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.

Liam Whitmore,Elizabeth Ryan,Jessica A Farrell,Whitney Daniel,Jennifer Shelby Walker,Devon Rollinson Ramia,David J Duffy,Annie Page-Karjian,Kelsey Yetsko,Hilary R Frandsen,Caitlin Bovery,Whitney Crowder,Brooke Burkhalter,Donna J Shaver

doi:10.3390/ani11092489

Abstract

Simple SummaryOur research aims to unravel uncertainties relating to the genetic and viral causes of the debilitating sea turtle disease fibropapillomatosis, which affects all seven species of sea turtle. This disease is likely caused by an alphaherpesvirus (ChHV5) and an environmental trigger (e.g., pollution). Fibropapillomatosis is characterised by multiple benign tumours which grow on the skin, eyes and internal organs, and is becoming a threat to sea turtle conservation globally. ChHV5 research is crucial to better provide effective management and conservation of turtles from this disease. This study aimed to compare ChHV5 genomes between geographic regions and sea turtle species and observe how this virus has evolved and changed. ChHV5 genomes harboured differences within and between geographic regions (88–2793 single nucleotide polymorphisms (SNPs) per sequenced genome). Multiple ChHV5 genes were also found to be under varying selective pressures. Phylogenomic and phylogenetic analyses revealed grouping of the virus, mostly by geography rather than by species, and found differences in ChHV5 genomes between tumours from the same individual. This study pioneers the phylogenomic approach to ChHV5 research. This study provides the most comprehensive picture to-date of whole-genome inter-species ChHV5 diversity and provides important baseline ChHV5 genomic data for future comparisons.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.

Highlights

Fibropapillomatosis (FP) is a debilitating neoplastic disease which has been reported in all seven species of sea turtle [1], these species range from vulnerable to critically endangered [2]
Whole genome sequences from 6 Kemp’s ridley samples, 1 olive ridley sample and 13 green sea turtle samples were analysed for chelonid alphaherpesvirus 5 (ChHV5) aligning reads
ChHV5 genome coverage ranged from 683× to 16,290×x coverage for virally enriched samples and from 7× to 585× coverage for non-enriched samples (Table 1)

Summary

Introduction

Fibropapillomatosis (FP) is a debilitating neoplastic disease which has been reported in all seven species of sea turtle [1], these species range from vulnerable to critically endangered [2]. Fibropapillomatosis manifests as multiple tumours that primarily arise from the soft tissues of sea turtles, including: cutaneous, ocular and visceral tumours (fibromas, fibrosarcomas, mixofibromas and mixomas), which can vary in size and distribution [12,13]. These tumours can be severely debilitating; impairing vision, locomotion, feeding, predator evasion and other natural behaviours, and preventing affected turtles from providing their valuable ecosystem services and keystone species functions [1,11,12,14,15]. Increases in incidence such as these are worrying as turtles are thought to have robust anti-cancer defences given the rarity of other forms of neoplasia [7,36]

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