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

SIMPLE SUMMARY: Our 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. ABSTRACT: 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.