DOI: 10.5061/dryad.wwpzgmsk6
title: Evolutionary comparisons of Chelonid alphaherpesvirus 5 (ChHV5) Genomes from Fibropapillomatosis-afflicted green (Chelonia mydas), Olive ridley (Lepidochelys olivacea) and Kemp’s ridley (Lepidochelys kempii) sea turtles

description: The spreading global sea turtle fibropapillomatosis (FP) epizootic is
 threatening some of Earth’s ancient reptiles, adding to the plethora of
 threats faced by these keystone species. Understanding this neoplastic
 disease and its likely aetiological pathogen, chelonid alphaherpesvirus 5
 (ChHV5), is crucial to understand how the disease impacts sea turtle
 populations and species and the future trajectory of disease incidence. We
 generated 20 ChHV5 genomes, from three sea turtle species, to better
 understand the viral variant diversity and gene evolution of this
 oncogenic virus. We revealed previously underappreciated genetic diversity
 within this virus (with an average of 2035 single nucleotide polymorphisms
 (SNPs), 1.54% of the ChHV5 genome) and identified genes under the
 strongest evolutionary pressure. Furthermore, we investigated the
 phylogeny of ChHV5 at both genome and gene level, confirming the
 propensity of the virus to be interspecific, with related variants able to
 infect multiple sea turtle species. Finally, we revealed unexpected
 intra-host diversity, with up to 0.15% of the viral genome varying between
 ChHV5 genomes isolated from different tumours concurrently arising within
 the same individual. These findings offer important insights into ChHV5
 biology and provide genomic resources for this oncogenic virus.
description: This 1._ChHV5_consensus_genome_sequences.txtreadme.txt file was
 generated on 2021-07-01 by Liam Whitmore GENERAL
 INFORMATION 1. Title of Dataset:
 1._ChHV5_consensus_genome_sequences.txt 2. Author
 Information<br>     A. Principal Investigator Contact
 Information<br>         Name: Liam Whitmore<br>       
  Institution: University of Limerick<br>         Address: University
 of Limerick, Limerick, V94 T9PX, Ireland​<br>         Email:
 Liam.Whitmore@ul.ie 3. Date of data collection (single
 date, range, approximate date): <br> Data collection spanned
 multiple papers as we used collaborators data as well as our
 own.<br> Information regarding this can be found in the methods
 section of this research paper
 (https://doi.org/10.3390/ani11092489). 4. Geographic
 location of data collection: <br> Samples collected from turtles for
 data analysis were collected<br> from coast of eastern USA (from
 Massachusetts to Texas). 5. Information about funding
 sources that supported the collection of the data: <br> Funding was
 generously provided by an Irish Research Council Government of Ireland
 Postgraduate Scholarship, <br> under project number GOIPG/2020/1056,
 by the National Save The Sea Turtle Foundation, Inc., and this
 research <br> was also supported by Gumbo Limbo Nature Center, Inc.
 d/b/a Friends of Gumbo Limbo (a 501c3 non-profit organization) <br>
 through a generous donation through their Graduate Research Grant
 programme. SHARING/ACCESS INFORMATION
 Links to publications that cite or use the data: <br>
 Whitmore, L., Yetsko, K., Farrell, J.A., Page-Karjian, A., Daniel, W.,
 Shaver, D.J., Frandsen, H.R., Walker, J.S., Crowder, W., Bovery,
 C. <br> and Rollinson Ramia, D., 2021. Evolutionary Comparisons of
 Chelonid Alphaherpesvirus 5 (ChHV5) Genomes from
 Fibropapillomatosis-Afflicted <br> Green (Chelonia mydas), Olive
 Ridley (Lepidochelys olivacea) and Kemp’s Ridley (Lepidochelys kempii) Sea
 Turtles. Animals, 11(9), p.2489<br>
 https://doi.org/10.3390/ani11092489  Recommended
 citation for this dataset: <br> Whitmore, L., Yetsko, K., Farrell,
 J.A., Page-Karjian, A., Daniel, W., Shaver, D.J., Frandsen, H.R., Walker,
 J.S., Crowder, W., Bovery, C. <br> and Rollinson Ramia, D., 2021.
 Evolutionary Comparisons of Chelonid Alphaherpesvirus 5 (ChHV5) Genomes
 from Fibropapillomatosis-Afflicted <br> Green (Chelonia mydas),
 Olive Ridley (Lepidochelys olivacea) and Kemp’s Ridley (Lepidochelys
 kempii) Sea Turtles. Animals, 11(9), p.2489<br>
 https://doi.org/10.3390/ani11092489  DATA &
 FILE OVERVIEW File information: <br> Dataset
 consists of 21 ChHV5 consensus sequences (genomes, including reference
 ChHV5 genome) generated from FP tumour tissue samples from three species
 of marine turtle (Green, Kemp's ridley and olive ridley) <br>
 in the western Atlantic (MA - TX). Please see associated paper for table
 with sample information. Are there multiple versions of
 the dataset? no METHODOLOGICAL INFORMATION
 Please see published manuscript with detailed information
 regarding data processing, along with additional information of how data
 was processed by collaborators<br>
 (https://doi.org/10.3390/ani11092489). DATA-SPECIFIC
 INFORMATION FOR: 1._ChHV5_consensus_genome_sequences.txt
 1. Number of variables: 21 2. Number of
 cases/rows: N/A