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

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.