The Concurrent Detection of Chelonid Alphaherpesvirus 5 and Chelonia mydas Papillomavirus 1 in Tumoured and Non-Tumoured Green Turtles

Case report: Diagnosis and autogenous vaccine treatment of herpesvirus in a green turtle (Chelonia mydas) in Santa Marta, Colombia

This study reports the first case of fibropapillomatosis (FP) in the green turtle Chelonia mydas that has been successfully diagnosed and treated in Colombia. Worldwide, FP has reached epizootic proportions as it has been reported in marine turtles of tropical and subtropical waters, and in severe cases, it reduces the probability of survival. Treatment has been elusive as multiple surgical excisions are needed due to tumor recurrence. In this case, one green turtle with multiple tumors was diagnosed by histopathology and molecular detection of the chelonid herpesvirus 5 (ChHV5) by means of amplification and sequencing of the DNA polymerase (DNApol) gene. Two separate treatments that consisted of autogenous vaccines and surgical excisions were applied; the first one had a partial success as one out of the tumors treated reappeared after 3 months post-treatment. Treatment 2 consisted of an autogenous vaccine enriched with adjuvants and applied at increasing doses, after which, the tumor significatively decreased in size and was surgically removed. At the end of the 6 months follow-up period, no tumor recurrence was observed, and the turtle was in apparent optimal health conditions. These findings, although limited, suggest a possible treatment that might help to contain this epizootic problem.

Detection of Hemopathogens in Chelonoidis carbonaria: Microscopic, Molecular, Hematological, and Clinical Biochemistry Aspects

Background: The growing contact between men and wild animals, caused by the increase in the population in urban centers and the destruction of the habitat of these animals, has been leading to a greater circulation of pathogens between humans and wildlife. Chelonoidis carbonaria, a tortoise found throughout South America, is one of the animals most rescued from animal trafficking and illegal breeding. Considering this situation, this study aimed to verify the occurrence of hemoparasites in C. carbonaria. Materials and Methods: Blood samples from 73 C. carbonaria were collected from animals located in (1) a rural commercial breeding unit, (2) an urban zoo, and (3) a center of rescued animal screening. Genomic DNA was extracted from these animals and used in PCRs to detect specific genomic fragments of haemogregarines (i.e., Hepatozoon and Hemolivia), and members of the Anaplasmataceae Family (i.e., Ehrlichia sp. and Anaplasma sp.). Blood samples were screened for hemopathogens by direct microscopy and were used for hematological assays, and serum samples were analyzed to determine the concentration of serum components. Results: It was found that 34.2% of the tortoises presented Sauroplasma sp. in their blood samples; these animals showed clinical biochemistry changes that indicate altered liver function. Two zoo animals were positive for Ehrlichia sp. in PCR, and also presented clinical biochemistry and hematological changes. Conclusion: The present project is pioneer in the detection of Ehrlichia sp. in C. carbonaria, and was able to identify changes in clinical biochemistry that can be a result of the infection by hemopathogens in this species.

Exploring the relationship between environmental drivers and the manifestation of fibropapillomatosis in green turtles (Chelonia mydas) in eastern Brazil

Fibropapillomatosis (FP) is a disease characterized by epithelial tumors that can impede life-sustaining activities of sea turtles, especially green turtles (Chelonia mydas). FP is caused by a herpesvirus, but environmental factors are also thought to play a role in triggering FP tumor growth. In this study, we evaluate the epidemiology of FP tumors in green turtles along the coast of Espírito Santo, Brazil, a region where juvenile green turtles are known to aggregate with high FP prevalence. A dataset comprising 2024 beach-cast green turtles recorded through daily beach surveys on 400 km of coastline from 2018 to 2021 (inclusive) was evaluated. FP tumors were recorded in 40.9% of the individuals in this dataset, and presence of FP tumors was predicted by individual variables (presence of marine leeches, stranding code, curved carapace length, body mass-size residual) and characteristics of the stranding site (distance to nearest metallurgical plant, mean sea surface salinity (SSS), annual range of sea surface temperature (SST)). Additionally, a second dataset comprising detailed information about the size and anatomical distribution of tumors in 271 green turtles with FP from the same region was evaluated. Hierarchical clustering analysis revealed these turtles could be classified in three groups according to the anatomical distribution of their tumors, and in turn the group to which each turtle was assigned could be predicted by the study period (2010-2014 vs. 2018-2022) and by characteristics of the stranding/capture site (green turtle stranding density, mean sea surface chlorophyll-a concentration, mean SSS, mean SST, annual range of SST). These results corroborate that individual and environmental factors play a significant role driving FP epidemiology. Furthermore, the results suggest that rather than behaving as a single entity, FP may be seen as a mosaic of distinct anatomical patterns that are not necessarily driven by the same environmental factors.

Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA

The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption of eDNA analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered and invasive species detection, and population genetics. Here we show that deep-sequencing-based eDNA approaches capture genomic information from humans (Homo sapiens) just as readily as that from the intended target species. We term this phenomenon human genetic bycatch (HGB). Additionally, high-quality human eDNA could be intentionally recovered from environmental substrates (water, sand and air), holding promise for beneficial medical, forensic and environmental applications. However, this also raises ethical dilemmas, from consent, privacy and surveillance to data ownership, requiring further consideration and potentially novel regulation. We present evidence that human eDNA is readily detectable from 'wildlife' environmental samples as human genetic bycatch, demonstrate that identifiable human DNA can be intentionally recovered from human-focused environmental sampling and discuss the translational and ethical implications of such findings.

Reptile Dermatology

Reptiles are being presented more frequently to veterinarians because they increase in popularity. As with domestic pets, dermatologic conditions are common findings in captive reptiles and can be associated with husbandry and nutritional deficiencies, infectious diseases, and neoplasia. To have success with these cases, it is important to take a stepwise and strategic approach, starting with a thorough anamnesis and physical examination. From there, diagnostic tests should be pursued, with an understanding of the limitations of each diagnostic test. By understanding these limitations, the veterinary scientist can determine the best path to a diagnosis and treatment for the case.

Revealing the uncharacterised diversity of amphibian and reptile viruses

Amphibians and non-avian reptiles represent a significant proportion of terrestrial vertebrates, however knowledge of their viruses is not proportional to their abundance. Many amphibians and reptiles have strict habitual environments and localised populations and are vulnerable to viral outbreaks and potential elimination as a result. We sought to identify viruses that were hidden in amphibian and reptile metatranscriptomic data by screening 235 RNA-sequencing datasets from a 122 species covering 25 countries. We identified 26 novel viruses and eight previously characterised viruses from fifteen different viral families. Twenty-five viruses had RNA genomes with identity to Arteriviridae, Tobaniviridae, Hantaviridae, Rhabdoviridae, Astroviridae, Arenaviridae, Hepeviridae, Picornaviridae, Orthomyxoviridae, Reoviridae, Flaviviridae and Caliciviridae. In addition to RNA viruses, we also screened datasets for DNA viral transcripts, which are commonly excluded from transcriptomic analysis. We identified ten DNA viruses with identity to Papillomaviridae, Parvoviridae, Circoviridae and Adomaviridae. With the addition of these viruses, we expand the global amphibian and reptile virome and identify new potentially pathogenic viruses that could challenge populations. We speculate that amphibian viruses often have simpler genomes than those in amniotes, as in the case of the Secondpapillomavirinae and Orthomyxoviridae viruses identified in this study. In addition, we find evidence of inter-family recombination in RNA viruses, and we also identify new members of the recombinant Adomaviridae family. Overall, we provide insights into the uncharacterised diversity of amphibian and reptile viruses with the aim of improving population management, treatment and conservation into the future.

Detection and population genomics of sea turtle species via non-invasive environmental DNA analysis of nesting beach sand tracks and oceanic water

Elusive aquatic wildlife, such as endangered sea turtles, are difficult to monitor and conserve. As novel molecular and genetic technologies develop, it is possible to adapt and optimize them for wildlife conservation. One such technology is environmental (e)DNA - the detection of DNA shed from organisms into their surrounding environments. We developed species-specific green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtle probe-based qPCR assays, which can detect and quantify sea turtle eDNA in controlled (captive tank water and sand samples) and free ranging (oceanic water samples and nesting beach sand) settings. eDNA detection complemented traditional in-water sea turtle monitoring by enabling detection even when turtles were not visually observed. Furthermore, we report that high throughput shotgun sequencing of eDNA sand samples enabled sea turtle population genetic studies and pathogen monitoring, demonstrating that non-invasive eDNA techniques are viable and efficient alternatives to biological sampling (e.g. biopsies and blood draws). Genetic information was obtained from sand many hours after nesting events, without having to observe or interact with the target individual. This greatly reduces the sampling stress experienced by nesting mothers and emerging hatchlings, and avoids sacrificing viable eggs for genetic analysis. The detection of pathogens from sand indicates significant potential for increased wildlife disease monitoring capacity and viral variant surveillance. Together, these results demonstrate the potential of eDNA approaches to ultimately help understand and conserve threatened species such as sea turtles.

Genotype data not consistent with clonal transmission of sea turtle fibropapillomatosis or goldfish schwannoma

Recent discoveries of transmissible cancers in multiple bivalve species suggest that direct transmission of cancer cells within species may be more common than previously thought, particularly in aquatic environments. Fibropapillomatosis occurs with high prevalence in green sea turtles ( Chelonia mydas) and the geographic range of disease has increased since fibropapillomatosis was first reported in this species. Widespread incidence of schwannomas, benign tumours of Schwann cell origin, reported in aquarium-bred goldfish (Carassius auratus), suggest an infectious aetiology. We investigated the hypothesis that cancers in these species arise by clonal transmission of cancer cells. Through analysis of polymorphic microsatellite alleles, we demonstrate concordance of host and tumour genotypes in diseased animals. These results imply that the tumours examined arose from independent oncogenic transformation of host tissue and were not clonally transmitted. Further, failure to experimentally transmit goldfish schwannoma via water exposure or inoculation suggest that this disease is unlikely to have an infectious aetiology.

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.

Environmental DNA monitoring of oncogenic viral shedding and genomic profiling of sea turtle fibropapillomatosis reveals unusual viral dynamics

Pathogen-induced cancers account for 15% of human tumors and are a growing concern for endangered wildlife. Fibropapillomatosis is an expanding virally and environmentally co-induced sea turtle tumor epizootic. Chelonid herpesvirus 5 (ChHV5) is implicated as a causative virus, but its transmission method and specific role in oncogenesis and progression is unclear. We applied environmental (e)DNA-based viral monitoring to assess viral shedding as a direct means of transmission, and the relationship between tumor burden, surgical resection and ChHV5 shedding. To elucidate the abundance and transcriptional status of ChHV5 across early, established, regrowth and internal tumors we conducted genomics and transcriptomics. We determined that ChHV5 is shed into the water column, representing a likely transmission route, and revealed novel temporal shedding dynamics and tumor burden correlations. ChHV5 was more abundant in the water column than in marine leeches. We also revealed that ChHV5 is latent in fibropapillomatosis, including early stage, regrowth and internal tumors; higher viral transcription is not indicative of poor patient outcome, and high ChHV5 loads predominantly arise from latent virus. These results expand our knowledge of the cellular and shedding dynamics of ChHV5 and can provide insights into temporal transmission dynamics and viral oncogenesis not readily investigable in tumors of terrestrial species.