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Detection and Molecular Characterization of Manatee Papillomavirus in Cutaneous Lesions of the Florida Manatee (Trichechus manatus latirostris)

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Title:
Detection and Molecular Characterization of Manatee Papillomavirus in Cutaneous Lesions of the Florida Manatee (Trichechus manatus latirostris)
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2008

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Subjects / Keywords:
Amino acids ( jstor )
DNA ( jstor )
Gels ( jstor )
Genomes ( jstor )
Lesions ( jstor )
Manatees ( jstor )
Open reading frames ( jstor )
Papilloma ( jstor )
Polymerase chain reaction ( jstor )
Skin ( jstor )

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University of Florida
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University of Florida
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7/30/2007

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DETECTION AND MOLECULAR CHARACTERIZATION OF MANATEE
PAPILLOMAVIRUS IN CUTANEOUS LESIONS OF THE FLORIDA
MANATEE (Trichechus manatus latirostris)













By

REBECCA ANN WOODRUFF


A THESIS PRESENTED TO THE GRADUATE SCHOOL
OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT
OF THE REQUIREMENTS FOR THE DEGREE OF
MASTER OF SCIENCE

UNIVERSITY OF FLORIDA


2005

































Copyright 2005

by

Rebecca Ann Woodruff

































This document is dedicated to the graduate students of the University of Florida.















ACKNOWLEDGMENT

I would like to extend my greatest appreciation and thanks to my mentor, Dr.

Carlos Romero, for allowing me to join his laboratory and enjoy many opportunities that

I would not have been able to elsewhere. I would also like to thank my committee

members, Dr. Peter McGuire and Dr. Ayalew Mergia, for their time, assistance, and

suggestions. I would like to thank Dr. Ellis Greiner for first introducing me to the

pathobiology graduate program at the University of Florida. I extend great thanks to Bob

Bonde, not only for obtaining all of the manatee samples used in this study, but also for

providing his expertise and knowledge of manatees. This project was funded by the

Florida Fish and Wildlife Commission through the Marine Mammal Animal Health

Program of the College of Veterinary Medicine at the University of Florida, and would

not have been possible without the U. S. Geological Survey (USGS) Department of the

Interior, contributions of collaborators affiliated with numerous zoological parks, and

those involved with manatee capture release studies. I would also like to thank my fellow

lab-mates, Alexa Bracht, Kara Smolarek-Benson, Shasta McClenahan, and Rebecca

Grant, for their much valued friendships. I am greatly appreciative of my best friend,

David Kottke, for supporting me unconditionally and following me to pursue my dreams,

even if it meant putting his own aside. I would also like to thank my family for their

constant encouragement during these past two years.
















TABLE OF CONTENTS

page

A C K N O W L E D G M E N T .......................................................................... .................... iv

LIST OF TABLES ...................... ................. ............... viii

LIST OF FIGURES ......... ........................................... ............ ix

ABSTRACT .............. .................. .......... .............. xi

CHAPTER

1 IN TR OD U CTION ............................................... .. ......................... ..

C classification of Papillom viruses ................. ................................. .. ....................1
Papillomavirus Genome Organization and Characterization ......................................2
Papillom avirus R eplication......................................... ................................. 4
P apillom avirus T ransm ission....................................... .......................................5
Papillom avirus Pathogenesis ........................................ ................................. 6
D iagnosis of Papillom avirus Infection ...................................................... .............. 8
Treatment and Prevention of Papillomavirus Infection..............................................9
H um an Papillom viruses ...................................... ................................................ 10
N on-Hum an Papillom aviruses................................................... .........................
Marine Mammal Papillomaviruses.................. ................................. 13
The Florida Manatee (Trichechus manatus latirostris).............................................13

2 M ATERIALS AND M ETHOD S ........................................ ......................... 16

Clinical Data ................................................... ........ ........ ............... 16
Source of Samples ........................... ............ .............. 16
DNA Extraction from Papillomatous Lesions......... .......................................17
G general M ethods of P C R ...................................................................... ......... 18
T aq Polym erase R actions .............. ......................................... ..................... 18
AccuprimeTM Taq DNA Polymerase Reactions ...............................................19
Expand High Fidelity Plus Reactions..... .......... ........................................ 19
PCR Targeting the L 458-bp Fragm ent ....................................... ............... 20
PCR Targeting the AL1 TmlPV 458-bp Fragment................. ............................20
PCR Targeting the TmlPV L1-El Region....................................... ............... 20
PCR Targeting the Complete TmlPV E6 Gene ................................ ............... 21
PCR Targeting the Complete TmlPV E7 Gene ................................ ............... 21


v









PCR Targeting the TmlPV L1-L2 Region................................................. 21
PCR Targeting the Complete TmlPV L1 Gene ................................ ............... 22
PCR Targeting the Complete TmlPV L2 Gene .............................................. .22
G el Electrophoresis....................................................... ......... ... 22
General Cloning of PCR Products................. ............ ............. ............... 23
Cloning into pCR 2.1 TOPO T/A Vector ............................. .................. 23
Cloning into P-TargetTM Mammalian Expression Vector ...............................24
Cloning into pcDNA '"3.1 Directional TOPO Expression Vector ................24
A nalyzing R ecom binants ......... .. ............... ...........................................................25
Sub-cloning of Purified Recombinants.......... .... .......................................... 27
Sub-Cloning into pcDNA 3.1/Zeo+ Expression Vector................ .......... 27
L1 Gene Sub-Cloning into pFastBacTM1 Vector..............................................29
L1 Gene Sub-Cloning into pBlueBac 4.5................................. ............... 30
Sequencing of PCR-amplified and Cloned Products............................................... 30
Transfection of Insect Cell Cultures ..................................................................... 31
Culturing Insect C ells ................ .......... .......... .. ....... ...... 31
Transformation of MAX Efficiency DH1OBacTM Competent E. coli .............32
Transfection of Insect Cells with Bacmid DNA Recombinants........................33
Harvest of Recombinant Baculovirus Stocks .................................................34
Reverse Transcription PCR (RT-PCR) of Infected Cell Cultures....................34
Generation of Recombinant Baculovirus .......................................................35
Transfection of M am m alian Cells .......................................................................... 36
Culturing African Green Monkey Kidney (COS-7) Cells..................................36
Electroporation of COS-7 Cells with Recombinants for Immunofluorescence
A s sa y s ................................. .... .. .......................... .... .............. 3 7
Culturing Florida Manatee Respiratory Epithelial Cells..................................38
Transfection of TmlRE Cells with DNA Recombinants for
Im m unofluorescence A says ........................................ ........ ............... 39

3 R E S U L T S .......................................................................... 4 4

P C R R results .................................................... ................................. . 44
PCR Targeting the Papillomavirus L1 458-bp Fragment...............................44
PCR Targeting the AL1 TmlPV Fragment.........................................................45
PCR Targeting the TmlPV L1-El Region................................ ............... 45
PCR Targeting the Complete TmlPV E6 Gene............................................45
PCR Targeting the Complete TmlPV E7 Gene ............................................45
PCR Targeting the TmlPV L1-L2 Region.................. ................. 46
PCR Targeting the Complete TmlPV L1 Gene.......... .......... ............... 46
PCR Targeting the Complete TmlPV L2 Gene .............................................. 46
Sequencing Results and Genetic Analyses............................... ............. ........... 46
Tm lPV L 1 458-bp Fragm ents.................................................. ......... .......... .. 46
L 1-E 1 T m lP V R egion ............................................................... .....................4 8
Tm lPV E6 G ene ............................................................. 49
Tm lPV E7 G ene ............................................................. 49
Tm lPV L1 -L2 R egion............................................. ......... ......................... 50
Complete TmlPV L1 Gene from Captive Manatee Lorelei .............................51









Com plete Tm lPV L2 Gene.................................................... .. ..................51
Immunofluorescence and Gene Expression Assays ................................................52
M am m alian Expression System s...................................................................... 52
Bac-to-Bac Baculovirus Expression System .....................................................52
Bac-N -Blue Baculovirus Expression System ....................................................... 53
Phylogenetic A analysis ...................................... ................. .... ....... 53

4 D ISC U S SIO N ............................................................................... 78

LIST OF REFEREN CES ............................................................................. 95

BIOGRAPHICAL SKETCH ............................................................. ............... 106
















LIST OF TABLES


Table page

2-1 Samples obtained from skin lesions of captive Florida manatees.....................39

2-2 Samples obtained from skin lesions of free-ranging Florida manatees ..............40

2-3 PCR primers designed to target manatee papillomavirus sequences ..................40

2-4 Sequencing primers used to obtain the complete sequence of PCR amplified
T m lP V gene fragm ents .......................................................................... .... ... 4 1

3-1 PCR results of DNAs obtained from captive manatee skin lesions tested for
the presence of TmlPV infection. .............................................. ............... 55

3-2 PCR results of DNAs obtained from free-ranging manatee skin lesions tested
for the presence of TmlPV infection. ...................................... ............... 56

3-3 Sum m ary of PCR results. ................................................................................57

3-4 Accession numbers of manatee papillomavirus sequences deposited into the
GenBank tool of the NCBI website ............................................................58

3-5 Pair-wise comparisons of the amino acid sequences of the L1, L2, E6, and E7
gene fragments of manatee papillomavirus (TmlPV) with several human and
non-human papillomaviruses..................................................... 59

3-6 Pair-wise comparisons of the amino acid sequences of the L1, L2, E6, and E7
gene fragments of manatee papillomavirus (TmlPV) with several human and
non-human papillomaviruses..................................................... 60

3-7 Summary of the pair-wise comparisons of the amino acid sequences of
manatee papillomavirus gene fragments with several human and non-human
p ap illo m av iru ses..................................................................................... 6 1















LIST OF FIGURES


Figure page

1-1 Illustration demonstrating the genetic organization of a typical
papillom avirus genom e.. ............................. .... .....................................15

2-1 Linear representation of the open reading frames (ORFs) of the circular
manatee papillomavirus (TmlPV) genome with the relative positions of the
PCR primers used to amplify TmlPV DNA ........................................... ........... 16

3-1 Agarose gel electrophoresis of PCR amplified 458-bp fragments of the L1
capsid protein gene of manatee papillomavirus. ............................. ............... 62

3-2 Agarose gel electrophoresis of PCR amplified 2,772-bp fragment of the Ll-
El region of manatee papillomavirus........................................................ 62

3-3 Agarose gel electrophoresis of PCR amplified 587-bp fragments of the E6
gene of manatee papillomavirus. ............. ................................. .................63

3-4 Agarose gel electrophoresis of PCR amplified 489-bp fragments of the E7
gene of manatee papillomavirus. ............ .. .................................. .................63

3-5 Agarose gel electrophoresis of PCR amplified 3,208-bp fragments of the L1
gene plus the L2 gene of manatee papillomavirus ............................................64

3-6 Agarose gel electrophoresis of PCR amplified 1,712-bp fragments of the
complete L1 gene of manatee papillomavirus.............................................64

3-7 Agarose gel electrophoresis of PCR amplified 1,660-bp fragments of the
complete L2 gene of manatee papillomavirus............................... ..............65

3-8 Multiple alignment of the amino acid sequences deduced from the nucleotide
sequences of the L1 gene fragment of manatee papillomavirus identified in
cutaneous lesions of captive and free-ranging Florida manatees ......................66

3-9 Electron micrograph of Sf21 insect cell cultures transfected with
pFastBacl/TmlPV L1 gene recombinant................................................67

3-10 Agarose gel electrophoresis demonstrating the PCR amplification of the
manatee papillomavirus complete L1 gene fragment from cDNAs obtained
from infected Sf21 cell cultures. .............................................. ............... 68









3-11 Agarose gel electrophoresis demonstrating restriction enzyme digests of the
manatee papillomavirus E6 gene and E7 gene recombinants. ..........................69

3-12 Agarose gel electrophoresis demonstrating restriction enzyme digests of the
manatee papillomavirus L1 complete gene recombinant...................................69

3-13 Neighbor-Joining phylogenetic tree of the deduced amino acid sequences of
the complete L1 gene of several human and non-human papillomaviruses........70

3-14 Neighbor-Joining phylogenetic tree of the deduced amino acid sequences of
the complete L2 gene of several human and non-human papillomaviruses........72

3-15 Neighbor-Joining phylogenetic tree of the deduced amino acid sequences of
the complete E6 gene of several human and non-human papillomaviruses ......74

3-16 Neighbor-Joining phylogenetic tree of the deduced amino acid sequences of
the complete E7 gene of several human and non-human papillomaviruses ........76

4-1 Papillomatous skin lesions on the flipper of a captive Florida manatee
(Trichechus manatus latirostris) housed at Homosassa Springs State Wildlife
Park, H om osassa, Florida .................................. ............... ............... 93

4-2 Typical papillomatous skin lesions of free-ranging Florida manatees ..............44















Abstract of Thesis Presented to the Graduate School
of the University of Florida in Partial Fulfillment of the
Requirements for the Master of Science

DETECTION AND MOLECULAR CHARACTERIZATION OF MANATEE
PAPILLOMAVIRUS IN CUTANEOUS LESIONS OF THE FLORIDA MANATEE
(Trichechus manatus latirostris)

By

Rebecca Ann Woodruff

August 2005

Chair: Carlos H. Romero
Major Department: Veterinary Medicine

Papillomaviruses are widespread and successful pathogens associated with the

development of benign warts and malignant neoplasia in humans and domestic and wild

animals. Phylogenetic comparisons have classified human and non-human

papillomaviruses into 16 genera within the Papillomaviridae family. With the advent of

PCR and molecular cloning, significant advances have been made in understanding

human papillomaviruses; however, little is known about marine mammal

papillomaviruses. DNA extracted from skin lesions of captive and free-ranging manatees

was assayed by polymerase chain reaction (PCR) to detect papillomavirus infection.

Initially, primers were based on the widely used MY11 and MY09 human papillomavirus

(HPV) primer set, which target a highly conserved region of the L1 capsid protein. The

MY11 and MY09 primers directed the amplification of a 458-bp fragment from DNA

extracted from captive and free-ranging Florida manatee (Trichechus manatus latirostris)

skin lesions. Sequences of this fragment led to the development of AL1 PCR primers,









which specifically target the L1 capsid protein of Florida manatee papilloma virus

(TmlPV). The L1 and AL1 DNA fragment sequences were 100% identical, suggesting

that there is only one genotype of manatee PV present in captive and free-ranging

manatees around Homosassa Springs State Wildlife Park. PCR primers were also

designed to specifically target the complete TmlPV E6, E7, L1, and L2 genes.

Amplification of the TmlPV E6 gene product yielded a 589-bp fragment, which included

the complete TmlPV E6 gene, and amplification of the TmlPV E7 gene product yielded a

487-bp fragment, which included the complete TmlPV E7 gene. Targeting the TmlPV

L1 capsid protein gene yielded amplification of a 1,712-bp fragment, which included the

complete TmlPV L1 gene, and targeting the TmlPV L2 capsid protein yielded

amplification of a 1,660-bp fragment, which included the complete TmlPV L2 gene. The

complete TmlPV L1, E6, and E7 genes were successfully cloned into mammalian and

insect expression vectors, allowing for the future production of recombinant genes and

the development of serologic assays, such as ELISA. The described assays based on

PCR and direct sequencing of amplicons have allowed for the molecular detection of

TmlPV in captive and free-ranging Florida manatees and have allowed for the

phylogenetic comparisons of TmlPV to several human and non-human papillomaviruses.

The TmlPV is a unique papillomavirus based on phylogenetic analyses of the deduced

amino acid sequences of the L1, L2, E6, and E7 proteins, quite distinct from another

marine papillomavirus of Burmeister's porpoises, most closely related to HPVs that cause

common skin warts, and least related to high-risk HPVs involved in malignancy.














CHAPTER 1
INTRODUCTION

The papillomaviruses (PVs) are a group of small DNA viruses that cause benign

warts and malignant neoplasia in humans (Walboomers et al., 1999) and domestic and

wild animals (Sundberg, 1987). To date, more than a hundred human PV (HPV) types

have been partially identified and a wide variety of PV types have also been detected in

mammals and birds (de Villiers et al., 2004). Papillomavirus infection has also been

detected in genital and cutaneous lesions of several species of marine mammals (Bossart

et al., 2002; Kennedy-Stoskopf, 2001; Van Bressem et al., 1996) and studies have shown

that the healthy skin of humans and animal species can harbor sub-clinical PV infections

in the absence of overt lesions (Antonsson and Hansson, 2002, and Antonsson et al.,

2000).

Classification of Papillomaviruses

Papillomaviruses were originally grouped together with the polyomaviruses in the

family Papovaviridae based on their small size, non-enveloped capsids, and circular,

double-stranded genomes. However, a lack of overall homology of particle size, genome

organization, and sequence similarities between the two viral genomes led to the

recognition of two separate families, Polvomaviridae and Papillomaviridae (Howley and

Lowy, 2001). Viruses within the Papillomaviridae family are defined by genomic

properties, rather than serology, and are therefore described as PV genotypes, not

serotypes. Papillomavirus genotypes are classified by analysis of only part of the viral

genome that encompasses the combined nucleotide sequences of the E6, E7, and L1 open









reading frames (ORFs) (Chan et al., 1995). Recent phylogenetic comparisons of the L1

ORF nucleotide sequences of 96 HPVs and 22 animal PVs have further classified PV

types into genera and species. Higher-order phylogenetic clusters (major branches) of

PV types have now been classified into genera, sharing less than 60% identity in the L1

ORF nucleotide sequences. Each genus within the 16 genera identified is defined by its

biological properties and genome organization. Lower-order clusters (minor branches) of

PV types, or PV subtypes, have now been termed species. Species within each genus

share 60-70% identity at the nucleotide level (de Villiers et al., 2004). Nucleotide

sequence analyses of the L1 ORF of various HPV types have been used to construct

phylogenetic trees that display clusters of PV types with similar tissue tropisms and

oncogenic potentials (Chan et al., 1995).

Papillomavirus Genome Organization and Characterization

Papillomaviruses have double-stranded, circular DNA genomes of about 8,000 base

pairs (bp) in size. The papillomavirus particles (52 to 55 nm in diameter) contain the

viral genome within a spherical capsid composed of 72 capsomers. All ORFs are located

on one strand, indicating that transcription occurs on only one strand. Transcription is

regulated by the differentiation state of the infected cells and is complex, due to the

presence of multiple promoters, alternate and multiple splice patterns, and differential

production of mRNA in different cells (Howley and Lowy, 2001).

A PV genome usually contains seven major ORFs that code for five early (E)

proteins and two late (L) capsid proteins, plus an upstream regulatory region (URR), or

long coding region (LCR) (Tachezy et al., 2002). The early region of the PV genome

encodes the viral regulatory proteins El, E2, E4, E6, and E7, which are necessary for

initiating viral DNA replication. The late region encapsulates the genome and encodes









the L1 and L2 capsid proteins (Howley and Lowy, 2001). The LCR does not contain any

ORFs, but does contain the origin of viral DNA replication. Elements present in the LCR

regulate viral DNA replication and transcription (Desaintes and Demeret, 1996).

Unusual ORFs have been described in several types of PVs (Tachezy et al., 2002). The

genomes of European elk (Odocoileus alces) PV, white-tail deer (Odocoileus virginianus)

PV, and reindeer (Odocoileus hemionus) PV contain a transforming E9 gene (Eriksson et

al., 1994). The African grey parrot (Psittacus erithacus timneh) papillomavirus (PePV)

genome does not contain the typical E6 or E7 ORFs (Tachezy et al., 2002) and the

Burmeister's porpoise (Phoecena spinipinnis) papillomavirus (PsPV-1) genome also

lacks the E7 ORF (Van Bressem et al., 1996). Two ORFs with unknown functions, E3

and E8, may also be present in a PV genome (Lowy and Howley, 2001). An illustration

of a typical PV genome is shown in Figure 1-1.

The PV genome is contained within the capsid region which consists of the major

and minor structural proteins, L1 and L2, respectively. The L1 ORF is the most highly

conserved ORF within the papillomavirus genome (de Villiers et al., 2004) and represents

80% of the total viral protein (Howley and Lowy, 2001). The L1 protein can self-

assemble into virus-like particles (VLPs) or in combination with L2, although the L2

protein is not required (Hagensee et al., 1993). The L2 protein may enhance packaging

(Stauffer et al., 1998) and infectivity (Roden et al., 2001).

The early genes E6 and E7, and in some PV types, E5, contain oncogenic

properties that can modulate the transformation process (Baker and Howley, 1987). The

E6 protein of bovine papilloma virus type 1 (BPV-1) and of the oncogenic HPVs is

believed to function through binding cellular targets (Howley and Lowy, 2001), such as









binding and degrading the p53 tumor suppressor protein (Scheffner et al., 1993). The E7

protein of the oncogenic HPVs binds a number of important cellular regulatory proteins,

such as the retinoblastoma tumor suppressor protein (pRB) and the related pocket

proteins, p107 and p130 (Dyson et al., 1989). The papillomaviruses may activate cellular

genes necessary for the replication of their own DNA through the binding of the viral E6

and E7 proteins to cellular factors (Howley and Lowy, 2001).

The early genes El and E2 are regulatory proteins that modulate transcription and

replication (Baker and Howley, 1987). The El and E2 proteins are essential for viral

DNA replication (Chiang et al., 1992). The El protein has been shown to bind a number

of cellular proteins, including the cellular DNA polymerase a-primase, thus recruiting the

cellular DNA replication initiation machinery to the viral origin of replication (Park et al.,

1994). The multifunctional E2 protein can activate or repress viral promoters, has critical

roles in viral DNA replication (Ham et al., 1991), and targets the El protein to the

replication origin (Sedman and Stenlund, 1995). Although the E4 ORF is located in the

early region of the PV genome, it is expressed as a late gene (Howley and Lowy, 2001).

The precise role of the E4 protein is unclear, but studies have shown E4 expression

coincides with the onset of viral genome amplification (Peh et al., 2002).

Papillomavirus Replication

Key life cycle events seem to be similarly regulated in both human and non-human

PVs (Peh et al., 2002). The PV life cycle is strictly dependent on differentiation of the

epithelial tissue (Barksdale and Baker, 1993) and PV replication can be divided into three

stages (McBride et al., 2000). First, the PV virion must bind to a basal keratinocyte,

although studies have shown that the PV virions can bind a wide variety of cell types

(Muller et al., 1995). During this stage, the viral genome is maintained as an episome









within the nucleus (McBride et al., 2000). The viral genome is then amplified and the

viral copy number is increased up to 1,000 per haploid cell genome (Lepik et al., 1998).

As the basal cells differentiate, the viral DNA is maintained as a stable plasmid (Howley

and Lowy, 2001). During this second, maintenance stage, the viral genome replicates in

synchrony with the host cell chromosome (Gilbert and Cohen, 1987). The PVs rely on

cellular replication factors and enzymes (Muller et al., 1994), such as replication protein

A (RPA) (Mannik et al., 2002), in order to replicate their genomes from a single origin of

replication (Melendy et al., 1995). The earliest PV DNA synthesis is within the fragment

containing the PV replication origin and synthesis proceeds in both directions from the

replication origin (Melendy et al., 1995). The third replication stage takes place in the

terminally differentiated epithelial cells of the papilloma (Howley and Lowy, 2001). In

this next layer of stratified epithelium, the stratum granulosum, late viral gene expression,

synthesis of capsid proteins, vegetative viral DNA synthesis, and assembly of virions

occur (McBride et al., 2000). The PV DNA is thought to remain in the basal epithelial

cells and to be reactivated when levels of immune system monitoring decline (Doorbar, J.

2005).

Papillomavirus Transmission

Papillomavirus enters infected skin via skin surface abrasions, allowing the virus

access to the proliferative cells of the skin (Egawa, 2003), where it promotes cellular

proliferation and accelerated epithelial growth (Silverberg, 2004). Infection with HPV is

primarily found on the extremities, face, and body, and moist skin is more likely to allow

viral transmission (Silverberg, 2004). Transmission of high-risk mucosal HPVs occurs

predominately through sexual contact, but horizontal and vertical routes have also been

identified. Vertical transmission of mucosal HPVs may be acquired from the mother in









utero, across the placenta, intrapartum, during birth through an infected birth canal, or

post partum (Cason and Mant, 2005). In 1989, Sedlacek et al. described the first

confirmed vertical transmission of HPV infection in nasopharyngeal samples of infants

born to HPV positive mothers.

Papillomavirus Pathogenesis

Papillomas (warts) are induced in the skin and mucosal epithelia at specific sites

(de Villiers et al., 2004) and differ in their tissue specificity and the associated disease

(McMurray et al., 2001). The highly tissue-specific papillomaviruses can be divided into

two groups: one group is primarily found in cutaneous epithelia (skin), in which there is

thickening of the epidermis, and the other group is predominantly present in mucosal

epithelia (Smits et al., 1992), involving the oral pharynx, esophagus, or genital tract

(Howley and Lowy, 2001). Warts are diagnosed by physical examination and are defined

by morphology, location, and host immune response. The three main types of lesions

observed are: common warts (rough plaques of skin), mosaic warts (groups of common

warts), and flat warts (smooth, flesh-colored papules). Mucosal warts may appear as

single plaques or as a group with a grapelike appearance (Silverberg, 2004).

The genital mucosal HPV types are defined as either high-risk or low-risk based on

their involvement with lower genital tract cancers (McMurray et al., 2001). In the low-

risk types, such as HPV-6 or HPV-11, benign warts proliferate. In the high-risk types,

such as HPV-16 or HPV-18, the virus deregulates checkpoints that normally monitor the

fidelity of chromosome replication and segregation, leading to the development of cancer

(Galloway, 2003). Anogenital carcinomas caused by HPV infection include penile

(Rubin et al., 2001), vaginal (Daling et al., 2002), vulvar (Trimble et al., 1996), and anal

cancers (Krzyzek et al., 1980). The high-risk HPV types are also associated with cervical









dysplasia (Kurman et al., 1982), uterine cancer (Parkin et al., 1999, and zur Hausen,

1996), and cervical cancer, one of the most common cancers of women world-wide

(Schiffman, 1992, and zur Hausen, 1991). The E6 and E7 genes of the high-risk types

are expressed in cervical cancer (Schwarz et al., 1985). The roles of E6 and E7 of the

low-risk types are unclear, but studies suggest that they may act in a similar manner as

observed in the high-risk E6 and E7 proteins (Oh et al., 2004). Risk factors associated

with cervical cancer and other anogenital tumors include cigarette smoking, sexual

factors, and, possibly, genetic susceptibility (Daling et al., 2002).

Both the low-risk and high-risk HPV types cause low-grade squamous

intraepithelial lesions (LSIL) of the cervix, but the high-risk HPV types cause high-grade

SIL (HSIL), carcinoma in situ, or invasive cancer. The steps leading to cervical

carcinogenesis include infection with an oncogenic (high-risk) HPV, development of

HSIL, progression of HSIL to carcinoma in situ, and, then, invasive cancer (Baseman and

Koutsky, 2005). Frequent integration of the HPV genome into the host genome usually

occurs in the case of high-risk PVs (Mannik et al., 2002).

At least 25 types of HPVs have also been detected in oral lesions on the lips, hard

palate, and gingiva (Syrjanen, 2003). The high risk HPV types 16 and 18 are highly

associated with oropharyngeal and laryngeal squamous cell carcinomas (Kreimer et al.,

2005) while the low risk HPV types 6 and 11 are predominant in benign lesions of the

oral mucosa (Syrjanen, 2003). Infection with HPV is a significant independent risk

factor for oral squamous cell carcinoma (Miller and Johnstone, 2001).

The pathogenesis of HPVs differs for viruses that are considered high risk or low

risk group members. In the case of epidermodysplasia verruciformis (EV), the disease









behaves like a genetic cancer of viral origin, which may result from an abnormal

recessive gene (Jablonska, 1991). Clinical forms of EV may be benign or malignant.

The benign form is associated with HPV-3 and/or HPV-10 and induces flat, wart-like

lesions over the trunk and limbs. The malignant form is associated with EV-HPV and

induces reddish, polymorphous lesions, flat wart-like lesions, and pre-malignant lesions

disseminated over the body. Epidermodysplasia verruciformis is the first human genetic

condition in which cutaneous cancer is associated with HPV infection (Majewski and

Jablonska, 1995).

There is an increased risk of developing cutaneous HPV-associated disease if the

virus is not cleared from the skin (Silverberg, 2004). Cutaneous HPV types, such as

HPV-5 and HPV-8, may contribute to skin cancer development in immunosuppressed

individuals (Stockfleth et al., 2004). In renal transplant studies, 90% of recipients

developed HPV-induced warts (Blessing et al., 1989) and up to 40% of recipients

developed nonmelanoma skin cancer within 15 years after transplantation (Birkeland et

al., 1995). HPV-5 and HPV-8 were also predominately detected in squamous cell

carcinoma of patients diagnosed with EV (Orth, 1987). Immunosuppression may

increase the activity of HPV, which may lead to the development of cancer (Stockfleth et

al., 2004).

Diagnosis of Papillomavirus Infection

Testing for the presence of HPV viral DNA includes methods such as Southern

blots, dot blots, in situ hybridization, polymerase chain reaction (PCR), and solution

hybridization (hybrid capture assay) (Trofatter, 1997). Detection of HPV by PCR is

more sensitive than the other methods, enables the detection of a single genome copy per

cell for HPV DNA that has integrated (Shamanin et al., 1994), and allows for the









detection of a broad spectrum of genital HPVs (Ting and Manos, 1990). The widely used

consensus PCR primers, MY09 and MY11, are based on sequences obtained from the

highly conserved PV L1 capsid protein gene (Manos et al., 1989). The primers were

designed from homologous regions 20 to 25 base pairs (bp) in length that were identified

in genital HPV types 6, 11, 16, 18, and 33 (Ting and Manos, 1990). These primers are

known to amplify a 458 base pair (bp) fragment when used with DNA from most types of

genital HPVs (Bernard et al., 1994). Human papillomavirus DNA can be detected by

method of PCR in fresh or frozen cervical biopsies (Li et al., 1988; Manos et al., 1989),

condylomata acuminata (genital warts) tissues (Brown et al., 1999), cutaneous wart

tissues (Harwood et al., 1999), and in swab samples taken from the top of lesions

(Forslund et al., 2004). Harwood et al. (1999) have described a degenerate nested PCR

that is capable of detecting cutaneous, mucosal, and EV HPV types. A new method of

HPV detection using high-density DNA microarrays is able to detect single and multiple

mucosal HPV infections (Klaassen et al., 2003).

Treatment and Prevention of Papillomavirus Infection

The host response to HPV infection is a complex process of skin barrier protection,

innate immunity, and acquired immunity (Silverberg, 2004). Warts generally will regress

over time and after six months of infection, 30 percent of warts will clear on their own

(Messing and Epstein, 1963). Following immune regression, PV DNA persists in a

latent state, with only a few cells, if any, capable of supporting the productive cycle that

occurs during epithelial cell differentiation (Doorbar, 2005). A possible approach to

controlling the level of HPV-associated disease is to prevent HPV infection (McMurray

et al., 2001); however, the PV life cycle requires a differentiated stratified epithelium to

replicate and this has been difficult to generate in cell culture (McBride et al., 2000).









Due to the fact that PVs could not previously be propagated in cell cultures, the

development of a capsid-directed vaccine was hindered for a long time (Biemelt et al.,

2003). A recently described raft system now allows for the genetic analysis of the

complete viral life cycle of BPV-1. Using a combination of organotypic raft cultures and

xenografts on nude mice, BPV-1 DNA can be amplified and capsid antigens and

infectious BPV-1 virus particles can be produced (McBride et al., 2000).

Several animal models of PV infection have shown that neutralizing antibodies can

block new infection (Galloway, 2003). Vaccination against PV infections using virus-

like particles (VLPs) based on the L1 capsid protein or the L1 plus the L2 protein is

currently being developed (Leder et al., 2001). Vaccines based on VLPs are desirable

because they retain repetitive, highly immunogenic epitopes found on the surface of

infectious virions, but lack the potentially harmful PV genomes. Three types of HPV

VLP-based vaccines are currently being developed. The first, most basic type is designed

to prevent genital HPVs by inducing virus-neutralizing antibodies against the L1 major

capsid protein. The second type of vaccine is based on chimeric VLPs which incorporate

polypeptides of other viral and cellular proteins into the VLPs. These vaccines induce

cell-mediated responses to nonstructural viral proteins, such as the HPV E7 protein. The

third type of vaccine incorporates self-peptides into the outer surface of the VLPs and is

designed to induce antibodies against central self-antigens (Schiller and Lowy, 2000).

Vaccination with HPV VLPs has been well tolerated, induces high titers of antibodies,

and shows evidence of T-cell responses (Galloway, 2003).

Human Papillomaviruses

Papillomaviruses are one of the most important viruses associated with benign and

malignant neoplasia in humans (Chan et al., 1995). Papillomaviruses were first isolated









almost 30 years ago (Orth et al., 1977) and the first HPVs fully sequenced were HPV-1

(Danos et al., 1982), HPV-6 (Schwarz et al., 1983), and HPV-16 (Seedorfet al., 1985).

To date, more than 100 types of human papilloma viruses (HPVs) have been identified,

of which 96 have been cloned and characterized (deVilliers et al., 2004). More than 50

types of HPVs have been found to infect the genital tract (Galloway, 2003). Low-risk

(benign) genital HPVs include: types 6, 11, 40, 42-45, 53-55, 57, 67, 69, 71, and 74.

High-risk (oncogenic) genital HPVs include: types 16, 18, 31-35, 51, 52, 56, 58, 66, 68,

70, and 73 (deVilliers et al., 2004 and McMurray et al., 2001), with types 26, 53, and 66

being probably oncogenic (Munoz et al., 2003). The HPV types 59, 61, and 82 may be

associated with benign or malignant lesions (deVilliers et al., 2004). Infection with a

single HPV type or infection with multiple HPV types can occur (Munoz et al., 2003).

Non-Human Papillomaviruses

Warts in animals have been recognized for centuries. Equine papillomas were

described as early as in the 9th century A. D. and the first experimental transmission of

animal papillomas occurred in 1898 (Lancaster and Olson, 1982). Warts in wild

cottontail rabbits were the first animal papillomas thoroughly examined for properties of

transmissibility, etiology, and histology. The activities and characteristics of the

papilloma-producing agent in cottontail rabbits classified it as a virus (Shope, 1933).

Additional non-human PVs initially characterized include: BPV (Lancaster and Olson,

1978), equine PV (Fulton et al., 1970), canine oral PV (Chambers and Evans, 1959), deer

fibromavirus (Shope et al., 1958), and chaffinch PV (Lina et al., 1973). Presently, 22

animal PVs have been fully characterized and classified into genera and species based on

the L1 ORF sequences (de Villiers et al., 2004). As many as 53 putative new animal PV

types have been identified by polymerase chain reaction (PCR) in 7 animal species,









including chimpanzees, gorillas, spider monkeys, long-tailed macaques, domestic cattle,

aurochs, and European elk (Antonsson and Hansson, 2002).

Animal papillomas can be divided into four groups based on tissue tropism and

histology of lesions. These groups comprise animal PVs that can induce neoplasia of

cutaneous stratified epithelium, fibromas with a minimally hyperplastic cutaneous

epithelium, cutaneous papillomas and fibropapillomas (an underlying fibroma of

connective tissue), and hyperplasia of either normal non-stratified squamous epithelium

or metaplastic squamous epithelium. Infection with non-human PVs is generally

contained to the skin or mucous membranes of the host species (Lancaster and Olson,

1982); however, canine oral PV can also infect the eyelid, conjunctival epithelium, and

skin around the nose and mouth (Chambers and Evans, 1959). Some animal PV types,

such as BPV, cottontail rabbit PV, and European harvest mice PV, have been implicated

in cancers (Antonsson and Hansson, 2002), with BPV being the most oncogenic of the

PVs (Lancaster et al., 1977). The E5 protein of BPV type 1 (BPV-1) transforms cells and

functions by altering the activity of cellular membrane proteins that are involved in

proliferation (DiMaio et al., 1986).

Most PVs are species-specific or may infect closely related animals within the

same genus (Sundberg et al., 2000), although BPV-1 and BPV-2 can induce fibroblastic

tumors in a strain of inbred mice (Boiron et al., 1964), hamsters (Cheville, 1966), and

rabbits (Breitburd et al., 1981). The presence ofBPV-specific DNA has also been

detected in both naturally occurring tumors and BPV-induced tumors of horses

(Lancaster et al., 1977). An oral PV that infected one coyote and three dogs has also

been described (Sundberg et al., 1991). Studies have shown that many domestic and









wild species of mammals and birds can be infected by one or more PVs (Sundberg et al.,

2000).

Marine Mammal Papillomaviruses

Viruses and viral diseases have long been identified in marine mammals (Smith

and Skilling, 1979) and new PVs in marine mammals have recently been described (Van

Bressem et al., 1996, and Bossart et al., 2002). Papillomavirus-like particles have been

observed in association with genital lesions of male sperm whales (Physeter catodon)

(Lambertsen et al., 1987), dusky dolphins (Lagenorhynchus obscurus), and Burmeister's

porpoises (Phocoena spinipinnis) (Van Bressem et al., 1996). The high prevalence of

papillomatous lesions in several small cetaceans (L. obscurus, P. spinipinnis, Delphinus

capensis, Tursiops truncatus) indicates a possible venereal transmission of the disease

(Van Bressem et al., 1996). Squamous papillomas and fibropapillomas have also been

identified on the skin, the surface of the penis, and the tongue of mysticetes and

odontocetes (Geraci et al., 1987) and gastric papillomas containing PV-like particles have

been observed in a significant amount of beluga (Delphinapterus leucas) inhabiting the

St. Lawrence River (Martineau et al., 2002).

The Florida Manatee (Trichechus manatus latirostris)

The Florida manatee is a marine mammal that is primarily found in the

southeastern United States waters and the Gulf of Mexico and is listed as endangered at

both the state and federal levels (U. S. Fish and Wildlife Service, 2001). The manatee

immune system appears to be highly developed and it has been hypothesized that natural

disease in manatees is uncommon (Bossart et al., 2002). Environmental diseases that

may represent emerging problems for the Florida manatee include brevetoxicosis and

cold stress syndrome (Bossart, 2001). Recently, it has been shown that exposure to









multiple stressors, such as cold weather and harmful algal blooms (Karenia brevis), may

have synergistic effects on the immune function of manatees (Walsh et al., 2005).

Papillomas in Florida manatees were initially identified in 1997 in a captive

population maintained at Homosassa Springs State Wildlife Park (HSSWP), Homosassa,

Florida. These seven captive manatees developed multiple, cutaneous, pedunculated

papillomas located on the pectoral flippers, upper lips, external nares, and periorbital

regions. Approximately three years later, four of the manatees developed papillomas that

were clinically distinct from the previously observed lesions. These lesions were sessile,

firm, and more diffuse and numerous than those biopsied in 1997. Based on histological,

ultrastructural, and immunohistochemical findings, PV was considered to be a theoretical

causative agent in both outbreaks. Electron microscopy evaluation of the lesions

revealed the presence of round to hexagonal 45- to 50-nm virions that were

ultrastructurally identical to those of known PVs. Positive immunohistochemical staining

was demonstrated with polyclonal antibodies against BPV-1. This was the first viral

infection described in Florida manatees (Bossart et al., 2002). Similar papillomatous skin

lesions have since been observed in free-ranging Florida manatees inhabiting two

locations in Florida waters (Woodruff et al., in press).

The first molecular detection of PV infection in Florida manatees was performed

by amplifying PV DNA from papillomatous lesions of captive and free-ranging manatees

using the degenerative HPV primers MY09 and MY11. These primers amplified a 458-

bp DNA fragment of the highly conserved L1 capsid protein gene of manatee

papillomavirus (TmlPV) (Woodruff et al., in press). Recently, the entire TmlPV genome

has been completely sequenced and characterized. The complete TmlPV genome









(TmPV-1) contains 7,722 bp and consists of seven major ORFs that encode five early

proteins and two late capsid proteins (Rector et al., 2004). Sequences of nine L1

fragments previously described by Woodruff et al. (2005) were 100% identical to the

corresponding L1 region of the published manatee papillomavirus, TmPV-1, suggesting

that there is only one type of manatee PV that causes skin lesions in manatees (Rector et

al., 2004). Although the existence of a manatee papillomavirus has been well

documented, further work is required in order to better understand the overall impact and

possible oncogenic potential of papillomavirus infection in the already endangered

Florida manatee. The goals of this study were to determine if more than one TmlPV is

associated with papillomatous lesions in captive and free-ranging manatees, to

genetically characterize the TmlPV genome(s), and to develop serological assays with the

potentially oncogenic E6 and E7 proteins and with the L1 capsid protein.

LCR

.9 5 E6 7




.00oo HPV 16 2.oo El



4.00



E5
Figure 1-1. Illustration demonstrating the genetic organization of a typical
papillomavirus genome. The HPV-16 genome is divided into early (E) and
late (L) regions depending on the timing of protein expression.














CHAPTER 2
MATERIALS AND METHODS

Clinical Data

Nine adult female Florida manatees (Trichechus manatus latirostris) comprised the

captive population dwelling at Homosassa Springs State Wildlife Park (HSSWP) located

in Homosassa, Florida. Manatees at HSSWP were housed in Homosassa Springs, a

natural freshwater spring at the headwaters of the Homosassa River, Citrus County,

Florida. An underwater fence placed at the junction of the spring and the river confined

the manatees to an area of approximately 2 acres (Bossart et al., 2002). Free-ranging

manatees were occasionally observed at the outer perimeter of the underwater fence. The

free-ranging manatees found in this area are winter residents that use the springs for

thermoregulation (Woodruff et al., in press).

Source of Samples

Between January, 2003, and February, 2005, skin lesions from captive and free-

ranging manatees were brought to our laboratory fresh, on ice, or fixed in either 10%

non-buffered formalin (NBF) or Dimethyl Sulfoxide (DMSO). Papillomatous skin

lesions from captive Florida manatees were received from various parks, including

HSSWP, Florida, and other marine parks in Florida and California. Papillomatous skin

lesions were also obtained from free-ranging Florida manatees inhabiting several bodies

of Florida waters, including Crystal River, Homosassa River, Port of Isles, and Tampa

Bay, and from free-ranging Antillean manatees (Trichechus manatus manatus) inhabiting

the offshore waters of the Drowned Keys, Belize. One papillomatous penile lesion









preserved in 10% NBF was obtained from a free-ranging manatee carcass examined at

the Fish and Wildlife Research Institute, St. Petersburg, Florida, and an uninfected,

normal manatee liver was obtained from the Marine Mammal Pathology Laboratory, St.

Petersburg, Florida. Samples biopsied from HSSWP captive manatees between July,

1998, and January, 2000, were preserved in 10% NBF or DMSO and samples biopsied

from free-ranging manatees in April, 2004, and August, 2004, were preserved in 10%

NBF. All other manatee tissue samples (captive and free-ranging) arrived fresh or on ice.

Sample description and information are located in Table 2-1 and Table 2-2.

Blood serum from captive manatees housed at HSSWP was brought to our

laboratory on dry ice, courtesy of Bob Bonde, U. S. Geological Survey, Gainesville,

Florida. Serum samples were obtained from the following captive manatees (date

obtained): Holly (July 9, 1998), Betsy (February, 1999), Oakley (Feb 25, 1999; June 20,

2002), Willoughby (January 13, 2000), Amanda (Jan 13, 2000), and Lorelei (Jun 20,

2002). Purified anti-manatee IgG monoclonal antibody (1.2 mg/ml) was obtained

courtesy of Dr. Peter McGuire, Department of Biochemistry, University of Florida, and

Ms. Linda Green, Hybridoma Core Laboratory, University of Florida, Gainesville,

Florida.

DNA Extraction from Papillomatous Lesions

Total DNA was extracted from all tissue samples using the DNeasy tissue kit

(Qiagen Inc, Valencia, California, USA) according to the protocol recommended by the

manufacturer. Working in a laminar flow cabinet equipped with an HEPA filter,

approximately 25 mg of each papillomatous skin lesion was minced with a sterile

surgical blade and placed and ground in a sterile 1.5-ml micro centrifuge tube. The

tissues were incubated overnight at 550C in a mixture containing 1801l of digestion









buffer ATL and 20 [tl proteinase K (20 mg/ml) until lysis was complete. Then, 200 ptl of

buffer AL and 200 [il of 100% molecular grade ethanol were added to precipitate the

DNA. The solution was centrifuged in a DNeasy Spin Column to bind the DNA to the

membrane and the membrane was washed with 500 ptl of buffers AW1 and AW2 for 1

minute each time. A final centrifugation step was performed to eliminate residual ethanol

remaining in the membrane. The DNA was eluted in 200 ptl of buffer AE and evaluated

for yield and purity by spectrophotometry using the Ultrospec 3000 (Amersham

Biosciences Corp., Piscataway, New Jersey, USA). A negative tissue sample from

uninfected manatee skin or uninfected manatee liver was extracted along with each set of

tissue samples for use as a negative control in PCR analyses. The eluted DNA samples

were stored in 1.5-ml screw-cap tubes at -800C.

General Methods of PCR

Taq Polymerase Reactions

The PCR reaction in a 0.2 ml tube contained: 200 nM of each primer (IDT,

Coralville, IA, USA), 2 mM MgSO4, 100 [IM of each deoxynucleoside triphosphate

(dNTP), 20 mM Tris-HCl (pH 8.4), 10 mM KC1, 0.1 % Triton X-100 (pH 8.8), 10 mM

(NH4)2S04, 1 unit of Taq DNA polymerase (New England BioLabs, Beverly,

Massachusetts, USA), 0.5-1.0 tg of template DNA, and ultrapure H20 in a final volume

of 50 l. A total of 40 PCR cycles were performed in a PTC-100 thermal cycler (MJ

Research, Inc., Waltham, Massachusetts, USA) for the amplification of the manatee

papillomavirus (TmlPV) L1 fragments using the modified MY11/MY09 primers

(CR333/CR332) and the AL1 TmlPV-specific primers (CR490/CR491). Following an

initial denaturation step at 940C for 1 min, reactions were subjected to 39 cycles of: a

denaturation step at 940C for 1 min, an annealing step at 480C for 1 min, and an









elongation step at 720C for 2 min. An elongation step at 720C for 10 min was

incorporated in the final cycle.

AccuprimeTM Taq DNA Polymerase Reactions

The PCR reaction in a 0.2 ml tube contained: 400 nM of each primer, 200 mM

Tris-HCl (pH 8.0), 500 mM KC1, 15 mM MgCl2, 2 mM of each dNTP, 2 units of

Accuprime Taq DNA polymerase (Invitrogen, Carlsbad, California, USA), 0.2-0.5 pg of

template DNA, and ultrapure H20 in a final volume of 50 il. Cycling conditions for the

amplification of the complete TmlPV E6 gene fragment included: an initial denaturation

step at 940C for 2 min, then, 39 cycles of: a denaturation step at 940C for 30 sec, an

annealing step at 530C for 30 sec, and an extension step at 680C for 1 min. Cycling

conditions for amplification of the L1 fragments and the complete E7 complete gene

were similar, except that the annealing temperatures were set at 590C and 510C,

respectively.

Expand High Fidelity Plus Reactions

The PCR reaction in a 0.2 ml tube contained: 400 nM of each primer, 200 iM of

each dNTP, 1.5 mM MgCl2, Expand High Fidelity Plus Reaction Buffer diluted to 1.5

mM MgCl2 (Roche Applied Science, Mannheim, Germany), 2.5 units of Expand High

Fidelity Plus Enzyme Blend (Roche Applied Science), 0.5 pg of template DNA, and

ultrapure H20 in a final volume of 50 [il. Cycling conditions for amplification of the

TmlPV L1-El region were: an initial denaturation at 940C for 2 min, followed by 39

cycles of 940C for 30 sec, 500C for 30 sec, and 720C for 3 min, with a final extension

step at 720C for 7 minutes. Cycling conditions for amplification of the TmlPV L1-L2

capsid region were similar, except that the annealing temperature was set at 590C and the

extension step was performed at 680C for 3.5 min. Cycling conditions for amplification









of the TmlPV complete L1 capsid gene were similar, but the extension steps were

performed at 720C for 1.5 min. For amplification of the TmlPV complete L2 capsid

gene, cycling conditions were similar and the annealing temperature was set at 530C and

the extension step performed at 720C for 2 min.

PCR Targeting the L1 458-bp Fragment

The MY11 and MY09 L1 consensus primers that amplify a 458-bp fragment of the

L1 capsid protein gene of several human papillomaviruses (HPVs) (Manos et al., 1989)

were modified in our laboratory to contain deoxyinosines at positions of nucleotide

degeneracy [forward primer (FP) CR333 and reverse primer (RP) CR332] (Table 2-3).

DNA obtained from a lesion from captive manatee Oakley was used as the positive

control. A blank sample (water) and DNA extracted from a liver of an uninfected

manatee were used as negative controls.

PCR Targeting the AL1 TmlPV 458-bp Fragment

Based on newly generated nucleotide sequences of the amplified TmlPV L1

fragment obtained in our laboratory, the MY11/MY09 HPV L1 primers (Manos et al.,

1989) were modified to contain TmlPV L1-specific nucleotides at positions of nucleotide

degeneracy. The AL1TmlPV primers, FP CR490 and RP CR491 (Table 2-3), target a

458-bp sequence contained within the L1 capsid gene of TmlPV. DNA obtained from a

lesion from captive manatee Oakley was used as the positive control. A blank sample

(water) and DNA from a negative tissue (manatee liver) were used as negative controls.

PCR Targeting the TmlPV L1-E1 Region

Using a PCR method described by Forslund and Hansson (1996), oligonucleotide

primers were designed to target a region of the TmlPV genome that spans an area from

within the 3' end of the TmlPV L1 ORF to an area within the 5' end of the TmlPV El









ORF. A plus-strand oligonucleotide primer designed from the TmlPV L1 458-bp

fragment nucleotide sequence was used in a PCR reaction together with a minus-strand

HPV consensus primer from the El ORF (Smits et al., 1992). The TmlPV L1 FP CR442

and the HPV El RP CR441 (Table 2-3) direct the amplification of an approximately

3,000-bp fragment. DNA obtained from a lesion from captive manatee Oakley was used

as the positive control. A blank sample (water) and DNA from a negative tissue

(manatee liver) were used as negative controls.

PCR Targeting the Complete TmlPV E6 Gene

Based on the nucleotide sequences of the TmlPV L1-El region obtained by us,

oligonucleotide primers FP CR498 and RP CR499 (Table 2-3) targeting the complete

TmlPV E6 gene were designed for cloning and expression. DNA obtained from a lesion

from captive manatee Oakley was used as the positive control. A blank sample (water)

and DNA from a negative tissue (manatee liver) were used as negative controls.

PCR Targeting the Complete TmlPV E7 Gene

Based on the nucleotide sequences of the TmlPV L1-El region obtained by us,

oligonucleotide primers FP CR500 and RP CR501 (Table 2-3) targeting the complete

TmlPV E7 gene were designed for cloning and expression. DNA obtained from a lesion

from captive manatee Oakley was used as the positive control. A blank sample (water)

and DNA from a negative tissue (manatee liver) were used as negative controls.

PCR Targeting the TmlPV L1-L2 Region

Based on nucleotide sequences of the complete TmlPV genome (AY609301)

(Rector et al., 2004), a plus strand oligonucleotide primer FP CR572 (Table 2-3) was

designed from an area upstream of the L2 ORF. Used together with an L1 minus strand

primer RP CR574 (Table 2-3), designed by us, these primers target a region of the









TmlPV genome that spans an area upstream of the 5'end of the TmlPV L2 ORF to an

area downstream of the 3'end of the TmlPV L1 ORF. DNA obtained from a lesion from

captive manatee Oakley was used as the positive control. A blank sample (water) and

DNA from a negative tissue (manatee liver) were used as negative controls.

PCR Targeting the Complete TmlPV L1 Gene

Based on nucleotide sequences of the L1-L2 fragment obtained in our laboratory, a

plus-strand oligonucleotide primer FP CR573 (Table 2-3) was designed upstream of the

L1 start codon to be used together with the L1 FP CR574 for amplification of the

complete L1 gene for cloning and expression. DNA obtained from a lesion from captive

manatee Oakley was used as the positive control. A blank sample (water) and DNA from

a negative tissue (manatee liver) were used as negative controls.

PCR Targeting the Complete TmlPV L2 Gene

Based on nucleotide sequences of the L1-L2 fragment obtained in our laboratory, a

minus-strand oligonucleotide primer RP CR622 (Table 2-3) was designed downstream of

the L2 stop codon to be used together with the L2 FP CR572 for amplification of the

complete L2 gene. DNA obtained from a lesion from captive manatee Oakley was used

as the positive control. A blank sample (water) and DNA from a negative tissue

(manatee liver) were used as negative controls. A linear representation of the circular

TmlPV genome with the relative positions of the PCR primers used in this study is shown

in Figure 2-1.

Gel Electrophoresis

Between 20-30 [tl of PCR products were resolved by horizontal electrophoresis in

1.0% agarose gels containing ethidium bromide (0.5 [g/ml). Amplified DNA fragments









were visualized under ultraviolet light and photographed using a gel documentation

system (Bio-Rad Laboratories, Inc., Hercules, California, USA).

General Cloning of PCR Products

As described under gel electrophoresis, PCR products containing amplified

fragments of only the expected size were purified for use in cloning reactions. PCR

products containing additional amplified fragments were resolved in 1.2% low-melting

point (LMP) agarose and the band of the appropriate size was excised and purified for

use in cloning reactions. PCR products and excised gel pieces were purified using the

Wizard SV Gel and PCR Clean-Up System (Promega Corporation, Madison, Wisconsin,

USA) according to the protocol provided by the manufacturer. Briefly, an equal volume

of membrane binding solution was added to the PCR product, the prepared PCR product

was added to the SV minicolumn assembly, and the minicolumn was washed twice with

the membrane wash solution. The purified DNA was eluted in 50 ptl of nuclease-free

water and stored at -800C until further use in cloning reactions.

Cloning into pCR 2.1 TOPO T/A Vector

Purified PCR products were cloned into the pCR 2.1 TOPO vector (Invitrogen

Life Technologies, Carlsbad, California, USA) for sequencing analysis. In a 0.2 ml tube,

ligation reactions contained: 1 itl of salt solution (1.2 M NaC1, 0.06 M MgC12), 1 Ol of the

TOPO T/A vector (Invitrogen), 50 ng of purified PCR or gel product, and ultrapure H20

in a final volume of 6 l. Reactions were incubated at room temperature for 1 hour; then,

3 l of the reaction were added to one vial (50tl) of DH5a or TOP-10 chemically

competent Escherichia coli cells (Invitrogen). Tubes were placed on ice for 1 hour, heat

shocked for 30 sec at 420C in a water bath, and returned to ice. After adding 250 pl of

S.O.C. medium (Invitrogen), the tubes were shaken horizontally at 220 rpm at 370C for 1









hour. Reactions (100-200 .il) were spread onto bacterial agar plates containing ampicillin

(100 pg/ml) (Roche Applied Science) and blue/white selection medium [75 pl 2XYT:

16g Bacto-tryptone, 10 g Bacto-Yeast Extract, 15 g Bacto-Agar (Beckton Dickinson,

Franklin Lakes, New Jersey, USA), 5g enzyme grade NaCl (Fisher Scientific

International Inc., Hampton, New Hampshire, USA) in 1 L of ultrapure H20, 20 pl IPTG

(100mg/ml) (Invitrogen), and 5 .l UltraPure Bluo-gal (100mg/ml) (Invitrogen)] spread

on the agar plates surface one hour before the plates were inoculated with cloning

reactions. Plates were incubated overnight at 370C.

Cloning into P-TargetTM Mammalian Expression Vector

Purified PCR products were directly cloned into the P-TargetTM mammalian

expression vector (Promega) to test for protein expression after transfection and

immunofluorescence. In a 0.5 ml tube, the ligation reaction contained: 1 p1 of T4 DNA

ligase constituents, 1 il of T4 DNA ligase, 1 il of pTargetTM cloning vector (ProMega),

51p of purified PCR product, and ultrapure H20 in a final volume of 10 il. The ligation

reaction was incubated at 40C overnight in a refrigerated block. Five il of the ligation

reaction were added to one vial (501l) of JM109 high efficiency competent cells

(Promega) and incubated on ice for 20 min. The cells were heat shocked for 45 sec at

420C in a water bath and returned to ice for 2 min. After adding 450p1 of S.O.C.

medium, the tubes were shaken at 150 rpm at 370C for 1.5 hrs. The transformation

reaction was spread in 100p1 volumes onto bacterial agar plates containing ampicillin

(100 lg/ml) and blue/white selection medium.

Cloning into pcDNA TM3.1 Directional TOPO Expression Vector

In order to pair with the -GTGG- overhang of the pcDNATM 3.1 Directional

TOPO Expression Vector, the TmlPV E7 FP CR 500 was modified at the 5'end to









contain a corresponding 4-bp CACC sequence. To amplify the complete TmlPV E7 gene

with the TOPO overhang, the modified E7 FP CR 530 (Table 2-3) was used in a PCR

reaction with the TmlPV E7 RP CR501. The PCR reaction in a 0.2 ml tube contained:

200 nM of each primer, 300 mM Tris-SO4 (pH 9.1), 90 mM (NH4)2SO4, 10 mM MgSO4,

200KM of each dNTP, 2 units of Elongase enzyme mix (Invitrogen), 0.5-1.0 [g of

template DNA, and ultrapure H20 to a final volume of 50 [il. Cycling conditions for the

amplification of the E7 TOPO PCR products were: an initial denaturation step at 940C

for 2 min, then 39 cycles of a denaturation step at 940C for 30 sec, an annealing step at

510C for 1 min, and an extension step at 680C for 1 min. Purified E7 TOPO PCR

products were directly cloned into the pcDNATM 3.1 Directional TOPO expression

vector for use in immunofluorescence assays. In a 0.2 ml tube, the ligation reaction

contained: 1 ll of salt solution (50 mM NaC1, 2.5 mM MgC12), 1 l1 of pcDNATM 3.1

TOPO vector (Invitrogen), 50 ng of purified E7 TOPO PCR product, and ultrapure

H20 in a final volume of 6[l. Ligation reactions were incubated at room temperature for

1 hour; then, 3 l of the reaction were added to one vial (50 l) of One-shot TOP10

chemically competent E. coli cells (Invitrogen). Tubes were placed on ice for 1 hour,

heat shocked for 30 sec at 420C in a water bath, and returned to ice. After adding 250 il

of S.O.C. medium (Invitrogen), the tubes were shaken horizontally at 220 rpm at 370C

for 1 hour. Transformations (100-200 pl) were spread onto bacterial agar plates

containing ampicillin (100 .g/ml) and the plates were incubated overnight at 370C.

Analyzing Recombinants

Using sterile toothpicks, bacterial colonies were selected from agar plates and

added to 10 ml sterile glass tubes containing 3 mL 2XYT and 3ptl ampicillin (100lg/ml)

and the tubes were shaken overnight at 275 rpm at 370C. DNA was extracted from









approximately 1 ml of overnight culture using the 10-minute Mini-Prep Protocol (Zhou et

al., 1990). Briefly, overnight cultures were centrifuged for 10 sec in a 1.5 ml capped

tube. The supernatant was discarded, 300.l of TENS was added to the cell pellet, and the

tube was vortexed for 2-5 sec. Then, 150 pl of 3.0 M sodium acetate (pH 5.2) (Gibco

Life Technologies, Carlsbad, California, USA) were added and the tube was vortexed and

centrifuged. The supernatant was transferred to a fresh 1.5 ml capped tube and mixed

thoroughly with 0.9 ml of 100% molecular grade ethanol which had been pre-cooled to -

200C. After centrifugation, the plasmid DNA pellet was washed twice with 1 ml of 70%

ethanol, allowed to dry, and resuspended in 50 [l of TE buffer (pH 8.0). Recombinants

were analyzed by restriction enzyme digestion using endonucleases HindIII, Apal,

BamHI, EcoRI, and the combination of Apal and BamHI (Invitrogen). Restriction digest

reactions contained: 0.3 [il of restriction enzyme, 3.0 [il of the appropriate enzyme buffer,

1.0 pl of mini-prep DNA, and ultrapure H20 in a final volume of 30 il. Reactions were

incubated at 370C for 1 hour in a dry block and analyzed by gel electrophoresis.

Recombinants containing inserts of the appropriate size were further propagated in

competent E. coli cells and purified with the AuruTM Plasmid Mini Kit (Bio-Rad

Laboratories, Inc., Hercules, CA, USA) for sub-cloning and sequencing. Following the

protocol provided by the manufacturer, 1 ml of overnight culture was added to a 2.0 ml

tube, centrifuged, and the supernatant decanted. Then, 250 [l of resuspension solution

and 2501l of lysis solution were added, the tube was inverted 6-8 times, and the mixture

was allowed to incubate at room temperature for 5 min to ensure lysis was complete.

After adding 350 [l of neutralization solution, the tube was inverted 6-8 times and

centrifuged. The cleared lysate was transferred to a mini spin column and the column









was washed once with 750 [l of wash solution. The DNA was eluted in 50 il of elution

solution and evaluated for yield and purity by spectrophotometry.

Sub-cloning of Purified Recombinants

In order to obtain a high yield and purity of vector and recombinant DNAs for sub-

cloning reactions, midi-prep DNAs were prepared with the Qiagen plasmid purification

kit (Qiagen, Hilden, Germany), according to the manufacturer's protocol.

Transformation reactions containing 1 pl of DNA were propagated overnight in 100 ml

of 2XYT medium (100.l ampicillin), the overnight cultures were centrifuged, and the

supernatants were removed. The bacterial pellets were resuspended and vortexed in 4 ml

of buffer P1 and mixed gently in 4 ml of buffer P2. The lysis reactions were allowed to

proceed at room temperature for 5 min and 4 ml of chilled buffer P3 were added. The

reactions were mixed gently, incubated on ice for 15 min, and centrifuged for 1 hour until

the supernatant was clear. Each supernatant was added to an equilibrated Qiagen-tip 100

and allowed to enter the resin by gravity flow. The Qiagen-tip was washed twice with

buffer QC and the DNA was eluted in 5 ml of buffer QF. The DNA was precipitated in 5

ml of isopropanol, washed with 2 ml of 70% ethanol, and allowed to dry for 15-20 min.

The DNA pellet was redissolved in 200 pl of buffer EB and evaluated for yield and

purity by spectrophotometry.

Sub-Cloning into pcDNA 3.1/Zeo+ Expression Vector

The complete TmlPV E6 and L1 capsid genes were sub-cloned from pCR 2.1

TOPO T/A into pcDNA 3.1/Zeo+ expression vector at positions of compatible restriction

sites present in the vector multiple cloning sites. The TmlPV E6 recombinants were sub-

cloned into the expression vector at the EcoRI site, and the TmlPV complete L1 gene

recombinants were sub-cloned into the expression vector at the HindIII and Xbal sites.









Purified recombinant DNAs and purified pcDNA 3.1/Zeo DNA were cut with identical

restriction enzyme(s) in separate digest reactions. Restriction digests of pcDNA 3.1/Zeo

contained: 3.0 .il of restriction enzyme, 6.0 .il of the corresponding buffer (Invitrogen),

3.0 pl of bovine serum albumin (Invitrogen), 1 pg of purified pcDNA 3.1/Zeo vector

DNA, and ultrapure H20 in a final volume of 601. Restriction digests of TOPO T/A

recombinants were similar, except that they contained 3 pg of purified recombinant DNA.

Digest reactions were incubated at 370C in a dry block for 2 hours and resolved by

horizontal electrophoresis in 1.2% low-melting point (LMP) agarose gels containing

ethidium bromide (0.5 ig/ml). The bands of the appropriate size for the digested pcDNA

3.1/Zeo+ vector and for the digested recombinants were excised from the LMP gel and

purified using the Wizard SV gel and PCR clean-up system. DNA from the purified gel

products was used in the ligation reaction that contained: 4 [il of 5X T4 ligase buffer, 1.5

pl of T4 ligase (Invitrogen), a 1 [1 of gel purified recombinant DNA, 3 pl of gel purified

pcDNA 3.1/Zeo and ultrapure H20 in a final volume of 20[l. Ligation reactions were

incubated overnight at 140C in a refrigeration block. Ten [il of the ligation reaction were

added to one vial (50 [l)ofDH5a competent E. coli cells, incubated on ice for 1 hour,

heat shocked at 420C for 30 sec, and returned to ice. Then, 600 pl of 2XYT containing

50 mM glucose were added and the vial was shaken horizontally at 220 rpm at 370C for 1

hour. Reactions (200p1) were spread onto agar plates containing ampicillin, and plates

were incubated overnight at 370C. Bacterial colonies were selected from the plates and

propagated in 2XYT medium containing ampicillin. Recombinant DNA was purified

using the 10 minute mini-prep protocol and inserts of the appropriate size cloned into the

pcDNA 3.1+ vector were confirmed by restriction digest using 6-base cutter enzymes









Nsil, known to cut the TmlPV E6 fragment once, and Spel, known to cut the TmlPV L1

fragment sequence once.

L1 Gene Sub-Cloning into pFastBacTM1 Vector

The TmlPV complete L1 gene was sub-cloned from pCR 2.1 TOPO T/A into the

pFastBacTM1 vector (Invitrogen) at positions of compatible restriction sites present in the

vector multiple cloning site for use in the Bac-to-Bac Baculovirus expression system

(Invitrogen). Purified L1 recombinant DNA and purified pFastBacTMI vector DNA were

cut with identical restriction enzyme(s) in separate digest reactions. Restriction digests of

pFastBacTMI contained: 3.0 .il of restriction enzyme EcoRI (Invitrogen), 6.0 .il of the

corresponding 10X buffer III (Invitrogen), 3.0 pl of bovine serum albumin (Invitrogen), 1

tg of purified pFastBacTM1 maxi-prep DNA, and ultrapure H20 in a final volume of

60p l. Restriction digests of the TOPO T/A TmlPV L1 complete gene recombinant were

similar, except that they contained 3 tg of purified maxi-prep recombinant DNA. Digest

reactions were incubated at 370C in a dry block for 2 hours and resolved by horizontal

electrophoresis in 1.2% low-melting point (LMP) agarose gels containing ethidium

bromide (0.5 [tg/ml). Bands of the appropriate size for the digested pFastBacTMI vector

and the digested TOPO T/A TmlPV L1 complete gene recombinant were excised from

the LMP gel and purified using the Wizard SV gel and PCR clean-up system. The

ligation and transformation reactions of the L1 complete gene into pFastBacTM1 were set

up similar to the reactions previously described for sub-cloning into the pcDNA 3.1+/Zeo

expression vector, except that transformations were performed in TOP-10 competent E.

coli cells (Invitrogen). Individual bacterial colonies were selected from the plates and

propagated in 2XYT medium containing ampicillin (100lg/ml). DNA was extracted

from the overnight cultures using the 10 minute mini-prep protocol (Zhou et al., 1990)









and pFastBacTM1 L1 recombinants were identified by restriction digest with enzymes

EcoRI, Hind III, and BamHI, a 6-base cutter enzyme known to cut the TmlPV L1

sequence at one site.

L1 Gene Sub-Cloning into pBlueBac 4.5

The TmlPV complete L1 gene was sub-cloned from pCR 2.1 TOPO T/A after

digesting with enzymes Xbal and SstI into the pBlueBac 4.5 vector (Invitrogen), which

was digested with the same enzymes. The ligation and transformation reaction of the

TmlPV L1 gene into the pBlueBac vector was set up similar to the described sub-cloning

reaction into the pFastBacI vector. Individual bacterial colonies were selected from agar

plates and propagated in 2XYT medium containing ampicillin (100lg/ml). DNA was

extracted from overnight cultures using the 10 minute mini-prep protocol (Zhou et al.,

1990) and pBlueBac L1 recombinants were identified by restriction digest with Xbal and

SstI enzymes.

Sequencing of PCR-amplified and Cloned Products

As described under gel electrophoresis, amplified PCR products of the expected

size were purified and sequenced directly using the PCR primers diluted 1:5 in sterile

H20. Cloned PCR products were sequenced with the corresponding vector sequencing

primers diluted 1:10 in sterile H20. Additional sequencing primers (1:5) were used to

obtain the complete sequence of cloned DNA fragments that were greater than 600

nucleotides in length. A list of sequencing primers is contained in Table 2-4. Between

50-100 fmol of purified PCR products or purified recombinants were sequenced in

duplicate using specific forward and reverse primers in the Beckman-Coulter CEQ

2000XL sequencing instrument (Beckman-Coulter Inc., Fullerton, California, USA).

Chromatograms were checked manually for errors in nucleotide sequences using the









Chromas 2.3 software (Technelysium Pty Ltd., Tewantin, Queensland, Australia), and the

assembled sequences were analyzed using the seqed, gap, translate, and multiple

alignment functions of the University of Wisconsin Package Version 10.2 (Genetics

Computer Group [GCG], University of Wisconsin, Madison, Wisconsin, USA). The

Basic Local Alignment Search Tool (BLAST) function of the National Center for

Biotechnology Information (NCBI) website (http://www.ncbi.nlm.nih.gov/) was used to

identify papillomavirus sequences most closely related to sequences obtained from

TmlPV fragments. Neighbor-Joining phylogenetic trees were generated by PAUP 4.0

(Sinauer Associates, Sunderland, Massachusetts, USA) software, using Clustal W slow

and accurate function using Gonnet residue weight table, gap penalty of 35 and gap

extension penalty of 0.75 for pairwise alignment parameters, and gap penalty of 15 and

gap extension penalty of 0.3 for multiple alignment parameters. Phylogenetic trees were

constructed with the deduced amino acid sequences of the TmlPV L1 ORF, L2 ORF, E6

ORF, and E7 ORF DNA fragments. Trees were based on the amino acid sequences of

human and non-human PVs obtained from the GenBank database through the NCBI

website and from the HPV database of the Los Alamos National Laboratory Theoretical

Biology and Biophysics website (http://hpv-web.lanl.gov/stdgen/virus/hpv/).

Transfection of Insect Cell Cultures

Culturing Insect Cells

Sf21 (Spodoptera frugiperda) insect cells (Invitrogen) were used as indicator cell

cultures to generate recombinant baculoviruses. Sf21 cells were cultured in 75 cm2 flasks

(TPP, Switzerland) in serum free Sf-900 II medium (Invitrogen) containing: 200 pg/ml

of antibiotic/antimycotic [penicillin (1X104 units/ml)], streptomycin sulfate (10 mg/ml),

amphotericin B (25 pg/ml)] (Gibco), 200 pg/ml of gentamicin (100 pg/ml) (Gibco), and









10% fetal bovine serum (Gibco). Insect cells were incubated at 270C in a humidified

incubator. After one week, the cell monolayer was scraped with a sterile, disposable cell

scraper (Greiner Bio-One, Kremsmuenster, Australia), resuspended in 10 ml of Sf-900

11/10% FBS, and counted with a hemocytometer (Reichert Scientific Instruments,

Buffalo, NY). Approximately 1 X 106 Sf21 cells in 2 ml of Sf-900 I1/10% FBS medium

were added to 35 mm dishes and incubated at 270C. All steps were performed in a

laminar-flow cabinet under sterile conditions.

Transformation of MAX Efficiency DH1OBacTM Competent E. coli

In order to transfect insect cell cultures and generate a recombinant baculovirus, the

pFastBacTM1 L1 constructs were first transformed into MAX Efficiency DH10BacTM

competent E. coli (Invitrogen) that contain a baculovirus shuttle vector (bacmid) and a

helper plasmid. Briefly, 1 [l of purified pFastBacTM1 recombinant (Ing/il) was added to

50pl of DH10BacTM E. coli, incubated on ice 30 min, heat shocked at 420C for 45 sec,

and returned to ice for 2 min. The reaction was transferred to a 15 ml screw-cap conical

tube (Sarstedt Inc., Newton, North Carolina, USA) and 900 pl of S.O.C. medium were

added. The reactions were shaken at 225 rpm at 370C for 4 hours and transformations

were spread onto bacterial agar plates containing kanamycin (50.g/ml), tetracycline

(10g/ml), gentamicin (7 pg/ml) (Gibco), and blue/white selection medium. Plates were

incubated overnight at 370C. Individual bacterial colonies were selected and propagated

in 3ml 2XYT medium containing kanamycin, tetracycline, and gentamicin and shaken

overnight at 275 rpm at 370C. Overnight cultures were purified using the 10 minute

mini-prep protocol and recombinant bacmids were confirmed by PCR analysis. The Bac-

to-Bac M13 primers, forward primer CR 613: 5'-CCC AGT CAC GAC GTT GTA

AAA CG-3' and reverse primer CR 614: 5'-AGC GGA TAA CAA TTT CAC ACA GG-









3', were used together in a PCR reaction that contained: 200 nM of each primer, 2 mM

MgSO4, 100 pM of each dNTP, 20 mM Tris-HCl (pH 8.4), 10 mM KC1, 0.1 % Triton X-

100 (pH 8.8), 10 mM (NH4)2S04, 1 unit of Taq DNA polymerase (New England

BioLabs), 1 [1 of mini-prep DNA, and ultrapure H20 in a final volume of 50il. For

amplification ofbacmid DNAs, cycling conditions were: an initial denaturation step at

930C for 3 min, followed by 29 cycles of denaturation at 940C for 45 sec, annealing at

510C for 45 sec, and extension at 720C for 5 min. An elongation step at 720C for 7 min

was incorporated into the final cycle. Bacmid DNA recombinants containing the L1

complete gene were expected to be approximately 4,000-bp in size (2,300 bp bacmid

DNA plus 1,712 bp L1 complete gene) and bacmid DNA amplicons that were not

recombinants were expected to be approximately 300-bp in size. PCR products were

resolved by horizontal electrophoresis in 1.0% agarose gels containing ethidium bromide

(0.5 [g/ml) and visualized under UV light. Recombinant bacmids were further

confirmed to contain the pFastBacTM1 L1 gene by PCR analysis targeting the TmlPV L1

complete gene.

Transfection of Insect Cells with Bacmid DNA Recombinants

In a 10 ml glass bacteriological tube (Fisher Scientific), 1 [tg of L1 bacmid DNA

was added to 100[l of unsupplemented Grace's insect cell culture medium (Gibco). In a

separate glass tube, 6 [il of Cellfectin Reagent (Img/ml) (Invitrogen) were added to

100p1 of unsupplemented Grace's insect cell culture medium. The mixtures were

combined and the tube was incubated at room temperature for 45 min. Prior to

transfecting Sf21 insect cells, the cell monolayer was washed with 2 ml of Grace's

medium and incubated for 5 min at room temperature. The medium was removed and

800 [l of Grace's medium were added gently and directly to the cells. The









Bacmid/Cellfectin transfection mix was then added dropwise onto the cells and the

cultures were incubated at 270C for 5 hours. At this time, the transfection mixture was

removed and 2 ml of unsupplemented Grace's medium was added to the transfected cells.

Cultures were incubated at 270C in a humidified incubator. Sf21 cells fed with

unsupplemented Grace's medium (without baculovirus DNA) and Sf21 cells transfected

with purified baculovirus DNA (without insert) were used as negative controls. All steps

were performed in a laminar-flow cabinet under sterile conditions.

Harvest of Recombinant Baculovirus Stocks

After the transfected cell cultures were incubated for approximately 96 hrs, the cell

monolayer and supernatant (-2 ml) were collected with a sterile pipette and inoculated

onto Sf21 cultures in 60 mm tissue culture dishes. One ml of the cell supernatant plus 1

ml of Sf-900 11/5% FBS medium were added to fresh 60 mm dishes containing

approximately 2 X 106 Sf21 cells. The cells were incubated at 270C for 1.5 hrs, the

inoculum was removed, and the cultures were transfected with 3 ml of unsupplemented

Grace's medium. Infected cultures were incubated at 270C for approximately 96 hrs and

sub-cultured again into fresh cultures. The infected cultures were sub-cultured a total of

5 times and the final harvest of cells and supernatants were obtained from 150 mm

dishes. All steps were performed in a laminar-flow cabinet under sterile conditions.

Harvests from infected cell cultures were analyzed by electron microscopy, by Mr.

Woody Frazer, from the Florida Animal Disease Diagnostic Laboratory, Florida

Department of Agriculture and Consumer Services, Kissimmee, Florida.

Reverse Transcription PCR (RT-PCR) of Infected Cell Cultures

RNA was extracted from infected Sf21 cell cultures transfected with the pBlueBac

plasmid containing the L1 capsid gene to determine whether messenger RNA (mRNA)









encoding the TmlPV L1 capsid protein was present. To use as negative controls, RNA

was extracted from untransfected Sf21 cell cultures and from Sf21 cells transfected with

purified parental pBlueBac vector. Cells and supernatants were harvested 96 hrs after

transfection, centrifuged at 4,000 rpm at 100C for 10 min, the supernatant was removed,

and RNA was extracted from the cell pellets using the Aurum total RNA mini kit (Bio-

Rad). The RNA samples were treated with twice the recommended amount (160p1) of

DNase I solution for 30 min, eluted from a mini column with 100l1 of elution solution,

and treated again with 160[l of DNase I solution. The alcohol precipitated RNA pellet

was resuspended in 601l of RNase-free H20 and analyzed for yield and purity by

spectrophotometry. Total RNA was used in reverse transcription reactions in order to

obtain a first-strand cDNA product for use in PCR analysis. Synthesis of cDNA was

performed with SuperScript II (Invitrogen) according to the manufacturer's protocol.

Reactions contained random hexamer primers (Invitrogen) or a TmlPV L1 gene-specific

primer (RP CR574) designed by us. The reverse transcription assays were performed in

duplicate with or without the incorporation of SuperScript II reverse transcriptase

enzyme (Invitrogen) in order to ensure that the DNA had been completely degraded by

the DNase I treatment during the RNA extraction process. The cDNAs were used as

templates for amplification in TmlPV L1 PCR assays according to the PCR protocol

targeting the TmlPV complete L1 gene.

Generation of Recombinant Baculovirus

Recombinant vector pBlueBac 4.5 containing the complete TmlPV L1 gene under

the control of the polyhedron promoter and the Bac-N-Blue baculovirus DNA

(Invitrogen) (0.5kg DNA in 10pl volume) were incubated at room temperature for 10

min. Then, 1 ml of unsupplemented Grace's insect medium (Invitrogen) was added to









the tube, followed by 20Cl of Cellfectin reagent (Invitrogen). The reaction was gently

mixed for 10 sec and allowed to incubate at room temperature for 15 minutes. Prior to

transfecting the Sf21 insect cultures (3X106) seeded in 60 mm dishes, the medium was

removed and the cell monolayer was rinsed gently twice with 2 ml of fresh,

unsupplemented Grace's insect medium without FBS. The transfection mixture was

added dropwise onto the cells and incubated at 270C for six hours in a humidified

incubator. After the incubation period, 2 ml of complete TNM-FH medium (Invitrogen)

containing gentamycin (10g/ml) and FBS (10%) were added to each dish. The dishes

were incubated at 270C for 10 days, at which time cells and medium were harvested and

stored at 40C prior to screening and purification of the recombinant viruses. A second

dish containing Sf21 cell cultures was transfected with the transfer vector pBlueBac 4.5

containing the L1 capsid gene, but no baculovirus DNA, and treated similarly. A third

culture ofuntransfected Sf21 cells served as a negative control. After 72 hrs, 500[l of

the medium was harvested from each dish and transferred to a sterile 15 ml screw-cap

tube to which 2[l ofBluo-gal substrate (200[g/pl in DMSO) was added. The tubes were

incubated at 270 and monitored for the development of a blue color.

Transfection of Mammalian Cells

Culturing African Green Monkey Kidney (COS-7) Cells

African green monkey kidney (COS-7) cells were propagated in 75 cm2 flasks in

Dulbecco's modified eagle medium (DMEM) (Gibco) containing gentamycin,

antibiotic/antimycotic, and 10% FBS. Cells were incubated at 370C in a humidified

incubator.









Electroporation of COS-7 Cells with Recombinants for Immunofluorescence Assays

COS-7 cells were dispersed with trypsin/EDTA (0.25% Trypsin/lmM EDTA)

(Gibco), resuspended in 10 ml DMEM/5% FBS in a 15 ml screw cap tube, and counted

with a hemocytometer. The cells were centrifuged at 1,500 rpm for 10 min at 100C in a

refrigerated centrifuge (Jouan, Unterhaching, Germany). The medium was aspirated

from the cells and the cell pellet was resuspended in cold, sterile IX PBS (Gibco). Then,

0.4 ml of cell suspension (1 X 107 cells) and 5 g of purified recombinant plasmid DNA

were added to a 0.4 cm cuvette placed inside the Gene Pulser II unit shocking chamber

(Bio-Rad Laboratories). COS-7 cell electroporation assays were performed using either

the E6 complete gene in pcDNA 3.1+/Zeo or the L1 complete gene in pcDNA 3.1+/Zeo

vector. Cells were electroporated in the Gene Pulser II Electroporation System (Bio-Rad

Laboratories) for 0.64 msec with the low capacitor set at 25[iF and the voltage set at 0.6

KVolts. Then, 200 [il of electroporated cells were added to each chamber of a four

chamber glass slide (Lab-Tek, Nalge Nunc Intl., Naperville, Illinois, USA), each

containing 1 ml ofDMEM/10 % FBS and zeocin, and the chambered coverglass sides

were incubated at 370C. Recombinant plasmid DNAs with the genes cloned in the wrong

orientation and parental plasmid DNA (without insert) were used as negative controls.

Cells in each chamber of the slide were fixed at four different times; 12 hrs, 24 hrs, 36

hrs, and 48 hrs. Briefly, the medium was aspirated from the chamber and the cells were

rinsed with lml of 1X Hanks balanced salt solution (Gibco). The cells were then fixed

for 1 min using 1 ml of cold acetone: methanol (1:1) solution, the fixative was removed,

and the chamber slide was stored at -200C until use. Immediately before use, to

equilibrate the cells, 1 ml of PBS/ 3% BSA was added to each slide chamber, allowed to

soak the monolayer for 5 minutes at room temperature, and removed. Serum obtained









from captive manatees (Holly, Betsy, Oakley, Willoughby, Amanda, and Lorelei) with a

history of papillomavirus infection was diluted 1:20 in PBS/3% BSA solution and 500 [l

of diluted serum were added to the appropriate chamber. The cells were incubated at

370C for 1 hr, the serum was removed, and the cells were washed three times with 1 ml

PBS/0.025% Tween 20 (Fisher Scientific, Fairland, New Jersey, USA) solution. Purified

anti-manatee IgG monoclonal antibody (1.2mg/ml) was diluted 1:20 in PBS/3% BSA

solution and 500 pl of diluted monoclonal antibody were added to each chamber. The

chambers were incubated at 370C for 1 hr, the monoclonal antibody was removed, and

the cell monolayer was washed three times with 1 ml PBS/0.025% Tween 20 solution.

Fluorescein-labeled protein G conjugate (250[g/ml) (Sigma-Aldrich, Steinheim,

Germany), was diluted 1:40 in PBS/3% BSA, 200 pl were added to each slide chamber,

and the chamber slides were incubated at 370C for 1 hr. The monolayers were gently

rinsed three times with 1 ml PBS/0.025% Tween 20 solution, the cover and lining of the

chamber were removed, and ProLong gold anti-fade reagent (Molecular Probes,

Carlsbad, California, USA) was added dropwise to the monolayer. Cover slips were

placed on the anti-fade reagent and the obtained monolayers were evaluated for specific

immunofluorescence using a fluorescent microscope (Zeiss Axiovert 25). Similar

immunofluorescence assays were also performed using fluorescein-labeled Protein A

(Sigma-Aldrich), instead of Protein G, according to the methods described.

Culturing Florida Manatee Respiratory Epithelial Cells

Florida manatee respiratory epithelial (TmlRE) cell cultures were obtained from

Dr. Mark Sweat (Fish and Wildlife Research Institute, St. Petersburg, Florida) and

propagated in 75 cm2 flasks in Dulbecco's modified eagle medium (DMEM) (Gibco)









containing antibiotic/antimycotic, gentamycin, and 10% FBS. Cells were incubated at

370C in a humidified incubator.

Transfection of TmlRE Cells with DNA Recombinants for Immunofluorescence
Assays

Methods for transfecting TmlRE cells were the same as the methods described for

transfecting COS-7 cells. TmlRE cell transfection assays were performed with E7

pcDNA 3.1+ TOPO and the L1 complete gene pcDNA 3.1 /Zeo recombinant plasmids.


Table 2-1. Samples obtained from skin lesions of captive Florida manatees. DNA
extracted from lesions was tested by PCR for the presence of papillomavirus
infection. HSSWP: Homosassa Springs State Wildlife Park, FL: Florida, SD:


San Diego, CA:California.
Sample I.D. Manatee I.D.
CR130 Oakley
V368 Betsy
V369 Holly
V370 Betsy
V371 Amanda
V372 Amanda
V373 Willowby
V374 Willowby
V375 Lorelei
V376 Lorelei
V377 Lorelei
V684 Rosie
V685 Lorelei
V686 Betsy
V687 Amanda
V909 SW04031
V910 SW04031
V989 TM0334
V991 Stubby
V995 TM0341
V996 TM0341


Location
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
HSSWP, FL
SD, CA
SD, CA
Orlando, FL
Orlando, FL
Orlando, FL
Orlando, FL


Date Obtained
July, 2002
July, 1998
July, 1998
July, 1998
January, 2000
January, 2000
January, 2000
January, 2000
January, 2000
January, 2000
January, 2000
October, 2003
October, 2003
October, 2003
October, 2003
January, 2004
January, 2004
January, 2004
January, 2004
January, 2004
January, 2004









Table 2-2. Samples obtained from skin lesions of free-ranging Florida manatees. DNA
extracted from lesions was tested by PCR for the presence of TmlPV
infection. CR: Crystal River, FL: Florida, HR: Homosassa River, DK:
Drowned Keys, BZ: Belize, POI: Port of Isles (Everglades City),
TB=Tampa Bay,*: manatee penile lesion, **: uninfected manatee liver.
Sample I. D. Manatee I. D. Location of Manatee Date Obtained
V378 RKB-1029-17 CR, FL January, 2003
V389 RKB-1035-31 CR, FL February, 2003
V390 RKB-1036-19 HR, FL February, 2003
V396 RKB-1040-23 HR, FL February, 2003
V397 RKB-1039-13 HR, FL February, 2003
V408 RKB-10474 CR, FL February, 2003
V556 BZ01M16 DK,BZ May, 2003
V1329 TNP-29 POI, FL April, 2004
V1330 TNP-29 POI, FL April, 2004
V1331 TNP-29 POI, FL April, 2004
V1332 TNP-31 POI, FL April, 2004
V1333 TNP-32 POI, FL April, 2004
V1334 Unidentified POI, FL April, 2004
V1335 Unidentified POI, FL April, 2004
V1343 BZ04M64 DK, BZ May, 2004
V1437* MEC0449 TB, FL August, 2004
V1351 BZ04M58 DK, BZ May, 2004
V1774 THR-02 HR, FL April, 2005
V1776 THR-03 HR, FL April, 2005
V1777 THR-04 HR, FL April, 2005
V1855** MEC-0515 TB, FL February, 2005

Table 2-3. PCR primers designed to target manatee papillomavirus sequences


Target
L1 458-bp
Fragment



L1--El
Region

Complete E6
Gene


E6 TOPO
Fragment


PCR Primer
FP CR333
RP CR332
FP CR490
RP CR491

FP CR442
RP CR441

FP CR498
RP CR499

FP CR529
RP CR499


PCR Primer Sequence
5'- GCI CAG GGI CAT AAI AAT GG-3'
5'- CGT CCI AII GGA IAC TGA TC-3'
5'- CAG GGG CAT AAG AAT GGT ATT G -3'
5'- GAG GGG AGA CTG ATC GAG TTC TG-3'

5'- CCT GCT GAA AAT GAT GAT CC -3'
5'- TTA TCA IAT GCC CAI TGT ACC AT -3'

5'- CAA CCA TCT TCT ACA TGC TTA GT-3'
5'- CGT ATT CTT GGA TAT GTG GTG -3'

5'- CAC CCA ACC ATC TTC TAC ATG CTT AGT-3'
5'- CGT ATT CTT GGA TAT GTG GTG -3'









Table 2-3. Continued


Target
E7 TOPO
Fragment

L1-L2
Region
Complete L1


Gene


Complete L2
Gene


PCR Primer
FP CR530
RP CR501

FP CR572
RP CR574
FP CR573

RP CR574

FP CR572
RP CR622


PCR Primer Sequence
5'-CAC CTT AGA AGAC ACA GCA CGT ATC-3'
5'- ATC TGT TGT ATC CGA GTC AC -3'

5'- TAA CCG CAT TTA ATG GGC AAT TTG -3'
5'- AAT AAA ATG ATG CAC AGT GCC AG -3'
5'- CAC CTA CAA TCC TTA TTG ATT TTC AAT C
-3'
5'- AAT AAA ATG ATG CAC AGT GCC AG -3'

5'- TAA CCG CAT TTA ATG GGC AAT TTG -3'
5'-TTC GGT ATT GAG GAT GCG GG-3'


Table 2-4. Sequencing primers used to obtain the complete sequence of PCR amplified
TmlPV gene fragments.
Target Sequencing Primer Primer Sequence
L1 458-bp FP CR333 5'- GCI CAG GGI CAT AAI AAT GG -3'
Fragment RP CR332 5'- CGT CCI All GGA IAC TGA TC -3'
FP M13 5'- GTA AAA CGA CGG CCA G -3'
RP M13 5'- CAG GAA ACA GCT ATG AC -3'


L1-El
Region


Complete E6
Gene



Complete E7
Gene


L1-L2
Region


T7 Promoter
RP CR216
FP CR579
RP CR478
FP CR492
RP CR493

FP M13
RPM13
T7 Promoter
RP CR532

FP M13
RPM13
T7 Promoter
RP CR532

FP M13
RPM13
FP CR583
RP CR580
FP CR588
RP CR601
FP CR 592


5'- TAA TAC GAC TCA CTA TAG GG -3'
5'- TAC AAG ACA GGT TTA AGG AGA C -3'
5'- TGC GCA TAG TTA CTT CTG AG -3'
5'- CAG TGT ACC ATT GAA GAT AAG TC -3'
5'- ATG TAT GAA GTA TAA ATA GCA C -3'
5'- CAA CTC TAC CTG TAC GTT CC -3'

5'- GTA AAA CGA CGG CCA G -3'
5'- CAG GAA ACA GCT ATG AC -3'
5'- TAA TAC GAC TCA CTA TAG GG -3'
5'-TAG AAG GCA CAG TCG AGG-3'

5'- GTA AAA CGA CGG CCA G -3'
5'- CAG GAA ACA GCT ATG AC -3'
5'- TAA TAC GAC TCA CTA TAG GG -3'
5'-TAG AAG GCA CAG TCG AGG-3'

5'- GTA AAA CGA CGG CCA G -3'
5'- CAG GAA ACA GCT ATG AC -3'
5'- AGA TTA CAC CAG AGG CTC C -3'
5'- ATT CAT TGT ATG TAT GTG GG -3'
5'- CCC TAT CTT TGA CAA TTC TG -3'
5'- GAG CGT CTG CTT TCG TGT GT -3'
5'-GGG AGA CTC CAC TGA TAC CA-3'






42


Table 2-4. Continued
Target Sequencing Primer Primer Sequence


Complete L1 FPM13
Gene RP M13
FP CR579
RP CR580


5'- GTA AAA CGA CGG CCA G -3'
5'- CAG GAA ACA GCT ATG AC -3'
5'- TGC GCA TAG TTA CTT CTG AG -3'
5'- ATT CAT TGT ATG TAT GTG GG -3'






















L2ORF FP CR572
-- I0


L1ORF FP CR573
-- 0


L1 FP CR333/
L1FP CI90
E6 FP CR498
L1FP CR442 -


S2 ORF L1 ORF NCR I ORF 7 ORF NCR E ORF


L20RF RP CR622
4-


L1ORF RP CR574
4-


E6 RP CR499
4-


E7 RP CR500
4-


E1 RP CR441
4-


L1 RP CR332/
L RPCR491

Figure 2-1. Linear representation of the open reading frames (ORFs) of the circular manatee papillomavirus (TmlPV) genome with
the relative positions of the PCR primers used to amplify TmlPV DNA. FP=Forward primer, RP=Reverse primer.


E7FP CR500













CHAPTER 3
RESULTS

PCR Results

Total DNA extracted from 13 skin lesions of captive Florida manatees (Trichechus

manatus latirostris) and six skin lesions of free-ranging Florida manatees from the

vicinity of Homosassa Springs State Wildlife Park (HSSWP) amplified DNA fragments

of the expected size in PCR assays for the detection of manatee papillomavirus (TmlPV).

DNA fragments of the expected size could not be amplified from DNA extracted from

three skin lesions of free-ranging Antillean manatees (T. manatus manatus) in PCR

assays and, therefore, served as negative controls in subsequent PCR assays. DNA

extracted from one manatee liver was also incorporated into the PCR in order to serve as

a negative control and to validate the results in subsequent PCR assays. PCR results of

manatee skin lesions assayed for the presence of TmlPV DNA are shown in Tables 3-1,

3-2, and 3-3 (summary).

PCR Targeting the Papillomavirus L1 458-bp Fragment

Oligonucleotide primers MY11 and MY09 (Manos et al., 1989), known to amplify

a 458-bp fragment within the L1 capsid gene of several human papillomaviruses and

modified by us to contain deoxyinosines at positions of nucleotide degeneracy (primers

CR333 and CR332), amplified DNA fragments of identical size from five captive

manatee skin lesions, out of 11 tested, and from four free-ranging manatee skin lesions

(near HSSWP), out of seven tested.









PCR Targeting the AL1 TmlPV Fragment

The AL1 TmlPV oligonucleotide primers CR490 and CR491, designed to amplify a

458-bp fragment within the L1 capsid gene of TmlPV, amplified DNA fragments of

identical size from 11 captive manatee skin lesions, out of 15 assayed, and from five free-

ranging manatee skin lesions, out of 15 tested for the presence of papillomavirus

infection. Total DNA from four skin lesions from which no amplification of the 458-bp

DNA fragments could be achieved using the MY11 and MY09 HPV L1 primer set

amplified DNA fragments of the expected size (458-bp) using the TmlPV-specific

CR490 and CR491 primer set (Figure 3-1).

PCR Targeting the TmlPV L1-E1 Region

Oligonucleotide primers CR442 and CR441, known to amplify an approximately

3,000 bp fragment of the L1-El region of the HPV-70 genome (Forslund and Hansson,

1996), amplified a fragment of similar size from one captive manatee skin lesion that

was tested with the CR442/CR441 primers (Figure 3-2).

PCR Targeting the Complete TmlPV E6 Gene

Oligonucleotide primers CR498 and CR499, designed to amplify a 587-bp

fragment of the TmlPV genome that contains the complete TmlPV E6 gene ORF,

amplified DNA fragments of the expected size from five captive manatee skin lesions

(Figure 3-3), out of eight tested for the presence of papillomavirus infection.

Amplification was not obtained from 12 free-ranging manatee skin lesions tested.

PCR Targeting the Complete TmlPV E7 Gene

Oligonucleotide primers CR500 and CR501, designed to amplify a 489-bp

fragment of the TmlPV genome that contains the complete TmlPV E7 gene ORF,

amplified DNA fragments of the expected size from five captive manatee skin lesions









(Figure 3-4), out of five tested for the presence of papillomavirus. Similar fragments

were not amplified from any of the seven free-ranging manatee skin lesions tested.

PCR Targeting the TmlPV L1-L2 Region

Oligonucleotide primers CR572 and CR574, designed to amplify a 3,208-bp

fragment of the TmlPV genome that contains the complete L1 gene ORF plus the

complete L2 gene ORF, amplified DNA fragments of the expected size from two skin

captive manatee skin lesions (Figure 3-5), out of two tested for the presence of

papillomavirus infection.

PCR Targeting the Complete TmlPV L1 Gene

Oligonucleotide primers CR573 and CR574, designed to amplify a 1,712-bp

fragment of the TmlPV genome that contains the complete L1 capsid gene ORF,

amplified DNA fragments of the expected size from three captive manatee skin lesions

(Figure 3-6), out of three tested for the presence of papillomavirus infection.

PCR Targeting the Complete TmlPV L2 Gene

Oligonucleotide primers CR572 and CR622, designed to amplify a 1,611-bp

fragment of the TmlPV genome that contains the complete L2 capsid gene ORF,

amplified DNA fragments of the expected size from two captive manatee skin lesions

(Figure 3-7), out of two tested for the presence of papillomavirus infection.

Sequencing Results and Genetic Analyses

TmlPV L1 458-bp Fragments

Sequencing of papillomavirus L1 capsid gene fragments amplified with the

modified HPV primers MY11 and MY09 (CR333/CR332) revealed that the fragments

were 458-bp in length, supporting the universality of the MY11 and MY09 primers,

which are known to amplify a 458-bp DNA fragment from most types of genital HPVs









(Bernard et al., 1994). Sequencing of papillomavirus L1 capsid gene fragments amplified

with the AL1 TmlPV-specific primers revealed that the fragments were also 458-bp in

length. Nucleotide sequences of the 458-bp TmlPV L1 gene fragments were entered into

the Basic Local Alignment Search Tool (BLAST) of the National Center for

Biotechnology Information Website (NCBI, Bethesda, Maryland) to identify

papillomavirus homologues that had the highest similarity and identity to TmlPV L1.

This demonstrated that the amplified TmlPV fragments were contained within a highly

conserved domain of the L1 capsid protein gene of papillomaviruses. Nine TmlPV L1

fragment sequences, obtained from the DNA of three captive manatee lesions and six

free-ranging manatee lesions, were submitted to the GenBank database of the NCBI

website (Table 3-4).

The TmlPV L1 gene fragments translated correctly from the first nucleotide of

forward primer (FP) MY11 and FPALITmlPV (CR 490) into protein fragments

consisting of 152 amino acids. The GAP function of the GCG Genetic Package (GCG,

University of Wisconsin, Madison, Wisconsin, USA) showed that the nine TmlPV L1

fragment sequences were 100% identical at the nucleotide and the amino acid level. The

multiple alignment of the deduced amino acid sequences of the TmlPV L1 fragments

demonstrated the identity of the TmlPV L1 sequences (Figure 3-8). Comparisons of the

TmlPV L1 amino acid sequence with homologues from human and non-human

papillomaviruses demonstrated identities that ranged between 36% and 57% (Table 3-5)

and similarities that ranged between 57% and 67% (Table 3-6). After removal of the L1

primer sequences, the L1 fragment sequence was 100% identical to the corresponding L1









region of the TmPV-1 sequence obtained by another research group and recently

deposited in the GenBank database (AY609301) and published (Rector et al., 2004).

L1-E1 TmlPV Region

Sequencing of the approximately 3,000-bp papillomavirus DNA fragment

amplified from one lesion of a captive manatee (V369, Holly) revealed that the fragment

was 2,772 nucleotides in length. The ORF(Open Reading Frame) Finder tool of the

NCBI website revealed that the 2,772-bp sequence contained partial sequences of the L1

ORF, the complete E6 ORF, the complete E7 ORF, and partial sequences of the El ORF.

Further genetic analysis of the 2,772-bp sequence showed that it contained: partial

sequences of the 3' end of the TmlPV L1 ORF (261-bp, including the L1 stop codon),

followed by a large non-coding region (816-bp), the TmlPV E6 ORF (414-bp, including

the E6 stop codon), then, separated by two nucleotides, the TmlPV E7 ORF (348-bp,

including the E7 stop codon), a small non-coding region (334-bp), and partial sequences

of the 5' end of the TmlPV El ORF (599-bp). The 2,772-bp sequence that spans the L1-

El region of the TmlPV genome was submitted to the GenBank database of the NCBI

website (Table 3-4). Nucleotide sequences of the TmlPV E6 ORF translated into a

protein consisting of 137 amino acid residues. Comparisons of the TmlPV E6 137 amino

acid sequence with homologues from human and non-human papillomaviruses

demonstrated identities that ranged between 22% and 32% (Table 3-5) and similarities

that ranged between 28% and 42% (Table 3-6). The TmlPV E6 ORF sequence obtained

from sequencing the 2,772-bp fragment was submitted to the GenBank database of the

NCBI website (Table 3-4). Nucleotide sequences of the TmlPV E7 ORF translated into a

protein consisting of 115 amino acid residues. Comparisons of the TmlPV E7 115 amino

acid sequence with homologues from human and non-human papillomaviruses









demonstrated identities that ranged between 23% and 41% (Table 3-5) and similarities

that ranged between 31% and 51% (Table 3-6). Pair-wise comparisons were not

performed with Phocoena spinipinnis PV (PsPV-1) because the PsPV-1 genome does not

encode an E7 ORF. The complete TmlPV E7 ORF sequence obtained from sequencing

the 2,772-bp fragment was submitted to the GenBank database of the NCBI website

(Table 3-4).

TmlPV E6 Gene

Sequencing of amplified DNA fragments containing the complete TmlPV E6 gene

from four lesions of captive manatees revealed that the fragments were 587 nucleotides in

length. Genetic analysis of the 587-bp TmlPV E6 gene fragment revealed that the

sequence contained the complete TmlPV E6 ORF (414-bp, including the E6 stop codon)

that translated into a protein consisting of 137 amino acid residues. Comparisons of the

four obtained TmlPV E6 sequences showed that the nucleotide identity ranged from 99.5-

100.0% and the amino acid identity was 100.0% (not shown). The TmlPV E6 gene

sequence obtained from the positive control manatee DNA (CR130) demonstrated 100%

identity and similarity to the corresponding region of the TmPV-1 genome described by

another research group (Rector et al., 2004). The TmlPV E6 ORF sequences were

submitted to the GenBank database of the NCBI website (Table 3-4).

TmlPV E7 Gene

Sequencing of amplified DNA fragments containing the complete TmlPV E7 gene

from four lesions of captive manatees revealed that the fragments were 489 nucleotides in

length. Genetic analysis of the 489-bp TmlPV E7 gene fragments revealed that the

sequences contained the complete TmlPV E7 ORF (348-bp, including the E7 stop codon)

that translated into a protein consisting of 115 amino acid residues. Comparisons of the









four obtained TmlPV E7 ORF sequences showed that the nucleotide identity ranged from

99.4% tol00.0 % and the amino acid identity ranged from 99.1% to 100.0% (not shown).

The TmlPV E7 sequence obtained from positive control manatee DNA (CR130) had

100% identity and similarity to the corresponding region of the recently published

TmPV1 genome (Rector et al., 2004). The TmlPV E7 ORF sequences were submitted to

the GenBank database of the NCBI website (Table 3-4).

TmlPV L1-L2 Region

Sequencing of the amplified TmlPV L1-L2 gene fragments from two papillomatous

lesions of captive manatees Oakley and Holly revealed that the fragments were 3,208

nucleotides in length. Genetic analysis revealed that the fragments contained the

complete TmlPV L1 ORF (1,518-bp, including the L1 stop codon) plus the complete

TmlPV L2 ORF (1,536-bp, including the L2 stop codon). The start codon of the

TmlPVL 1 ORF sequence was contained within the TmlPV L2 ORF sequence, and the

TmlPV L1 and TmlPVL2 ORFs had an overlapping region of 20 nucleotides. Nucleotide

sequences of the TmlPV L1 ORF translated into a protein of 505 amino acid residues.

Comparisons of the TmlPV L1 505 amino acid sequence with homologues from human

and non-human papillomaviruses demonstrated identities that ranged between 31% and

57% (Table 3-5) and similarities that ranged between 41% and 68% (Table 3-6). The

complete TmlPV L1 sequence obtained from a lesion of manatee Oakley (CR130)

demonstrated 100% identity and similarity to the corresponding region of the TmPV1

genome deposited in the GenBank database by another research group (AY609301). The

two TmlPV L1 ORF sequences obtained from lesions of captive manatees Oakley and

Holly shared 99.7% nucleotide identity and 99.8% amino acid identity (not shown). The

TmlPV L1 ORF sequences were submitted to the GenBank database of the NCBI website









(Table 3-4). Nucleotide sequences of the TmlPV L2 ORF translated into a protein of 511

amino acid residues. Comparisons of the TmlPV L2 511 amino acid sequence with

homologues from human and non-human papillomaviruses showed identities that ranged

between 35% and 42% (Table 3-5) and similarities that ranged between 43% and 51%

(Table 3-6). The complete TmlPV L2 sequence obtained from positive control manatee

DNA (CR130) demonstrated 100% identity and similarity to the corresponding region of

the TmPV1 genome (AY609301). The two TmlPV L2 ORF sequences obtained from

lesions of captive manatees Holly and Oakley shared 99.9% nucleotide identity and

99.6% amino acid identity (not shown). The TmlPV L2 ORF sequences were submitted

to the GenBank database of the NCBI website (Table 3-4).

Complete TmlPV L1 Gene from Captive Manatee Lorelei

Sequencing of the amplified fragment containing the complete TmlPV L1 gene

fragment from one lesion of captive manatee Lorelei (V685) revealed that the fragment

was 1,712 nucleotides in length. Genetic analysis revealed that the fragment contained

the complete TmlPV L1 ORF sequence that translated into a protein of 505 amino acid

residues. The complete TmlPV L1 ORF sequence was shown to be 99.7% and 99.4%-

99.7% identical to the previously obtained TmlPV L1 ORF sequences at the nucleotide

and amino acid levels, respectively (not shown). The TmlPV L1 ORF sequence (Lorelei)

was submitted to the GenBank database of the NCBI website (Table 3-4).

Complete TmlPV L2 Gene

Total DNA extracted from two lesions of captive manatees Oakley and Holly from

which the complete TmlPV L2 gene (1,611-bp) was amplified was also positive for

amplification of the TmlPV L1-L2 fragment (3,208-bp). This fragment had previously









been sequenced; therefore, sequencing of the complete TmlPV L2 genes from these

DNAs (V369 and CR130) was not repeated.

Immunofluorescence and Gene Expression Assays

Mammalian Expression Systems

Fluorescence was not detected in immunologic assays utilizing monkey kidney

(COS-7) cells transfected with TmlPV L1 or TmlPV E6 genes cloned in eukaryotic

vectors under the control of the CMV promoter. Likewise, specific fluorescence was not

observed in assays using Florida manatee respiratory epithelial (TmlRE) cells transfected

with the eukaryotic vectors containing the TmlPV L1 gene under control of the CMV

promoter. A few TmlRE cells transfected with the E7 gene displayed a faint halo of

fluorescence; however, fluorescence was considered subjective and ambiguous and did

not provide conclusive evidence of protein expression. Restriction digests of the TmlPV

E6 and E7 pcDNA3.1+/Zeo recombinants are shown in Figure 3-11.

Bac-to-Bac Baculovirus Expression System

Supernatant and cell harvests from Sf21 insect cell cultures transfected with TmlPV

L1 capsid protein bacmid DNA were analyzed by electron microscopy by Mr. Woody

Frazer, Florida Animal Disease Diagnostic Laboratory, Florida Department of

Agriculture and Consumer Services, Kissimmee, Florida for the presence of virus-like

particles (VLPs). Amorphous clumps were observed after negative staining that

resembled capsid protein particles; however, papillomavirus-like particles of the expected

size (50-55 nm) were not observed (Figure 3-9). The cDNAs obtained by RT-PCR of

RNAs extracted from infected cell cultures showed that mRNA expressing the TmlPV L1

gene was being produced in the cell cultures (Figure 3-10). Restriction digests of the









TmlPV L1 pFastBacl recombinant used in the transfection experiment are shown in

Figure 3-12.

Bac-N-Blue Baculovirus Expression System

After ninety-six hours of incubation at 270C, supernatants were harvested from

Sf21 cell cultures transfected with the recombinant pBlueBac 4.5 L1 vector DNA. The

baculovirus DNA developed blue color after 48 hrs of incubation (270C) in the presence

of the P-galactosidase substrate Bluo-gal (Invitrogen). This finding indicated that

recombination had occurred between the homologous sequences in the baculovirus DNA

(Bac-N-Blue DNA) and the transfer vector (pBlueBac 4.5 L1 plasmid), reconstituting the

essential sequences necessary for replication of the newly generated recombinant virus.

Supernatants corresponding to the cultures transfected with the pBlueBac 4.5 L1 vector

(no baculovirus DNA) and those from the untransfected cultures did not express the P-

galactosidase enzyme, as judged by the lack of development of blue color. Although no

direct proof has yet been obtained on the expression of the L1 capsid protein by the

generated baculoviruses, it is speculated at this point that unless the L1 capsid gene has

been inadvertently mutagenized, protein expression after the isolation and purification of

recombinant baculovirus will be demonstrated by Western blot analysis.

Phylogenetic Analysis

Multiple sequence alignments and the construction of phylogenetic trees

demonstrated the genetic relatedness of the TmlPV amino acid sequences to the amino

acid sequences of several human and non-human papillomaviruses. Trees were

constructed using the following PVs (with their GenBank accession numbers): Human

papillomavirus type la HPV-la (V01116), HPV-2a (X55964), HPV-3 (X74462), HPV-4

(X70827), HPV-5 (M17463), HPV-6 (AF092932), HPV-7 (X74463), HPV-9 (X74464),









HPV-11 (M14119), HPV-13 (X62843), HPV-15 (X74468), HPV-16 (K02718), HPV-18

(X05015), HPV-20 (U31778), HPV-21 (U31779), HPV-26 (X74472), HPV-27

(X74473), HPV-30 (X74474), HPV-32 (X74475), HPV-33 (M12732), HPV-34

(X74476), HPV-41 (X56147), HPV-51 (M62877), HPV-63 (X70828), HPV-65

(X70829), HPV-92 (NC_004500), HPV-95 (AJ62010), Bovine PV type 1 BPV-1

(X02346), BPV-2 (M20219), Canine oral PV COPV (L22695), Cottontail rabbit PV

CRPV (AJ243287), White-tail deer PV DEERPV (M11910), Equus caballus PV ECPV

(NC_003748), European elk PV EEPV (M15953), Ovine PV type 1 OPV-1 (U83594),

OPV-2 (U83595), Rhesus monkey PV RhMPV (M60184), Phocoena spinipinnis PV

PsPV1(AJ238373), and Manatee papillomavirus type 1 TmPV1 (AY609301). Florida

manatee PV (TmlPV) sequences obtained from positive control manatee DNA (CR130)

were used in all phylogenetic analyses. The L1 capsid protein gene phylograms indicated

that the TmlPV sequence formed a unique branch, distinct from known human and

animal papillomavirus L1 sequences (Figure 13). The TmlPV complete L2 capsid

protein gene also formed a separate branch in the L2 capsid protein phylograms (Figure

14), indicating the uniqueness of this virus. The E6 protein gene based phylograms

indicated that TmlPV was the sole member of a unique branch (Figure 3-15). Similarly,

the E7 protein gene claded by itself to form a branch that is closely rooted to the

papillomaviruses of hoofed animals (Figure 3-16).












Table 3-1. PCR results of DNAs obtained from captive manatee skin lesions tested for the presence of
TmlPV infection. POS: positive, DNA fragments of the expected size were amplified;
NEG: negative, DNA fragments of the expected size were not amplified; X: assay not


ORF: open reading frame.


Sample
I. D. No.
CR130
V368
V369
V370
V371
V372
V373
V374
V375
V376
V377
V684
V685
V686
V687
V909
V910
V989
V991
V995
V996


performed,
L1 458-bp
Fragment
POS
NEG
POS
NEG
NEG
NEG
NEG
POS
POS
POS
NEG
X
X
X
X
X
X
X
X
X
X


TmlPV AL1
Fragment
POS
X
X
POS
POS
X
X
X
POS
POS
X
POS
POS
POS
POS
NEG
POS
NEG
NEG
POS
NEG


L1-L2
Region
POS
X
POS
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X


L1-El
Region
X
X
POS
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X


E6 ORF
POS
X
POS
X
NEG
X
X
X
POS
X
X
X
POS
POS
X
X
NEG
X
X
NEG
X


E7 ORF
POS
X
POS
POS
X
X
X
X
X
X
X
X
POS
POS
X
X
X
X
X
X
X


L1 ORF
POS
X
POS
X
X
X
X
X
X
X
X
X
POS
X
X
X
X
X
X
X
X


L2 ORF
POS
X
POS
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X












Table 3-2. PCR results of DNAs obtained from free-ranging manatee skin lesions tested for the presence of TmlPV infection. POS:
positive, DNA fragments of the expected size were amplified; NEG: negative, DNA fragments of the expected size were
not amplified; X: assay not performed, ORF: open reading frame, *= penile skin lesion, **= normal manatee liver DNA


Location of
Animal
CR, FL
CR, FL
HR, FL
HR, FL
HR, FL
CR, FL
DK, BZ
POI, FL
POI, FL
POI, FL
POI, FL
POI, FL
POI, FL
POI, FL
DK, BZ
DK, BZ
TB, FL
HR, FL
HR, FL
HR, FL
TB, FL


Animal L1 458-bp
I. D. Fragment


V378
V389
V390
V396
V397
V408
V556
V1329
V1330
V1331
V1332
V1333
V1334
V1335
V1343
V1351
V1437*
V1774
V1776
V1777
V1855**


POS
NEG
NEG
POS
POS
POS
NEG
X
X
X
X
X
X
X
X
X
X
X
X
X
X


TmlPV AL1
Fragment
X
POS
POS
POS
POS
POS
NEG
NEG
NEG
NEG
NEG
NEG
NEG
NEG
NEG
NEG
NEG
NEG
NEG
NEG
NEG


L1-L2
Region
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
NEG
NEG
NEG
X


L1
ORF
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
NEG
NEG
NEG
X


L2
ORF
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
NEG
NEG
NEG
X


L1-E1
Region
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X


E6
ORF
X
NEG
NEG
NEG
NEG
NEG
X
NEG
NEG
NEG
NEG
NEG
NEG
NEG
X
X
X
X
X
X
X


E7
ORF
X
X
X
X
X
X
X
NEG
NEG
NEG
NEG
NEG
NEG
NEG
X
X
X
X
X
X
X













Table 3-3. Summary of PCR results. DNAs obtained from skin lesions of captive and free-ranging manatees were tested for the
presence of manatee papillomavirus infection.


CAPTIVE
MANATEES


FREE-RANGING
MANATEES


Tissues
No. +ve

No. tested

No. +ve
No. tested


CR332/CR333
Fragment
5
11


AL1
Fragment
11
15


L1-L2
Region
2


L1-El
L1 ORF L2 ORF Region


E6 ORF E7 ORF
5 5
8 5









Table 3-4. Accession numbers of manatee papillomavims
GenBank tool of the NCBI website.
Animal
Amplicon I.D. No.
TmlPV L1 458-bp Fragment V369
V396
V389
V390
V397
V408
V375
V378
CR130


TmlPV L1-El Region

TmlPV Complete E6 Gene





TmlPV Complete E7 Gene





TmlPV L -L2 Region


TmlPV Complete L1 Gene



TmlPV Complete L2 Gene


V369

CR130
V369
V685
V686

CR130
V369
V685
V686

CR130
V685

CR130
V369
V686

CR130
V369


sequences deposited into the

GenBank
Accession No.
AY455940
AY455941
AY496568
AY496569
AY496570
AY496571
AY496572
AY496574
AY496575


DQ099425

DQ099425
AY830703
AY830704
AY830705

DQ099427
AY830706
AY830707
AY830708

DQ099423
DQ099424

AY994164
AY994166
DQ099422

AY994165
AY994167









Table 3-5. Pair-wise comparisons of the amino acid sequences of the L1, L2, E6, and E7
gene fragments of manatee papillomavirus (TmlPV) with several human and
non-human papillomaviruses. Numbers represent percent identity to
corresponding TmlPV sequences obtained from Oakley's DNA. X=no
sequence available.

PV Type L1 Fragment L1 ORF L2 ORF E6 ORF E7 ORF
HPVla 55.0 53.0 37.0 32.0 40.0
HPV2a 51.0 52.0 37.0 30.0 36.0
HPV3 57.0 53.0 37.0 29.0 39.0
HPV4 57.0 56.0 40.0 28.0 32.0
HPV5 53.0 56.0 41.0 26.0 35.0
HPV6 55.0 54.0 37.0 25.0 40.0
HPV7 50.0 54.0 37.0 27.0 27.0
HPV9 54.0 56.0 40.0 29.0 40.0
HPV11 56.0 54.0 36.0 23.0 38.0
HPV13 56.0 55.0 37.0 22.0 39.0
HPV15 50.0 54.0 41.0 26.0 41.0
HPV16 51.0 52.0 37.0 30.0 35.0
HPV18 43.0 52.0 38.0 22.0 31.0
HPV20 57.0 58.0 39.0 31.0 35.0
HPV21 57.0 57.0 40.0 30.0 38.0
HPV26 55.0 54.0 38.0 26.0 28.0
HPV27 51.0 51.0 39.0 28.0 35.0
HPV30 56.0 55.0 39.0 23.0 30.0
HPV32 52.0 52.0 40.0 31.0 31.0
HPV33 54.0 31.0 38.0 30.0 28.0
HPV34 53.0 52.0 36.0 25.0 32.0
HPV41 55.0 51.0 36.0 31.0 28.0
HPV51 55.0 54.0 37.0 28.0 32.0
HPV63 55.0 51.0 36.0 31.0 27.0
HPV65 57.0 57.0 39.0 28.0 28.0
HPV92 51.0 55.0 40.0 30.0 38.0
HPV95 57.0 57.0 40.0 32.0 24.0
BPV1 49.0 50.0 36.0 28.0 28.0
BPV2 50.0 50.0 35.0 28.0 27.0
OPV1 49.0 50.0 36.0 25.0 31.0
OPV2 51.0 50.0 35.0 22.0 28.0
CRPV 53.0 57.0 37.0 32.0 25.0
DeerPV 47.0 46.0 35.0 22.0 23.0
ECPV 55.0 51.0 40.0 29.0 32.0
EEPV 50..0 51.0 37.0 25.0 21.0
RhMPV 54.0 53.0 38.0 27.0 39.0
COPV 53.0 54.0 41.0 27.0 34.0
PsPV1 53.0 51.0 42.0 26.0 X
TmPV1 100.0 100.0 100.0 100.0 100.0









Table 3-6. Pair-wise comparisons of the amino acid sequences of the L1, L2, E6, and E7
gene fragments of manatee papillomavirus (TmlPV) with several human and
non-human papillomaviruses. Numbers represent percent similarity to
corresponding TmlPV sequence obtained from Oakley's DNA. X=no sequence
available
PV Type L1 Fragment L1 ORF L2 ORF E6 ORF E7 ORF
HPVla 65.0 63.0 47.0 42.0 51.0
HPV2a 60.0 62.0 47.0 36.0 40.0
HPV3 66.0 63.0 45.0 36.0 44.0
HPV4 66.0 65.0 49.0 36.0 43.0
HPV5 64.0 66.0 51.0 40.0 44.0
HPV6 64.0 63.0 46.0 34.0 50.0
HPV7 61.0 63.0 47.0 35.0 36.0
HPV9 65.0 66.0 49.0 39.0 50.0
HPV11 63.0 62.0 47.0 33.0 48.0
HPV13 64.0 64.0 45.0 32.0 45.0
HPV15 63.0 64.0 51.0 39.0 49.0
HPV16 60.0 61.0 48.0 36.0 43.0
HPV18 66.0 62.0 47.0 32.0 41.0
HPV20 66.0 62.0 49.0 42.0 44.0
HPV21 67.0 68.0 50.0 41.0 45.0
HPV26 66.0 64.0 47.0 33.0 40.0
HPV27 61.0 62.0 48.0 37.0 40.0
HPV30 64.0 64.0 46.0 30.0 38.0
HPV32 63.0 63.0 48.0 42.0 40.0
HPV33 64.0 41.0 48.0 37.0 36.0
HPV34 62.0 62.0 47.0 32.0 42.0
HPV41 65.0 62.0 46.0 41.0 36.0
HPV51 65.0 64.0 46.0 37.0 43.0
HPV63 65.0 62.0 46.0 41.0 36.0
HPV65 66.0 65.0 48.0 37.0 40.0
HPV92 64.0 65.0 50.0 40.0 45.0
HPV95 67.0 67.0 50.0 38.0 36.0
BPV1 63.0 61.0 44.0 36.0 31.0
BPV2 64.0 61.0 44.0 34.0 31.0
OPV1 60.0 61.0 43.0 33.0 34.0
OPV2 61.0 60.0 44.0 31.0 31.0
CRPV 65.0 66.0 46.0 36.0 34.0
DeerPV 57.0 56.0 46.0 28.0 31.0
ECPV 62.0 60.0 51.0 36.0 37.0
EEPV 60.0 61.0 46.0 32.0 32.0
RhMPV 63.0 62.0 46.0 38.0 51.0
COPV 62.0 64.0 51.0 40.0 41.0
PsPV1 62.0 61.0 50.0 36.0 X
TmPV1 100.0 100.0 100.0 100.0 100.0









Table 3-7. Summary of the pair-wise comparisons of the amino acid sequences of
manatee papillomavirus gene fragments with several human and non-human
papillomaviruses.
TmlPV Fragment Most Similar PV Type (%) Least Similar PV type (%)
L1 458-bp HPV-21 (67.0%) DeerPV (57.0%)


HPV-21 (67.0%)
HPV-20 (66.0%)
HPV-65 (66.0%)


OPV-1 (60.0%)
EEPV (60.0%)
HPV-2a (60.0%)


Complete L1 ORF





Complete L2 ORF





Complete E6 ORF





Complete E7 ORF


HPV-21 (68.0%)
HPV-95 (67.0%)
HPV-5 (66.0%)
HPV-9 (66.0%)

HPV-5 (51.0%)
HPV-15 (51.0%)
COPV (51.0%)
ECPV (51.0%)

HPV-la (42.0%)
HPV-20 (42.0%)
HPV-32 (42.0%)
HPV-63 (41.0%)

HPV-la (51.0%)
RhMPV (51.0%)
HPV-15 (49.0%)
HPV-11 (48.0%)


Fragment


HPV-33
DeerPV
OPV-2
ECPV

OPV-1
OPV-2
BPV-1
BPV-2

DeerPV
HPV-30
OPV-2
HPV-18

BPV-1
BPV-2
OPV-2
DeerPV


(41.0%)
(56.0%)
(60.0%)
(60.0%)

(43.0%)
(44.0%)
(44.0%)
(44.0%)

(28.0 %)
(30.0%)
(31.0%)
(32.0%)

(31.0%)
(31.0%)
(31.0%)
(31.0%)
























MM 1 2 3 4 5 6 7 8 9 10 11 12
Figure 3-1. Agarose gel electrophoresis of PCR amplified 458-bp fragments of the L1
capsid protein gene of manatee papillomavirus. MM: 1 Kb Molecular marker,
Lane 1: V375, Lane 2: V376, Lane 3: V389, Lane 4: V390, Lane 5: V396,
Lane 6: V397, Lane 7: V408, Lane 8:V370, Lane 9:V371, Lane 10:V556,
negative tissue; Lane 11: negative tube, water; Lane 12: Positive control
captive manatee Oakley (CR130). C: Captive manatee, FR: Free-ranging
manatee


MM 1 2 3
Figure 3-2. Agarose gel electrophoresis of PCR amplified 2,772-bp fragment of the Ll-
El region of manatee papillomavirus. MM: 1 Kb Molecular marker, Lane 1:
Captive manatee Holly (V369), Lane 2: negative tube, no DNA; Lane 3:
negative tissue control (V1855).


C, C, P- IP- IP- IP- IP- C, C






















MM 1 2 3 4 5 6
Figure 3-3. Agarose gel electrophoresis of PCR amplified 587-bp fragments of the E6
gene of manatee papillomavirus. MM: 1 Kb Molecular marker, Lane 1:
Captive manatee Holly (V369), Lane 2: Captive manatee Betsy (V686), Lane
3: Captive manatee Lorelei (V685), Lane 4: Positive control captive manatee
Oakley (CR130), Lane 5: negative tube, no DNA; Lane 6: negative tissue
control (V1855).


.. ... ... .











MM 1 2 3 4 5 6
Figure 3-4. Agarose gel electrophoresis of PCR amplified 489-bp fragments of the E7
gene of manatee papillomavirus. MM: 1 Kb Molecular marker, Lane 1:
Captive manatee Holly (V369), Lane 2: Captive manatee Betsy (V686), Lane
3: Captive manatee Lorelei (V685), Lane 4: Positive control captive manatee
Oakley (CR130), Lane 5: negative tube, no DNA; Lane 6: negative tissue
control (V1855).






















MM 1 2 3 4
Figure 3-5. Agarose gel electrophoresis of PCR amplified 3,208-bp fragments of the L1
gene plus the L2 gene of manatee papillomavirus. MM: 1 Kb Molecular
marker, Lane 1: Captive manatee Holly (V369), Lane 2: Positive control
captive manatee Oakley (CR130), Lane 3: negative tube, no DNA; Lane 4:
negative tissue control (V1855).


MM 1 2 3 4 5
Figure 3-6. Agarose gel electrophoresis of PCR amplified 1,712-bp fragments of the
complete L1 gene of manatee papillomavirus. MM: 1 Kb Molecular marker,
Lane 1: Captive manatee Holly (V369), Lane 2: Captive manatee Lorelei
(V685), Lane 3: Positive control captive manatee Oakley (CR130), Lane 4:
negative tube, no DNA; Lane 5: negative tissue control, (V1855).


























1 2 3 4
SAgarose gel electrophoresis of PCR amplified 1,660-bp fragments of the
complete L2 gene of manatee papillomavirus. MM: 1 Kb Molecular marker,
Lane 1: Captive manatee Lorelei (V685), Lane 2: Positive control captive
manatee Oakley (CR130), Lane 3: negative tube, no DNA; Lane 4: negative
tissue control (V1855).


MM
Figure 3-7






















































V408



V397



V396



V390



V389



V378



V375



V369



P31


Consensus AQGHKNGIAW QNQLFVTILD NTRGTNMTVS VSTQNALVVD HYDDNDYAQY LRHAEEFELS FVFQLCKVQL TTEALAHIHT MNPKILEDWH IGLRPPPSAS


V408



V397



V396



V390



V389



V378



V375



V369



P31


Consensus VEDQYRYIQS LATRCPPKEV PAENDDPYKT KKFWVVDLST RFSTELDQSP LG












Figure 3-8. Multiple alignment of the amino acid sequences deduced from the nucleotide sequences of the L1 gene fragment of




manatee papillomavirus identified in cutaneous lesions of captive and free-ranging Florida manatees.


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Rod-shaped
Baculovirus particles


Amorphous
viral clumps











Figure 3-9. Electron micrograph of Sf21 insect cell cultures transfected with pFastBacl
TmlPV L1 gene recombinant. Amorphous viral clumps that resemble capsid
protein particles and rod-shaped Baculovirus (non-recombinant) particles
were found present. Photo supplied by Mr. Woody Fraser.









MM 1R 2S 3R 4S 5R 6S 7R 8S 9 10 MM











Figure 3-10. Agarose gel electrophoresis demonstrating the PCR amplification of the
manatee papillomavirus complete L1 gene fragment from cDNAs obtained
from infected Sf21 cell cultures. R= Random hexamer primers used in RT-
PCR reactions, S= TmlPV L1 gene-specific primers used in RT-PCR
reactions; MM=Molecular marker, 1 KB ladder; Lanes 1 and 2=Sf21 cell
cultures (negative control); Lanes 3 and 4=Sf21 cell cultures infected with
bacmid DNA (no recombinant); Lanes 5 and 6=Sf21 cell cultures infected
with TmlPV L1 gene recombinant; Lanes 7 and 8= Sf21 cell cultures infected
with TmlPV L1 gene recombinant (no SuperScript); Lane 9=blank sample
(H20), negative PCR control; Lane 10=TmlPV L1 plasmid DNA, positive
PCR control. All of the samples were treated with Dnasel solution, but the
samples in Lanes 7 and 8 were not treated with the SuperScript enzyme and
were not transcribed to cDNA. This demonstrates that the Dnase I solution
effectively degraded the DNA in these samples and validated the results of
this assay. Samples in lanes 5 and 6 were treated with the Dnasel solution and
also with SuperScript enzyme, therefore the TmlPV L1 DNA fragment was
able to be amplified from the cDNA.























MM 1 2 3 4
Figure 3-11. Agarose gel electrophoresis demonstrating restriction enzyme digests of the
manatee papillomavirus E6 gene and E7 gene recombinants. MM: 1 Kb
Molecular marker, Lane 1: pcDNA 3. l+/Zeo E6 recombinant, Hind III; Lane
2: pcDNA 3.1+/Zeo E6 recombinant, EcoRI; Lane 3: pcDNA 3.1+/Zeo E7
recombinant, Hind III; Lane 4: pcDNA 3. 1+/Zeo E7 recombinant, EcoRI
















MM 1 2 3 4
Figure 3-12. Agarose gel electrophoresis demonstrating restriction enzyme digests of the
manatee papillomavirus L1 complete gene recombinant. MM: 1 Kb
Molecular marker, Lane 1: pcDNA 3. 1+/Zeo L1 recombinant, Hind III; Lane
2: pcDNA 3.1+/Zeo L1 recombinant, HindIII plus Xhol; Lane 3: pFastBacl
L1 recombinant, Hind III; Lane 4: pFastBacl L1 recombinant, EcoRI.











HPVla
HPV63

CFPV
PsPV1

I TPV-1
M-.0- E HP"2a,
-- HFV27
HPV2
s HPV3
HPV13
HPV30
HPV26
~~~____~~______________--- HPkr41
HPVr51
HPV7
HPV13
HPW1
LE HPV B
&&-7Joao PV11
HPV 32
RIiMPV
t 7-- HPV34
S HPV16
.4 HPV33
HPVB95
HPV4
HPBkr 55
Rs HPV5

HPV21





ECPV
BPV 1
--4 BPV2
SOPV1
p opyl

A DEERPV
EEPV

Figure 3-13. A. Neighbor-Joining phylogenetic tree of the deduced amino acid sequences
of the complete LI gene of several human and non-human papillomaviruses.
The tree was generated by Clustal W slow and accurate function using Gonnet
250 residue weight table, gap penalty of 35 and gap extension penalty of 0.75
(pairwise alignment parameters), gap penalty of 15 and gap extension penalty
of 0.3 (multiple alignment parameters). In the rectangular cladogram format,
numbers represent the percent confidence of 1000 bootstrap replications. B. In
the radial format, the 0.1 divergence scale represents 0.1 substitutions per site











DEERPV



EEPV



TmPV1
TmlPV

SCRPV
COPV

HPV63
SHPV1a






HPV3

HPV2a
HPV27


B


0.1


Figure 3-13. Continued


S I HPV13
HPV11 HPV6
HPV7

















































Figure 3-14. A. Neighbor-Joining phylogenetic tree of the deduced amino acid sequences
of the complete L2 gene of several human and non-human papillomaviruses.
The tree was generated by Clustal W slow and accurate function using Gonnet
250 residue weight table, gap penalty of 35 and gap extension penalty of 0.75
(pairwise alignment parameters), gap penalty of 15 and gap extension penalty
of 0.3 (multiple alignment parameters). In the rectangular cladogram format,
numbers represent the percent confidence of 1000 bootstrap replications. B. In
the radial format, the 0.1 divergence scale represents 0.1 substitutions per site.













HPV4
HPV95 \


HPV20
HPV65 HPV5 I


HPV41

ECPV

PsPV1





OPV2
OPV1


DEERPV


BPV2 '0
BPV1


HPV11 / I
HPV6 /
HPV13 HPV32
HPV7 RhMPV


B 0.1


HPV21
HPV9
HPV15 TmPV1
/ TmlPV

CRPV


HPV63
HPVla


HPV27
HPV2a
HPV18
HPV26


HPV3
116


Figure 3-14. Continued












HPVZ'

HPV2T
H PY*
F8PV1
H FY'ZT


H PVI ?



H PY1F

H PV51
H P'~4








Tm1--lPV
Tl7 hM PV

H PY25

HFr41



T00 PV

H PAI

HPV1



1.4H P92
HPVW

HPV
---------- ( BP1
W S------------- T H P19 3








9.A HEVE2P
H P.
HPV15
ECPV
_BPW

Ii- [DEH RPV

A E EPV
O PV1




Figure 3-15. A. Neighbor-Joining phylogenetic tree of the deduced amino acid sequences
of the complete E6 gene of several human and non-human papillomaviruses.
The tree was generated by Clustal W slow and accurate function using Gonnet
250 residue weight table, gap penalty of 35 and gap extension penalty of 0.75
(pairwise alignment parameters), gap penalty of 15 and gap extension penalty
of 0.3 (multiple alignment parameters). In the rectangular cladogram format,
numbers represent the percent confidence of 1000 bootstrap replications. B. In
the radial format, the 0.1 divergence scale represents 0.1 substitutions per site.











HPV30 HPV51 PsPV1
HPV26I HPV32 HPV7
/ / HPV13
hMIHPV6
SI / HPV11


EEPV
DEERPV


HPV41

-- CRPV

TmPV1
TmlPV


0.1


Figure 3-15. Continued











COPV
H PV7
H PV13
H PV3
H PV32
H PV1a
RhHPV
H PV34
H PVl1
HPM3,
H PW S
H PV20
.0 H PV2T
HP V1
HPV11
HP V3D
HPV2B
SHPV51
HPV1B
HPV33
EC PV
BPV1
SBPV2
s;B I DEERPV
73A1
EE PV



I TniI _

CPV'
HP V41
H PV5
H PV20
H PuV21
H PV92
H PV'15
H PV9
SH PV95
H PV4
1 .0
H PLWS5


Figure 3-16. A. Neighbor-Joining phylogenetic tree of the deduced amino acid sequences
of the complete E7 gene of several human and non-human papillomaviruses.
The tree was generated by Clustal W slow and accurate function using Gonnet
250 residue weight table, gap penalty of 35 and gap extension penalty of 0.75
(pairwise alignment parameters), gap penalty of 15 and gap extension penalty
of 0.3 (multiple alignment parameters). In the rectangular cladogram, numbers
represent the percent confidence of 1000 bootstrap replications. B. In the
radial format, the 0.1 divergence scale represents 0.1 substitutions per site.













HPV26 HPV18


HPVla
S.HPV63


ECPV


% BPV2
BPV1

DEERPV


0.1 TmlPV
TmPV1


Figure 3-16. Continued














CHAPTER 4
DISCUSSION

Papillomatous lesions harvested from the skin of captive and free-ranging manatees

contained manatee papillomavirus (TmlPV) DNA and were morphologically similar to

the previously described papillomatous lesions of captive Florida manatees (Trichechus

manatus latirostris) housed at Homosassa Springs State Wildlife Park (HSSWP),

Homosassa, Florida (Bossart et al., 2002). Lesions were either flat and sessile or

pedunculated and distributed over the manatee body, including the flippers, nares, and

contact regions of the anterior body (Figure 4-1 and Figure 4-2). Conclusions could not

be made about the stage of the infection based on the appearance of the lesions; however,

the TmlPV L1 fragment sequence (GenBank Accession number AY496572) isolated

from a pedunculated skin lesion in the present study was 100% identical to the manatee

papillomavirus type 1 (TmPV-1) sequence that had been deposited in the GenBank

(AY609301) from another research group and had been isolated from a sessile skin

lesion. These findings strongly suggest that the same virus may cause both types of

papillomatous skin lesions in manatees, and is also suggested by those authors (Rector et

al., 2004).

Until recently, papillomavirus studies dealt mainly with transmission experiments,

virus ultrastructure and chemical composition, and pathological description of lesions.

The main impediment for the analysis of these viruses has been the lack of a reproducible

cell culture system permissive for their replication (Lancaster and Olson, 1982). The

study of PVs has been limiting, as only a few HPV types have been purified in quantities









sufficient for structural analysis, due to the low virus load of many lesions and the

inability to develop tissue culture systems for large scale propagation of the virus

(Rommel et al., 2005). However, the papillomavirus field has advanced recently,

especially in the areas of molecular biology techniques and molecular cloning, which

have made these viruses more amenable to study (Lancaster and Olson, 1982). Despite

the absence of advanced molecular tools, immunohistochemical data from previous

studies of papillomatous lesions in manatees indicated the presence of a species-specific

PV. The immunologic data also suggested that manatee PV (TmlPV) infection might be

latent and, possibly, that it might have been activated after immunosuppression (Bossart

et al., 2002). While electron microscopy evaluation and immunohistochemistry staining

of lesions showed the presence of a PV, these assays did not provide genetic information

about the type of PV involved. The primary objectives of this study were: 1.) To develop

a molecular diagnostic assay for the detection of TmlPV infection in skin lesions, 2.) to

molecularly characterize the TmlPV genome and define some of its organization, and 3.)

to develop a serological assay based on virus-like particles (VLPs) absorbed to an ELISA

plate for the detection and quantitation of antibodies against TmlPV.

The steps for developing a molecular diagnostic assay included: extracting DNA

from papillomatous lesions; designing PCR primers and PCR protocols; and sequencing

amplified products to confirm the identity of the virus involved. Due to the lack of

sequence data available on marine mammal papillomaviruses, specifically, of the

manatee, PCR assays for the molecular detection of TmlPV DNA were initially based on

the MY11 and MY09 primer set that targets a highly conserved region of the human PV

(HPV) L1 ORF. Our PCR protocol utilized annealing temperatures 100 below the









primers melting temperatures, in order to maximize the chances of amplifying the TmlPV

L1 DNA fragment, and incorporated deoxyinosines at positions of nucleotide degeneracy

in the primer sequences. After testing the modified MY11 and MY09 primers

(CR333/CR332) with positive TmlPV DNA, the annealing temperatures of the primers

were gradually increased until amplification of a single band of the appropriate size was

obtained. Using these primers in PCR assays, five TmlPV positive lesions were

identified from captive manatees and four positive skin lesions from free-ranging

manatees. These results confirmed the usefulness of the widely used MY11 and MY09

consensus primers and provided an improved method for the detection of TmlPV in

cutaneous lesions. Based on the sequences generated from the TmlPV L1 fragment using

the MY11 and MY09 primers, these primers were modified to contain TmlPV L1-

specific sequences at positions of nucleotide degeneracy. These TmlPV L1 specific

primers effectively amplified DNA fragments of the expected size from DNA samples

extracted from lesions of 11 captive and five free ranging manatees. Four manatee DNA

samples that had been negative for L1 fragment amplification of fragments of the

expected size using the modified MY11 and MY09 primers were shown to contain

TmlPV DNA fragments of the expected size using the more TmlPV L1-specific primers

(CR490/CR491). These results demonstrated the robustness of the TmlPV L1-specific

primers and improved the use of PCR as a tool for the detection of TmlPV in skin lesions.

Nucleotide sequences and deduced amino acid sequences of L1 fragments amplified with

the MY11/MY09 primer set and with the TmlPV Li-specific primer set were 100%

identical (Figure 3-8), indicating that only one genotype of TmlPV was detected in the

captive manatees of HSSWP and a few of the free-ranging animals that swim around









HSSWP. Three skin lesions (V372, V373, V377) obtained from captive manatees

preserved in DMSO were negative for amplification of the TmlPV L1 fragment;

however, DMSO is known to crosslink DNA, making it difficult to amplify DNA

fragments from these samples. These manatees may have been infected with TmlPV, but

due to the method of sample preservation, the TmlPV DNA fragments were not able to be

amplified from these samples. This demonstrates the need for fresh tissue samples in the

diagnosis of TmlPV infection and has implications on the methods of sample

preservation.

Positive TmlPV skin lesions, identified by PCR amplification of DNA fragments of

the appropriate size, were purified and sequenced directly or purified, cloned, and

sequenced. Nucleotide sequences of cloned products and of directly sequenced products

were compared to confirm the nucleotide identity of the sequences. In a study by Saiki et

al. (1988), an overall error frequency of 0.25% was observed in the sequences of 239-bp

amplified products after 30 cycles of amplification of the fragment. In our PCR assays,

whenever long DNA fragments (>1 Kb) were amplified, high fidelity enzymes that are

endowed with proofreading activity were used in order to minimize possible nucleotide

incorporation errors made by the polymerase during DNA amplification. Furthermore, at

least two clones from each recombinant DNA were completely sequenced and analyzed

and, often, both the purified mini-prep recombinant DNAs and the purified maxi-prep

recombinant DNAs of cloned products were sequenced, as the bacteria could have

possibly introduced nucleotide copying errors during transformations. Nucleotide

sequence differences were observed between the TmlPV E6 ORF sequences (99.5-

100.0% identity), E7 ORF sequences (99.4-100.0 % identity), L1 ORF sequences (99.7%









identity), and L2 ORF sequences (99.9% identity). These minor sequence variations may

have been due to nucleotide errors made either by the polymerase in PCR assays or by

the bacteria after transformation with plasmid DNA. Comparisons of the E6 ORF, E7

ORF, L1 ORF, and L2 ORF sequences obtained from the TmlPV DNA (CR130), used as

positive control throughout this study, with the corresponding sequences of the TmPV-1

genome recently published by another group (Rector et al., 2004) revealed that the

sequences were almost 100% identical at the nucleotide and amino acid levels. These

results indicated the truthfulness of the sequences obtained from the positive control

TmlPV DNA (CR130) and also validated the use of this DNA (CR130) for all future

genetic and phylogenetic analyses. Additionally, the identities shared by the manatee PV

sequences obtained from two different manatee papilloma isolates supports the presence

of only one type of manatee PV in skin lesions from captive and free-ranging manatees

around HSSWP.

Our results confirmed the presence of TmlPV in skin lesions of captive manatees

and extended the knowledge to encompass skin lesions from a few free-ranging manatees

inhabiting Crystal River and Homosassa River, Florida, the nearby waters of HSSWP.

Free-ranging manatees are often seen at the perimeter of the underwater fence that

separates the known TmlPV-positive captive HSSWP manatees from the free-ranging

manatees in this area. DNA samples obtained from skin lesions of free-ranging manatees

inhabiting more distant bodies of water in Florida (Port of the Isles, Tampa Bay) and

Belize (Drowned Keys) were always negative for TmlPV DNA. Therefore, it is thought

that a few of the free-ranging manatees that swim in the vicinity of the infected

population at HSSWP may have acquired the infection by direct contact through this









underwater fence. Manatee papillomavirus DNA was detected in skin lesions that were

harvested from free-ranging manatees during winter months (Table 2-2). Low water

temperatures have been suspected as a potential factor in immunologic suppression in the

known TmlPV-infected HSSWP manatees (Bossart et al., 2002), and exposure to cold

water has been directly correlated with impairment of the immune function in free-

ranging Florida manatees (Walsh et al., 2005). Cold stress syndrome (CSS), induced by

prolonged exposure to cold water, followed by nutritional, metabolic, and immunologic

disturbances culminating in multi-systemic, life-threatening opportunistic infectious

disease (Bossart et al., 2003), has been documented as a frequent (18%) cause of death in

Florida manatees (Bossart et al., 2004). It is likely, then, that when the manatee immune

system is compromised by ill-defined immunosuppressive factors, such as CSS, the

papilloma virus may become activated, invasive, and produce cutaneous lesions.

Exposure to harmful algal blooms (Karenia brevis) can also impair immune function in

manatees (Walsh et al., 2005) and may be involved in TmlPV activation and production

of lesions.

In an attempt to obtain the entire nucleotide sequence of the TmlPV genome, PCR

primers were designed to amplify overlapping PCR products that, if obtained, would

together span the complete TmlPV genome. PCR primers effectively amplified the first

amplimer that spans the L1-El region of the TmlPV genome; however, additional PCR

primers that were based on the overlapping PCR product method (Forslund and Hansson,

1996) did not amplify the subsequent amplimers. Problems encountered in amplifying

the overlapping PCR products included: the lack of sequence data of marine mammal

PVs available for primer design, low quantities and/or poor quality of starting extracted









DNA, and, leastly, significant sequence variation between the targeted regions of TmlPV

and homologous regions in the HPVs. Sequences obtained from the first amplimer

allowed for the partial characterization of the TmlPV genome, which included partial

sequences of the L1 ORF, the complete sequence of the E6 ORF, the complete sequence

of the E7 ORF, and partial sequence of the El ORF. Sequences obtained from the first

amplimer also allowed for the design of PCR primers that specifically targeted the

TmlPV complete E6 and E7 ORFs, widening the targets for the diagnosis of papillomas

of manatees. Primers targeting the TmlPV E6 ORF and E7 ORF effectively amplified

DNA fragments of the expected size from five DNA samples from HSSWP captive

manatees. These results expanded the use of molecular tools for the detection of TmlPV

infection and provided a method for complete gene amplification for gene expression

assays. However, the TmlPV E6 and E7 ORF primers did not effectively amplify

fragments of the expected size from five free-ranging manatee DNA samples and two

captive manatee DNA samples that had previously been positive for amplification of the

L1 458-bp fragment. These captive manatees were housed at marine parks (other than

HSSWP) in Florida and California and the TmlPV E6 and E7 ORF primers were specific

for TmlPV sequences obtained from the HSSWP captive manatees. The E6 and E7 ORFs

are less conserved among PV types than the L1 ORF, the most highly conserved region

of the PV genome (deVilliers et al., 2004), and sequence variation within the E6 and E7

ORFs may have lowered the efficiency of the E6 and E7 primers. Also, the primers that

targeted the E6 and E7 ORFs were located upstream and downstream of the ORFs, within

the non-coding regions of the TmlPV genome; unlike the TmlPV L1 fragment primers

that targeted a very highly conserved region within the L1 ORF. The quality and quantity









of the manatee DNA samples may have adversely affected the efficiency with which the

TmlPV E6 and E7 primers amplified DNA fragments of the expected size. The DNA

samples were frozen and thawed several times for the development of PCR assays, which

may have caused the DNAs to degrade. These results demonstrate the importance of

sequencing more than one genome of TmlPV. A reverse primer based on our own

sequences and a forward primer based on the sequence revealed in a recent publication of

the TmPV-1 genome (Rector et al., 2004) effectively amplified the complete L1 and L2

capsid protein genes from three captive manatee DNA samples and from two captive

manatee DNA samples, respectively. These results also expanded the use of molecular

tools for the detection of TmlPV infection and provided a method for complete gene

amplification for gene expression assays. Sequences obtained from the L1-E1 amplimer

plus the sequences obtained from the complete L1 and complete L2 amplimers allowed

for further characterization of the TmlPV genome.

Pair-wise comparisons of the TmlPV sequences with the corresponding sequences

of several human and non-human PVs revealed amino acid identities (Table 3-5) and

similarities (Table 3-6) of these viruses. Identities refer to the extent to which two amino

acid sequences are invariant and similarities refer to changes at a specific position of an

amino acid sequence that preserve the physico-chemical properties of the original

residue. Sequence identities and similarities also give an idea of the overall similarity

homologyy) of the TmlPV sequence to each virus to which it was compared, but do not

provide phylogenetic data on the genetic relatedness of the viruses. Comparisons of the

TmlPV L1 fragment with several human and non-human PV types suggested that the

TmlPV L1 fragment sequence was more similar to the sequences of cutaneous HPV types









(HPV-3, HPV-4, HPV-20, HPV-21, HPV-65, HPV-95) than to sequences of the high risk

genital mucosal HPV types (HPV-16, -18) and ungulate PV types that induce

fibropapillomas (Deer PV, OPV-1, EEPV). Comparisons of the TmlPV complete L1

ORF with several human and non-human PV types suggested that the TmlPV L1 ORF

sequence was more similar to the sequences of the cutaneous PV types (HPV-20, HPV-

65, HPV-95) than to the high-risk genital mucosal HPV-33 sequence and the

fibropapilloma-inducing Deer PV sequence. These L1 ORF sequence comparison results

were as expected, as TmlPV infection has so far only been associated with the presence

of benign skin lesions and not with genital mucosal lesions or aggressive fibropapillomas.

Since the L1 ORF is the most highly conserved region among all members of the PV

family (deVilliers et al., 2004), results of the L1 ORF comparisons are, possibly, more

reliable than results of comparisons made with less conserved, more variable regions of

the PV genome.

Comparisons of the TmlPV L2 ORF with several human and non-human PV types

shows that the TmlPV L2 ORF was more similar to another genetically characterized

marine mammal PV sequence (PsPV-1) isolated from a Burmeister's porpoise (Phocoena

spinipinnis) and to sequences of cutaneous HPV types (HPV-5, HPV-15), than to the

sequences of the fibropapilloma PV types (BPV, OPV, Deer PV). The TmlPV L2 ORF

sequence would be expected to be more similar to cutaneous PV types than to mucosal or

malignant papillomas, as TmlPV infection has so far only been associated with the

presence of skin lesions. The TmlPV L2 ORF sequence showed the greatest similarity to

the Burmeister's porpoise (Phocoena spinipinnis) papillomavirus (PsPV-1) (Van Bressem

et al., 1996), the only other papillomavirus of marine mammals that has been molecularly









characterized. Although marine in nature, these viruses do not seem to share a common

ancestor, as PsPV-1 and TmlPV clade independently of each other in phylogenetic trees.

Also, PsPV-1 is known to have caused genital warts in cetaceans (Van Bressem et al.,

1996), whereas the TmlPV has so far only been associated with cutaneous lesions. These

results demonstrated the overall similarity of the TmlPV L2 ORF sequence to that of the

L2 ORF sequences of several PV types, but did not provide an accurate phylogenetic

relationship of the viruses.

Comparisons of the TmlPV E6 ORF with several human and non-human PV types

suggested that the TmlPV E6 ORF sequence was similar to sequences of a wide variety

of PV types, including a rabbit PV, a high risk mucosal genital PV type (HPV-32), and

cutaneous PV types (HPV-la, HPV-20, HPV-95). Inferences could not be made from

these results, as they suggested that the TmlPV E6 ORF sequence is similar to both non-

oncogenic (HPV-la, HPV-20, HPV-95) and oncogenic (HPV-32) PV types. However,

the oncogenic potential of TmlPV has not yet been determined, and it is possible that the

oncogenic determination of the TmlPV may be a consequence of a fine balance between

the E6 and E7 regions and unidentified sequences in a different region of the TmlPV

genome. This is partially the case in other types of terrestrial PVs, such as deer PV,

European elk PV, and reindeer PV, which contain a novel, transforming E9 gene in their

genomes (Erikkson et. al, 1994). The results of the E6 ORF sequence comparisons

showed more variability than the comparisons of the highly conserved L1 and L2 regions,

as the E6 ORF is a segment with little sequence conservation among PV viruses (de

Villiers et al., 2004).









Comparisons of the TmlPV E7 ORF with several human and non-human PV types

suggested that this sequence is most similar to sequences of cutaneous PV types (HPV-9,

HPV-15) and a benign mucosal PV type (HPV-6). Results from these comparisons were

not surprising, as TmlPV, so far, has only been associated with benign cutaneous lesions.

Cladistic phylogenetic diagrams reflect hypotheses about the evolutionary

relationships of organisms. A clade is formed by all species which share derived

ancestral characters and a most common ancestor (Chan et al., 1995). The bootstrapped

cladograms and the radial divergence trees representing the L1 ORF, L2 ORF, and E6

ORF sequences demonstrated that TmlPV forms a single, distinct branch, or constitutes

its own clade. Since no PVs have been characterized from species closely related to the

manatee, it is not surprising that TmlPV clades by itself in these phylograms (Figure 3-

13, -14, -15, -16). These results indicated that TmlPV is a unique virus, distinct from the

known human and non-human PVs. The single branch formed by the TmlPV in the L1

ORF phylograms may be associated with the type of cell surface receptors used by the

virus. The PVs enter a wide range of cells and the tropism of infection by the different

PVs is controlled by events downstream of the initial binding and uptake (Muller et al.,

1995). Studies have shown that the L1 major capsid proteins of low-risk HPV-11 binds

to the Kap alpha-2 adapter and the Kap beta-2 import receptor and also interacts with the

Kap beta-3 import receptor (Nelson et al., 2003), while the L1 capsid protein of high-risk

HPV-45 interacts with Kap alpha-2 beta-1 heterodimers (Nelson et al., 2000). It has not

yet been determined what the specific receptor of the TmlPV L1 capsid protein is;

however, if these receptors differ from those described in other PV types, it may explain

why the TmlPV L1 protein is phylogenetically characterized as a single, distinct branch.




Full Text

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DETECTION AND MOLECULAR CH ARACTERIZATION OF MANATEE PAPILLOMAVIRUS IN CUTANEOUS LESIONS OF THE FLORIDA MANATEE (Trichechus manatus latirostris ) By REBECCA ANN WOODRUFF A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLOR IDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2005

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Copyright 2005 by Rebecca Ann Woodruff

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This document is dedicated to the graduate students of the University of Florida.

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iv ACKNOWLEDGMENT I would like to extend my greatest appreciation and th anks to my mentor, Dr. Carlos Romero, for allowing me to join hi s laboratory and enjoy many opportunities that I would not have been able to elsewhere. I would also like to thank my committee members, Dr. Peter McGuire and Dr. Ayalew Mergia, for their time, assistance, and suggestions. I would like to thank Dr. Elli s Greiner for first introducing me to the pathobiology graduate program at the University of Florida. I extend great thanks to Bob Bonde, not only for obtaining all of the manatee samples used in this study, but also for providing his expertise and know ledge of manatees. This project was funded by the Florida Fish and Wildlife Commission th rough the Marine Mammal Animal Health Program of the College of Veterinary Medicine at the University of Florida, and would not have been possible without the U. S. Ge ological Survey (USGS) Department of the Interior, contributions of collaborators affiliated with numerous zoological parks, and those involved with manatee capture release st udies. I would also like to thank my fellow lab-mates, Alexa Bracht, Kara Smolarek-Benson, Shasta McClenahan, and Rebecca Grant, for their much valued friendships. I am greatly appreciative of my best friend, David Kottke, for supporting me unconditionally and following me to pursue my dreams, even if it meant putting his own aside. I w ould also like to thank my family for their constant encouragement during these past two years.

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v TABLE OF CONTENTS page ACKNOWLEDGMENT....................................................................................................iv LIST OF TABLES...........................................................................................................viii LIST OF FIGURES...........................................................................................................ix ABSTRACT....................................................................................................................... xi CHAPTER 1 INTRODUCTION........................................................................................................1 Classification of Papillomaviruses...............................................................................1 Papillomavirus Genome Organization and Characterization.......................................2 Papillomavirus Replication...........................................................................................4 Papillomavirus Transmission........................................................................................5 Papillomavirus Pathogenesis........................................................................................6 Diagnosis of Papillomavirus Infection.........................................................................8 Treatment and Prevention of Papillomavirus Infection................................................9 Human Papillomaviruses............................................................................................10 Non-Human Papillomaviruses....................................................................................11 Marine Mammal Papillomaviruses.............................................................................13 The Florida Manatee (Trichechus manatus latirostris)...............................................13 2 MATERIALS AND METHODS...............................................................................16 Clinical Data...............................................................................................................16 Source of Samples......................................................................................................16 DNA Extraction from Papillomatous Lesions............................................................17 General Methods of PCR............................................................................................18 Taq Polymerase Reactions..................................................................................18 Accuprime Taq DNA Polymerase Reactions..................................................19 Expand High Fidelity Plus Reactions..................................................................19 PCR Targeting the L1 458-bp Fragment....................................................................20 PCR Targeting the L1 TmlPV 458-bp Fragment.....................................................20 PCR Targeting the TmlPV L1-E1 Region..................................................................20 PCR Targeting the Complete TmlPV E6 Gene..........................................................21 PCR Targeting the Complete TmlPV E7 Gene..........................................................21

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vi PCR Targeting the TmlPV L1-L2 Region..................................................................21 PCR Targeting the Complete TmlPV L1 Gene..........................................................22 PCR Targeting the Complete TmlPV L2 Gene..........................................................22 Gel Electrophoresis.....................................................................................................22 General Cloning of PCR Products..............................................................................23 Cloning into pCR 2.1 TOPO T/A Vector........................................................23 Cloning into P-Target Mamm alian Expression Vector...................................24 Cloning into pcDNA .1 Directio nal TOPO Expression Vector.................24 Analyzing Recombinants............................................................................................25 Sub-cloning of Purified Recombinants.......................................................................27 Sub-Cloning into pcDNA 3.1/ Zeo+ Expression Vector......................................27 L1 Gene Sub-Cloning into pFastBac Vector.................................................29 L1 Gene Sub-Cloning into pBlueBac 4.5............................................................30 Sequencing of PCR-amplif ied and Cloned Products..................................................30 Transfection of Insect Cell Cultures...........................................................................31 Culturing Insect Cells..........................................................................................31 Transformation of MAX Efficiency DH10Bac Competent E. coli..............32 Transfection of Insect Cells with Bacmid DNA Recombinants..........................33 Harvest of Recombinant Baculovirus Stocks......................................................34 Reverse Transcription PCR (RT-PCR) of Infected Cell Cultures.......................34 Generation of Recombinant Baculovirus............................................................35 Transfection of Mammalian Cells..............................................................................36 Culturing African Green Monkey Kidney (COS-7) Cells...................................36 Electroporation of COS-7 Cells with Recombinants for Immunofluorescence Assays..............................................................................................................37 Culturing Florida Manatee Respiratory Epithelial Cells.....................................38 Transfection of TmlRE Cells with DNA Recombinants for Immunofluorescence Assays...........................................................................39 3 RESULTS...................................................................................................................44 PCR Results................................................................................................................44 PCR Targeting the Papillomavirus L1 458-bp Fragment....................................44 PCR Targeting the L1 TmlPV Fragment..........................................................45 PCR Targeting the TmlPV L1-E1 Region...........................................................45 PCR Targeting the Complete TmlPV E6 Gene...................................................45 PCR Targeting the Complete TmlPV E7 Gene...................................................45 PCR Targeting the TmlPV L1-L2 Region...........................................................46 PCR Targeting the Complete TmlPV L1 Gene...................................................46 PCR Targeting the Complete TmlPV L2 Gene..........................................................46 Sequencing Results and Genetic Analyses.................................................................46 TmlPV L1 458-bp Fragments..............................................................................46 L1-E1 TmlPV Region..........................................................................................48 TmlPV E6 Gene..................................................................................................49 TmlPV E7 Gene..................................................................................................49 TmlPV L1-L2 Region..........................................................................................50 Complete TmlPV L1 Gene from Captive Manatee Lorelei................................51

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vii Complete TmlPV L2 Gene..................................................................................51 Immunofluorescence and Ge ne Expression Assays...................................................52 Mammalian Expression Systems.........................................................................52 Bac-to-Bac Baculovirus Expression System.......................................................52 Bac-N-Blue Baculovirus Expression System.............................................................53 Phylogenetic Analysis................................................................................................53 4 DISCUSSION.............................................................................................................78 LIST OF REFERENCES...................................................................................................95 BIOGRAPHICAL SKETCH...........................................................................................106

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viii LIST OF TABLES Table page 2-1 Samples obtained from skin lesions of captive Florida manatees.......................39 2-2 Samples obtained from skin lesions of free-ranging Florida manatees...............40 2-3 PCR primers designed to target manatee papillomavirus sequences..................40 2-4 Sequencing primers used to obtain th e complete sequence of PCR amplified TmlPV gene fragments........................................................................................41 3-1 PCR results of DNAs obtained from captive manatee skin lesions tested for the presence of TmlPV infection.........................................................................55 3-2 PCR results of DNAs obtained from free-ranging manatee skin lesions tested for the presence of TmlPV infection...................................................................56 3-3 Summary of PCR results.....................................................................................57 3-4 Accession numbers of ma natee papillomavirus sequen ces deposited into the GenBank tool of the NCBI website.....................................................................58 3-5 Pair-wise comparisons of the amino aci d sequences of the L1, L2, E6, and E7 gene fragments of manatee papillomavi rus (TmlPV) with several human and non-human papillomaviruses...............................................................................59 3-6 Pair-wise comparisons of the amino aci d sequences of the L1, L2, E6, and E7 gene fragments of manatee papillomavi rus (TmlPV) with several human and non-human papillomaviruses...............................................................................60 3-7 Summary of the pair-wise comparis ons of the amino acid sequences of manatee papillomavirus gene fragments with several human and non-human papillomaviruses..................................................................................................61

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ix LIST OF FIGURES Figure page 1-1 Illustration demonstrating the genetic organization of a typical papillomavirus genome.......................................................................................15 2-1 Linear representation of the open re ading frames (ORFs) of the circular manatee papillomavirus (TmlPV) genome with the relative positions of the PCR primers used to amplify TmlPV DNA........................................................16 3-1 Agarose gel electrophoresis of PCR amplified 458-bp fragments of the L1 capsid protein gene of manatee papillomavirus..................................................62 3-2 Agarose gel electrophoresis of PCR amplified 2,772-bp fragment of the L1E1 region of manatee papillomavirus..................................................................62 3-3 Agarose gel electrophoresis of PCR amplified 587-bp fragments of the E6 gene of manatee papillomavirus..........................................................................63 3-4 Agarose gel electrophoresis of PCR amplified 489-bp fragments of the E7 gene of manatee papillomavirus..........................................................................63 3-5 Agarose gel electrophoresis of PCR amplified 3,208-bp fragments of the L1 gene plus the L2 gene of manatee papillomavirus..............................................64 3-6 Agarose gel electrophoresis of P CR amplified 1,712-bp fragments of the complete L1 gene of ma natee papillomavirus.....................................................64 3-7 Agarose gel electrophoresis of P CR amplified 1,660-bp fragments of the complete L2 gene of manatee papillomavirus.....................................................65 3-8 Multiple alignment of the amino acid sequences deduced from the nucleotide sequences of the L1 gene fragment of manatee papillomavirus identified in cutaneous lesions of captive and free-ranging Florida manatees........................66 3-9 Electron micrograph of Sf21 ins ect cell cultures transfected with pFastBac1/TmlPV L1 gene recombinant............................................................67 3-10 Agarose gel electrophoresis demonstr ating the PCR amplification of the manatee papillomavirus complete L1 gene fragment from cDNAs obtained from infected Sf21 cell cultures..........................................................................68

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x 3-11 Agarose gel electrophoresis demonstra ting restriction enzyme digests of the manatee papillomavirus E6 gene and E7 gene recombinants.............................69 3-12 Agarose gel electrophoresis demonstra ting restriction enzyme digests of the manatee papillomavirus L1 complete gene recombinant....................................69 3-13 Neighbor-Joining phylogenetic tree of the deduced amino acid sequences of the complete L1 gene of several human and non-human papillomaviruses........70 3-14 Neighbor-Joining phylogenetic tree of the deduced amino acid sequences of the complete L2 gene of several human and non-human papillomaviruses........72 3-15 Neighbor-Joining phylogenetic tree of the deduced amino acid sequences of the complete E6 gene of several hum an and non-human papillomaviruses ......74 3-16 Neighbor-Joining phylogenetic tree of the deduced amino acid sequences of the complete E7 gene of several human and non-human papillomaviruses........76 4-1 Papillomatous skin lesions on the flipper of a captive Florida manatee (Trichechus manatus latirostris) housed at Homosassa Springs State Wildlife Park, Homosassa, Florida....................................................................................93 4-2 Typical papillomatous skin lesions of free-ranging Florida manatees................44

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xi Abstract of Thesis Presen ted to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Master of Science DETECTION AND MOLECULAR CH ARACTERIZATION OF MANATEE PAPILLOMAVIRUS IN CUTANEOUS LES IONS OF THE FLORIDA MANATEE (Trichechus manatus latirostris ) By Rebecca Ann Woodruff August 2005 Chair: Carlos H. Romero Major Department: Veterinary Medicine Papillomaviruses are widespread and succe ssful pathogens associated with the development of benign warts and malignant ne oplasia in humans and domestic and wild animals. Phylogenetic comparisons have classified human and non-human papillomaviruses into 16 genera within the Papillomaviridae family. With the advent of PCR and molecular cloning, si gnificant advances have been made in understanding human papillomaviruses; however, l ittle is known about marine mammal papillomaviruses. DNA extracted from skin lesions of captive and free-ranging manatees was assayed by polymerase chain reaction (PCR) to detect papillomavirus infection. Initially, primers were based on the widely used MY11 and MY09 human papillomavirus (HPV) primer set, which target a highly c onserved region of the L1 capsid protein. The MY11 and MY09 primers directed the amplif ication of a 458-bp fragment from DNA extracted from captive and free-ranging Florida manatee (Trichechus manatus latirostris ) skin lesions. Sequences of this fragment led to the development of L1 PCR primers,

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xii which specifically target the L1 capsid pr otein of Florida manatee papilloma virus (TmlPV). The L1 and L1 DNA fragment sequences were 100% identic al, suggesting that there is only one genot ype of manatee PV present in captive and free-ranging manatees around Homosassa Springs State W ildlife Park. PCR primers were also designed to specifically target the comple te TmlPV E6, E7, L1, and L2 genes. Amplification of the TmlPV E6 gene product yielded a 589-bp fragment, which included the complete TmlPV E6 gene, and amplifica tion of the TmlPV E7 gene product yielded a 487-bp fragment, which included the complete TmlPV E7 gene. Targeting the TmlPV L1 capsid protein gene yielded amplifica tion of a 1,712-bp fragment which included the complete TmlPV L1 gene, and targeti ng the TmlPV L2 capsid protein yielded amplification of a 1,660-bp fragment, which included the complete TmlPV L2 gene. The complete TmlPV L1, E6, and E7 genes were successfully cloned into mammalian and insect expression vectors, allowing for the future production of recombinant genes and the development of serologic assays, such as ELISA. The described assays based on PCR and direct sequencing of amplicons have allowed for the molecular detection of TmlPV in captive and free-ranging Florid a manatees and have allowed for the phylogenetic comparisons of TmlPV to severa l human and non-human papillomaviruses. The TmlPV is a unique papillomavirus base d on phylogenetic analyses of the deduced amino acid sequences of the L1, L2, E6, and E7 proteins, quite distinct from another marine papillomavirus of Burmeisters porpoise s, most closely related to HPVs that cause common skin warts, and leas t related to high-risk HPVs involved in malignancy.

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1 CHAPTER 1 INTRODUCTION The papillomaviruses (PVs) are a group of small DNA viruses that cause benign warts and malignant neoplasia in humans (Walboomers et al., 1999) and domestic and wild animals (Sundberg, 1987). To date, more than a hundred human PV (HPV) types have been partially identified and a wide vari ety of PV types have also been detected in mammals and birds (de Villiers et al., 2004). Papillomavirus infection has also been detected in genital and cutaneous lesions of several species of marine mammals (Bossart et al., 2002; Kennedy-Stoskopf, 2001; Van Bresse m et al., 1996) and studies have shown that the healthy skin of humans and animal sp ecies can harbor sub-cl inical PV infections in the absence of overt lesions (Antonss on and Hansson, 2002, and Antonsson et al., 2000). Classification of Papillomaviruses Papillomaviruses were originally grouped together with the polyomaviruses in the family Papovaviridae based on their small size, nonenveloped capsids, and circular, double-stranded genomes. However, a lack of overall homology of particle size, genome organization, and sequence similarities be tween the two viral genomes led to the recognition of two separate families, Polyomaviridae and Papillomaviridae (Howley and Lowy, 2001). Viruses within the Papillomaviridae family are defined by genomic properties, rather than serology, and are therefore described as PV genotypes, not serotypes. Papillomavirus ge notypes are classified by analysis of only part of the viral genome that encompasses the combined nucleo tide sequences of the E6, E7, and L1 open

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2 reading frames (ORFs) (Chan et al., 1995). Recent phylogenetic comparisons of the L1 ORF nucleotide sequences of 96 HPVs and 22 animal PVs have further classified PV types into genera and species. Higher-orde r phylogenetic clusters (major branches) of PV types have now been classified into gene ra, sharing less than 60% identity in the L1 ORF nucleotide sequences. Each genus within the 16 genera identified is defined by its biological properties and genome organization. Lower-order clusters (minor branches) of PV types, or PV subtypes, have now been termed species. Species within each genus share 60-70% identity at the nucleotide leve l (de Villiers et al., 2004). Nucleotide sequence analyses of the L1 ORF of various HPV types have been used to construct phylogenetic trees that display clusters of PV types with similar tissue tropisms and oncogenic potentials (Chan et al., 1995). Papillomavirus Genome Organization and Characterization Papillomaviruses have double-stranded, circular DNA genomes of about 8,000 base pairs (bp) in size. The papillomavirus part icles (52 to 55 nm in diameter) contain the viral genome within a spherica l capsid composed of 72 capsome rs. All ORFs are located on one strand, indicating that transcription occurs on only one stra nd. Transcription is regulated by the differentiati on state of the infected cells and is complex, due to the presence of multiple promoters, alternate and multiple splice patterns, and differential production of mRNA in different cel ls (Howley and Lowy, 2001). A PV genome usually contains seven majo r ORFs that code for five early (E) proteins and two late (L) cap sid proteins, plus an upstream regulatory region (URR), or long coding region (LCR) (Tachezy et al., 2002). The early region of the PV genome encodes the viral regulatory proteins E1, E2, E4, E6, and E7, which are necessary for initiating viral DNA replication. The late region encapsulates the genome and encodes

PAGE 15

3 the L1 and L2 capsid proteins (Howley a nd Lowy, 2001). The LCR does not contain any ORFs, but does contain the origin of viral DNA replication. Elements present in the LCR regulate viral DNA replication and transcri ption (Desaintes and Demeret, 1996). Unusual ORFs have been described in severa l types of PVs (Tachezy et al., 2002). The genomes of European elk (Odocoileus alces ) PV, white-tail deer (Odocoileus virginianus ) PV, and reindeer (Odocoileus hemionus ) PV contain a transformi ng E9 gene (Eriksson et al., 1994). The African grey parrot (Psittacus erithacus timneh ) papillomavirus (PePV) genome does not contain the typical E6 or E7 ORFs (Tachezy et al., 2002) and the Burmeisters porpoise (Phoecena spinipinnis ) papillomavirus (PsPV-1) genome also lacks the E7 ORF (Van Bressem et al., 1996). Two ORFs with unknown functions, E3 and E8, may also be present in a PV ge nome (Lowy and Howley, 2001). An illustration of a typical PV genome is shown in Figure 1-1. The PV genome is contained within the capsid region which consists of the major and minor structural proteins, L1 and L2, re spectively. The L1 ORF is the most highly conserved ORF within the papillomavirus genom e (de Villiers et al., 2004) and represents 80% of the total viral prot ein (Howley and Lowy, 2001). The L1 protein can selfassemble into virus-like part icles (VLPs) or in combination with L2, although the L2 protein is not required (Hag ensee et al., 1993). The L2 pr otein may enhance packaging (Stauffer et al., 1998) and inf ectivity (Roden et al., 2001). The early genes E6 and E7, and in some PV types, E5, contain oncogenic properties that can modulate the transforma tion process (Baker and Howley, 1987). The E6 protein of bovine papilloma virus type 1 (BPV-1) and of the oncogenic HPVs is believed to function through bi nding cellular target s (Howley and Lowy, 2001), such as

PAGE 16

4 binding and degrading the p53 tumor suppressor protein (Scheffner et al., 1993). The E7 protein of the oncogenic HPVs binds a number of important cellular regulatory proteins, such as the retinoblastoma tumor suppre ssor protein (pRB) and the related pocket proteins, p107 and p130 (Dyson et al., 1989). Th e papillomaviruses may activate cellular genes necessary for the replication of thei r own DNA through the binding of the viral E6 and E7 proteins to cellular f actors (Howley and Lowy, 2001). The early genes E1 and E2 are regulatory proteins that modulat e transcription and replication (Baker and Howley, 1987). The E1 and E2 proteins are essential for viral DNA replication (Chiang et al., 1992). The E1 protein has been shown to bind a number of cellular proteins, including the cellular DNA polymerase -primase, thus recruiting the cellular DNA replication initiation machinery to the viral origin of re plication (Park et al., 1994). The multifunctional E2 protein can activate or repress viral promoters, has critical roles in viral DNA replication (Ham et al., 1991), and targets the E1 protein to the replication origin (Sedman and Stenlund, 1995). Although the E4 ORF is located in the early region of the PV genome, it is expresse d as a late gene (Howley and Lowy, 2001). The precise role of the E4 protein is unc lear, but studies have shown E4 expression coincides with the onset of viral geno me amplification (Peh et al., 2002). Papillomavirus Replication Key life cycle events seem to be simila rly regulated in both human and non-human PVs (Peh et al., 2002). The PV life cycle is strictly depe ndent on differentiation of the epithelial tissue (Barksdale and Baker, 1993) an d PV replication can be divided into three stages (McBride et al., 2000). First, the PV virion must bind to a basal keratinocyte, although studies have shown that the PV viri ons can bind a wide variety of cell types (Muller et al., 1995). During this stage, the viral genome is maintained as an episome

PAGE 17

5 within the nucleus (McBride et al., 2000). Th e viral genome is then amplified and the viral copy number is increased up to 1,000 per haploid cell genome (Lepik et al., 1998). As the basal cells differentiate, the viral DNA is maintained as a stable plasmid (Howley and Lowy, 2001). During this second, maintena nce stage, the viral ge nome replicates in synchrony with the host cell chromosome (G ilbert and Cohen, 1987). The PVs rely on cellular replication factors a nd enzymes (Muller et al., 1994), such as replication protein A (RPA) (Mannik et al., 2002), in order to repl icate their genomes from a single origin of replication (Melendy et al., 1995) The earliest PV DNA synthesis is within the fragment containing the PV replication origin and synt hesis proceeds in both directions from the replication origin (Melendy et al., 1995). The third replicat ion stage takes place in the terminally differentiated epith elial cells of the papilloma (Howley and Lowy, 2001). In this next layer of stratified epithelium, the stratum granulos um, late viral gene expression, synthesis of capsid proteins, vegetative vira l DNA synthesis, and assembly of virions occur (McBride et al., 2000). The PV DNA is thought to remain in the basal epithelial cells and to be reactivated when levels of immune system monitoring decline (Doorbar, J. 2005). Papillomavirus Transmission Papillomavirus enters infected skin via skin surface abrasions, allowing the virus access to the proliferative cells of the skin (Egawa, 2003), where it promotes cellular proliferation and accelerated epithelial growth (Silverberg, 2004). Infection with HPV is primarily found on the extremities, face, and body, and moist skin is more likely to allow viral transmission (Silverberg, 2004). Transm ission of high-risk mucosal HPVs occurs predominately through sexual contact, but horizon tal and vertical rout es have also been identified. Vertical transmi ssion of mucosal HPVs may be acquired from the mother in

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6 utero, across the placenta, intr apartum, during birth through an infected birth canal, or post partum (Cason and Mant, 2005). In 1989, Sedlacek et al. described the first confirmed vertical transmissi on of HPV infection in nasoph aryngeal samples of infants born to HPV positive mothers. Papillomavirus Pathogenesis Papillomas (warts) are induced in the skin and mucosal epithelia at specific sites (de Villiers et al., 2004) and di ffer in their tissue specificity and the associated disease (McMurray et al., 2001). The highly tissue-specific papilloma viruses can be divided into two groups: one group is primarily found in cuta neous epithelia (skin), in which there is thickening of the epidermis, and the other group is predominantly present in mucosal epithelia (Smits et al., 1992), involving th e oral pharynx, esophagus, or genital tract (Howley and Lowy, 2001). Warts are diagnos ed by physical examination and are defined by morphology, location, and host immune response. The three main types of lesions observed are: common warts (r ough plaques of skin), mosaic warts (groups of common warts), and flat warts (smooth, flesh-colore d papules). Mucosal warts may appear as single plaques or as a group with a grap elike appearance (Silverberg, 2004). The genital mucosal HPV types are defined as either high-risk or low-risk based on their involvement with lower genital tract can cers (McMurray et al ., 2001). In the lowrisk types, such as HPV-6 or HPV-11, benign wa rts proliferate. In the high-risk types, such as HPV-16 or HPV-18, the virus deregu lates checkpoints that normally monitor the fidelity of chromosome replication and segreg ation, leading to the development of cancer (Galloway, 2003). Anogenital carcinomas caused by HPV infection include penile (Rubin et al., 2001), vaginal (Daling et al., 2002), vulvar (Trimble et al., 1996), and anal cancers (Krzyzek et al., 1980). The high-risk HP V types are also associated with cervical

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7 dysplasia (Kurman et al., 1982), uterine can cer (Parkin et al., 1999, and zur Hausen, 1996), and cervical cancer, one of the mo st common cancers of women world-wide (Schiffman, 1992, and zur Hausen, 1991). The E6 and E7 genes of the high-risk types are expressed in cervical cancer (Schwarz et al., 1985). The roles of E6 and E7 of the low-risk types are unclear, but studies suggest that they may act in a similar manner as observed in the high-risk E6 and E7 proteins (Oh et al., 2004). Risk factors associated with cervical cancer and ot her anogenital tumors include cigarette smoking, sexual factors, and, possibly, genetic sus ceptibility (Daling et al., 2002). Both the low-risk and high-risk HP V types cause low-grade squamous intraepithelial lesions (LSIL) of the cervix, but the high-risk HPV types cause high-grade SIL (HSIL), carcinoma in situ, or invasive cancer. The steps leading to cervical carcinogenesis include infecti on with an oncogenic (high-risk) HPV, development of HSIL, progression of HSIL to carcinoma in s itu, and, then, invasive cancer (Baseman and Koutsky, 2005). Frequent integration of th e HPV genome into the host genome usually occurs in the case of high-risk PVs (Mannik et al., 2002). At least 25 types of HPVs have also been detected in oral lesi ons on the lips, hard palate, and gingiva (Syrjane n, 2003). The high risk HPV types 16 and 18 are highly associated with oropharyngeal and laryngeal squamous cell ca rcinomas (Kreimer et al., 2005) while the low risk HPV types 6 and 11 are predominant in benign lesions of the oral mucosa (Syrjanen, 2003). Infection w ith HPV is a significan,t independent risk factor for oral squamous cell carcinoma (Miller and Johnstone, 2001). The pathogenesis of HPVs differs for viruse s that are considered high risk or low risk group members. In the case of epidermodysplasia verruciformis (EV), the disease

PAGE 20

8 behaves like a genetic cancer of viral or igin, which may result from an abnormal recessive gene (Jablonska, 1991). Clinical forms of EV may be benign or malignant. The benign form is associated with HPV-3 and/or HPV-10 and induces flat, wart-like lesions over the trunk and limbs. The maligna nt form is associated with EV-HPV and induces reddish, polymorphous lesions, flat wa rt-like lesions, and pr e-malignant lesions disseminated over the body. Epidermodysplasia verruciformis is the first human genetic condition in which cutaneous cancer is asso ciated with HPV infection (Majewski and Jablonska, 1995). There is an increased risk of developing cutaneous HPV-associated disease if the virus is not cleared from the skin (Silverb erg, 2004). Cutaneous HPV types, such as HPV-5 and HPV-8, may contribute to skin cancer development in immunosuppressed individuals (Stockfleth et al ., 2004). In renal transplant studies, 90% of recipients developed HPV-induced warts (Blessing et al., 1989) and up to 40% of recipients developed nonmelanoma skin cancer within 15 years after transplantation (Birkeland et al., 1995). HPV-5 and HPV-8 were also pr edominately detected in squamous cell carcinoma of patients diagnosed with EV (Orth, 1987). Immunosuppression may increase the activity of HPV, which may lead to the development of cancer (Stockfleth et al., 2004). Diagnosis of Papillomavirus Infection Testing for the presence of HPV viral DNA includes methods such as Southern blots, dot blots, in situ hybridization, polymerase chai n reaction (PCR), and solution hybridization (hybrid capture assay) (Trofatter, 1997). Detection of HPV by PCR is more sensitive than the other methods, enab les the detection of a single genome copy per cell for HPV DNA that has integrated (Sha manin et al., 1994), and allows for the

PAGE 21

9 detection of a broad spectrum of genital HPVs (Ting and Manos, 1990). The widely used consensus PCR primers, MY09 and MY11, are based on sequences obtained from the highly conserved PV L1 capsid protein gene (Manos et al., 1989). The primers were designed from homologous regions 20 to 25 base pairs (bp) in length that were identified in genital HPV types 6, 11, 16, 18, and 33 (T ing and Manos, 1990). These primers are known to amplify a 458 base pair (bp) fragment when used with DNA from most types of genital HPVs (Bernard et al., 1994 ) Human papillomavirus DNA can be detected by method of PCR in fresh or frozen cervical biopsies (Li et al., 1988; Manos et al., 1989), condylomata acuminata (genital warts) tissu es (Brown et al., 1999), cutaneous wart tissues (Harwood et al., 1999), and in swab samples taken from the top of lesions (Forslund et al., 2004). Ha rwood et al. (1999) have described a degenerate nested PCR that is capable of detecting cutaneous, mucosal, and EV HPV types. A new method of HPV detection using high-density DNA microarrays is able to detect single and multiple mucosal HPV infections (K laassen et al., 2003). Treatment and Prevention of Papillomavirus Infection The host response to HPV infection is a co mplex process of skin barrier protection, innate immunity, and acquired immunity (Sil verberg, 2004). Warts generally will regress over time and after six months of infecti on, 30 percent of warts will clear on their own (Messing and Epstein, 1963). Following immu ne regression, PV DNA persists in a latent state, with only a few cells, if any, capable of supporting th e productive cycle that occurs during epithelia l cell differentiation (Doorbar, 2005). A possible approach to controlling the level of HPV-a ssociated disease is to prevent HPV infection (McMurray et al., 2001); however, the PV life cycle requires a differentia ted stratified epithelium to replicate and this has been difficult to genera te in cell culture (McB ride et al., 2000).

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10 Due to the fact that PVs could not previ ously be propagated in cell cultures, the development of a capsid-directed vaccine wa s hindered for a long time (Biemelt et al., 2003). A recently described raft system now allows for the genetic analysis of the complete viral life cycle of BPV-1. Using a combination of organotyp ic raft cultures and xenografts on nude mice, BPV-1 DNA can be amplified and capsid antigens and infectious BPV-1 virus particles can be produced (McBride et al., 2000). Several animal models of PV infection ha ve shown that neutralizing antibodies can block new infection (Galloway, 2003). Vacci nation against PV infections using viruslike particles (VLPs) based on the L1 capsid pr otein or the L1 plus the L2 protein is currently being developed (Leder et al., 2001). Vaccines based on VLPs are desirable because they retain repetitive, highly immunogenic epitopes found on the surface of infectious virions, but lack the potentially harmful PV ge nomes. Three types of HPV VLP-based vaccines are currently being developed. The first, most basic type is designed to prevent genital HPVs by inducing virus-ne utralizing antibodies against the L1 major capsid protein. The second type of vaccine is based on chimeric VLPs which incorporate polypeptides of other viral a nd cellular proteins into the VLPs. These vaccines induce cell-mediated responses to nonstructural viral proteins, such as the HPV E7 protein. The third type of vaccine incorpor ates self-peptides into the ou ter surface of the VLPs and is designed to induce antibodies against central self-antigens (Schiller and Lowy, 2000). Vaccination with HPV VLPs has been well tole rated, induces high titers of antibodies, and shows evidence of T-cell responses (Galloway, 2003). Human Papillomaviruses Papillomaviruses are one of the most impor tant viruses associated with benign and malignant neoplasia in humans (Chan et al., 199 5). Papillomaviruses were first isolated

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11 almost 30 years ago (Orth et al., 1977) and the first HPVs fully sequenced were HPV-1 (Danos et al., 1982), HPV-6 (Schwarz et al ., 1983), and HPV-16 (Seedorf et al., 1985). To date, more than 100 types of human papi lloma viruses (HPVs) have been identified, of which 96 have been cloned and characterized (deVilliers et al., 2004). More than 50 types of HPVs have been found to infect th e genital tract (Gallo way, 2003). Low-risk (benign) genital HPVs include: t ypes 6, 11, 40, 42-45, 53-55, 57, 67, 69, 71, and 74. High-risk (oncogenic) genital HPVs include: types 16, 18, 31-35, 51, 52, 56, 58, 66, 68, 70, and 73 (deVilliers et al., 2004 and McMurr ay et al., 2001), with types 26, 53, and 66 being probably oncogenic (Munoz et al., 2003) The HPV types 59, 61, and 82 may be associated with benign or malignant lesions (deVilliers et al., 2004) Infection with a single HPV type or infection with multiple HPV types can occur (Munoz et al., 2003). Non-Human Papillomaviruses Warts in animals have been recognized for centuries. Equine papillomas were described as early as in the 9th century A. D. and the first experimental transmission of animal papillomas occurred in 1898 (Lan caster and Olson, 1982). Warts in wild cottontail rabbits were the fi rst animal papillomas thoroughly examined for properties of transmissibility, etiology, and histology. The activities and char acteristics of the papilloma-producing agent in co ttontail rabbits classified it as a virus (Shope, 1933). Additional non-human PVs initi ally characterized include: BPV (Lancaster and Olson, 1978), equine PV (Fulton et al., 1970), canine oral PV (Chambers and Evans, 1959), deer fibromavirus (Shope et al., 1958), and chaffi nch PV (Lina et al., 1973). Presently, 22 animal PVs have been fully characterized and classified into genera and species based on the L1 ORF sequences (de Villiers et al., 2004). As many as 53 putative new animal PV types have been identified by polymerase ch ain reaction (PCR) in 7 animal species,

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12 including chimpanzees, gorillas, spider monke ys, long-tailed macaques, domestic cattle, aurochs, and European elk (Antonsson and Hansson, 2002). Animal papillomas can be divided into four groups based on tissue tropism and histology of lesions. These groups comprise animal PVs that can induce neoplasia of cutaneous stratified epithelium, fibromas with a minimally hyperplastic cutaneous epithelium, cutaneous papillomas and fibropapillomas (an underlying fibroma of connective tissue), and hyperplasia of either normal non-stratified squamous epithelium or metaplastic squamous epithelium. Infection with non-human PVs is generally contained to the skin or mucous membrane s of the host species (Lancaster and Olson, 1982); however, canine oral PV can also infect the eyelid, conjunctival epithelium, and skin around the nose and mouth (Chambers and Evans, 1959). Some animal PV types, such as BPV, cottontail rabbit PV, and Europ ean harvest mice PV, have been implicated in cancers (Antonsson and Hansson, 2002), w ith BPV being the most oncogenic of the PVs (Lancaster et al., 1977). The E5 protein of BPV type 1 (BPV-1) transforms cells and functions by altering the activ ity of cellular membrane prot eins that are involved in proliferation (DiMaio et al., 1986). Most PVs are species-specific or may inf ect closely related animals within the same genus (Sundberg et al., 2000), although BPV-1 and BPV-2 can induce fibroblastic tumors in a strain of inbred mice (Boir on et al., 1964), hamsters (Cheville, 1966), and rabbits (Breitburd et al., 1981). The pres ence of BPV-specific DNA has also been detected in both naturally occurring tu mors and BPV-induced tumors of horses (Lancaster et al., 1977). An oral PV that infected one coyote a nd three dogs has also been described (Sundberg et al., 1991). St udies have shown that many domestic and

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13 wild species of mammals and birds can be in fected by one or more PVs (Sundberg et al., 2000). Marine Mammal Papillomaviruses Viruses and viral diseases have long been identified in marine mammals (Smith and Skilling, 1979) and new PVs in marine ma mmals have recently been described (Van Bressem et al., 1996, and Bossart et al., 2002). Papillomavirus-like particles have been observed in association with genital le sions of male sperm whales (Physeter catodon ) (Lambertsen et al., 1987), dusky dolphins (Lagenorhynchus obscurus ), and Burmeisters porpoises (Phocoena spinipinnis ) (Van Bressem et al., 1996). The high prevalence of papillomatous lesions in se veral small cetaceans (L. obscurus P. spinipinnis Delphinus capensis Tursiops truncatus ) indicates a possible venereal transmission of the disease (Van Bressem et al., 1996). Squamous papill omas and fibropapillomas have also been identified on the skin, the surface of the penis, and the tongue of mysticetes and odontocetes (Geraci et al., 1987) and gastric papillomas contai ning PV-like particles have been observed in a significant am ount of beluga (Delphinapterus leucas ) inhabiting the St. Lawrence River (M artineau et al., 2002). The Florida Manatee (Trichechus manatus latirostris ) The Florida manatee is a marine mammal that is primarily found in the southeastern United States waters and the Gulf of Mexico and is li sted as endangered at both the state and federal levels (U. S. Fi sh and Wildlife Service, 2001). The manatee immune system appears to be highly devel oped and it has been hypothesized that natural disease in manatees is uncommon (Bossart et al., 2002). Environmental diseases that may represent emerging problems for the Flor ida manatee include brevetoxicosis and cold stress syndrome (Bossart, 2001). Recen tly, it has been shown that exposure to

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14 multiple stressors, such as cold weat her and harmful algal blooms (Karenia brevis ), may have synergistic effects on the immune f unction of manatees (Walsh et al., 2005). Papillomas in Florida manatees were initially identified in 1997 in a captive population maintained at Homosassa Springs State Wildlife Park (HSSWP), Homosassa, Florida. These seven captive manatees developed multiple, cutaneous, pedunculated papillomas located on the pectoral flippers, upper lips, external nares, and periorbital regions. Approximately three y ears later, four of the manat ees developed papillomas that were clinically distinct from the previously observed lesions. These lesions were sessile, firm, and more diffuse and numerous than those biopsied in 1997. Based on histological, ultrastructural, and immunohistochemical findings PV was considered to be a theoretical causative agent in both outbreaks. El ectron microscopy evaluation of the lesions revealed the presence of round to hexa gonal 45to 50-nm virions that were ultrastructurally identical to those of know n PVs. Positive immunohistochemical staining was demonstrated with polyclonal antibodies against BPV-1. This was the first viral infection described in Florida manatees (Bossa rt et al., 2002). Similar papillomatous skin lesions have since been observed in free -ranging Florida manatees inhabiting two locations in Florida waters (W oodruff et al., in press). The first molecular detection of PV inf ection in Florida manatees was performed by amplifying PV DNA from papillomatous le sions of captive and free-ranging manatees using the degenerative HPV primers MY09 and MY11. These primers amplified a 458bp DNA fragment of the highly conserved L1 capsid protein gene of manatee papillomavirus (TmlPV) (Woodruff et al., in pr ess). Recently, the entire TmlPV genome has been completely sequenced and characterized. The complete TmlPV genome

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15 (TmPV-1) contains 7,722 bp and consists of seven major ORFs that encode five early proteins and two late capsid proteins (Rector et al., 2004) Sequences of nine L1 fragments previously described by Woodruff et al. (2005) were 100% identical to the corresponding L1 region of the published ma natee papillomavirus, TmPV-1, suggesting that there is only one type of manatee PV that causes skin le sions in manatees (Rector et al., 2004). Although the exis tence of a manatee papillomavirus has been well documented, further work is required in orde r to better understand th e overall impact and possible oncogenic potential of papillomavir us infection in th e already endangered Florida manatee. The goals of this study were to determine if more than one TmlPV is associated with papillomatous lesions in captive and free-ranging manatees, to genetically characterize the TmlPV genome(s), a nd to develop serological assays with the potentially oncogenic E6 and E7 protei ns and with the L1 capsid protein. Figure 1-1. Illustration de monstrating the genetic organization of a typical papillomavirus genome. The HPV-16 genome is divided into early (E) and late (L) regions depending on th e timing of protein expression.

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16 CHAPTER 2 MATERIALS AND METHODS Clinical Data Nine adult female Florida manatees (Trichechus manatus latirostris ) comprised the captive population dwelling at Homosassa Springs State Wildlife Park (HSSWP) located in Homosassa, Florida. Ma natees at HSSWP were housed in Homosassa Springs, a natural freshwater spring at the headwaters of the Homo sassa River, Citrus County, Florida. An underwater fence placed at the junction of the spring and the river confined the manatees to an area of approximately 2 acres (Bossart et al., 2002). Free-ranging manatees were occasionally observed at the ou ter perimeter of the unde rwater fence. The free-ranging manatees found in this area are winter residents that use the springs for thermoregulation (Woodruff et al., in press). Source of Samples Between January, 2003, and February, 2005, sk in lesions from captive and freeranging manatees were brought to our laborator y fresh, on ice, or fixed in either 10% non-buffered formalin (NBF) or Dimethyl Sulfoxide (DMSO). Papillomatous skin lesions from captive Florida manatees were received from various parks, including HSSWP, Florida, and other marine parks in Florida and California. Papillomatous skin lesions were also obtained from free-ranging Florida manatees inhabiting several bodies of Florida waters, including Cr ystal River, Homosassa River, Port of Isles, and Tampa Bay, and from free-ranging Antillean manatees (Trichechus manatus manatus ) inhabiting the offshore waters of the Drowned Keys, Belize. One papillomatous penile lesion

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17 preserved in 10% NBF was obtained from a free-ranging manatee carcass examined at the Fish and Wildlife Research Institute, St. Petersburg, Florida, and an uninfected, normal manatee liver was obtained from th e Marine Mammal Pathology Laboratory, St. Petersburg, Florida. Samples biopsied fr om HSSWP captive manatees between July, 1998, and January, 2000, were preserved in 10% NBF or DMSO and samples biopsied from free-ranging manatees in April, 2004, and August, 2004, were preserved in 10% NBF. All other manatee tissue samples (captive and free-ranging) arrived fresh or on ice. Sample description and information ar e located in Table 2-1 and Table 2-2. Blood serum from captive manatees hous ed at HSSWP was brought to our laboratory on dry ice, courte sy of Bob Bonde, U. S. Geol ogical Survey, Gainesville, Florida. Serum samples were obtained fr om the following captive manatees (date obtained): Holly (July 9, 1998), Betsy (Febru ary, 1999), Oakley (Feb 25, 1999; June 20, 2002), Willoughby (January 13, 2000), Amanda (Jan 13, 2000), and Lorelei (Jun 20, 2002). Purified anti-manatee IgG monoc lonal antibody (1.2 mg/ml) was obtained courtesy of Dr. Peter McGuire, Department of Biochemistry, University of Florida, and Ms. Linda Green, Hybridoma Core Laboratory, University of Florida, Gainesville, Florida. DNA Extraction from Papillomatous Lesions Total DNA was extracted from all tissue samples using the DNeasy tissue kit (Qiagen Inc, Valencia, California, USA) acco rding to the protocol recommended by the manufacturer. Working in a laminar flow cabinet equipped with an HEPA filter, approximately 25 mg of each papillomatous skin lesion was minced with a sterile surgical blade and placed and ground in a sterile 1.5-ml micro centrifuge tube. The tissues were incubated overnight at 55C in a mixture containing 180l of digestion

PAGE 30

18 buffer ATL and 20 l proteinase K (20 mg/ml) until lysis was complete. Then, 200 l of buffer AL and 200 l of 100% molecular grad e ethanol were added to precipitate the DNA. The solution was centrifuged in a DNeasy Spin Column to bind the DNA to the membrane and the membrane was washed with 500 l of buffers AW1 and AW2 for 1 minute each time. A final centrifugation step was performed to eliminate residual ethanol remaining in the membrane. The DNA was el uted in 200 l of buf fer AE and evaluated for yield and purity by spectrophotometr y using the Ultros pec 3000 (Amersham Biosciences Corp., Piscataway, New Jerse y, USA). A negative tissue sample from uninfected manatee skin or uninfected manatee liver was extracted along with each set of tissue samples for use as a negative contro l in PCR analyses. The eluted DNA samples were stored in 1.5-ml scre w-cap tubes at -80C. General Methods of PCR Taq Polymerase Reactions The PCR reaction in a 0.2 ml tube contained: 200 nM of each primer (IDT, Coralville, IA, USA), 2 mM MgSO4, 100 M of each deoxynucleoside triphosphate (dNTP), 20 mM Tris-HCl (pH 8.4), 10 mM KCl, 0.1 % Triton X-100 (pH 8.8), 10 mM (NH4)2SO4, 1 unit of Taq DNA polymerase (New England BioLabs, Beverly, Massachusetts, USA), 0.5-1.0 g of template DNA, and ultrapure H2O in a final volume of 50 l. A total of 40 PCR cycles were performed in a PTC-100 thermal cycler (MJ Research, Inc., Waltham, Mass achusetts, USA) for the amp lification of the manatee papillomavirus (TmlPV) L1 fragments using the modified MY11/MY09 primers (CR333/CR332) and the L1 TmlPV-specific primers (CR490/CR491). Following an initial denaturation step at 94C for 1 min, r eactions were subjected to 39 cycles of: a denaturation step at 94C for 1 min, an a nnealing step at 48C for 1 min, and an

PAGE 31

19 elongation step at 72C for 2 min. An elongation step at 72C for 10 min was incorporated in the final cycle. Accuprime Taq DNA Polymerase Reactions The PCR reaction in a 0.2 ml tube cont ained: 400 nM of each primer, 200 mM Tris-HCl (pH 8.0), 500 mM KCl, 15 mM MgCl2, 2 mM of each dNTP, 2 units of Accuprime Taq DNA polymerase (Invitrogen, Carlsbad, California, USA), 0.2-0.5 g of template DNA, and ultrapure H20 in a final volume of 50 l. Cycling conditions for the amplification of the complete TmlPV E6 gene fragment included: an initial denaturation step at 94C for 2 min, then, 39 cycles of: a denaturation step at 94C for 30 sec, an annealing step at 53C for 30 sec, and an ex tension step at 68C for 1 min. Cycling conditions for amplification of the L1 fragments and the complete E7 complete gene were similar, except that the annealing temperatures were set at 59C and 51C, respectively. Expand High Fidelity Plus Reactions The PCR reaction in a 0.2 ml tube contai ned: 400 nM of each primer, 200 M of each dNTP, 1.5 mM MgCl2, Expand High Fidelity Plus Reaction Buffer diluted to 1.5 mM MgCl2 (Roche Applied Science, Mannheim, Germany), 2.5 units of Expand High Fidelity Plus Enzyme Blend (Roche App lied Science), 0.5 g of template DNA, and ultrapure H2O in a final volume of 50 l. Cyclin g conditions for amplification of the TmlPV L1-E1 region were: an initial denaturation at 94C for 2 min, followed by 39 cycles of 94C for 30 sec, 50C for 30 sec, and 72C for 3 min, w ith a final extension step at 72C for 7 minutes. Cycling conditi ons for amplification of the TmlPV L1-L2 capsid region were similar, except that the annealing temperature was set at 59C and the extension step was performed at 68C for 3.5 min. Cycling conditions for amplification

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20 of the TmlPV complete L1 capsid gene were similar, but the extension steps were performed at 72C for 1.5 min. For amplifi cation of the TmlPV complete L2 capsid gene, cycling conditions were similar and th e annealing temperatur e was set at 53C and the extension step performed at 72C for 2 min. PCR Targeting the L1 458-bp Fragment The MY11 and MY09 L1 consensus primers th at amplify a 458-bp fragment of the L1 capsid protein gene of several human papillomaviruses (HPVs) (Manos et al., 1989) were modified in our laboratory to contai n deoxyinosines at positions of nucleotide degeneracy [forward primer (FP) CR333 and re verse primer (RP) CR332] (Table 2-3). DNA obtained from a lesion from captive ma natee Oakley was used as the positive control. A blank sample (water) and DNA extracted from a liver of an uninfected manatee were used as negative controls. PCR Targeting the L1 TmlPV 458-bp Fragment Based on newly generated nucleotide se quences of the amplified TmlPV L1 fragment obtained in our la boratory, the MY11/MY09 HPV L1 primers (Manos et al., 1989) were modified to contain TmlPV L1-speci fic nucleotides at pos itions of nucleotide degeneracy. The L1TmlPV primers, FP CR490 and RP CR491 (Table 2-3), target a 458-bp sequence contained within the L1 capsid gene of TmlPV. DNA obtained from a lesion from captive manatee Oakley was used as the positive control. A blank sample (water) and DNA from a negative tissue (manatee liver) were used as negative controls. PCR Targeting the TmlPV L1-E1 Region Using a PCR method described by Forslund and Hansson (1996), oligonucleotide primers were designed to target a region of the TmlPV genome that spans an area from within the 3 end of the TmlPV L1 ORF to an area within the 5 end of the TmlPV E1

PAGE 33

21 ORF. A plus-strand oligonucleotide prim er designed from the TmlPV L1 458-bp fragment nucleotide sequence was used in a PCR reaction together with a minus-strand HPV consensus primer from the E1 ORF (Smits et al., 1992). The TmlPV L1 FP CR442 and the HPV E1 RP CR441 (Table 2-3) direct the amplification of an approximately 3,000-bp fragment. DNA obtained from a lesi on from captive manatee Oakley was used as the positive control. A blank samp le (water) and DNA from a negative tissue (manatee liver) were used as negative controls. PCR Targeting the Complete TmlPV E6 Gene Based on the nucleotide sequences of th e TmlPV L1-E1 region obtained by us, oligonucleotide primers FP CR498 and RP CR499 (Table 2-3) targeting the complete TmlPV E6 gene were designed for cloning and expression. DNA obt ained from a lesion from captive manatee Oakley was used as the positive control. A blank sample (water) and DNA from a negative tissue (manatee liver ) were used as negative controls. PCR Targeting the Complete TmlPV E7 Gene Based on the nucleotide sequences of th e TmlPV L1-E1 region obtained by us, oligonucleotide primers FP CR500 and RP CR501 (Table 2-3) targeting the complete TmlPV E7 gene were designed for cloning and expression. DNA obt ained from a lesion from captive manatee Oakley was used as the positive control. A blank sample (water) and DNA from a negative tissue (manatee liver ) were used as negative controls. PCR Targeting the TmlPV L1-L2 Region Based on nucleotide sequences of the complete TmlPV genome (AY609301) (Rector et al., 2004), a plus strand oligonuc leotide primer FP CR572 (Table 2-3) was designed from an area upstream of the L2 ORF. Used together with an L1 minus strand primer RP CR574 (Table 2-3), designed by us these primers target a region of the

PAGE 34

22 TmlPV genome that spans an area upstream of the 5end of the TmlPV L2 ORF to an area downstream of the 3end of the TmlPV L1 ORF. DNA obtaine d from a lesion from captive manatee Oakley was used as the posi tive control. A blank sample (water) and DNA from a negative tissue (manatee liver) were used as negative controls. PCR Targeting the Complete TmlPV L1 Gene Based on nucleotide sequences of the L1-L2 fragment obtained in our laboratory, a plus-strand oligonucleotide prim er FP CR573 (Table 2-3) was designed upstream of the L1 start codon to be used together with the L1 FP CR574 for am plification of the complete L1 gene for cloning and expression. DNA obtained from a lesion from captive manatee Oakley was used as the positive co ntrol. A blank sample (water) and DNA from a negative tissue (manatee liver) were used as negative controls. PCR Targeting the Complete TmlPV L2 Gene Based on nucleotide sequences of the L1-L2 fragment obtained in our laboratory, a minus-strand oligonucleotide primer RP CR622 (Table 2-3) was designed downstream of the L2 stop codon to be used together with the L2 FP CR572 for amplification of the complete L2 gene. DNA obtained from a le sion from captive manatee Oakley was used as the positive control. A blank samp le (water) and DNA from a negative tissue (manatee liver) were used as negative contro ls. A linear representation of the circular TmlPV genome with the relative positions of th e PCR primers used in this study is shown in Figure 2-1. Gel Electrophoresis Between 20-30 l of PCR products were re solved by horizontal electrophoresis in 1.0% agarose gels containing ethidium brom ide (0.5 g/ml). Amplified DNA fragments

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23 were visualized under ultr aviolet light and photographe d using a gel documentation system (Bio-Rad Laboratories, In c., Hercules, California, USA). General Cloning of PCR Products As described under gel electrophoresis PCR products containing amplified fragments of only the expected size were purified for use in cloning reactions. PCR products containing additional amplified fragments were resolved in 1.2% low-melting point (LMP) agarose and the band of the a ppropriate size was exci sed and purified for use in cloning reactions. PCR products and excised gel pieces were purified using the Wizard SV Gel and PCR Clean-Up System (P romega Corporation, Madison, Wisconsin, USA) according to the protocol provided by the manufacturer. Br iefly, an equal volume of membrane binding solution was added to the PCR product, the prepared PCR product was added to the SV minicolumn assembly, and the minicolumn was washed twice with the membrane wash solution. The purified DNA was eluted in 50 l of nuclease-free water and stored at -80C until further use in cloning reactions. Cloning into pCR 2.1 TOPO T/A Vector Purified PCR products were cloned into the pCR 2.1 TOPO vector (Invitrogen Life Technologies, Carlsbad, California, USA) for sequencing analysis. In a 0.2 ml tube, ligation reactions contained: 1 l of salt solution (1.2 M NaCl, 0.06 M MgCl2), 1l of the TOPO T/A vector (Invitrogen), 50 ng of purifie d PCR or gel product, and ultrapure H2O in a final volume of 6 l. Reactions were incubated at room temperature for 1 hour; then, 3l of the reaction were adde d to one vial (50l) of DH5 or TOP-10 chemically competent Escherichia coli cells (Invitrogen). Tubes were placed on ice for 1 hour, heat shocked for 30 sec at 42C in a water bath, a nd returned to ice. After adding 250 l of S.O.C. medium (Invitrogen), the tubes were shaken horizontally at 220 rpm at 37C for 1

PAGE 36

24 hour. Reactions (100-200 l) were spread onto bacterial agar plates containing ampicillin (100 g/ml) (Roche Applied Science) and bl ue/white selection me dium [75 l 2XYT: 16g Bacto-tryptone, 10 g Bacto-Yeast Extract, 15 g Bacto-Agar (Beckton Dickinson, Franklin Lakes, New Jersey, USA), 5g enzyme grade NaCl (Fisher Scientific International Inc., Hampton, New Hampshire, USA) in 1 L of ultrapure H2O, 20 l IPTG (100mg/ml) (Invitrogen), and 5 l UltraPure Bluo-gal (100mg/ml) (Invitrogen)] spread on the agar plates surface one hour before the plates were inoculated with cloning reactions. Plates were in cubated overnight at 37C. Cloning into P-Target Ma mmalian Expression Vector Purified PCR products were directly cloned into the P-Target mammalian expression vector (Promega) to test for protein expre ssion after tran sfection and immunofluorescence. In a 0.5 ml tube, the li gation reaction contained: 1l of T4 DNA ligase constituents, 1 l of T4 DNA ligase, 1 l of pTarget cloni ng vector (ProMega), 5l of purified PCR product, and ultrapure H2O in a final volume of 10 l. The ligation reaction was incubated at 4C overnight in a re frigerated block. Five l of the ligation reaction were added to one vial (50l) of JM109 high efficiency competent cells (Promega) and incubated on ice for 20 min. Th e cells were heat shocked for 45 sec at 42C in a water bath and returned to i ce for 2 min. After adding 450l of S.O.C. medium, the tubes were shaken at 150 rpm at 37C for 1.5 hrs. The transformation reaction was spread in 100l volumes onto bacterial agar plates containing ampicillin (100g/ml) and blue/white selection medium. Cloning into pcDNA .1 Directional TOPO Expression Vector In order to pair with the -GTGGoverhang of the pcDNA 3.1 Directional TOPO Expression Vector, the TmlPV E7 FP CR 500 was modified at the 5end to

PAGE 37

25 contain a corresponding 4-bp CA CC sequence. To amplify the complete TmlPV E7 gene with the TOPO overhang, the modified E7 FP CR 530 (Table 2-3) was used in a PCR reaction with the TmlPV E7 RP CR501. The P CR reaction in a 0.2 ml tube contained: 200 nM of each primer, 300 mM Tris-SO4 (pH 9.1), 90 mM (NH4)2SO4, 10 mM MgSO4, 200M of each dNTP, 2 units of Elongase enzyme mix (Invitrogen), 0.5-1.0 g of template DNA, and ultrapure H2O to a final volume of 50 l. Cycling conditions for the amplification of the E7 TOPO PCR products were: an initia l denaturation step at 94C for 2 min, then 39 cycles of a denaturation st ep at 94C for 30 sec, an annealing step at 51C for 1 min, and an extension step at 68C for 1 min. Purified E7 TOPO PCR products were directly cloned into th e pcDNA 3.1 Directional TOPO expression vector for use in immunofluorescence assays. In a 0.2 ml tube, the ligation reaction contained: 1l of salt solu tion (50 mM NaCl, 2.5 mM MgCl2), 1l of pcDNA 3.1 TOPO vector (Invitrogen), 50 ng of purified E7 TOPO PCR product, and ultrapure H2O in a final volume of 6l. Ligation reacti ons were incubated at room temperature for 1 hour; then, 3l of the reaction were added to one vial (50l) of One-shot TOP10 chemically competent E. coli cells (Invitrogen). Tubes were placed on ice for 1 hour, heat shocked for 30 sec at 42C in a water bat h, and returned to ice. After adding 250 l of S.O.C. medium (Invitrogen) the tubes were shaken horizontally at 220 rpm at 37C for 1 hour. Transformations (100-200 l) we re spread onto bacterial agar plates containing ampicillin (100 g/ml) and the plat es were incubated overnight at 37C. Analyzing Recombinants Using sterile toothpicks, bacterial colonies were selected from agar plates and added to 10 ml sterile glass tubes containi ng 3 mL 2XYT and 3l ampicillin (100g/ml) and the tubes were shaken overnight at 275 rpm at 37C. DNA was extracted from

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26 approximately 1 ml of overnight culture usi ng the 10-minute Mini-Prep Protocol (Zhou et al., 1990). Briefly, overnight cultures were centrifuged for 10 sec in a 1.5 ml capped tube. The supernatant was discarded, 300l of TENS was added to the cell pellet, and the tube was vortexed for 2-5 sec. Then, 150 l of 3.0 M sodium acetate (pH 5.2) (Gibco Life Technologies, Carlsbad, California, USA) were added and the tube was vortexed and centrifuged. The supernatant was transferred to a fresh 1.5 ml capped tube and mixed thoroughly with 0.9 ml of 100% mo lecular grade ethanol which had been pre-cooled to 20C. After centrifugation, the plasmid DNA pe llet was washed twice with 1 ml of 70% ethanol, allowed to dry, and resuspended in 50 l of TE buffer (pH 8.0). Recombinants were analyzed by restriction enzyme dige stion using endonucleases HindIII, ApaI, BamHI, EcoRI, and the combination of ApaI and BamHI (Invitrogen). Restriction digest reactions contained: 0.3 l of restriction enzyme, 3.0 l of the appropriate enzyme buffer, 1.0 l of mini-prep DNA, and ultrapure H2O in a final volume of 30 l. Reactions were incubated at 37C for 1 hour in a dry block and analyzed by gel electrophoresis. Recombinants containing inserts of the a ppropriate size were fu rther propagated in competent E. coli cells and purified with the Auru m Plasmid Mini Kit (Bio-Rad Laboratories, Inc., Hercules CA, USA) for sub-cloning a nd sequencing. Following the protocol provided by the manufacturer, 1 ml of overnight culture was added to a 2.0 ml tube, centrifuged, and the supernatant decanted. Then, 250 l of resuspension solution and 250l of lysis solution were added, the tu be was inverted 6-8 times, and the mixture was allowed to incubate at room temperature for 5 min to ensure lysis was complete. After adding 350 l of neut ralization solution, the tube was inverted 6-8 times and centrifuged. The cleared lysate was transferre d to a mini spin column and the column

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27 was washed once with 750 l of wash solutio n. The DNA was eluted in 50 l of elution solution and evaluated for yield and purity by spectrophotometry. Sub-cloning of Purified Recombinants In order to obtain a high yield and purity of vector and recombinant DNAs for subcloning reactions, midi-prep DNAs were prepar ed with the Qiagen plasmid purification kit (Qiagen, Hilden, Germany), according to the manufacturers protocol. Transformation reactions cont aining 1 l of DNA were pr opagated overnight in 100 ml of 2XYT medium (100l ampicillin), the overnight cultures were centrifuged, and the supernatants were removed. The bacterial pell ets were resuspended and vortexed in 4 ml of buffer P1 and mixed gently in 4 ml of buf fer P2. The lysis reactions were allowed to proceed at room temperature for 5 min and 4 ml of chilled buffer P3 were added. The reactions were mixed gently, incubated on ice for 15 min, and centrifuged for 1 hour until the supernatant was clear. Each supernatant wa s added to an equilibr ated Qiagen-tip 100 and allowed to enter the resin by gravity flow The Qiagen-tip was washed twice with buffer QC and the DNA was eluted in 5 ml of buffer QF. The DNA was precipitated in 5 ml of isopropanol, washed with 2 ml of 70% ethanol, and allowed to dry for 15-20 min. The DNA pellet was redissolved in 200 l of buffer EB and evaluated for yield and purity by spectrophotometry. Sub-Cloning into pcDNA 3.1/Zeo+ Expression Vector The complete TmlPV E6 and L1 capsid genes were sub-cloned from pCR 2.1 TOPO T/A into pcDNA 3.1/Zeo+ expression vector at positions of compatible restriction sites present in the vector multiple cloning sites. The TmlPV E6 recombinants were subcloned into the expression vector at the Ec oRI site, and the TmlPV complete L1 gene recombinants were sub-cloned into the expression vector at the HindIII and XbaI sites.

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28 Purified recombinant DNAs and purified pcDNA 3.1/Zeo+ DNA were cut with identical restriction enzyme(s) in separate digest re actions. Restriction digests of pcDNA 3.1/Zeo+ contained: 3.0 l of restri ction enzyme, 6.0 l of the corresponding buffer (Invitrogen), 3.0 l of bovine serum albumin (Invitrogen), 1 g of purified pcDNA 3.1/Zeo+ vector DNA, and ultrapure H2O in a final volume of 60l. Re striction digests of TOPO T/A recombinants were similar, except that they contained 3g of purified recombinant DNA. Digest reactions were incubated at 37C in a dry block for 2 hours and resolved by horizontal electrophoresis in 1.2% low-melting point (LMP) agarose gels containing ethidium bromide (0.5 g/ml). The bands of the appropriate size for the digested pcDNA 3.1/Zeo+ vector and for the digested recombinants were excised from the LMP gel and purified using the Wizard SV gel and PCR cl ean-up system. DNA from the purified gel products was used in the ligation reaction that contained: 4 l of 5X T4 ligase buffer, 1.5 l of T4 ligase (Invitrogen), a 1l of gel purified recombinant DNA, 3l of gel purified pcDNA 3.1/Zeo+, and ultrapure H2O in a final volume of 20l. Ligation reactions were incubated overnight at 14C in a refrigeration block. Ten l of the ligation reaction were added to one vial (50 l)of DH5 competent E. coli cells, incubated on ice for 1 hour, heat shocked at 42C for 30 sec, and returned to ice. Then, 600 l of 2XYT containing 50 mM glucose were added and the vial was shaken horizontally at 220 rpm at 37C for 1 hour. Reactions (200l) were spread onto agar plates containing ampicillin, and plates were incubated overnight at 37C. Bacterial colonies were selected from the plates and propagated in 2XYT medium containing am picillin. Recombinant DNA was purified using the 10 minute mini-prep protocol and in serts of the appropriate size cloned into the pcDNA 3.1+ vector were confirmed by restricti on digest using 6-ba se cutter enzymes

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29 NsiI, known to cut the TmlPV E6 fragment on ce, and SpeI, known to cut the TmlPV L1 fragment sequence once. L1 Gene Sub-Cloning into pFastBac Vector The TmlPV complete L1 gene was subcloned from pCR 2.1 TOPO T/A into the pFastBac1 vector (Invitrogen) at positions of compatible restriction sites present in the vector multiple cloning site for use in the Bac-to-Bac B aculovirus expression system (Invitrogen). Purified L1 recombinant DNA and purified pFastBac vector DNA were cut with identical restriction enzyme(s) in sepa rate digest reactions. Restriction digests of pFastBac contained: 3.0 l of restriction enzyme EcoR I (Invitrogen), 6.0 l of the corresponding 10X buffer III (Invitrogen), 3.0 l of bovine serum albumin (Invitrogen), 1 g of purified pFastBac ma xi-prep DNA, and ultrapure H2O in a final volume of 60l. Restriction digests of the TOPO T/A TmlPV L1 complete gene recombinant were similar, except that they contained 3g of purified maxi-prep recombinant DNA. Digest reactions were incubated at 37C in a dry block for 2 hours and resolved by horizontal electrophoresis in 1.2% low-melting point (L MP) agarose gels containing ethidium bromide (0.5 g/ml). Bands of the appropria te size for the digested pFastBac vector and the digested TOPO T/A TmlPV L1 comple te gene recombinant were excised from the LMP gel and purified using the Wizard SV gel and PCR clean-up system. The ligation and transformation reac tions of the L1 complete gene into pFastBac were set up similar to the reactions pr eviously described for sub-cl oning into the pcDNA 3.1+/Zeo expression vector, except that transformati ons were performed in TOP-10 competent E. coli cells (Invitrogen). Individua l bacterial colonies were se lected from the plates and propagated in 2XYT medium containing ampi cillin (100g/ml). DNA was extracted from the overnight cultures using the 10 minute mini-prep protocol (Zhou et al., 1990)

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30 and pFastBac L1 recombinants were iden tified by restriction digest with enzymes EcoRI, Hind III, and BamHI, a 6-base cu tter enzyme known to cut the TmlPV L1 sequence at one site. L1 Gene Sub-Cloning into pBlueBac 4.5 The TmlPV complete L1 gene was su b-cloned from pCR 2.1 TOPO T/A after digesting with enzymes XbaI and SstI into the pBlueBac 4.5 vector (Invitrogen), which was digested with the same enzymes. Th e ligation and transformation reaction of the TmlPV L1 gene into the pBlueBac vector was set up similar to the described sub-cloning reaction into the pFastBacI vect or. Individual bacterial coloni es were selected from agar plates and propagated in 2XYT medium containing ampicillin (100g/ml). DNA was extracted from overnight cu ltures using the 10 minute mini -prep protocol (Zhou et al., 1990) and pBlueBac L1 recombinants were identi fied by restriction digest with XbaI and SstI enzymes. Sequencing of PCR-amplified and Cloned Products As described under gel electrophoresis, amp lified PCR products of the expected size were purified and sequenced directly us ing the PCR primers diluted 1:5 in sterile H2O. Cloned PCR products were sequenced with the corresponding vector sequencing primers diluted 1:10 in sterile H2O. Additional sequencing pr imers (1:5) were used to obtain the complete sequence of cloned DNA fragments that were greater than 600 nucleotides in length. A list of sequencing pr imers is contained in Table 2-4. Between 50 fmol of purified PCR products or purif ied recombinants were sequenced in duplicate using specific forward and revers e primers in the Beckman-Coulter CEQ 2000XL sequencing instrument (Beckman-Coulte r Inc., Fullerton, California, USA). Chromatograms were checked manually for errors in nucleotide sequences using the

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31 Chromas 2.3 software (Technelysium Pty Ltd., Tewantin, Queensland, Australia), and the assembled sequences were analyzed using the seqed, gap, translate, and multiple alignment functions of the University of Wisconsin P ackage Version 10.2 (Genetics Computer Group [GCG], Univ ersity of Wisconsin, Madi son, Wisconsin, USA). The Basic Local Alignment Search Tool (BLA ST) function of the National Center for Biotechnology Information (NCBI) website ( http://www.ncbi.nlm.nih.gov/ ) was used to identify papillomavirus sequences most cl osely related to sequences obtained from TmlPV fragments. Neighbor-Joining phyloge netic trees were generated by PAUP 4.0 (Sinauer Associates, Sunderland, Massachuse tts, USA) software, using Clustal W slow and accurate function using Gonnet residue weight table, gap penalty of 35 and gap extension penalty of 0.75 for pairwise alignment parameters, and gap penalty of 15 and gap extension penalty of 0.3 fo r multiple alignment parameters. Phylogenetic trees were constructed with the deduced amino acid sequ ences of the TmlPV L1 ORF, L2 ORF, E6 ORF, and E7 ORF DNA fragments. Trees we re based on the amino acid sequences of human and non-human PVs obtained from th e GenBank database through the NCBI website and from the HPV database of the Los Alamos National Laboratory Theoretical Biology and Biophysics website ( http://hpv-web.lanl.gov /stdgen/virus/hpv/ ). Transfection of Insect Cell Cultures Culturing Insect Cells Sf21 (Spodoptera frugiperda ) insect cells (Invitrogen) we re used as indicator cell cultures to generate recombinant baculovi ruses. Sf21 cells were cultured in 75 cm2 flasks (TPP, Switzerland) in serum free Sf-900 II medium (Invitrogen) containing: 200 g/ml of antibiotic/antimycotic [penicillin (1X104 units/ml)], streptomycin sulfate (10 mg/ml), amphotericin B (25 g/ml)] (Gibco), 200 g/ml of gentamicin (100 g/ml) (Gibco), and

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32 10% fetal bovine serum (Gibco). Insect ce lls were incubated at 27C in a humidified incubator. After one week, th e cell monolayer was scraped w ith a sterile, disposable cell scraper (Greiner Bio-One, Kremsmuenster, Australia), resuspende d in 10 ml of Sf-900 II/10% FBS, and counted with a hemocytome ter (Reichert Scientific Instruments, Buffalo, NY). Approximately 1 X 106 Sf21 cells in 2 ml of Sf-900 II/10% FBS medium were added to 35 mm dishes and incubated at 27C. All steps were performed in a laminar-flow cabinet under sterile conditions. Transformation of MAX Efficiency DH10Bac Competent E coli In order to transfect insect cell cultures a nd generate a recombin ant baculovirus, the pFastBac L1 constructs were firs t transformed into MAX Efficiency DH10Bac competent E. coli (Invitrogen) that contain a bacul ovirus shuttle vector (bacmid) and a helper plasmid. Briefly, 1 l of purified pF astBac recombinant (1ng/l) was added to 50l of DH10Bac E. coli incubated on ice 30 min, heat shocked at 42C for 45 sec, and returned to ice for 2 min. The reaction was transferred to a 15 ml screw-cap conical tube (Sarstedt Inc., Newton, North Carolina, USA) and 900 l of S.O.C. medium were added. The reactions were shaken at 225 rp m at 37C for 4 hours and transformations were spread onto bacterial agar plates c ontaining kanamycin (50g/ml), tetracycline (10g/ml), gentamicin (7 g/ml) (Gibco), a nd blue/white selection medium. Plates were incubated overnight at 37C. Individual bact erial colonies were selected and propagated in 3ml 2XYT medium containing kanamycin, tetracycline, and gentamicin and shaken overnight at 275 rpm at 37C. Overnight cultures were purifie d using the 10 minute mini-prep protocol and recombinant bacmid s were confirmed by PCR analysis. The Bacto-Bac M13 primers, forward primer CR 613: 5-CCC AGT CAC GAC GTT GTA AAA CG-3 and reverse primer CR 614: 5-AGC GGA TAA CAA TTT CAC ACA GG-

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33 3, were used together in a PCR reaction th at contained: 200 nM of each primer, 2 mM MgSO4, 100 M of each dNTP, 20 mM Tris-HCl (pH 8.4), 10 mM KCl, 0.1 % Triton X100 (pH 8.8), 10 mM (NH4)2SO4, 1 unit of Taq DNA polymerase (New England BioLabs), 1l of mini-prep DNA, and ultrapure H2O in a final volume of 50l. For amplification of bacmid DNAs, cycling conditi ons were: an initial denaturation step at 93C for 3 min, followed by 29 cycles of dena turation at 94C for 45 sec, annealing at 51C for 45 sec, and extension at 72C for 5 min. An elongation step at 72C for 7 min was incorporated into the final cycle. Bacmid DNA recombinants containing the L1 complete gene were expected to be a pproximately 4,000-bp in size (2,300 bp bacmid DNA plus 1,712 bp L1 complete gene) a nd bacmid DNA amplicons that were not recombinants were expected to be approxi mately 300-bp in size. PCR products were resolved by horizontal electropho resis in 1.0% agarose gels containing ethidium bromide (0.5 g/ml) and visualized under UV light. Recombinant bacmids were further confirmed to contain the pFas tBac L1 gene by PCR analysis targeting the TmlPV L1 complete gene. Transfection of Insect Cells with Bacmid DNA Recombinants In a 10 ml glass bacteriological tube (Fis her Scientific), 1 g of L1 bacmid DNA was added to 100l of unsupplemented Graces ins ect cell culture medium (Gibco). In a separate glass tube, 6 l of Cellfectin Reagent (1mg/ml) (Invitrogen) were added to 100l of unsupplemented Graces insect cell culture medium. The mixtures were combined and the tube was incubated at room temperature for 45 min. Prior to transfecting Sf21 insect cells, the cell m onolayer was washed with 2 ml of Graces medium and incubated for 5 min at room temperature. The medium was removed and 800 l of Graces medium were added gen tly and directly to the cells. The

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34 Bacmid/Cellfectin transfection mix was th en added dropwise ont o the cells and the cultures were incubated at 27C for 5 hours. At this time, the transfection mixture was removed and 2 ml of unsupplemented Graces me dium was added to the transfected cells. Cultures were incubated at 27C in a humi dified incubator. Sf21 cells fed with unsupplemented Graces medium (without bacu lovirus DNA) and Sf21 cells transfected with purified baculovirus DNA (w ithout insert) were used as negative controls. All steps were performed in a laminar-flo w cabinet under sterile conditions. Harvest of Recombinant Baculovirus Stocks After the transfected cell cultures were incubated for approximately 96 hrs, the cell monolayer and supernatant (~2 ml) were collect ed with a sterile pipette and inoculated onto Sf21 cultures in 60 mm tissue culture dishes One ml of the ce ll supernatant plus 1 ml of Sf-900 II/5% FBS medium were added to fresh 60 mm dishes containing approximately 2 X 106 Sf21 cells. The cells were incubated at 27C for 1.5 hrs, the inoculum was removed, and the cultures were transfected with 3 ml of unsupplemented Graces medium. Infected cultures were incubated at 27C for approximately 96 hrs and sub-cultured again into fresh cultures. The infected cultures were sub-cultured a total of 5 times and the final harvest of cells and supernatants were obtained from 150 mm dishes. All steps were performed in a la minar-flow cabinet under sterile conditions. Harvests from infected ce ll cultures were analyzed by electron microscopy, by Mr. Woody Frazer, from the Florida Animal Disease Diagnostic Laboratory, Florida Department of Agriculture and Consum er Services, Kissimmee, Florida. Reverse Transcription PCR (RT-PCR) of Infected Cell Cultures RNA was extracted from infected Sf21 cell cultures transfected with the pBlueBac plasmid containing the L1 capsid gene to determine whether messenger RNA (mRNA)

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35 encoding the TmlPV L1 capsid protein was pres ent. To use as negative controls, RNA was extracted from untransfected Sf21 cell cu ltures and from Sf21 ce lls transfected with purified parental pBlueBac vect or. Cells and supernatants were harvested 96 hrs after transfection, centrifuged at 4,000 rpm at 10C for 10 min, the supernatant was removed, and RNA was extracted from the cell pellets using the Aurum total RNA mini kit (BioRad). The RNA samples were treated with twice the recommended amount (160l) of DNase I solution for 30 min, eluted from a mi ni column with 100l of elution solution, and treated again with 160l of DNase I so lution. The alcohol pr ecipitated RNA pellet was resuspended in 60l of RNase-free H2O and analyzed for yield and purity by spectrophotometry. Total RNA was used in reve rse transcription reactions in order to obtain a first-strand cDNA product for use in PCR analysis. Synthesis of cDNA was performed with SuperScript II (Invitrogen) acco rding to the manufacturers protocol. Reactions contained random hexamer primers (Invitrogen) or a TmlPV L1 gene-specific primer (RP CR574) designed by us. The revers e transcription assays were performed in duplicate with or without the incorporation of SuperScript II reverse transcriptase enzyme (Invitrogen) in order to ensure that the DNA had been completely degraded by the DNase I treatment during the RNA extrac tion process. The cDNAs were used as templates for amplification in TmlPV L1 PCR assays according to the PCR protocol targeting the TmlPV complete L1 gene. Generation of Recombinant Baculovirus Recombinant vector pBlueBac 4.5 containi ng the complete TmlPV L1 gene under the control of the polyhedron promoter and the Bac-N-Blue baculovirus DNA (Invitrogen) (0.5g DNA in 10l volume) were incubated at room temperature for 10 min. Then, 1 ml of unsupplemented Graces insect medium (Invitrogen) was added to

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36 the tube, followed by 20l of Cellfectin reag ent (Invitrogen). The reaction was gently mixed for 10 sec and allowed to incubate at room temperature for 15 minutes. Prior to transfecting the Sf21 in sect cultures (3X106) seeded in 60 mm dishes, the medium was removed and the cell monolayer was rinsed gently twice with 2 ml of fresh, unsupplemented Graces insect medium wit hout FBS. The transfection mixture was added dropwise onto the cells and incubate d at 27C for six hours in a humidified incubator. After the incuba tion period, 2 ml of complete TNM-FH medium (Invitrogen) containing gentamycin (10g/ml) and FBS (10%) were added to each dish. The dishes were incubated at 27C for 10 days, at which time cells and medium were harvested and stored at 4C prior to screen ing and purification of the reco mbinant viruses. A second dish containing Sf21 cell cultures was transfec ted with the transfer vector pBlueBac 4.5 containing the L1 capsid gene, but no bacul ovirus DNA, and treated similarly. A third culture of untransfected Sf21 cells served as a negative control. After 72 hrs, 500l of the medium was harvested from each dish a nd transferred to a st erile 15 ml screw-cap tube to which 2l of Bluo-gal substrate (200 g/l in DMSO) was added. The tubes were incubated at 27 and monitored for the development of a blue color. Transfection of Mammalian Cells Culturing African Green Monkey Kidney (COS-7) Cells African green monkey kidney (COS-7 ) cells were propagated in 75 cm2 flasks in Dulbeccos modified eagle medium (D MEM) (Gibco) containing gentamycin, antibiotic/antimycotic, and 10% FBS. Cells were incubated at 37C in a humidified incubator.

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37 Electroporation of COS-7 Cells with Recombinants for Immunofluorescence Assays COS-7 cells were dispersed with tr ypsin/EDTA (0.25% Trypsin/1mM EDTA) (Gibco), resuspended in 10 ml DMEM/5% FBS in a 15 ml screw cap tube, and counted with a hemocytometer. The cells were cen trifuged at 1,500 rpm for 10 min at 10C in a refrigerated centrifuge (Jouan, Unterhachi ng, Germany). The medium was aspirated from the cells and the cell pellet was resuspe nded in cold, sterile 1X PBS (Gibco). Then, 0.4 ml of cell suspension (1 X 107 cells) and 5g of purified recombinant plasmid DNA were added to a 0.4 cm cuvette placed inside the Gene Pulser II unit shocking chamber (Bio-Rad Laboratories). COS7 cell electroporation assays we re performed using either the E6 complete gene in pcDNA 3.1+/Zeo or the L1 complete gene in pcDNA 3.1+/Zeo vector. Cells were electroporated in the Gene Pulser II Electroporation System (Bio-Rad Laboratories) for 0.64 msec with the low capacito r set at 25F and the voltage set at 0.6 KVolts. Then, 200 l of electroporated cells were added to each chamber of a four chamber glass slide (Lab-Tek, Nalge Nunc Intl., Naperville, Illinois, USA), each containing 1 ml of DMEM/10 % FBS and zeoci n, and the chambered coverglass sides were incubated at 37C. Recombinant plasmid DNAs with the genes cloned in the wrong orientation and parental plas mid DNA (without insert) were used as negative controls. Cells in each chamber of the slide were fixe d at four different times; 12 hrs, 24 hrs, 36 hrs, and 48 hrs. Briefly, the medium was as pirated from the chamber and the cells were rinsed with 1ml of 1X Hanks balanced salt solution (Gibco). The cells were then fixed for 1 min using 1 ml of cold acetone: meth anol (1:1) solution, the fixative was removed, and the chamber slide was stored at -20C until use. Immediately before use, to equilibrate the cells, 1 ml of PBS/ 3% BSA wa s added to each slide chamber, allowed to soak the monolayer for 5 minutes at room temperature, and removed. Serum obtained

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38 from captive manatees (Holly, Betsy, Oakl ey, Willoughby, Amanda, and Lorelei) with a history of papillomavirus infection was diluted 1:20 in PBS/3% BSA solution and 500 l of diluted serum were added to the appropriate chamber. The cells were incubated at 37C for 1 hr, the serum was removed, and the cells were washed three times with 1 ml PBS/0.025% Tween 20 (Fisher Scientific, Fairla nd, New Jersey, USA) solution. Purified anti-manatee IgG monoclonal antibody (1.2mg/ ml) was diluted 1:20 in PBS/3% BSA solution and 500 l of diluted monoclonal an tibody were added to each chamber. The chambers were incubated at 37C for 1 hr, the monoclonal antibody was removed, and the cell monolayer was washed three times with 1 ml PBS/0.025% Tween 20 solution. Fluorescein-labeled protein G conjugat e (250g/ml) (Sigma-Aldrich, Steinheim, Germany), was diluted 1:40 in PBS/3% BSA, 200 l were added to each slide chamber, and the chamber slides were incubated at 37C for 1 hr. The monolayers were gently rinsed three times with 1 ml PBS/0.025% Tw een 20 solution, the cove r and lining of the chamber were removed, and ProLong gold anti-fade reagent (Molecular Probes, Carlsbad, California, USA) was added dropw ise to the monolayer. Cover slips were placed on the anti-fade reagen t and the obtained monolayers were evaluated for specific immunofluorescence using a fluorescent micr oscope (Zeiss Axiovert 25). Similar immunofluorescence assays were also perf ormed using fluorescein-labeled Protein A (Sigma-Aldrich), instead of Protein G, according to the methods described. Culturing Florida Manatee Respiratory Epithelial Cells Florida manatee respiratory epithelial (TmlRE) cell cultures were obtained from Dr. Mark Sweat (Fish and Wildlife Research Institute, St. Petersburg, Florida) and propagated in 75 cm2 flasks in Dulbeccos modified eagle medium (DMEM) (Gibco)

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39 containing antibiotic/antimycotic, gentamycin, and 10% FBS. Cells were incubated at 37C in a humidified incubator. Transfection of TmlRE Cells with DNA Recombinants for Immunofluorescence Assays Methods for transfecting TmlRE cells were the same as the methods described for transfecting COS-7 cells. TmlRE cell transfection assays were performed with E7 pcDNA 3.1+ TOPO and the L1 complete gene pcDNA 3.1+/Zeo recombinant plasmids. Table 2-1. Samples obtained from skin lesions of captive Florida manatees. DNA extracted from lesions was tested by P CR for the presence of papillomavirus infection. HSSWP: Homosassa Springs St ate Wildlife Park, FL: Florida, SD: San Diego, CA:California. Sample I.D. Manatee I.D. Location Date Obtained CR130 Oakley HSSWP, FL July, 2002 V368 Betsy HSSWP, FL July, 1998 V369 Holly HSSWP, FL July, 1998 V370 Betsy HSSWP, FL July, 1998 V371 Amanda HSSWP, FL January, 2000 V372 Amanda HSSWP, FL January, 2000 V373 Willowby HSSWP, FL January, 2000 V374 Willowby HSSWP, FL January, 2000 V375 Lorelei HSSWP, FL January, 2000 V376 Lorelei HSSWP, FL January, 2000 V377 Lorelei HSSWP, FL January, 2000 V684 Rosie HSSWP, FL October, 2003 V685 Lorelei HSSWP, FL October, 2003 V686 Betsy HSSWP, FL October, 2003 V687 Amanda HSSWP, FL October, 2003 V909 SW04031 SD, CA January, 2004 V910 SW04031 SD, CA January, 2004 V989 TM0334 Orlando, FL January, 2004 V991 Stubby Orlando, FL January, 2004 V995 TM0341 Orlando, FL January, 2004 V996 TM0341 Orlando, FL January, 2004

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40 Table 2-2. Samples obtained from skin lesi ons of free-ranging Fl orida manatees. DNA extracted from lesions was tested by PCR for the presence of TmlPV infection. CR: Crystal River, FL: Florida, HR: Homosassa River, DK: Drowned Keys, BZ: Belize, POI: Po rt of Isles (Everglades City), TB=Tampa Bay,*: manatee penile le sion, **: uninfected manatee liver. Sample I. D. Manatee I. D. Location of Manatee Date Obtained V378 RKB-1029-17 CR, FL January, 2003 V389 RKB-1035-31 CR, FL February, 2003 V390 RKB-1036-19 HR, FL February, 2003 V396 RKB-1040-23 HR, FL February, 2003 V397 RKB-1039-13 HR, FL February, 2003 V408 RKB-10474 CR, FL February, 2003 V556 BZ01M16 DK,BZ May, 2003 V1329 TNP-29 POI, FL April, 2004 V1330 TNP-29 POI, FL April, 2004 V1331 TNP-29 POI, FL April, 2004 V1332 TNP-31 POI, FL April, 2004 V1333 TNP-32 POI, FL April, 2004 V1334 Unidentified POI, FL April, 2004 V1335 Unidentified POI, FL April, 2004 V1343 BZ04M64 DK, BZ May, 2004 V1437* MEC0449 TB, FL August, 2004 V1351 BZ04M58 DK, BZ May, 2004 V1774 THR-02 HR, FL April, 2005 V1776 THR-03 HR, FL April, 2005 V1777 THR-04 HR, FL April, 2005 V1855** MEC-0515 TB, FL February, 2005 Table 2-3. PCR primers designed to targ et manatee papillomavirus sequences Target PCR Primer PCR Primer Sequence L1 458-bp FP CR333 5GCI CAG GGI CAT AAI AAT GG-3 Fragment RP CR332 5CGT CCI AII GGA IAC TGA TC-3 FP CR490 5CAG GGG CAT AAG AAT GGT ATT G -3 RP CR491 5GAG GGG AGA CTG ATC GAG TTC TG-3 L1--E1 FP CR442 5CCT GCT GAA AAT GAT GAT CC -3 Region RP CR441 5TTA TCA IA T GCC CAI TGT ACC AT -3 Complete E6 FP CR498 5CAA CCA TCT TCT ACA TGC TTA GT-3 Gene RP CR499 5CGT ATT CTT GGA TAT GTG GTG -3 E6 TOPO FP CR529 5CAC CCA AC C ATC TTC TAC ATG CTT AGT-3 Fragment RP CR499 5CGT ATT CTT GGA TAT GTG GTG -3

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41 Table 2-3. Continued Target PCR Primer PCR Primer Sequence E7 TOPO FP CR530 5-CAC CTT AGA AGAC ACA GCA CGT ATC-3 Fragment RP CR501 5ATC TGT TGT ATC CGA GTC AC -3 L1L2 FP CR572 5TAA CCG CA T TTA ATG GGC AAT TTG -3 Region RP CR574 5AAT AAA ATG ATG CAC AGT GCC AG -3 Complete L1 FP CR573 5-CAC CTA CAA TCC TTA TTG ATT TTC AAT C -3 Gene RP CR574 5AAT AAA ATG ATG CAC AGT GCC AG -3 Complete L2 FP CR572 5TAA CCG CAT TTA ATG GGC AAT TTG -3 Gene RP CR622 5-TTC GG T ATT GAG GAT GCG GG-3 Table 2-4. Sequencing primers used to obtain the complete sequence of PCR amplified TmlPV gene fragments. Target Sequencing Primer Primer Sequence L1 458-bp FP CR333 5GCI CAG GGI CAT AAI AAT GG -3 Fragment RP CR332 5CGT CCI AII GGA IAC TGA TC -3 FP M13 5GTA AAA CGA CGG CCA G -3 RP M13 5CAG GAA ACA GCT ATG AC -3 L1E1 T7 Promoter 5T AA TAC GAC TCA CTA TAG GG -3 Region RP CR216 5TAC AAG ACA GGT TTA AGG AGA C -3 FP CR579 5TGC GCA TAG TTA CTT CTG AG -3 RP CR478 5CAG TGT ACC ATT GAA GAT AAG TC -3 FP CR492 5ATG TAT GAA GTA TAA ATA GCA C -3 RP CR493 5CAA CTC TAC CTG TAC GTT CC -3 Complete E6 FP M13 5GTA AAA CGA CGG CCA G -3 Gene RP M13 5CAG GAA ACA GCT ATG AC -3 T7 Promoter 5TAA TA C GAC TCA CTA TAG GG -3 RP CR532 5-TAG AAG GCA CAG TCG AGG-3 Complete E7 FP M13 5GTA AAA CGA CGG CCA G -3 Gene RP M13 5CAG GAA ACA GCT ATG AC -3 T7 Promoter 5TAA TA C GAC TCA CTA TAG GG -3 RP CR532 5-TAG AAG GCA CAG TCG AGG-3 L1L2 FP M13 5GTA AAA CGA CGG CCA G -3 Region RP M13 5CAG GAA ACA GCT ATG AC -3 FP CR583 5AGA TTA CAC CAG AGG CTC C -3 RP CR580 5ATT CAT TGT ATG TAT GTG GG -3 FP CR588 5CCC TAT CTT TGA CAA TTC TG -3 RP CR601 5GAG CGT CTG CTT TCG TGT GT -3 FP CR 592 5-GGG AGA CT C CAC TGA TAC CA-3

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42 Table 2-4. Continued Target Sequencing Primer Primer Sequence Complete L1 FP M13 5GTA AAA CGA CGG CCA G -3 Gene RP M13 5CAG GAA ACA GCT ATG AC -3 FP CR579 5TGC GCA TAG TTA CTT CTG AG -3 RP CR580 5ATT CAT TGT ATG TAT GTG GG -3

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43 E6 FP CR498 E6 RP CR499 E6ORF E7 ORF E1 ORF NC R L1 ORF L2 ORF NC R E 7 FP CR500 E 7 R P CR500E1 R P CR441 L2ORF FP CR572 L2OR F RP CR622 L1OR F FP CR573 L1ORF RP CR574 L1 FP CR333/ L1 FP CR490 L1 RP CR332/ L1 RP CR491 L1FP CR442 Figure 2-1. Linear representati on of the open reading frames (ORFs) of the ci rcular manatee papillomavirus (TmlPV) genome with the relative positions of the PCR primers used to amp lify TmlPV DNA. FP=Forward primer, RP=Reverse primer.

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44 CHAPTER 3 RESULTS PCR Results Total DNA extracted from 13 skin lesions of captive Florida manatees (Trichechus manatus latirostris ) and six skin lesions of free-ra nging Florida manatees from the vicinity of Homosassa Springs State Wild life Park (HSSWP) amplified DNA fragments of the expected size in PCR assays for the de tection of manatee papillomavirus (TmlPV). DNA fragments of the expected size could not be amplified from DNA extracted from three skin lesions of free-ra nging Antillean manatees (T. manatus manatus ) in PCR assays and, therefore, served as negative controls in subsequent PCR assays. DNA extracted from one manatee liver was also inco rporated into the PCR in order to serve as a negative control and to validate the results in subsequent PCR assays. PCR results of manatee skin lesions assayed for the presen ce of TmlPV DNA are shown in Tables 3-1, 3-2, and 3-3 (summary). PCR Targeting the Papillomavirus L1 458-bp Fragment Oligonucleotide primers MY11 and MY09 (M anos et al., 1989), known to amplify a 458-bp fragment within the L1 capsid gene of several human papillomaviruses and modified by us to contain deoxyinosines at pos itions of nucleotide degeneracy (primers CR333 and CR332), amplified DNA fragments of identical size from five captive manatee skin lesions, out of 11 tested, and fr om four free-ranging manatee skin lesions (near HSSWP), out of seven tested.

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45 PCR Targeting the L1 TmlPV Fragment The L1 TmlPV oligonucleotide primers CR4 90 and CR491, designed to amplify a 458-bp fragment within the L1 capsid gene of TmlPV, amplified DNA fragments of identical size from 11 captive manatee skin le sions, out of 15 assayed, and from five freeranging manatee skin lesions, out of 15 tested for the presence of papillomavirus infection. Total DNA from four skin lesions from which no amplification of the 458-bp DNA fragments could be ach ieved using the MY11 and MY09 HPV L1 primer set amplified DNA fragments of the expected size (458-bp) using the TmlPV-specific CR490 and CR491 primer set (Figure 3-1). PCR Targeting the TmlPV L1-E1 Region Oligonucleotide primers CR442 and CR441, kno wn to amplify an approximately 3,000 bp fragment of the L1-E1 region of the HPV-70 genome (Forslund and Hansson, 1996), amplified a fragment of similar size fr om one captive manatee skin lesion that was tested with the CR442/CR441 primers (Figure 3-2). PCR Targeting the Complete TmlPV E6 Gene Oligonucleotide primers CR498 and CR 499, designed to amplify a 587-bp fragment of the TmlPV genome that contai ns the complete TmlPV E6 gene ORF, amplified DNA fragments of the expected size from five captive manatee skin lesions (Figure 3-3), out of eight tested for the presence of papillomavirus infection. Amplification was not obtained from 12 fr ee-ranging manatee skin lesions tested. PCR Targeting the Complete TmlPV E7 Gene Oligonucleotide primers CR500 and CR 501, designed to amplify a 489-bp fragment of the TmlPV genome that contai ns the complete TmlPV E7 gene ORF, amplified DNA fragments of the expected size from five captive manatee skin lesions

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46 (Figure 3-4), out of five tested for the pres ence of papillomavirus. Similar fragments were not amplified from any of the seven free-ranging manatee skin lesions tested. PCR Targeting the TmlPV L1-L2 Region Oligonucleotide primers CR572 and CR574, designed to amplify a 3,208-bp fragment of the TmlPV genome that contai ns the complete L1 gene ORF plus the complete L2 gene ORF, amplified DNA frag ments of the expected size from two skin captive manatee skin lesions (Figure 3-5), out of two tested for the presence of papillomavirus infection. PCR Targeting the Complete TmlPV L1 Gene Oligonucleotide primers CR573 and CR574, designed to amplify a 1,712-bp fragment of the TmlPV genome that contai ns the complete L1 capsid gene ORF, amplified DNA fragments of the expected si ze from three captive manatee skin lesions (Figure 3-6), out of three tested for the presence of papillomavirus infection. PCR Targeting the Complete TmlPV L2 Gene Oligonucleotide primers CR572 and CR622, designed to amplify a 1,611-bp fragment of the TmlPV genome that contai ns the complete L2 capsid gene ORF, amplified DNA fragments of the expected size from two captive manatee skin lesions (Figure 3-7), out of two tested for the pr esence of papillomavirus infection. Sequencing Results and Genetic Analyses TmlPV L1 458-bp Fragments Sequencing of papillomavirus L1 capsid gene fragments amplified with the modified HPV primers MY11 and MY09 (CR3 33/CR332) revealed that the fragments were 458-bp in length, s upporting the universal ity of the MY11 and MY09 primers, which are known to amplify a 458-bp DNA fragme nt from most types of genital HPVs

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47 (Bernard et al., 1994). Sequencing of papillo mavirus L1 capsid gene fragments amplified with the L1 TmlPV-specific primers revealed th at the fragments were also 458-bp in length. Nucleotide sequences of the 458-bp Tm lPV L1 gene fragments were entered into the Basic Local Alignment Search Tool (BLAST) of the National Center for Biotechnology Information Website (NCBI Bethesda, Maryland) to identify papillomavirus homologues that had the highest similarity and identity to TmlPV L1. This demonstrated that the amplified TmlP V fragments were contained within a highly conserved domain of the L1 capsid protein ge ne of papillomaviruses. Nine TmlPV L1 fragment sequences, obtained from the DNA of three captive manatee lesions and six free-ranging manatee lesions, were submitted to the GenBank database of the NCBI website (Table 3-4). The TmlPV L1 gene fragments translated correctly from the first nucleotide of forward primer (FP) MY11 and FP L1TmlPV (CR 490) into protein fragments consisting of 152 amino acids. The GAP f unction of the GCG Genetic Package (GCG, University of Wisconsin, Madison, Wisconsi n, USA) showed that the nine TmlPV L1 fragment sequences were 100% id entical at the nucleotide an d the amino acid level. The multiple alignment of the deduced amino aci d sequences of the TmlPV L1 fragments demonstrated the identity of the TmlPV L1 sequences (Figure 3-8). Comparisons of the TmlPV L1 amino acid sequence with homologues from human and non-human papillomaviruses demonstrated identities th at ranged between 36% and 57% (Table 3-5) and similarities that ranged between 57% and 67% (Table 3-6) Af ter removal of the L1 primer sequences, the L1 fragment sequence was 100% identical to the corresponding L1

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48 region of the TmPV-1 sequence obtained by another research group and recently deposited in the GenBank database (AY 609301) and published (Rect or et al., 2004). L1-E1 TmlPV Region Sequencing of the approximately 3,000-bp papillomavirus DNA fragment amplified from one lesion of a captive mana tee (V369, Holly) revealed that the fragment was 2,772 nucleotides in length. The ORF(Op en Reading Frame) Finder tool of the NCBI website revealed that the 2,772-bp seque nce contained partial sequences of the L1 ORF, the complete E6 ORF, the complete E7 ORF, and partial sequenc es of the E1 ORF. Further genetic analysis of the 2,772-bp sequence showed that it contained: partial sequences of the 3 end of the TmlPV L1 ORF (261-bp, including the L1 stop codon), followed by a large non-coding region (816bp), the TmlPV E6 ORF (414-bp, including the E6 stop codon), then, separated by tw o nucleotides, the TmlPV E7 ORF (348-bp, including the E7 stop codon), a small non-codi ng region (334-bp), and partial sequences of the 5 end of the TmlPV E1 ORF (599bp). The 2,772-bp sequence that spans the L1E1 region of the TmlPV genome was submitted to the GenBank database of the NCBI website (Table 3-4). Nucleotide sequences of the TmlPV E6 ORF translated into a protein consisting of 137 amino acid residues. Comparisons of the TmlPV E6 137 amino acid sequence with homologues from hu man and non-human papillomaviruses demonstrated identities that ranged between 22% and 32% (Table 3-5) and similarities that ranged between 28% and 42% (Table 36). The TmlPV E6 ORF sequence obtained from sequencing the 2,772-bp fragment was submitted to the GenBank database of the NCBI website (Table 3-4). Nucleotide sequenc es of the TmlPV E7 ORF translated into a protein consisting of 115 amino acid residues. Comparisons of the TmlPV E7 115 amino acid sequence with homologues from hu man and non-human papillomaviruses

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49 demonstrated identities that ranged between 23% and 41% (Table 3-5) and similarities that ranged between 31% and 51% (Table 3-6). Pair-wise co mparisons were not performed with Phocoena spinipinnis PV (PsPV-1) because the PsPV-1 genome does not encode an E7 ORF. The complete TmlPV E7 ORF sequence obtained from sequencing the 2,772-bp fragment was submitted to the GenBank database of the NCBI website (Table 3-4). TmlPV E6 Gene Sequencing of amplified DNA fragments co ntaining the complete TmlPV E6 gene from four lesions of captive manatees revealed that the fragments were 587 nucleotides in length. Genetic analysis of the 587-bp TmlP V E6 gene fragment revealed that the sequence contained the complete TmlPV E6 ORF (414-bp, including the E6 stop codon) that translated into a protein consisting of 137 amino acid residues. Comparisons of the four obtained TmlPV E6 sequences showed th at the nucleotide iden tity ranged from 99.5100.0% and the amino acid identity was 100.0% (not shown). The TmlPV E6 gene sequence obtained from the positive cont rol manatee DNA (CR130) demonstrated 100% identity and similarity to the corresponding region of the TmPV-1 genome described by another research group (Rector et al., 2004). The TmlPV E6 ORF sequences were submitted to the GenBank database of the NCBI website (Table 3-4). TmlPV E7 Gene Sequencing of amplified DNA fragments co ntaining the complete TmlPV E7 gene from four lesions of captive manatees revealed that the fragments were 489 nucleotides in length. Genetic analysis of the 489-bp TmlP V E7 gene fragments revealed that the sequences contained the comp lete TmlPV E7 ORF (348-bp, including the E7 stop codon) that translated into a protein consisting of 115 amino acid residues. Comparisons of the

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50 four obtained TmlPV E7 ORF sequences showed that the nucleotide identity ranged from 99.4% to100.0 % and the amino acid identity ra nged from 99.1% to 100.0% (not shown). The TmlPV E7 sequence obtained from positive control manatee DNA (CR130) had 100% identity and similarity to the corresponding region of the recently published TmPV1 genome (Rector et al., 2004). The TmlPV E7 ORF sequences were submitted to the GenBank database of the NCBI website (Table 3-4). TmlPV L1-L2 Region Sequencing of the amplified TmlPV L1-L2 gene fragments from two papillomatous lesions of captive manatees Oakley and Ho lly revealed that the fragments were 3,208 nucleotides in length. Genetic analysis re vealed that the fragments contained the complete TmlPV L1 ORF (1,518-bp, including the L1 stop codon) plus the complete TmlPV L2 ORF (1,536-bp, including the L2 stop codon). The start codon of the TmlPVL1 ORF sequence was contained within the TmlPV L2 ORF sequence, and the TmlPV L1 and TmlPVL2 ORFs had an overla pping region of 20 nucleotides. Nucleotide sequences of the TmlPV L1 ORF translated in to a protein of 505 amino acid residues. Comparisons of the TmlPV L1 505 amino aci d sequence with homologues from human and non-human papillomaviruses demonstrated identities that ranged between 31% and 57% (Table 3-5) and similari ties that ranged between 41% and 68% (Table 3-6). The complete TmlPV L1 sequence obtained from a lesion of manatee Oakley (CR130) demonstrated 100% identity and similarity to the corresponding region of the TmPV1 genome deposited in the GenBank database by another research group (AY609301). The two TmlPV L1 ORF sequences obtained from lesions of captive manatees Oakley and Holly shared 99.7% nucleotide identity and 99.8% amino acid identity (not shown). The TmlPV L1 ORF sequences were submitted to the GenBank database of the NCBI website

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51 (Table 3-4). Nucleotide sequences of the Tm lPV L2 ORF translated into a protein of 511 amino acid residues. Comparisons of th e TmlPV L2 511 amino acid sequence with homologues from human and non-human papillom aviruses showed identities that ranged between 35% and 42% (Table 3-5) and simila rities that ranged between 43% and 51% (Table 3-6). The complete TmlPV L2 sequence obtained from positive control manatee DNA (CR130) demonstrated 100% identity and si milarity to the corresponding region of the TmPV1 genome (AY609301). The two TmlP V L2 ORF sequences obtained from lesions of captive manatees Holly and Oa kley shared 99.9% nucleotide identity and 99.6% amino acid identity (not shown). The TmlPV L2 ORF sequences were submitted to the GenBank database of the NCBI website (Table 3-4). Complete TmlPV L1 Gene from Captive Manatee Lorelei Sequencing of the amplified fragment c ontaining the complete TmlPV L1 gene fragment from one lesion of captive manatee Lorelei (V685) revealed that the fragment was 1,712 nucleotides in length. Genetic analys is revealed that the fragment contained the complete TmlPV L1 ORF sequence that tr anslated into a protein of 505 amino acid residues. The complete TmlPV L1 ORF sequence was shown to be 99.7% and 99.4%99.7% identical to the previous ly obtained TmlPV L1 ORF sequences at the nucleotide and amino acid levels, respectively (not show n). The TmlPV L1 ORF sequence (Lorelei) was submitted to the GenBank database of the NCBI website (Table 3-4). Complete TmlPV L2 Gene Total DNA extracted from two lesions of captive manatees Oakley and Holly from which the complete TmlPV L2 gene (1,611-bp) was amplified was also positive for amplification of the TmlPV L1-L2 fragment (3,208-bp). This fragment had previously

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52 been sequenced; therefore, sequencing of the complete TmlPV L2 genes from these DNAs (V369 and CR130) was not repeated. Immunofluorescence and Gene Expression Assays Mammalian Expression Systems Fluorescence was not detected in im munologic assays utilizing monkey kidney (COS-7) cells transfected with TmlPV L1 or TmlPV E6 genes cloned in eukaryotic vectors under the control of the CMV promot er. Likewise, specifi c fluorescence was not observed in assays using Florida manatee resp iratory epithelial (TmlRE) cells transfected with the eukaryotic vectors containing th e TmlPV L1 gene under control of the CMV promoter. A few TmlRE cells transfected with the E7 gene displayed a faint halo of fluorescence; however, fluorescence was cons idered subjective and ambiguous and did not provide conclusive eviden ce of protein expression. Rest riction digests of the TmlPV E6 and E7 pcDNA3.1+/Zeo recombinants are shown in Figure 3-11. Bac-to-Bac Baculovirus Expression System Supernatant and cell harvests from Sf21 in sect cell cultures transfected with TmlPV L1 capsid protein bacmid DNA were anal yzed by electron microscopy by Mr. Woody Frazer, Florida Animal Disease Diagnostic Laboratory, Florida Department of Agriculture and Consumer Services, Kissimmee, Florida for the pres ence of virus-like particles (VLPs). Amorphous clumps were observed after negative staining that resembled capsid protein particles; however, pa pillomavirus-like particles of the expected size (50-55 nm) were not observed (Figure 39). The cDNAs obtained by RT-PCR of RNAs extracted from infected cell cultures showed that mRNA expressing the TmlPV L1 gene was being produced in the cell cultures (Figure 3-10). Restriction digests of the

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53 TmlPV L1 pFastBac1 recombinant used in the transfection experi ment are shown in Figure 3-12. Bac-N-Blue Baculovirus Expression System After ninety-six hours of incubation at 27 C, supernatants were harvested from Sf21 cell cultures transfected with the recombinant pBlueB ac 4.5 L1 vector DNA. The baculovirus DNA developed blue color after 48 hrs of incubation (27C) in the presence of the -galactosidase substrate Bluo-gal (Invi trogen). This finding indicated that recombination had occurred between the hom ologous sequences in the baculovirus DNA (Bac-N-Blue DNA) and the transf er vector (pBlueBac 4.5 L1 plasmid), reconstituting the essential sequences necessary for replication of the newly generated recombinant virus. Supernatants corresponding to the cultures transfected with the pBlueBac 4.5 L1 vector (no baculovirus DNA) and those from the unt ransfected cultures did not express the galactosidase enzyme, as judged by the lack of development of blue color. Although no direct proof has yet been obt ained on the expression of the L1 capsid protein by the generated baculoviruses, it is speculated at this point that unless the L1 capsid gene has been inadvertently mutagenized, protein expres sion after the isolati on and purification of recombinant baculovirus will be demonstrated by Western blot analysis. Phylogenetic Analysis Multiple sequence alignments and th e construction of phylogenetic trees demonstrated the genetic relatedness of th e TmlPV amino acid sequences to the amino acid sequences of several human and non-human papillomaviruses. Trees were constructed using the following PVs (with their GenBank accession numbers): Human papillomavirus type 1a HPV-1a (V 01116), HPV-2a (X55964), HPV-3 (X74462), HPV-4 (X70827), HPV-5 (M17463), HPV-6 (AF 092932), HPV-7 (X74463), HPV-9 (X74464),

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54 HPV-11 (M14119), HPV-13 (X62843), HPV15 (X74468), HPV-16 (K02718), HPV-18 (X05015), HPV-20 (U31778), HPV-21 (U31779), HPV-26 (X74472), HPV-27 (X74473), HPV-30 (X74474), HPV-32 (X74475), HPV-33 (M12732), HPV-34 (X74476), HPV-41 (X56147), HPV-51 (M62877), HPV-63 (X70828), HPV-65 (X70829), HPV-92 (NC_004500), HPV-95 (AJ 62010), Bovine PV type 1 BPV-1 (X02346), BPV-2 (M20219), Canine oral PV COPV (L22695), Cottontail rabbit PV CRPV (AJ243287), White-tail deer PV DEERPV (M11910), Equus caballus PV ECPV (NC_003748), European elk PV EEPV (M15953), Ovine PV type 1 OPV-1 (U83594), OPV-2 (U83595), Rhesus monke y PV RhMPV (M60184), Phocoena spinipinnis PV PsPV1(AJ238373), and Manatee papillomaviru s type 1 TmPV1 (AY609301). Florida manatee PV (TmlPV) sequences obtained fr om positive control manatee DNA (CR130) were used in all phylogenetic analyses. The L1 capsid pr otein gene phylograms indicated that the TmlPV sequence formed a unique branch, distinct from known human and animal papillomavirus L1 sequences (Figur e 13). The TmlPV complete L2 capsid protein gene also formed a separate branch in the L2 capsid protein phylograms (Figure 14), indicating the uniqueness of this virus. The E6 protein gene based phylograms indicated that TmlPV was the sole member of a unique branch (Figure 3-15). Similarly, the E7 protein gene claded by itself to form a branch that is closely rooted to the papillomaviruses of hoofed animals (Figure 3-16).

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55Table 3-1. PCR results of DNAs ob tained from captive manatee skin lesions tested for the presence of TmlPV infection. POS: positive, DNA fragment s of the expected size were amplified; NEG: negative, DNA fragments of the expected size were not amplified; X: assay not performed, ORF: open reading frame. Sample I. D. No. L1 458-bp Fragment TmlPV L1 Fragment L1-L2 Region L1 ORF L2 ORF L1-E1 Region E6 ORF E7 ORF CR130 POS POS POS POS POS X POS POS V368 NEG X X X X X X X V369 POS X POS POS POS POS POS POS V370 NEG POS X X X X X POS V371 NEG POS X X X X NEG X V372 NEG X X X X X X X V373 NEG X X X X X X X V374 POS X X X X X X X V375 POS POS X X X X POS X V376 POS POS X X X X X X V377 NEG X X X X X X X V684 X POS X X X X X X V685 X POS X POS X X POS POS V686 X POS X X X X POS POS V687 X POS X X X X X X V909 X NEG X X X X X X V910 X POS X X X X NEG X V989 X NEG X X X X X X V991 X NEG X X X X X X V995 X POS X X X X NEG X V996 X NEG X X X X X X

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56Table 3-2. PCR results of DNAs obtained from free-ranging manat ee skin lesions tested for the pr esence of TmlPV infection. PO S: positive, DNA fragments of the expected si ze were amplified; NEG: negative, DNA fragments of the expected size were not amplified; X: assay not performed, ORF: open reading frame, *= penile sk in lesion, **= normal manatee liver DNA Location of Animal Animal I. D. L1 458-bp Fragment TmlPV L1 Fragment L1-L2 Region L1 ORF L2 ORF L1-E1 Region E6 ORF E7 ORF CR, FL V378 POS X X X X X X X CR, FL V389 NEG POS X X X X NEG X HR, FL V390 NEG POS X X X X NEG X HR, FL V396 POS POS X X X X NEG X HR, FL V397 POS POS X X X X NEG X CR, FL V408 POS POS X X X X NEG X DK, BZ V556 NEG NEG X X X X X X POI, FL V1329 X NEG X X X X NEG NEG POI, FL V1330 X NEG X X X X NEG NEG POI, FL V1331 X NEG X X X X NEG NEG POI, FL V1332 X NEG X X X X NEG NEG POI, FL V1333 X NEG X X X X NEG NEG POI, FL V1334 X NEG X X X X NEG NEG POI, FL V1335 X NEG X X X X NEG NEG DK, BZ V1343 X NEG X X X X X X DK, BZ V1351 X NEG X X X X X X TB, FL V1437* X NEG X X X X X X HR, FL V1774 X NEG NEG NEG NEG X X X HR, FL V1776 X NEG NEG NEG NEG X X X HR, FL V1777 X NEG NEG NEG NEG X X X TB, FL V1855** X NEG X X X X X X

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57Table 3-3. Summary of PCR results. DNAs obt ained from skin lesions of captive and fr ee-ranging manatees were tested for the presence of manatee papillomavirus infection. Tissues CR332/CR333 Fragment L1 Fragment L1-L2 Region L1 ORF L2 ORF L1-E1 Region E6 ORF E7 ORF No. +ve 5 11 2 3 2 1 5 5 No. tested 11 15 2 3 2 1 8 5 No. +ve 4 5 0 0 0 X 0 0 CAPTIVE MANATEES FREE-RANGING MANATEES No. tested 7 20 3 3 3 X 12 7

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58 Table 3-4. Accession numbers of manatee papillomavirus se quences deposited into the GenBank tool of the NCBI website. Amplicon Animal I.D. No. GenBank Accession No. TmlPV L1 458-bp Fragment V369 AY455940 V396 AY455941 V389 AY496568 V390 AY496569 V397 AY496570 V408 AY496571 V375 AY496572 V378 AY496574 CR130 AY496575 TmlPV L1-E1 Region V369 DQ099425 TmlPV Complete E6 Gene CR130 DQ099425 V369 AY830703 V685 AY830704 V686 AY830705 TmlPV Complete E7 Gene CR130 DQ099427 V369 AY830706 V685 AY830707 V686 AY830708 TmlPV L1-L2 Region CR130 DQ099423 V685 DQ099424 TmlPV Complete L1 Gene CR130 AY994164 V369 AY994166 V686 DQ099422 TmlPV Complete L2 Gene CR130 AY994165 V369 AY994167

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59 Table 3-5. Pair-wise comparisons of the ami no acid sequences of the L1, L2, E6, and E7 gene fragments of manatee papillomavi rus (TmlPV) with several human and non-human papillomaviruses. Numbers represent percent identity to corresponding TmlPV sequences obtained from Oakleys DNA. X=no sequence available. PV Type L1 Fragment L1 ORF L2 ORF E6 ORF E7 ORF HPV1a 55.0 53.0 37.0 32.0 40.0 HPV2a 51.0 52.0 37.0 30.0 36.0 HPV3 57.0 53.0 37.0 29.0 39.0 HPV4 57.0 56.0 40.0 28.0 32.0 HPV5 53.0 56.0 41.0 26.0 35.0 HPV6 55.0 54.0 37.0 25.0 40.0 HPV7 50.0 54.0 37.0 27.0 27.0 HPV9 54.0 56.0 40.0 29.0 40.0 HPV11 56.0 54.0 36.0 23.0 38.0 HPV13 56.0 55.0 37.0 22.0 39.0 HPV15 50.0 54.0 41.0 26.0 41.0 HPV16 51.0 52.0 37.0 30.0 35.0 HPV18 43.0 52.0 38.0 22.0 31.0 HPV20 57.0 58.0 39.0 31.0 35.0 HPV21 57.0 57.0 40.0 30.0 38.0 HPV26 55.0 54.0 38.0 26.0 28.0 HPV27 51.0 51.0 39.0 28.0 35.0 HPV30 56.0 55.0 39.0 23.0 30.0 HPV32 52.0 52.0 40.0 31.0 31.0 HPV33 54.0 31.0 38.0 30.0 28.0 HPV34 53.0 52.0 36.0 25.0 32.0 HPV41 55.0 51.0 36.0 31.0 28.0 HPV51 55.0 54.0 37.0 28.0 32.0 HPV63 55.0 51.0 36.0 31.0 27.0 HPV65 57.0 57.0 39.0 28.0 28.0 HPV92 51.0 55.0 40.0 30.0 38.0 HPV95 57.0 57.0 40.0 32.0 24.0 BPV1 49.0 50.0 36.0 28.0 28.0 BPV2 50.0 50.0 35.0 28.0 27.0 OPV1 49.0 50.0 36.0 25.0 31.0 OPV2 51.0 50.0 35.0 22.0 28.0 CRPV 53.0 57.0 37.0 32.0 25.0 DeerPV 47.0 46.0 35.0 22.0 23.0 ECPV 55.0 51.0 40.0 29.0 32.0 EEPV 50..0 51.0 37.0 25.0 21.0 RhMPV 54.0 53.0 38.0 27.0 39.0 COPV 53.0 54.0 41.0 27.0 34.0 PsPV1 53.0 51.0 42.0 26.0 X TmPV1 100.0 100.0 100.0 100.0 100.0

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60 Table 3-6. Pair-wise comparisons of the ami no acid sequences of the L1, L2, E6, and E7 gene fragments of manatee papillomavi rus (TmlPV) with several human and non-human papillomaviruses. Numbers represent percent similarity to corresponding TmlPV sequence obtained fr om Oakleys DNA. X=no sequence available PV Type L1 Fragment L1 ORF L2 ORF E6 ORF E7 ORF HPV1a 65.0 63.0 47.0 42.0 51.0 HPV2a 60.0 62.0 47.0 36.0 40.0 HPV3 66.0 63.0 45.0 36.0 44.0 HPV4 66.0 65.0 49.0 36.0 43.0 HPV5 64.0 66.0 51.0 40.0 44.0 HPV6 64.0 63.0 46.0 34.0 50.0 HPV7 61.0 63.0 47.0 35.0 36.0 HPV9 65.0 66.0 49.0 39.0 50.0 HPV11 63.0 62.0 47.0 33.0 48.0 HPV13 64.0 64.0 45.0 32.0 45.0 HPV15 63.0 64.0 51.0 39.0 49.0 HPV16 60.0 61.0 48.0 36.0 43.0 HPV18 66.0 62.0 47.0 32.0 41.0 HPV20 66.0 62.0 49.0 42.0 44.0 HPV21 67.0 68.0 50.0 41.0 45.0 HPV26 66.0 64.0 47.0 33.0 40.0 HPV27 61.0 62.0 48.0 37.0 40.0 HPV30 64.0 64.0 46.0 30.0 38.0 HPV32 63.0 63.0 48.0 42.0 40.0 HPV33 64.0 41.0 48.0 37.0 36.0 HPV34 62.0 62.0 47.0 32.0 42.0 HPV41 65.0 62.0 46.0 41.0 36.0 HPV51 65.0 64.0 46.0 37.0 43.0 HPV63 65.0 62.0 46.0 41.0 36.0 HPV65 66.0 65.0 48.0 37.0 40.0 HPV92 64.0 65.0 50.0 40.0 45.0 HPV95 67.0 67.0 50.0 38.0 36.0 BPV1 63.0 61.0 44.0 36.0 31.0 BPV2 64.0 61.0 44.0 34.0 31.0 OPV1 60.0 61.0 43.0 33.0 34.0 OPV2 61.0 60.0 44.0 31.0 31.0 CRPV 65.0 66.0 46.0 36.0 34.0 DeerPV 57.0 56.0 46.0 28.0 31.0 ECPV 62.0 60.0 51.0 36.0 37.0 EEPV 60.0 61.0 46.0 32.0 32.0 RhMPV 63.0 62.0 46.0 38.0 51.0 COPV 62.0 64.0 51.0 40.0 41.0 PsPV1 62.0 61.0 50.0 36.0 X TmPV1 100.0 100.0 100.0 100.0 100.0

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61 Table 3-7. Summary of the pair-wise comp arisons of the amino acid sequences of manatee papillomavirus gene fragments with several human and non-human papillomaviruses. TmlPV Fragment Most Similar PV Type (%) Least Similar PV type (%) HPV-21 (67.0%) DeerPV (57.0%) L1 458-bp Fragment HPV-21 (67.0%) OPV-1 (60.0%) HPV-20 (66.0%) EEPV (60.0%) HPV-65 (66.0%) HPV-2a (60.0%) HPV-21 (68.0%) HPV-33 (41.0%) Complete L1 ORF HPV-95 (67.0%) DeerPV (56.0%) HPV-5 (66.0%) OPV-2 (60.0%) HPV-9 (66.0%) ECPV (60.0%) Complete L2 ORF HPV-5 (51.0%) OPV-1 (43.0%) HPV-15 (51.0%) OPV-2 (44.0%) COPV (51.0%) BPV-1 (44.0%) ECPV (51.0%) BPV-2 (44.0%) Complete E6 ORF HPV-1a (42.0%) DeerPV (28.0 %) HPV-20 (42.0%) HPV-30 (30.0%) HPV-32 (42.0%) OPV-2 (31.0%) HPV-63 (41.0%) HPV-18 (32.0%) Complete E7 ORF HPV-1a (51.0%) BPV-1 (31.0%) RhMPV (51.0%) BPV-2 (31.0%) HPV-15 (49.0%) OPV-2 (31.0%) HPV-11 (48.0%) DeerPV (31.0%)

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62 Figure 3-1. Agarose gel electrophoresis of PCR amplified 458-bp fragments of the L1 capsid protein gene of ma natee papillomavirus. MM: 1 Kb Molecular marker, Lane 1: V375, Lane 2: V376, Lane 3: V389, Lane 4: V390, Lane 5: V396, Lane 6: V397, Lane 7: V408, Lane 8:V370, Lane 9:V371, Lane 10:V556, negative tissue; Lane 11: negative tube, water; Lane 12: Positive control captive manatee Oakley (CR130). C: Captive manatee, FR: Free-ranging manatee Figure 3-2. Agarose gel electrophoresis of PCR amplified 2,772-bp fragment of the L1E1 region of manatee papillomavirus. MM: 1 Kb Molecular marker, Lane 1: Captive manatee Holly (V369), Lane 2: negative tube, no DNA; Lane 3: negative tissue control (V1855). MM1 23456789101112 CCFRFRFRFRFRCC MM123

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63 Figure 3-3. Agarose gel electrophoresis of PCR amplified 587-bp fragments of the E6 gene of manatee papillomavirus. MM: 1 Kb Molecular marker, Lane 1: Captive manatee Holly (V369), Lane 2: Captive manatee Betsy (V686), Lane 3: Captive manatee Lorelei (V685), Lane 4: Positive contro l captive manatee Oakley (CR130), Lane 5: negative tube, no DNA; Lane 6: negative tissue control (V1855). Figure 3-4. Agarose gel electrophoresis of PCR amplified 489-bp fragments of the E7 gene of manatee papillomavirus. MM: 1 Kb Molecular marker, Lane 1: Captive manatee Holly (V369), Lane 2: Captive manatee Betsy (V686), Lane 3: Captive manatee Lorelei (V685), Lane 4: Positive contro l captive manatee Oakley (CR130), Lane 5: negative tube, no DNA; Lane 6: negative tissue control (V1855). MM123456 MM12345 6

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64 Figure 3-5. Agarose gel electrophoresis of PCR amplified 3,208-bp fragments of the L1 gene plus the L2 gene of manatee papillomavirus. MM: 1 Kb Molecular marker, Lane 1: Captive manatee Holly (V369), Lane 2: Positive control captive manatee Oakley (CR130), Lane 3: negative tube, no DNA; Lane 4: negative tissue control (V1855). Figure 3-6. Agarose gel electrophoresis of PCR amplified 1,712-bp fragments of the complete L1 gene of manatee papilloma virus. MM: 1 Kb Molecular marker, Lane 1: Captive manatee Holly (V369) Lane 2: Captive manatee Lorelei (V685), Lane 3: Positive control capti ve manatee Oakley (CR130), Lane 4: negative tube, no DNA; Lane 5: ne gative tissue control, (V1855). MM 12345 MM1234

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65 Figure 3-7. Agarose gel electrophoresis of PCR amplified 1,660-bp fragments of the complete L2 gene of manatee papillo mavirus. MM: 1 Kb Molecular marker, Lane 1: Captive manatee Lorelei (V6 85), Lane 2: Positive control captive manatee Oakley (CR130), Lane 3: nega tive tube, no DNA; Lane 4: negative tissue control (V1855). MM1234

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66 1 51 100 V408 .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... V397 .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... V396 .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... V390 .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... V389 .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... V378 .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... V375 .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... V369 .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... P31 .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... Consensus AQGHKNGIAW QNQLFVTILD NTRGTNMTVS VSTQNALVVD HYDDNDYAQY LRHAEEFELS FVFQLCKVQL TTEALAHIHT MNPKILEDWH IGLRPPPSAS 101 151 V408 .......... .......... .......... .......... .......... .. V397 .......... .......... .......... .......... .......... .. V396 .......... .......... .......... .......... .......... .. V390 .......... .......... .......... .......... .......... .. V389 .......... .......... .......... .......... .......... .. V378 .......... .......... .......... .......... .......... .. V375 .......... .......... .......... .......... .......... .. V369 .......... .......... .......... .......... .......... .. P31 .......... .......... .......... .......... .......... .. Consensus VEDQYRYIQS LATRCPPKEV PAENDDPYKT KKFWVVDLST RFSTELDQSP LG Figure 3-8. Multiple alignment of the amino acid sequences deduced from the nucleotide sequences of the L1 gene fragment of manatee papillomavirus identified in cutaneous lesions of captive and free-ranging Florida manatees.

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67 Figure 3-9. Electron micrograph of Sf21 insect cell cultures transfected with pFastBac1 TmlPV L1 gene recombinant. Amorphous viral clumps that resemble capsid protein particles and rodshaped Baculovirus (non-recombinant) particles were found present. Photo s upplied by Mr. Woody Fraser. 200 n m Rod-shaped Baculovirus particles Amorphous viral clumps

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68 Figure 3-10. Agarose gel electrophoresis de monstrating the PCR amplification of the manatee papillomavirus complete L1 gene fragment from cDNAs obtained from infected Sf21 cell cultures. R= Random hexamer primers used in RTPCR reactions, S= TmlPV L1 gene-s pecific primers used in RT-PCR reactions; MM=Molecular marker, 1 KB ladder; Lanes 1 and 2=Sf21 cell cultures (negative control); Lanes 3 and 4=Sf21 cell cultures infected with bacmid DNA (no recombinant); Lanes 5 and 6=Sf21 cell cultures infected with TmlPV L1 gene recombinant; Lanes 7 and 8= Sf21 cell cultures infected with TmlPV L1 gene recombinant (no SuperScript); Lane 9=blank sample (H2O), negative PCR control; Lane 10=TmlPV L1 plasmid DNA, positive PCR control. All of the samples were treated with DnaseI solution, but the samples in Lanes 7 and 8 were not trea ted with the SuperScript enzyme and were not transcribed to cDNA. This de monstrates that the Dnase I solution effectively degraded the DNA in these samples and validated the results of this assay. Samples in lanes 5 and 6 were treated with the DnaseI solution and also with SuperScript enzyme, therefore the TmlPV L1 DNA fragment was able to be amplified from the cDNA. MM 1R 2S 3R 4S 5R 6S 7R 8S 9 10 MM

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69 Figure 3-11. Agarose gel electrophoresis demons trating restriction enzyme digests of the manatee papillomavirus E6 gene and E7 gene recombinants. MM: 1 Kb Molecular marker, Lane 1: pcDNA 3.1+/Zeo E6 recombinant, Hind III; Lane 2: pcDNA 3.1+/Zeo E6 recombinant, EcoRI; Lane 3: pcDNA 3.1+/Zeo E7 recombinant, Hind III; Lane 4: pcDNA 3.1+/Zeo E7 recombinant, EcoRI Figure 3-12. Agarose gel electrophoresis demons trating restriction enzyme digests of the manatee papillomavirus L1 complete gene recombinant. MM: 1 Kb Molecular marker, Lane 1: pcDNA 3.1+/Zeo L1 recombinant, Hind III; Lane 2: pcDNA 3.1+/Zeo L1 recombinant, HindIII plus XhoI; Lane 3: pFastBac1 L1 recombinant, Hind III; Lane 4: pFastBac1 L1 recombinant, EcoRI. MM12 34 MM1 2 3 4

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70 Figure 3-13. A. Neighbor-Joining phylogeneti c tree of the deduced amino acid sequences of the complete L1 gene of severa l human and non-human papillomaviruses. The tree was generated by Clustal W slow and accurate function using Gonnet 250 residue weight table, gap penalty of 35 and gap extension penalty of 0.75 (pairwise alignment parameters), gap pe nalty of 15 and gap extension penalty of 0.3 (multiple alignment parameters). In the rectangular cladogram format, numbers represent the percent confiden ce of 1000 bootstrap replications. B. In the radial format, the 0.1 divergence s cale represents 0.1 substitutions per site A

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71 Figure 3-13. Continued 0.1 HPV3 HPV2a HPV27 HPV26 HPV41 HPV51 HPV18 HPV30 HPV13 HPV6 HPV11 HPV7 HPV32 HPV16 HPV33 RhMPV HPV34 PsPV1 HPV95 HPV4 HPV65 HPV5 HPV21 HPV20 HPV92 HPV9 HPV15 ECPV BPV1 BPV2 OPV1 OPV2 DEERPV EEPV TmlPV TmPV1 CRPV COPV HPV63 HPV1a B

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72 Figure 3-14. A. Neighbor-Joining phylogenetic tree of the deduced amino acid sequences of the complete L2 gene of severa l human and non-human papillomaviruses. The tree was generated by Clustal W slow and accurate function using Gonnet 250 residue weight table, gap penalty of 35 and gap extension penalty of 0.75 (pairwise alignment parameters), gap pe nalty of 15 and gap extension penalty of 0.3 (multiple alignment parameters). In the rectangular cladogram format, numbers represent the percent confiden ce of 1000 bootstrap replications. B. In the radial format, the 0.1 divergence scal e represents 0.1 substitutions per site. A

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73 Figure 3-14. Continued 0.1 HPV2 a HPV27 HPV1 8 HPV2 6 HPV 5 1 HPV30 HPV 3 HPV16 HPV 33 HPV34 RhMPV HPV 3 2 HPV7 HPV13 HPV 6 HPV11 BPV1 BPV2 DEERPV EEPV OPV1 O PV2 P s PV1 E C PV HPV41 HPV95 HPV4 HPV65 HPV 9 2 HPV5 HPV20 HPV21 HPV9 HPV15 TmlPV TmPV1 CRPV COPV HPV63 HPV1a B

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74 Figure 3-15. A. Neighbor-Joining phylogeneti c tree of the deduced amino acid sequences of the complete E6 gene of several human and non-human papillomaviruses. The tree was generated by Clustal W slow and accurate function using Gonnet 250 residue weight table, gap penalty of 35 and gap extension penalty of 0.75 (pairwise alignment parameters), gap pe nalty of 15 and gap extension penalty of 0.3 (multiple alignment parameters). In the rectangular cladogram format, numbers represent the percent confiden ce of 1000 bootstrap replications. B. In the radial format, the 0.1 divergence scal e represents 0.1 substitutions per site. A

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75 Figure 3-15. Continued 0.1 HPV41 CRPV TmlPV TmPV1 HPV95 HPV4 HPV65 COPV HPV1a HPV92 HPV5 HPV20 HPV21 HPV9 HPV15 ECPV BPV1 BPV2 OPV1 OPV2 DEERPV EEPV HPV18 HPV16 HPV34 RhMPV HPV30 HPV26 HPV51 PsPV1 HPV32 HPV7 HPV13 HPV6 HPV11 HPV3 HPV27 HPV2a HPV33 HPV63B

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76 Figure 3-16. A. Neighbor-Joining phylogeneti c tree of the deduced amino acid sequences of the complete E7 gene of severa l human and non-human papillomaviruses. The tree was generated by Clustal W slow and accurate function using Gonnet 250 residue weight table, gap penalty of 35 and gap extension penalty of 0.75 (pairwise alignment parameters), gap pe nalty of 15 and gap extension penalty of 0.3 (multiple alignment parameters). In the rectangular cladogram, numbers represent the percent co nfidence of 1000 bootstrap replications. B. In the radial format, the 0.1 divergence scale represents 0.1 substitutions per site. A

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77 Figure 3-16. Continued 0.1 HPV1a HPV63 ECPV BPV1 BPV2 DEERPV EEPV OPV2 OPV1 TmlPV TmPV1 CRPV HPV41 HPV95 HPV4 HPV65 HPV5 HPV20 HPV21 HPV92 HPV15 HPV9 RhMPV HPV34 HPV16 HPV33 HPV30 HPV26 HPV51 HPV18 HPV32 HPV3 HPV2a HPV27 HPV7 HPV13 HPV6 HPV11 COPV B

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78 CHAPTER 4 DISCUSSION Papillomatous lesions harvested from the skin of captive and free-ranging manatees contained manatee papillomavirus (TmlPV) DNA and were morphologically similar to the previously described papillomatous lesi ons of captive Florida manatees (Trichechus manatus latirostris ) housed at Homosassa Springs State Wildlife Park (HSSWP), Homosassa, Florida (Bossart et al., 2002). Lesions were ei ther flat and sessile or pedunculated and distributed over the manat ee body, including the f lippers, nares, and contact regions of the anterior body (Figure 4-1 and Figure 4-2). Conclusions could not be made about the stage of the infection ba sed on the appearance of the lesions; however, the TmlPV L1 fragment sequence (GenBa nk Accession number AY496572) isolated from a pedunculated skin lesion in the pres ent study was 100% identical to the manatee papillomavirus type 1 (TmPV-1) sequence that had been deposited in the GenBank (AY609301) from another research group and had been isolated from a sessile skin lesion. These findings strongly suggest that the same virus may cause both types of papillomatous skin lesions in manatees, and is also suggested by thos e authors (Rector et al., 2004). Until recently, papillomavirus studies dealt mainly with transmission experiments, virus ultrastructure and chemical composition, and pathological desc ription of lesions. The main impediment for the analysis of thes e viruses has been the lack of a reproducible cell culture system permissive for their replication (Lancaster and Olson, 1982). The study of PVs has been limiting, as only a few HP V types have been purified in quantities

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79 sufficient for structural analysis, due to the low virus load of many lesions and the inability to develop tissue culture systems for large scale propagation of the virus (Rommel et al., 2005). However, the papi llomavirus field has advanced recently, especially in the areas of molecular bi ology techniques and molecular cloning, which have made these viruses more amenable to study (Lancaster and Olson, 1982). Despite the absence of advanced molecular tools, immunohistochemical data from previous studies of papillomatous lesions in manatees indicated the presence of a species-specific PV. The immunologic data also suggested th at manatee PV (TmlPV) infection might be latent and, possibly, that it might have been activated after imm unosuppression (Bossart et al., 2002). While electron microscopy ev aluation and immunohistochemistry staining of lesions showed the presence of a PV, these assays did not provide genetic information about the type of PV involve d. The primary objectives of th is study were: 1.) To develop a molecular diagnostic assay for the detection of TmlPV infection in skin lesions, 2.) to molecularly characterize the TmlPV genome and define some of its organization, and 3.) to develop a serological assay based on viruslike particles (VLPs) absorbed to an ELISA plate for the detection an d quantitation of antibodies against TmlPV. The steps for developing a molecular di agnostic assay included: extracting DNA from papillomatous lesions; designing PCR primers and PCR protocols; and sequencing amplified products to confirm th e identity of the virus invo lved. Due to the lack of sequence data available on marine mammal papillomaviruses, specifically, of the manatee, PCR assays for the molecular det ection of TmlPV DNA were initially based on the MY11 and MY09 primer set that targets a highly conserved region of the human PV (HPV) L1 ORF. Our PCR protocol utili zed annealing temperatures 10 below the

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80 primers melting temperatures, in order to ma ximize the chances of amplifying the TmlPV L1 DNA fragment, and incorporat ed deoxyinosines at positions of nucleotide degeneracy in the primer sequences. After testing the modified MY11 and MY09 primers (CR333/CR332) with positive TmlPV DNA, the annealing temperatures of the primers were gradually increased until amplification of a single band of the appropriate size was obtained. Using these primers in PCR assays, five TmlPV positive lesions were identified from captive manatees and four positive skin lesions from free-ranging manatees. These results confirmed the usef ulness of the widely used MY11 and MY09 consensus primers and provided an improve d method for the detection of TmlPV in cutaneous lesions. Based on the sequences ge nerated from the TmlPV L1 fragment using the MY11 and MY09 primers, these primers were modified to contain TmlPV L1specific sequences at positions of nucleotide degeneracy. These TmlPV L1 specific primers effectively amplified DNA fragments of the expected size from DNA samples extracted from lesions of 11 captive and five free ranging manatees. Four manatee DNA samples that had been negative for L1 frag ment amplification of fragments of the expected size using the modified MY11 and MY09 primers were shown to contain TmlPV DNA fragments of the expected size using the more TmlPV L1-specific primers (CR490/CR491). These results demonstrated the robustness of the TmlPV L1-specific primers and improved the use of PCR as a tool for the detection of TmlPV in skin lesions. Nucleotide sequences and deduced amino acid se quences of L1 fragments amplified with the MY11/MY09 primer set and with the Tm lPV L1-specific primer set were 100% identical (Figure 3-8), indicat ing that only one genotype of TmlPV was detected in the captive manatees of HSSWP and a few of th e free-ranging animals that swim around

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81 HSSWP. Three skin lesions (V372, V 373, V377) obtained from captive manatees preserved in DMSO were negative for am plification of the TmlPV L1 fragment; however, DMSO is known to crosslink DNA, making it difficult to amplify DNA fragments from these samples. These manatees may have been infected with TmlPV, but due to the method of sample preservation, the TmlPV DNA fragments we re not able to be amplified from these samples. This demonstrates the need for fresh tissue samples in the diagnosis of TmlPV infection and has im plications on the methods of sample preservation. Positive TmlPV skin lesions, identified by PCR amplification of DNA fragments of the appropriate size, were purified and se quenced directly or purified, cloned, and sequenced. Nucleotide sequences of cloned prod ucts and of directly sequenced products were compared to confirm the nucleotide iden tity of the sequences. In a study by Saiki et al. (1988), an overall error frequency of 0.25% was observed in the sequences of 239-bp amplified products after 30 cycles of amplification of the fr agment. In our PCR assays, whenever long DNA fragments (>1 Kb) were amplified, high fidelity enzymes that are endowed with proofreading activ ity were used in order to minimize possible nucleotide incorporation errors made by the polymerase during DNA amplification. Furthermore, at least two clones from each recombinant DNA were completely sequenced and analyzed and, often, both the purified mini-prep r ecombinant DNAs and the purified maxi-prep recombinant DNAs of cloned products were sequenced, as the b acteria could have possibly introduced nucleotide copying errors during transformations. Nucleotide sequence differences were observed betw een the TmlPV E6 ORF sequences (99.5100.0% identity), E7 ORF sequences (99.4-100.0 % identity), L1 ORF sequences (99.7%

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82 identity), and L2 ORF sequen ces (99.9% identity). These mi nor sequence variations may have been due to nucleotide errors made ei ther by the polymerase in PCR assays or by the bacteria after transformation with plasmi d DNA. Comparisons of the E6 ORF, E7 ORF, L1 ORF, and L2 ORF sequences obtai ned from the TmlPV DNA (CR130), used as positive control throughout this study, with the corresponding sequences of the TmPV-1 genome recently published by another group (Rec tor et al., 2004) revealed that the sequences were almost 100% identical at th e nucleotide and amino acid levels. These results indicated the truthfulness of the se quences obtained from the positive control TmlPV DNA (CR130) and also validated the use of this DNA (CR130) for all future genetic and phylogenetic analyses. Additionally, the identities shared by the manatee PV sequences obtained from two different mana tee papilloma isolates supports the presence of only one type of manatee PV in skin lesions from captive and free-ranging manatees around HSSWP. Our results confirmed the presence of TmlP V in skin lesions of captive manatees and extended the knowledge to encompass skin lesions from a few free-ranging manatees inhabiting Crystal River and Homosassa River, Florida, the nearby waters of HSSWP. Free-ranging manatees are often seen at th e perimeter of the underwater fence that separates the known TmlPV-pos itive captive HSSWP manatees from the free-ranging manatees in this area. DNA samples obtaine d from skin lesions of free-ranging manatees inhabiting more distant bodies of water in Florida (Port of the Isles, Tampa Bay) and Belize (Drowned Keys) were always negativ e for TmlPV DNA. Therefore, it is thought that a few of the free-ranging manatees that swim in the vicinity of the infected population at HSSWP may have acquired the infection by direct contact through this

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83 underwater fence. Manatee papillomavirus DNA was detected in skin lesions that were harvested from free-ranging manatees during winter months (Table 2-2). Low water temperatures have been suspected as a poten tial factor in immunol ogic suppression in the known TmlPV-infected HSSWP manatees (Bossa rt et al., 2002), and exposure to cold water has been directly correlated with im pairment of the immune function in freeranging Florida manatees (Walsh et al., 2005) Cold stress syndrome (CSS), induced by prolonged exposure to cold water, followed by nutritional, metabolic, and immunologic disturbances culminating in multi-systemic, life-threatening opportunistic infectious disease (Bossart et al., 2003), has been documented as a freque nt (18%) cause of death in Florida manatees (Bossart et al ., 2004). It is likely, then, that when the manatee immune system is compromised by ill-defined imm unosuppressive factors, such as CSS, the papilloma virus may become activated, i nvasive, and produce cu taneous lesions. Exposure to harmful algal blooms (Karenia brevis ) can also impair immune function in manatees (Walsh et al., 2005) and may be involved in TmlPV activation and production of lesions. In an attempt to obtain the entire nucle otide sequence of the TmlPV genome, PCR primers were designed to amplify overlapp ing PCR products that, if obtained, would together span the complete TmlPV genome. PCR primers effectively amplified the first amplimer that spans the L1-E1 region of the TmlPV genome; however, additional PCR primers that were based on the overlappi ng PCR product method (Forslund and Hansson, 1996) did not amplify the subsequent amplim ers. Problems encountered in amplifying the overlapping PCR products included: the l ack of sequence data of marine mammal PVs available for primer design, low quantitie s and/or poor quality of starting extracted

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84 DNA, and, leastly, significant se quence variation between the targeted regions of TmlPV and homologous regions in the HPVs. Seque nces obtained from the first amplimer allowed for the partial characterization of the TmlPV genome, which included partial sequences of the L1 ORF, the complete sequ ence of the E6 ORF, the complete sequence of the E7 ORF, and partial sequence of the E1 ORF. Sequences obtained from the first amplimer also allowed for the design of PCR primers that specifically targeted the TmlPV complete E6 and E7 ORFs, widening the targets for the diagnosis of papillomas of manatees. Primers targeting the TmlPV E6 ORF and E7 ORF effectively amplified DNA fragments of the expected size from five DNA samples from HSSWP captive manatees. These results expanded the use of molecular tools for the detection of TmlPV infection and provided a method for complete gene amplification for gene expression assays. However, the TmlPV E6 and E7 ORF primers did not effectively amplify fragments of the expected size from five free-ranging manatee DNA samples and two captive manatee DNA samples that had previously been positive for amplification of the L1 458-bp fragment. These captive manatees we re housed at marine parks (other than HSSWP) in Florida and Califor nia and the TmlPV E6 and E7 ORF primers were specific for TmlPV sequences obtained from the HS SWP captive manatees. The E6 and E7 ORFs are less conserved among PV types than the L1 ORF, the most hi ghly conserved region of the PV genome (deVilliers et al., 2004), and sequence vari ation within the E6 and E7 ORFs may have lowered the efficiency of the E6 and E7 primers. Also, the primers that targeted the E6 and E7 ORFs were located upstream and downstream of the ORFs, within the non-coding regions of the TmlPV genome; unlike the TmlPV L1 fragment primers that targeted a very highly conserved region within the L1 ORF. The quality and quantity

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85 of the manatee DNA samples may have adversel y affected the efficiency with which the TmlPV E6 and E7 primers amplified DNA fragments of the expected size. The DNA samples were frozen and thawed several times for the development of PCR assays, which may have caused the DNAs to degrade. Th ese results demonstrate the importance of sequencing more than one genome of TmlP V. A reverse primer based on our own sequences and a forward primer based on the se quence revealed in a recent publication of the TmPV-1 genome (Rector et al., 2004) eff ectively amplified the complete L1 and L2 capsid protein genes from three captive manatee DNA samples and from two captive manatee DNA samples, respectively. These re sults also expanded the use of molecular tools for the detection of TmlPV infecti on and provided a method for complete gene amplification for gene expre ssion assays. Sequences obtaine d from the L1-E1 amplimer plus the sequences obtained from the complete L1 and complete L2 amplimers allowed for further characterization of the TmlPV genome. Pair-wise comparisons of the TmlPV se quences with the corresponding sequences of several human and non-human PVs revealed amino acid identities (Table 3-5) and similarities (Table 3-6) of these viruses. Id entities refer to the extent to which two amino acid sequences are invariant and similarities refer to changes at a specific position of an amino acid sequence that preserve the physic o-chemical properties of the original residue. Sequence identities a nd similarities also give an idea of the overall similarity (homology) of the TmlPV sequence to each vi rus to which it was compared, but do not provide phylogenetic data on the genetic relate dness of the viruses. Comparisons of the TmlPV L1 fragment with seve ral human and non-human PV types suggested that the TmlPV L1 fragment sequence was more similar to the sequences of cutaneous HPV types

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86 (HPV-3, HPV-4, HPV-20, HPV-21, HPV-65, HPV-95) than to se quences of the high risk genital mucosal HPV types (HPV-16, -18) and ungulate PV types that induce fibropapillomas (Deer PV, OP V-1, EEPV). Comparisons of the TmlPV complete L1 ORF with several human and non-human PV types suggested that the TmlPV L1 ORF sequence was more similar to the sequences of the cutaneous PV types (HPV-20, HPV65, HPV-95) than to the high-risk ge nital mucosal HPV-33 sequence and the fibropapilloma-inducing Deer PV sequence. These L1 ORF sequence comparison results were as expected, as TmlPV infection has so far only been associated with the presence of benign skin lesions and not with genital mu cosal lesions or aggres sive fibropapillomas. Since the L1 ORF is the most highly cons erved region among all members of the PV family (deVilliers et al., 2004) results of the L1 ORF comparisons are, possibly, more reliable than results of comp arisons made with less conserve d, more variable regions of the PV genome. Comparisons of the TmlPV L2 ORF with several human and non-human PV types shows that the TmlPV L2 ORF was more sim ilar to another genetically characterized marine mammal PV sequence (PsPV-1) isolat ed from a Burmeisters porpoise (Phocoena spinipinnis ) and to sequences of cutaneous HPV types (HPV-5, HPV-15), than to the sequences of the fibropapilloma PV types (B PV, OPV, Deer PV). The TmlPV L2 ORF sequence would be expected to be more simila r to cutaneous PV types than to mucosal or malignant papillomas, as TmlPV infection has so far only been associated with the presence of skin lesions. The TmlPV L2 ORF sequence showed the greatest similarity to the Burmeisters porpoise (Phocoena spinipinnis ) papillomavirus (PsPV-1) (Van Bressem et al., 1996), the only other papillomavirus of marine mammals that has been molecularly

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87 characterized. Although marine in nature, th ese viruses do not seem to share a common ancestor, as PsPV-1 and TmlPV clade independe ntly of each other in phylogenetic trees. Also, PsPV-1 is known to have caused genita l warts in cetaceans (V an Bressem et al., 1996), whereas the TmlPV has so far only been a ssociated with cutaneous lesions. These results demonstrated the overall similarity of the TmlPV L2 ORF sequence to that of the L2 ORF sequences of several PV types, but did not provide an accurate phylogenetic relationship of the viruses. Comparisons of the TmlPV E6 ORF with several human and non-human PV types suggested that the TmlPV E6 ORF sequence wa s similar to sequences of a wide variety of PV types, including a ra bbit PV, a high risk mucosal ge nital PV type (HPV-32), and cutaneous PV types (HPV-1a, HPV-20, HPV-95). Inferences could not be made from these results, as they suggested that the Tm lPV E6 ORF sequence is similar to both nononcogenic (HPV-1a, HPV-20, HPV-95) and oncoge nic (HPV-32) PV types. However, the oncogenic potential of TmlPV has not yet been determined, and it is possible that the oncogenic determination of the TmlPV may be a consequence of a fine balance between the E6 and E7 regions and unidentified seque nces in a different region of the TmlPV genome. This is partially the case in other types of terrestrial PVs, such as deer PV, European elk PV, and reindeer PV, which cont ain a novel, transforming E9 gene in their genomes (Erikkson et. al, 1994). The result s of the E6 ORF sequence comparisons showed more variability than the comparisons of the highly conserved L1 and L2 regions, as the E6 ORF is a segment with little sequence conservation among PV viruses (de Villiers et al., 2004).

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88 Comparisons of the TmlPV E7 ORF with several human and non-human PV types suggested that this sequence is most similar to sequences of cutaneous PV types (HPV-9, HPV-15) and a benign mucosal PV type (HPV-6). Results from these comparisons were not surprising, as TmlPV, so far, has only been associated with benign cutaneous lesions. Cladistic phylogenetic diagrams refl ect hypotheses about the evolutionary relationships of organisms. A clade is formed by all species which share derived ancestral characters and a most common ancestor (Chan et al., 1995). The bootstrapped cladograms and the radial divergence trees representing the L1 ORF, L2 ORF, and E6 ORF sequences demonstrated that TmlPV forms a single, distinct branch, or constitutes its own clade. Since no PVs have been charac terized from species closely related to the manatee, it is not surprising that TmlPV cl ades by itself in these phylograms (Figure 313, -14, -15, -16). These results indicated that TmlPV is a unique virus, distinct from the known human and non-human PVs. The single branch formed by the TmlPV in the L1 ORF phylograms may be associated with the type of cell surface receptors used by the virus. The PVs enter a wide range of cells and the tropism of infection by the different PVs is controlled by events downstream of th e initial binding and upt ake (Muller et al., 1995). Studies have shown that the L1 major capsid proteins of low-risk HPV-11 binds to the Kap alpha-2 adapter and the Kap beta-2 import receptor and also interacts with the Kap beta-3 import receptor ( Nelson et al., 2003), while the L1 capsid protein of high-risk HPV-45 interacts with Kap alpha-2 beta-1 hete rodimers (Nelson et al., 2000). It has not yet been determined what the specific r eceptor of the TmlPV L1 capsid protein is; however, if these receptors differ from those described in other PV types, it may explain why the TmlPV L1 protein is phylogenetically ch aracterized as a single, distinct branch.

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89 The bootstrapped cladograms representing the E6 ORF and E7 ORF sequences displayed the TmlPV branch in a multi-species clade that also contained cottontail rabbit PV (CRPV). The E6 ORF and E7 ORF radial divergence phylograms (Figure 3-15 and Figure 3-16) also showed that the TmlPV and CRPV branches arose from a close point of origin. The terrestrial an cestry of the manatee may s upport the results of this phylogenetic relatedness. The closest modern relatives of manatees are hyraxes, furry mammals that are similar to ra bbits (Dawson, 1967). It is possible, then, that the manatee and rabbit may have evolved from a common placental ancestor and that the manatee PV and cottontail rabbit PV may have diverged as they evolved with thei r host species. The E7 ORF cladogram demonstrated that TmlPV is contained within a clade that includes the ungulate PVs (Figure 3-16); however, manat ee PV induces cutaneous lesions, rather than the fibropapillomas that are seen in th e ungulate PV types. A possible explanation for this difference in lesion morphology may be due to the fact that many host-specific PVs have specifically adapted to different eco logical niches (Chan et al., 1995). Since the PsPV-1 genome lacks the E7 ORF, the PsPV -1 and the TmlPV most likely do not share a common ancestor. In the L2 ORF bootst rapped cladogram (Figure 3-14), the two characterized marine mammal PVs, PsPV-1 a nd TmlPV, seem to be the outliers of a clade that includes several benign, cutaneous HPV types (HPV-4, -9, -15, -20, -21-92, 65). Data from the E6 and E7 radial di vergence trees (Figure 3-15 and Figure 3-16) suggested that the described TmlPV genotype found in cutane ous lesions of captive and free-ranging manatees might not have the complete genetic potential to induce the invasive malignancies observed in huma ns infected with high-risk oncogenic

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90 papillomaviruses, such as HPV-16, -18, -30, 33, -34, and -51, that are evolutionarily distant from TmlPV. Virus-like particles (VLPs) have be en produced using recombinant vaccinia viruses, baculoviruses, yeast, or Escherichia coli that express the major L1 capsid protein (Rommel et al., 2005). In our study, insect cells transfected with the TmlPV L1 recombinant bacmid DNA examined by el ectron microscopy were found to contain amorphous clumps resembling capsid particle s, but definitive papilloma virus-like particles of the appropriate si ze (50-55 nm diameter) could not be seen (Figure3-9). However, RT-PCR and PCR analyses performe d on RNAs extracted from the infected cell cultures showed the presen ce of mRNA encoding the TmlPV L1 capsid protein gene. This indicates that the message was being made for the expression of the TmlPV L1 capsid protein; but, for reasons unknown, the expressed protein in the form of VLPs could not be seen. Problems encountered in the detection of VLPs were: possible degradation of protein, protein toxicity to cells, and incorrect multiplicity of infection (MOI) used. A major problem of VLPs is th eir instability at low protein concentrations and their tendency to aggregate at high concentrations, both negatively affecting the performance of the immunologi cal assay (Rommel et al., 200 5). Even though L1 in RNA was produced in Sf21 insect cell cultures tr ansfected with the recombinant vector pFastBac/Bacmid L1, protein expression could not be detected when supernatants from apparently virus-containing cultu res were assayed by ELISA. In view of this setback, the pBlueBac 4.5 expression system, which in corporates blue/white screening of recombinant virus, was explored as a next altern ative. Using this system, we were able to detect the generation of reco mbinant virus that expressed -galactosidase and, if properly

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91 engineered, should express the TmlPV L1 capsi d protein from the polyhedron promoter. Using blue/white selection criteria, this system has provided a positive result for the detection of recombinant virus. Lack of specific fluorescence in the immunofluorescence assay may have arisen from the lack of similar assays used with marine mammal sera. Problems encountered with immunofluorescence detection assays ar ose from the lack of data available for marine mammal papilloma viruses. The immune response to TmlPV is not yet understood, and it is not known if the manatee develops specific l ong-lasting antibodies against E6, E7, or L1 after natu ral infection that can be dete cted with serological assays, such as an ELISA. Sera from animals that had skin lesions and were positive by PCR to TmlPV were assayed as the source of primar y antibodies to detect protein expression in the transfected cell cultures. However, no sp ecific fluorescence was observed. It is not known at this time what the reasons for th e lack of protein ex pression are. The cytomegalovirus (CMV) promoter of the expr ession vector is known to drive high-level expression in a wide variety of mammalian cells, especially in the case of COS-7 cell cultures. On the other hand, it is not known if the CMV prom oter could efficiently drive the expression of the TmlPV proteins in the manatee respiratory epithelial cells used in these assays, since similar work has not been done on this type of cell culture. As suggested before, it is conceivable that the levels of antibodies developing after TmlPV infection were not high. This, plus the re lative sensitivity of the immunofluorescence assay may have contributed to the negative results. Finally, the genes cloned into the eukaryotic expression vectors were not seque nced to confirm their integrity in the

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92 mammalian vector. It is possi ble that a deletion(s) may have occurred that made it impossible for proper protein expres sion in the transfected cells. It is unlikely that PVs have recently been transmitted to manatees; therefore, it is assumed that manatees have been latently in fected with PV on their healthy skin for a long time and that the appearance of PV le sions may have been triggered by impaired immunity or immunosuppression (Rector et al., 2004). Latency has been demonstrated in several animal papillomavirus infections, such as: Mastomys natalensis PV in inbred rodents (Amtmann et al., 1984), bovine PV (B PV) in cattle (Campo et al., 1994), canine oral PV (COPV) in domestic dogs (Nicholls et al., 1999), and several feline PVs (FPVs) in immunosuppressed domestic cats (Sundberg et al., 2000). Many PVs appear to occur preferentially in a latent stage and studies ha ve shown that the appare ntly healt hy skin of humans and animals may harbor multiple PV types in the absence of overt lesions (Antonsson and Hansson, 2002, and Antonsson et al., 2000). Under normal conditions, these PV infections do not exhibit any c linical symptoms, but in immunosuppressed individuals, the amount of virus increases and warts develop (Antonsson and Hansson, 2002). The pathogenesis of PV in marine mammals has not been extensively studied. It has been proposed that the type of squa mous epithelium necessary to protect these mammals from the harsh aquatic environmen t could make them susceptible to PV infection from other marine species (Bossart et al., 2002). Several re ports have described the presence of squamous papillomas and fibropapillomas in other marine mammals, specifically whales, dolphins, and porpoise s (Geraci et al., 1987). The PCR assays developed as part of this study targeted seve ral genes of TmlPV and will aid in the rapid

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93 diagnosis and identification of papilloma vi rus infections of manatees. Cloning and expression of TmlPV genes into mammalian and insect expression vectors will allow the development of new assays, such as ELISA, most likely using recombinant L1 antigens in the form of VLPs. This advance will make possible the detection of antibodies in seroepidemiological surveys in order to determine the prevalence of the infection in different geographical locations. Although the developm ent of a vaccine is within reach, its usefulness and efficacy, at this point, are que stionable, as the infection has only been detected around the HSSWP in an affected popula tion. Further efforts need to be made to better understand the underlying transformation pot ential of manatee papillomavirus. If papillomatous skin lesions became more wide spread in the natura l environment of the manatees, they could pose a more serious health problem for these already endangered animals. Figure 4-1. Papillomatous skin lesions on the flipper of a captive Florida manatee (Trichechus manatus latirostris ) housed at Homosassa Springs State Wildlife Park, Homosassa, Florida. Sessile skin lesion Pedunculated skin lesion

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94 Figure 4-2. A. Typical papillom atous skin lesions of free-ra nging Florida manatees. One lesion (sample V389) was harvested fr om a male calf in Crystal River, Florida, the nearby waters of Homosa ssa Springs State Wildlife Park, and tested for the presence of manatee papillomavirus infection. B. One lesion (sample V396) was harvested from an adult male in Homosassa River, Florida, the nearby waters of Homosa ssa Springs State Wildlife Park, and tested for the presence of manatee papillomavirus infection. B A

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106 BIOGRAPHICAL SKETCH Rebecca Ann Woodruff, daughter of Mike and Debbie Woodruff, was born and raised in Bradenton, Florida, along with her siblings, Jessica and Mike. Rebecca graduated from Bradenton Christian Hi gh School in 1997 and went on to Florida Southern College, Lakeland, Florida, where she majored in biology. Hoping to gain more opportunities and experiences in a larg e, public college, sh e transferred to the University of Florida after the completion of her sophomore year. Rebecca graduated from UF in May, 2001, with a bachelor of science in microbiology and cell sciences. After working for about a year at a plant viro logy research lab, she decided to go back to UF to obtain a masters degree. Upon meeti ng several professors, she decided to take the opportunity to become one of Dr. Carlos Ro meros students and conduct research in the exciting field of marine mammal viruses. After completing her masters defense, planning a wedding, and making a big move, sh e will be ready to relax in her new hometown of Fort Collins, Colorado.