Dataset Information

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.

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.

SUBMITTER: Whitmore L

PROVIDER: S-EPMC8465875 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The Kemp's ridley (Lepidochelys kempii) is the world's most endangered sea turtle species and is primarily distributed in the Gulf of Mexico. In the United States, South Padre Island, Texas serves as a key nesting ground for the species. Genetic studies of the Kemp's ridley have been used to aid in conservation and management practices, with the mitochondrial control region as the most commonly used marker due to its perceived hypervariability and ease of sequencing. However, with the advent of next generation sequencing technology, targeting complete mitochondrial genomes is now feasible. Here, we describe a more complete mitochondrial genome for the Kemp's ridley than has been previously published in literature and demonstrate a cost-effective and efficient method for obtaining complete mitochondrial genomes from sea turtles. We compare the genetic diversity and taxonomic resolution obtained from whole mitochondrial genomes to that obtained from the mitochondrial control region alone. We compare current genetic diversity with previous records. Furthermore, we evaluate the genetic structure between the breeding stock in South Padre Island and that of deceased Kemp's ridleys recovered on the Northern coast of the Gulf of Mexico after the 2010 BP Deepwater Horizon oil spill, and of Kemp's ridleys stranded on the East Coast of the United States. Our results show that complete mitochondrial genomes provide greater resolution than the control region alone. They also show that the genetic diversity of the Kemp's ridley has remained stable, despite large population declines, and that the genetic makeup of deceased turtles stranded after the Deepwater Horizon oil spill is indistinguishable from the breeding stock in South Padre Island, Texas.Open data badgeThis article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/genbank/.

Project description:Many juvenile Kemp's ridley (Lepidochelys kempii) and loggerhead (Caretta caretta) turtles strand during fall on the beaches of Cape Cod (MA, USA), with total stranding numbers sometimes exceeding 300 turtles per year. Once rehabilitated, turtles must be released at beaches with appropriate water temperatures, often requiring transportation to southeastern coastal states of the USA. These transportation events (transports) may approach or exceed 24 h in duration. Kemp's ridley turtles are known to exhibit an adrenal stress response during such transports, but the effect of transport duration has been unclear, and no other sea turtle species has been investigated. To assess whether transport duration and/or species affects physiological reactions to transport, we studied pre- and post-transport physiological measures in Kemp's ridley and loggerhead turtles transported by ground for <6, ∼12, ∼18, or ∼24 h, comparing with matched "control events" in which turtles were studied without transport. Blood samples were analyzed for four stress-associated measures (corticosterone, glucose, total white blood cell [WBC] count, and heterophil/lymphocyte ratio [H/L]) and nine measures of clinical status (pH, pO2, pCO2, HCO3, sodium, potassium, ionized calcium, lactate, and hematocrit). In both species, stress-associated measures elevated significantly during transport, while handling without transport had no significant effects. Loggerheads exhibited a greater stress response than Kemp's ridleys across all transport durations. These results indicate that sea turtles do react physiologically to ground transport; therefore, minimizing transport time and streamlining transport logistics (where feasible) may help ensure release of rehabilitated turtles to sea in the best possible condition. Nonetheless, both species remained in good clinical condition even after 24 h transport, indicating that current transport protocols are generally safe for sea turtles from a clinical perspective.

Dataset Information

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.

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