Evolutionary comparisons of chelonid alphaherpesvirus 5 (ChHV5) genomes from fibropapillomatosis-afflicted green (chelonia mydas), Ooive ridley (lepidochelys olivacea) and kemp’s ridley (lepidochelys kempii) sea turtles

peer-reviewedThe 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 viru

Development of genomic resources for a thraustochytrid pathogen and investigation of temperature influences on gene expression.

Understanding how environmental changes influence the pathogenicity and virulence of infectious agents is critical for predicting epidemiological patterns of disease. Thraustochytrids, part of the larger taxonomic class Labyrinthulomycetes, contain several highly pathogenic species, including the hard clam pathogen quahog parasite unknown (QPX). QPX has been associated with large-scale mortality events along the northeastern coast of North America. Growth and physiology of QPX is temperature-dependent, and changes in local temperature profiles influence pathogenicity. In this study we characterize the partial genome of QPX and examine the influence of temperature on gene expression. Genes involved in several biological processes are differentially expressed upon temperature change, including those associated with altered growth and metabolism and virulence. The genomic and transcriptomic resources developed in this study provide a foundation for better understanding virulence, pathogenicity and life history of thraustochytrid pathogens

Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression

Understanding how environmental changes influence the pathogenicity and virulence of infectious agents is critical for predicting epidemiological patterns of disease. Thraustochytrids, part of the larger taxonomic class Labyrinthulomycetes, contain several highly pathogenic species, including the hard clam pathogen quahog parasite unknown (QPX). QPX has been associated with large-scale mortality events along the northeastern coast of North America. Growth and physiology of QPX is temperature-dependent, and changes in local temperature profiles influence pathogenicity. In this study we characterize the partial genome of QPX and examine the influence of temperature on gene expression. Genes involved in several biological processes are differentially expressed upon temperature change, including those associated with altered growth and metabolism and virulence. The genomic and transcriptomic resources developed in this study provide a foundation for better understanding virulence, pathogenicity and life history of thraustochytrid pathogens.</p

Chelonid Alphaherpesvirus 5 Prevalence and First Confirmed Case of Sea Turtle Fibropapillomatosis in Grenada, West Indies

Chelonid alphaherpesvirus 5 (ChHV5) is strongly associated with fibropapillomatosis, a neoplastic disease of sea turtles that can result in debilitation and mortality. The objectives of this study were to examine green (Chelonia mydas), hawksbill (Eretmochelys imbricata), and leatherback (Dermochelys coriacea) sea turtles in Grenada, West Indies, for fibropapillomatosis and to utilize ChHV5-specific PCR, degenerate herpesvirus PCR, and serology to non-invasively evaluate the prevalence of ChHV5 infection and exposure. One-hundred and sixty-seven turtles examined from 2017 to 2019 demonstrated no external fibropapilloma-like lesions and no amplification of ChHV5 DNA from whole blood or skin biopsies. An ELISA performed on serum detected ChHV5-specific IgY in 18/52 (34.6%) of green turtles tested. In 2020, an adult, female green turtle presented for necropsy from the inshore waters of Grenada with severe emaciation and cutaneous fibropapillomas. Multiple tumors tested positive for ChHV5 by qPCR, providing the first confirmed case of ChHV5-associated fibropapillomatosis in Grenada. These results indicate that active ChHV5 infection is rare, although viral exposure in green sea turtles is relatively high. The impact of fibropapillomatosis in Grenada is suggested to be low at the present time and further studies comparing host genetics and immunologic factors, as well as examination into extrinsic factors that may influence disease, are warranted

Factors influencing survivorship of rehabilitating green sea turtles (Chelonia mydas) with fibropapillomatosis

Marine turtle fibropapillomatosis (FP) is a debilitating, infectious neoplastic disease that has reached epizootic proportions in several tropical and subtropical populations of green turtles (Chelonia mydas). FP represents an important health concern in sea turtle rehabilitation facilities. The objectives of this study were to describe the observed epidemiology, biology, and survival rates of turtles affected by FP (FP+ turtles) in a rehabilitation environment; to evaluate clinical parameters as predictors of survival in affected rehabilitating turtles; and to provide information about case progression scenarios and potential outcomes for FP+ sea turtle patients. A retrospective case series analysis was performed using the medical records of the Georgia Sea Turtle Center (GSTC), Jekyll Island, Georgia, USA, during 2009–2013. Information evaluated included signalment, morphometrics, presenting complaint, time to FP onset, tumor score (0–3), co-morbid conditions, diagnostic test results, therapeutic interventions, and case outcomes. Overall, FP was present in 27/362 (7.5%) of all sea turtles admitted to the GSTC for rehabilitation, either upon admittance or during their rehabilitation. Of these, 25 were green and 2 were Kemp's ridley turtles. Of 10 turtles that had only plaque-like FP lesions, 60% had natural tumor regression, all were released, and they were significantly more likely to survive than those with classic FP (P = 0.02 [0.27–0.75, 95% CI]). Turtles without ocular FP were eight times more likely to survive than those with ocular FP (odds ratio = 8.75, P = 0.032 [1.21–63.43, 95% CI]). Laser-mediated tumor removal surgery is the treatment of choice for FP+ patients at the GSTC; number of surgeries was not significantly related to case outcome

Average number of SNPs per kilobase pair in 152 contigs associated with GO Slim biological processes.

<p>Bar heights represent the average SNP rate per kilobase pair for select GO Slim biological processes. Color intensity of the bars indicates number of contigs for each GO Slim term.</p

Classification of annotated QPX contigs based on Gene Ontology.

<p>Representation of (a) biological processes, (b) molecular function, and (c) cellular components from Gene Ontology Slim terms based on Swiss-Prot gene annotations. The gene ontology categories ‘other biological processes functions’ (a), ‘other molecular functions’ (b), and ‘other cellular components’ (c) were excluded from these graphs.</p

Relative gene expression levels (RPKM) between QPX10 and QPX21 libraries.

<p>Each circle represents a single contig, with blue circles indicating those contigs that are differentially expressed. The diagonal line represents equal expression between the two libraries.</p