Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis
Chelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of mul...
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PeerJ Inc.
2018-02-01
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| author | Cheryl L. Morrison Luke Iwanowicz Thierry M. Work Elizabeth Fahsbender Mya Breitbart Cynthia Adams Deb Iwanowicz Lakyn Sanders Mathias Ackermann Robert S. Cornman |
| author_facet | Cheryl L. Morrison Luke Iwanowicz Thierry M. Work Elizabeth Fahsbender Mya Breitbart Cynthia Adams Deb Iwanowicz Lakyn Sanders Mathias Ackermann Robert S. Cornman |
| author_sort | Cheryl L. Morrison |
| collection | DOAJ |
| description | Chelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of multi-locus genomic sequence data hinders understanding of the rate and mechanisms of ChHV5 evolutionary divergence, as well as how these genomic changes may contribute to differences in disease manifestation. To assess genomic variation in ChHV5 among five Hawaii and three Florida green sea turtles, we used high-throughput short-read sequencing of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. The average nucleotide divergence between geographic populations was 1.5%; most of the substitutions were fixed differences between regions. Protein divergence was generally low (average 0.08%), and ranged between 0 and 5.3%. Several atypical genes originally identified and annotated in the reference genome were confirmed in ChHV5 genomes from both geographic locations. Unambiguous recombination events between geographic regions were identified, and clustering of private alleles suggests the prevalence of recombination in the evolutionary history of ChHV5. This study significantly increased the amount of sequence data available from ChHV5 strains, enabling informed selection of loci for future population genetic and natural history studies, and suggesting the (possibly latent) co-infection of individuals by well-differentiated geographic variants. |
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| language | English |
| last_indexed | 2024-03-09T07:28:12Z |
| publishDate | 2018-02-01 |
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| spelling | doaj.art-63c2cf54026a40609735ec54f3565ea42023-12-03T06:48:00ZengPeerJ Inc.PeerJ2167-83592018-02-016e438610.7717/peerj.4386Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosisCheryl L. Morrison0Luke Iwanowicz1Thierry M. Work2Elizabeth Fahsbender3Mya Breitbart4Cynthia Adams5Deb Iwanowicz6Lakyn Sanders7Mathias Ackermann8Robert S. Cornman9National Fish Health Research Laboratory, Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of AmericaNational Fish Health Research Laboratory, Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of AmericaNational Wildlife Health Center, Honolulu Field Station, US Geological Survey, Honolulu, HI, United States of AmericaCollege of Marine Science, University of South Florida, St. Petersburg, FL, United States of AmericaCollege of Marine Science, University of South Florida, St. Petersburg, FL, United States of AmericaNational Fish Health Research Laboratory, Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of AmericaNational Fish Health Research Laboratory, Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of AmericaNational Fish Health Research Laboratory, Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of AmericaInstitute of Virology, University of Zurich, Zurich, SwitzerlandFort Collins Science Center, US Geological Survey, Fort Collins, CO, United States of AmericaChelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of multi-locus genomic sequence data hinders understanding of the rate and mechanisms of ChHV5 evolutionary divergence, as well as how these genomic changes may contribute to differences in disease manifestation. To assess genomic variation in ChHV5 among five Hawaii and three Florida green sea turtles, we used high-throughput short-read sequencing of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. The average nucleotide divergence between geographic populations was 1.5%; most of the substitutions were fixed differences between regions. Protein divergence was generally low (average 0.08%), and ranged between 0 and 5.3%. Several atypical genes originally identified and annotated in the reference genome were confirmed in ChHV5 genomes from both geographic locations. Unambiguous recombination events between geographic regions were identified, and clustering of private alleles suggests the prevalence of recombination in the evolutionary history of ChHV5. This study significantly increased the amount of sequence data available from ChHV5 strains, enabling informed selection of loci for future population genetic and natural history studies, and suggesting the (possibly latent) co-infection of individuals by well-differentiated geographic variants.https://peerj.com/articles/4386.pdfGreen sea turtlesFibropapillomatosisRecombinationProtein divergenceViral genomicsHigh-throughput sequencing |
| spellingShingle | Cheryl L. Morrison Luke Iwanowicz Thierry M. Work Elizabeth Fahsbender Mya Breitbart Cynthia Adams Deb Iwanowicz Lakyn Sanders Mathias Ackermann Robert S. Cornman Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis PeerJ Green sea turtles Fibropapillomatosis Recombination Protein divergence Viral genomics High-throughput sequencing |
| title | Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis |
| title_full | Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis |
| title_fullStr | Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis |
| title_full_unstemmed | Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis |
| title_short | Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis |
| title_sort | genomic evolution recombination and inter strain diversity of chelonid alphaherpesvirus 5 from florida and hawaii green sea turtles with fibropapillomatosis |
| topic | Green sea turtles Fibropapillomatosis Recombination Protein divergence Viral genomics High-throughput sequencing |
| url | https://peerj.com/articles/4386.pdf |
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