Donna J. Shaver

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.

Fibropapillomatosis (FP), a debilitating, infectious neoplastic disease, is rarely reported
in endangered Kemp’s ridley sea turtles (Lepidochelys kempii). With this study, we describe FP and
the associated chelonid alphaherpesvirus 5 (ChHV5) in Kemp’s ridley turtles encountered in the
United States during 2006–2020. Analysis of 22 case reports of Kemp’s ridley turtles with FP revealed
that while the disease was mild in most cases, 54.5% were adult turtles, a reproductively valuable
age class whose survival is a priority for population recovery. Of 51 blood samples from tumor-free
turtles and 12 tumor samples from turtles with FP, 7.8% and 91.7%, respectively, tested positive for
ChHV5 DNA via quantitative polymerase chain reaction (qPCR). Viral genome shotgun sequencing
and phylogenetic analysis of six tumor samples show that ChHV5 sequences in Kemp’s ridley
turtles encountered in the Gulf of Mexico and northwestern Atlantic cluster with ChHV5 sequences
identified in green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtles from Hawaii, the southwestern Atlantic Ocean, and the Caribbean. Results suggest an interspecific, spatiotemporal
spread of FP among Kemp’s ridley turtles in regions where the disease is enzootic. Although FP is
currently uncommon in this species, it remains a health concern due to its uncertain pathogenesis
and potential relationship with habitat degradation.