Three novel herpesviruses of endangered Clemmys and Glyptemys turtles

Development and analytical validation of a novel quantitative PCR assay for the detection of Trachemys herpesvirus 1

Emerging infectious diseases are a threat that contributes to the decline of global chelonian species. Herpesviruses are among the most impactful pathogens described in chelonians and are frequently associated with a range of presentations across hosts with the potential for severe morbidity and mortality. Trachemys herpesvirus 1 (TrHV1) has been reported in red-eared and yellow-bellied sliders (Trachemys scripta elegans and Trachemys scripta scripta, respectively) but is largely understudied. Invasive red-eared sliders may serve as a reservoir for transmission to sympatric native species. This study aimed to develop a sensitive and specific quantitative real-time PCR (qPCR) assay for the detection of TrHV1 DNA to aid in the characterization of the epidemiology of this virus in aquatic turtles. Two TaqMan-MGB FAM-dye labeled primer-probe sets were designed and evaluated using plasmid dilutions. The higher performing assay was specific for TrHV1 DNA and had a linear dynamic range of 1.0 × 107 to 1.0 × 101 copies per reaction with an R2 of 0.999, slope of -3.386, and efficiency of 97.39%. The limit of detection was 101 copies per reaction, and there was no loss of reaction efficiency in the presence of TrHV1-negative chelonian oral-cloacal DNA. Overall, the Trachemys herpesvirus 1 assay meets established criteria for acceptable qPCR assays and will be a valuable tool in characterizing the epidemiology of Trachemys herpesvirus 1 in chelonians.

EMYDID HERPESVIRUS 1 INFECTIONS IN WESTERN POND TURTLES (ACTINEMYS MARMORATA) AND A RED-EARED SLIDER (TRACHEMYS SCRIPTA ELEGANS) WITH FATAL AND NONFATAL OUTCOMES

Herpesviruses are important pathogens in zoologic chelonian collections and have been associated with fatal disease in turtles of the family Emydidae. In this report, three western pond turtles (Actinemys marmorata), living in a mixed-species freshwater turtle exhibit, presented with varying degrees of lethargy, pallor, generalized edema, and cloacal hemorrhage before death within a 2-wk period. Postmortem findings included necrohemorrhagic enterocolitis, necrotizing splenitis, hepatic necrosis, esophagitis, thymic necrosis, and pneumonia with epithelial necrosis and degeneration of the trachea and kidneys. Intraepithelial, intranuclear, amphophilic to eosinophilic, Cowdry type A viral inclusion bodies were identified in the intestinal tract, liver, spleen, kidney, trachea, lung, and thymus. PCR amplification and sequencing of liver tissue produced amplicons that were 100% homologous with emydid herpesvirus 1 (EmyHV-1). Molecular screening of cohoused emydid turtles revealed that a red-eared slider (Trachemys scripta elegans) and a western pond turtle, both asymptomatic, were PCR-positive for EmyHV-1 on combined oral-cloacal swabs. This report describes, for the first time, EmyHV-1-associated disease in western pond turtles and molecularly identifies EmyHV-1 in an asymptomatic red-eared slider.

Herpesviruses in Captive Chelonians in Europe Between 2016 and 2020

Herpesviruses are important pathogens in tortoises and turtles, yet little is known about the epidemiology of these viruses. We analyzed herpesviruses detected by PCR in samples from captive chelonians in Europe according to virus strain, host species, year and season in which the animal was tested, and country in which the animal was kept. A total of 4,797 samples submitted to a diagnostic laboratory in Europe between January 2016 and December 2020 were evaluated. Of these, 312 (6.50%) were positive for herpesviruses. The types most commonly found were testudinid herpesvirus (TeHV)1 (143 positive, 45.83%) and TeHV3 (153 positive, 49.04%), but also included TeHV2 (1 positive, 0.32%), TeHV4 (3 positive, 0.96%), Terrapene herpesvirus 1 (7 positive, 2.24%), Trachemys herpesvirus 1 (2 positive, 0.64%), and three previously undescribed herpesviruses (0.96%). Herpesviruses were detected in chelonians in the families Testudinidae, Emydidae, Geoemydidae, and in the suborder Pleurodira. Among the species for which 100 samples or more were available, the highest proportions of positive samples (positivity rates) were found in samples from Horsfield's tortoises (Testudo horsfieldii) (14.96%), and radiated tortoises (Astrochelys radiata) (14.05%). Among tortoises (Testudinidae), viruses were most often detected in the spring, while in emydid turtles (Emydidae) they were most often detected in the summer. A comparison of the positivity rates according to country showed significant differences, with the highest rate in samples from Italy (16.01%). This study indicated possible differences in herpesvirus positivity rates depending on host species, virus strain, year of sampling, season, and country of origin. It provides useful information in further understanding fluctuations in infection rates as well as in helping to guide decision making for herpesvirus diagnostics in chelonian patients. It also provides evidence for the international dispersal of herpesviruses with their hosts through international trade.

Nidoviruses in Reptiles: A Review

Since their discovery in 2014, reptile nidoviruses (also known as serpentoviruses) have emerged as significant pathogens worldwide. They are known for causing severe and often fatal respiratory disease in various captive snake species, especially pythons. Related viruses have been detected in other reptiles with and without respiratory disease, including captive and wild populations of lizards, and wild populations of freshwater turtles. There are many opportunities to better understand the viral diversity, species susceptibility, and clinical presentation in different species in this relatively new field of research. In captive snake collections, reptile nidoviruses can spread quickly and be associated with high morbidity and mortality, yet the potential disease risk to wild reptile populations remains largely unknown, despite reptile species declining on a global scale. Experimental studies or investigations of disease outbreaks in wild reptile populations are scarce, leaving the available literature limited mostly to exploring findings of naturally infected animals in captivity. Further studies into the pathogenesis of different reptile nidoviruses in a variety of reptile species is required to explore the complexity of disease and routes of transmission. This review focuses on the biology of these viruses, hosts and geographic distribution, clinical signs and pathology, laboratory diagnosis and management of reptile nidovirus infections to better understand nidovirus infections in reptiles.

A NOVEL IGUANID HERPESVIRUS DETECTED IN ASYMPTOMATIC GREEN IGUANAS (IGUANA IGUANA) IN POLAND

While herpesviruses are well-known pathogens in a wide variety of chelonian species, they have only sporadically been documented in squamate reptiles. Those that have been described have most often been associated with hepatic disease and oral lesions. During a study on infectious disease in pet reptiles in Poland, herpesviruses were detected in swabs from three green iguanas (Iguana iguana) from two different owners that were presented to two different veterinary clinics in Warsaw. One iguana was presented for abscesses on the head, while the other two were partner animals and remained clinically healthy throughout the course of this study. Virus was detected in oral swabs as well as combined swab samples from the oral cavity and cloaca using a panherpesvirus PCR. PCR products from all three animals were sequenced, and the detected viruses were most closely related to iguanid herpesvirus 2 from a San Esteban chuckwalla (Sauromalus varius) in the United States (GenBank accession No. AY236869.1). The single animal was retested again 1 y later and remained clinically healthy and continued to shed the same herpesvirus. This is the first description of a herpesvirus infection in pet iguanas in Europe. While the clinical relevance of the infection is not known, it is of interest that the infected animals appeared to continue to shed virus over an extended period of time.

Herpesviruses in Reptiles

Since the 1970s, several species of herpesviruses have been identified and associated with significant diseases in reptiles. Earlier discoveries placed these viruses into different taxonomic groups on the basis of morphological and biological characteristics, while advancements in molecular methods have led to more recent descriptions of novel reptilian herpesviruses, as well as providing insight into the phylogenetic relationship of these viruses. Herpesvirus infections in reptiles are often characterised by non-pathognomonic signs including stomatitis, encephalitis, conjunctivitis, hepatitis and proliferative lesions. With the exception of fibropapillomatosis in marine turtles, the absence of specific clinical signs has fostered misdiagnosis and underreporting of the actual disease burden in reptilian populations and hampered potential investigations that could lead to the effective control of these diseases. In addition, complex life histories, sampling bias and poor monitoring systems have limited the assessment of the impact of herpesvirus infections in wild populations and captive collections. Here we review the current published knowledge of the taxonomy, pathogenesis, pathology and epidemiology of reptilian herpesviruses.

EPIDEMIOLOGY OF EMYDOIDEA HERPESVIRUS 1 IN FREE-RANGING BLANDING'S TURTLES (EMYDOIDEA BLANDINGII) FROM ILLINOIS

Herpesvirus infections have been associated with high morbidity and mortality in populations of captive emydid chelonians worldwide, but novel herpesviruses have also recently been identified in apparently healthy free-ranging emydid populations. Blanding's turtle (Emydoidea blandingii), an endangered species in Illinois, has experienced range-wide declines because of habitat loss, degradation, and fragmentation. A novel herpesvirus, Emydoidea herpesvirus 1 (EBHV1), was identified in Blanding's turtles in DuPage County, IL, in 2015. Combined oral-cloacal swabs were collected from radio transmitter-fitted and trapped (n = 54) turtles multiple times over the 2016 activity season. In addition, swabs were collected at a single time point from trapped and incidentally captured (n = 84) Blanding's turtles in DuPage (n = 33) and Lake (n = 51) counties over the same field season. Each sample was tested for EBHV1 using quantitative polymerase chain reaction (qPCR). EBHV1 was detected in 15 adult females for an overall prevalence of 10.8% (n = 15/138; 95% confidence interval [CI]: 6.2-17.3%). In radio transmitter-fitted females, there was a significantly higher prevalence of EBHV1 DNA in May (23.8%, n = 10/42) than June (3.6%, n = 1/28), July (0%, n = 0/42), August (0%, n = 0/47), or September (7.7%, n = 3/39) (odds ratio: 12.19; 95% CI: 3.60-41.30). The peak in May corresponds to the onset of nesting and may be associated with increased physiologic demands. Furthermore, all positive turtles were qPCR negative in subsequent months. There were no clinical signs associated with EBHV1 detection. This investigation is the critical first step to characterizing the implications of EBHV1 for Blanding's turtle population health and identifying management changes that may improve sustainability.

CHARACTERIZING THE EPIDEMIOLOGY OF HISTORIC AND NOVEL PATHOGENS IN BLANDING'S TURTLES (EMYDOIDEA BLANDINGII)

Pathogens such as herpesviruses, Mycoplasma spp., and frog virus 3-like ranavirus have contributed to morbidity and mortality in many species of free-living and zoo-maintained chelonians. However, their prevalence is understudied in Blanding's turtles (Emydoidea blandingii) across North America. To assess the presence of these pathogens, Blanding's turtles were sampled in Lake County, Illinois, in 2017 (N = 213) and 2018 (N = 160). DNA from cloacal-oral swabs was assayed for four ranaviruses, three Mycoplasma spp., two Salmonella spp., Emydoidea herpesvirus 1 (EBHV1), and tortoise intranuclear coccidiosis (TINC) using a multiplex quantitative polymerase chain reaction (qPCR). Pathogens were most frequently detected in adult turtles (n = 25) and rarely in subadults (n = 2) or juveniles (n = 1). EBHV1 was detected in 22 individuals with no clinical signs of illness, most (n = 20) occurring in the month of May (P < 0.0001). EBHV1 cases at one study site significantly clustered within the same 0.64-km area from 17 to 22 May 2017 (P < 0.0001) and 14 to 15 May 2018 (P = 0.0006). Individuals were rarely positive for Salmonella typhimurium (n = 6). A novel Mycoplasma sp. sharing high homology with other emydid Mycoplasma spp. was detected in one turtle with nasal discharge. Neither TINC nor any ranaviruses were detected. Continued monitoring of this population and habitat may facilitate identification of risk factors for pathogen occurrence and clarify the impact of infectious diseases on Blanding's turtle conservation outcomes.

Detection of a novel herpesvirus associated with squamous cell carcinoma in a free-ranging Blanding's turtle

The spread of both infectious and noninfectious diseases through wildlife populations is of increasing concern. Neoplastic diseases are rarely associated with population-level impacts in wildlife; however, impacts on individual health can be severe and might reflect deteriorating environmental conditions. An adult male free-ranging Blanding's turtle (Emydoidea blandingii) originally captured in 2005 and deemed healthy, was recaptured in 2018 with a 1 × 1.5 cm intra-oral broad-based right mandibular mass. An excisional biopsy was performed, and histopathology revealed squamous cell carcinoma (SCC). Consensus herpesvirus PCR identified a novel herpesvirus (proposed name Emydoidea herpesvirus 2 [EBHV-2]) within the tumor. EBHV-2 shares 85% sequence homology with Terrapene herpesvirus 2 (TerHV-2), a herpesvirus linked to fibropapillomas in eastern box turtles (Terrapene carolina carolina). Virus-associated fibropapillomas have been identified in multiple marine turtle species and have had debilitating effects on their populations, but to date, virus-associated SCCs are rarely reported.

HEALTH ASSESSMENT OF FREE-RANGING CHELONIANS IN AN URBAN SECTION OF THE BRONX RIVER, NEW YORK, USA

The Bronx River in Bronx, New York, US spans an area of significant human development and has been subject to historic and ongoing industrial contamination. We evaluated the health of freeranging native common snapping turtles ( Chelydra serpentina) and nonnative invasive red-eared sliders ( Trachemys scripta) in a segment of the Bronx River between May and July 2012. In 18 snapping turtles and nine sliders, complete physical examinations were performed, ectoparasites collected, and blood was analyzed for contaminants (mercury, thallium, cadmium, arsenic, lead, selenium, oxychlordane, alpha-chlordane, dieldrin, DDD, DDE, polychlorinated biphenyls). Complete blood counts and the presence of hemoparasites were determined in 16 snapping turtles and nine sliders. Swabs of the choana and cloaca were screened for ranavirus, adenovirus, herpesvirus, and Mycoplasma spp. by PCR in 39 snapping turtles and 28 sliders. Both turtle species exhibited bioaccumulation of various environmental contaminants, particularly organochlorines and polychlorinated biphenyls. Molecular screening revealed a unique herpesvirus in each species. A Mycoplasma sp. previously isolated from emydid turtles was detected in red-eared sliders while a unique Mycoplasma sp. was identified in common snapping turtles. Ranaviruses and adenoviruses were not detected. Our study established a baseline health assessment to which future data can be compared. Moreover, it served to expand the knowledge and patterns of health markers, environmental contaminants, and microorganisms of freeranging chelonians.

Molecular evolution of fibropapilloma-associated herpesviruses infecting juvenile green and loggerhead sea turtles

Chelonid Alphaherpesvirus 5 (ChHV5) has long been associated with fibropapillomatosis (FP) tumor disease in marine turtles. Presenting primarily in juvenile animals, FP results in fibromas of the skin, connective tissue, and internal organs, which may indirectly affect fitness by obstructing normal turtle processes. ChHV5 is near-universally present in tumorous tissues taken from affected animals, often at very high concentrations. However, there is also considerable asymptomatic carriage amongst healthy marine turtles, suggesting that asymptomatic hosts play an important role in disease ecology. Currently, there is a paucity of studies investigating variation in viral genetics between diseased and asymptomatic hosts, which could potentially explain why only some ChHV5 infections lead to tumor formation. Here, we generated a database containing DNA from over 400 tissue samples taken from green and loggerhead marine turtles, including multiple tissue types, a twenty year time span, and both diseased and asymptomatic animals. We used two molecular detection techniques, quantitative (q)PCR and nested PCR, to characterize the presence and genetic lineage of ChHV5 in each sample. We found that nested PCR across multiple loci out-performed qPCR and is a more powerful technique for determining infection status. Phylogenetic reconstruction of three viral loci from all ChHV5-positive samples indicated widespread panmixia of viral lineages, with samples taken across decades, species, disease states, and tissues all falling within the same evolutionary lineages. Haplotype networks produced similar results in that viral haplotypes were shared across species, tissue types and disease states with no evidence that viral lineages associated significantly with disease dynamics. Additionally, tests of selection on viral gene trees indicated signals of selection dividing major clades, though this selection did not divide sample categories. Based on these data, neither the presence of ChHV5 infection nor neutral genetic divergence between viral lineages infecting a juvenile marine turtle is sufficient to explain the development of FP within an individual.

Development and validation of a quantitative PCR assay for detection of Emydoidea herpesvirus 1 in free-ranging Blanding's turtles (Emydoidea blandingii)

Blanding's turtles (Emydoidea blandingii), an endangered species in Illinois, have experienced range-wide declines because of habitat degradation and fragmentation, predation, and road mortality. While ongoing studies are crucial to a thorough understanding of the natural history and demographics in these disjointed Illinois populations, infectious disease threats have been largely unevaluated. Herpesvirus outbreaks have been associated with high morbidity and mortality in populations of captive tortoises and turtles worldwide, including the family Emydidae (pond and box turtles). However, novel herpesviruses including Terrapene herpesvirus 1, Emydid herpesvirus 1 and 2, and Glyptemys herpesvirus 1 and 2, have recently been identified in apparently healthy free-ranging freshwater turtles. In 2015, 20 free-ranging Blanding's turtles in DuPage County, Illinois were screened for a herpesvirus using consensus PCR. A novel herpesvirus species (Emydoidea herpesvirus 1; EBHV1) was identified in two animals and shared a high degree of sequence homology to other freshwater turtle herpesviruses. Two quantitative real-time PCR assays, using EBHV1 primer-1 and primer-2, were developed to target an EBHV1-specific segment of the DNA-dependent DNA polymerase gene and validated. Both assays performed with high efficiency (slope = -3.2; R² = 1), low intra-assay variability, and low inter-assay variability (coefficient of variation <2% at all dilutions). However, EBHV1 primer-2 displayed less variation and was selected to test clinical samples and five closely related herpesvirus control samples. Results indicate that this assay is specific for EBHV1, has a linear range of detection from 10⁸ to 10¹ viral copies per reaction, and can categorically detect as few as 1 viral copy per reaction. This qPCR assay provides a valuable diagnostic tool for future characterization of EBHV1 epidemiology.

Detection of Mycoplasma spp., herpesviruses, topiviruses, and ferlaviruses in samples from chelonians in Europe

We tested samples from 1,015 chelonians in Europe for Mycoplasma spp., herpesviruses, ranaviruses, picornaviruses, and ferlaviruses by PCR. Mycoplasma spp. were detected in 42.1% and herpesviruses were detected in 8.0% of tested chelonians. Differentiation of the herpesviruses revealed that 46.9% of the detected chelonian viruses were testudinid herpesvirus 1 (TeHV-1) and 54.3% were TeHV-3, including co-detections of TeHV-1 and -3 in 3 tortoises. TeHV-4 was detected in a leopard tortoise ( Stigmochelys pardalis), and a herpesvirus that could not be further characterized was found in a pond slider ( Trachemys scripta). Picornaviruses (topiviruses) were detected in 2.2% of the tested animals; ferlaviruses were found in 0.6%; no ranaviruses were detected in any of the animals tested. Mycoplasma spp. were detected significantly more often in Horsfield’s tortoises ( Testudo horsfieldii), leopard tortoises, and Indian star tortoises ( Geochelone elegans) than in other species. Horsfield’s tortoises were also significantly more often positive for TeHV-1. Mycoplasma and TeHV-1 were co-detected in 3.0%, and mycoplasma and TeHV-3 in 2.3%. The TeHV-4–positive tortoise was also positive for mycoplasma. Mycoplasma and picornaviruses were co-detected in 1.2% of the tortoises. A spur-thighed tortoise ( Testudo graeca) was positive for mycoplasma and a ferlavirus. In some cases, >2 pathogens were detected. A significant correlation between mycoplasma and herpesvirus detection was found. Of all tested animals, 47.6% were positive for at least one pathogen, demonstrating the importance of pathogen detection in captive chelonians.

PREVALENCE OF TERRAPENE HERPESVIRUS 1 IN FREE-RANGING EASTERN BOX TURTLES (TERRAPENE CAROLINA CAROLINA) IN TENNESSEE AND ILLINOIS, USA

Diseases affecting the upper respiratory tract, such as herpesviruses, are well described in captive chelonians worldwide, but their importance in free-ranging populations is less well known. To characterize the disease epidemiology of terrapene herpesvirus 1 (TerHV1), 409 free-ranging eastern box turtles ( Terrapene carolina carolina) in Tennessee and Illinois, US were tested for TerHV1 in 2013 and 2014 using TaqMan quantitative PCR. Whole blood and swabs of the oral mucosa were collected from 365 adults (154 females, 195 males, 16 unknown sex) and 44 juveniles. The prevalence of detection was 31.3% (n=128). Turtles were more likely to be positive for TerHV1 in July (50%; n=67) compared to September (38%; n=44) and May (11%; n=17). Turtles sampled in 2014 had a significantly higher prevalence (50%; n=98) than in 2013 (14%; n=30). In a multivariate model, only season, year, and the interaction between season and year were maintained; turtles were most likely to be positive in July (odds ratio: 30.5) and September (odds ratio: 41.8) 2014 compared to May 2013. The prevalence was not statistically different by state of collection, sex, or age class. Packed cell volume (25.5%) and total solids (4.8 mg/dL) in positive turtles were significantly higher than in negative turtles (23.0%; 4.3 mg/dL). Positive turtles had increased eosinophil concentrations, fewer lymphocytes, and fewer monocytes. No clinical sign was associated with detection of herpesvirus. Widespread DNA evidence of TerHV1 infection was detected in eastern box turtles, and knowledge of the epidemiology of this virus may aid in management of free-ranging and captive individuals.

A Genomic Approach to Unravel Host-Pathogen Interaction in Chelonians: The Example of Testudinid Herpesvirus 3

We report the first de novo sequence assembly and analysis of the genome of Testudinid herpesvirus 3 (TeHV3), one of the most pathogenic chelonian herpesviruses. The genome of TeHV3 is at least 150,080 nucleotides long, is arranged in a type D configuration and comprises at least 102 open reading frames extensively co-linear with those of Human herpesvirus 1. Consistently, the phylogenetic analysis positions TeHV3 among the Alphaherpesvirinae, closely associated with Chelonid herpesvirus 5, a Scutavirus. To date, there has been limited genetic characterization of TeHVs and a resolution beyond the genotype was not feasible because of the lack of informative DNA sequences. To exemplify the potential benefits of the novel genomic information provided by this first whole genome analysis, we selected the glycoprotein B (gB) gene, for detailed comparison among different TeHV3 isolates. The rationale for selecting gB is that it encodes for a well-conserved protein among herpesviruses but is coupled with a relevant antigenicity and is consequently prone to accumulate single nucleotide polymorphisms. These features were considered critical for an ideal phylogenetic marker to investigate the potential existence of distinct TeHV3 genogroups and their associated pathology. Fifteen captive tortoises presumptively diagnosed to be infected with TeHVs or carrying compatible lesions on the basis of either the presence of intranuclear inclusions (presumptively infected) and/or diphtheronecrotic stomatitis-glossitis or pneumonia (compatible lesions) were selected for the study. Viral isolation, TeHV identification, phylogenetic analysis and pathological characterization of the associated lesions, were performed. Our results revealed 1) the existence of at least two distinct TeHV3 genogroups apparently associated with different pathologies in tortoises and 2) the first evidence for a putative homologous recombination event having occurred in a chelonian herpesvirus. This novel information is not only fundamental for the genetic characterization of this virus but is also critical to lay the groundwork for an improved understanding of host-pathogen interactions in chelonians and contribute to tortoise conservation.