Ecopathology of ranaviruses infecting amphibians

Leveraging machine learning to uncover multi-pathogen infection dynamics across co-distributed frog families

Background

Amphibians are experiencing substantial declines attributed to emerging pathogens. Efforts to understand what drives patterns of pathogen prevalence and differential responses among species are challenging because numerous factors related to the host, pathogen, and their shared environment can influence infection dynamics. Furthermore, sampling across broad taxonomic and geographic scales to evaluate these factors poses logistical challenges, and interpreting the roles of multiple potentially correlated variables is difficult with traditional statistical approaches. In this study, we leverage frozen tissues stored in natural history collections and machine learning techniques to characterize infection dynamics of three generalist pathogens known to cause mortality in frogs.

Methods

We selected 12 widespread and abundant focal taxa within three ecologically distinct, co-distributed host families (Bufonidae, Hylidae, and Ranidae) and sampled them across the eastern two-thirds of the United States of America. We screened and quantified infection loads via quantitative PCR for three major pathogens: the fungal pathogen Batrachochytrium dendrobatidis (Bd), double-stranded viruses in the lineage Ranavirus (Rv), and the alveolate parasite currently referred to as Amphibian Perkinsea (Pr). We then built balanced random forests (RF) models to predict infection status and intensity based on host taxonomy, age, sex, geography, and environmental variables and to assess relative variable importance across pathogens. Lastly, we used one-way analyses to determine directional relationships and significance of identified predictors.

Results

We found approximately 20% of individuals were infected with at least one pathogen (231 single infections and 25 coinfections). The most prevalent pathogen across all taxonomic groups was Bd (16.9%; 95% CI [14.9-19%]), followed by Rv (4.38%; 95% CI [3.35-5.7%]) and Pr (1.06%; 95% CI [0.618-1.82%]). The highest prevalence and intensity were found in the family Ranidae, which represented 74.3% of all infections, including the majority of Rv infection points, and had significantly higher Bd intensities compared to Bufonidae and Hylidae. Host species and environmental variables related to temperature were key predictors identified in RF models, with differences in importance among pathogens and host families. For Bd and Rv, infected individuals were associated with higher latitudes and cooler, more stable temperatures, while Pr showed trends in the opposite direction. We found no significant differences between sexes, but juvenile frogs had higher Rv prevalence and Bd infection intensity compared to adults. Overall, our study highlights the use of machine learning techniques and a broad sampling strategy for identifying important factors related to infection in multi-host, multi-pathogen systems.

Abiotic and biotic factors jointly influence the contact and environmental transmission of a generalist pathogen

The joint influence of abiotic and biotic factors is important for understanding the transmission of generalist pathogens. Abiotic factors such as temperature can directly influence pathogen persistence in the environment and will also affect biotic factors, such as host community composition and abundance. At intermediate spatial scales, the effects of temperature, community composition, and host abundance are expected to contribute to generalist pathogen transmission. We use a simple transmission model to explain and predict how host community composition, host abundance, and environmental pathogen persistence times can independently and jointly influence transmission. Our transmission model clarifies how abiotic and biotic factors can synergistically support the transmission of a pathogen. The empirical data show that high community competence, high abundance, and low temperatures correlate with high levels of transmission of ranavirus in larval amphibian communities. Discrete wetlands inhabited by larval amphibians in the presence of ranavirus provide a compelling case study comprising distinct host communities at a spatial scale anticipated to demonstrate abiotic and biotic influence on transmission. We use these host communities to observe phenomena demonstrated in our theoretical model. These findings emphasize the importance of considering both abiotic and biotic factors, and concomitant direct and indirect mechanisms, in the study of pathogen transmission and should extend to other generalist pathogens with the capacity for environmental transmission.

Environmental DNA concentrations vary greatly across productive and degradative conditions, with implications for the precision of population estimates

Population size is an important metric to inform the conservation and management of species. For aquatic species, environmental DNA (eDNA) concentration has been suggested for non-invasively estimating population size. However, many biotic and abiotic factors simultaneously influence the production and degradation of eDNA which can alter the relationship between population size and eDNA concentration. We investigated the influence of temperature, salinity, and ranavirus infection on eDNA concentrations using tadpole mesocosms. Using linear regression models, we tested the influence of each experimental treatment on eDNA concentrations at three time points before and during epidemics. Prior to infection, elevated temperatures lowered eDNA concentrations, indicating that degradation was the driving force influencing eDNA concentrations. During early epidemics, no treatments strongly influenced eDNA concentrations and in late epidemics, productive forces dominated as ranavirus intensity and dead organisms increased eDNA concentrations. Finally, population size was only an important predictor of eDNA concentration in late epidemics and we observed high levels of variation between samples of replicate mesocosms. We demonstrate the complexities of several interacting factors influencing productive and degradative forces, variation in influences on eDNA concentration over short time spans, and examine the limitations of estimating population sizes from eDNA with precision in semi-natural conditions.

Host Jump of an Exotic Fish Rhabdovirus into a New Class of Animals Poses a Disease Threat to Amphibians

Spring viremia of carp virus (SVCV) is a rhabdovirus that primarily infects cyprinid finfishes and causes a disease notifiable to the World Organization for Animal Health. Amphibians, which are sympatric with cyprinids in freshwater ecosystems, are considered non-permissive hosts of rhabdoviruses. The potential host range expansion of SVCV in an atypical host species was evaluated by testing the susceptibility of amphibians native to the Pacific Northwest. Larval long-toed salamanders Ambystoma macrodactylum and Pacific tree frog Pseudacris regilla tadpoles were exposed to SVCV strains from genotypes Ia, Ib, Ic, or Id by either intraperitoneal injection, immersion, or cohabitation with virus-infected koi Cyprinus rubrofuscus. Cumulative mortality was 100% for salamanders injected with SVCV, 98-100% for tadpoles exposed to virus via immersion, and 0-100% for tadpoles cohabited with SVCV-infected koi. Many of the animals that died exhibited clinical signs of disease and SVCV RNA was found by in situ hybridization in tissue sections of immersion-exposed tadpoles, particularly in the cells of the gastrointestinal tract and liver. SVCV was also detected by plaque assay and RT-qPCR testing in both amphibian species regardless of the virus exposure method, and viable virus was detected up to 28 days after initial exposure. Recovery of infectious virus from naïve tadpoles cohabited with SVCV-infected koi further demonstrated that SVCV transmission can occur between classes of ectothermic vertebrates. Collectively, these results indicated that SVCV, a fish rhabdovirus, can be transmitted to and cause lethal disease in two amphibian species. Therefore, members of all five of the major vertebrate groups (mammals, birds, reptiles, fish, and amphibians) appear to be vulnerable to rhabdovirus infections. Future research studying potential spillover and spillback infections of aquatic rhabdoviruses between foreign and domestic amphibian and fish species will provide insights into the stressors driving novel interclass virus transmission events.

High prevalence and concomitant infection of Ranavirus and Eustrongylides sp. in the invasive American Bullfrog in Brazil

American Bullfrogs, Aquarana catesbeiana, are invasive anuran species distributed worldwide. One of the adverse impacts that this species causes in native communities is as a reservoir host for pathogens and parasites. Here, we report the coinfection of two pathogenic organisms in A. catesbeiana: Ranavirus and the nematode Eustrongylides. Bullfrogs were collected in the wild in a pond close to the urban area of São Paulo, Brazil. The prevalence of both pathogens was high: 77% were infected with ranavirus with a mean viral load of 1010.3 viral copies, and 100% of the bullfrogs were infected by Eustrongylides sp. with a mean intensity of infection of 13.4 specimens per host. Four host specimens (31%) presented pathological signs that seemed to be related to the Eustrongylides sp. infection, such as internal organs adhered to each other due to high intensity and large size of the nematodes, ulcers, and raw flesh wounds caused by the nematode. The pathogenic and concomitant infections have potential zoonotic implications and raise concerns about human infection risks for Eustrongylides infection. Moreover, such infections may represent an additional level of threat to native communities through the potential shifts in patterns of parasite and pathogen transmission. Future research involving the native anuran community is essential to ascertain whether invasive bullfrogs are attenuating or exacerbating diseases such as ranavirosis and eustrongylidiosis.

First Report of Endemic Frog Virus 3 (FV3)-like Ranaviruses in the Korean Clawed Salamander (Onychodactylus koreanus) in Asia

Frog virus 3 (FV3) in the genus Ranavirus of the family Iridoviridae causes mass mortality in both anurans and urodeles worldwide; however, the phylogenetic origin of FV3-like ranaviruses is not well established. In Asia, three FV3-like ranaviruses have been reported in farmed populations of amphibians and reptiles. Here, we report the first case of endemic FV3-like ranavirus infections in the Korean clawed salamander Onychodactylus koreanus, caught in wild mountain streams in the Republic of Korea (ROK), through whole-genome sequencing and phylogenetic analysis. Two isolated FV3-like ranaviruses (Onychodactylus koreanus ranavirus, OKRV1 and 2) showed high similarity with the Rana grylio virus (RGV, 91.5%) and Rana nigromaculata ranavirus (RNRV, 92.2%) but relatively low similarity with the soft-shelled turtle iridovirus (STIV, 84.2%) in open reading frame (ORF) comparisons. OKRV1 and 2 formed a monophyletic clade with previously known Asian FV3-like ranaviruses, a sister group of the New World FV3-like ranavirus clade. Our results suggest that OKRV1 and 2 are FV3-like ranaviruses endemic to the ROK, and RGV and RNRV might also be endemic strains in China, unlike previous speculation. Our data have great implications for the study of the phylogeny and spreading routes of FV3-like ranaviruses and suggest the need for additional detection and analysis of FV3-like ranaviruses in wild populations in Asian countries.

Ranavirus and helminth parasite co-infection in invasive American bullfrogs in the Atlantic forest, Brazil

Emerging infectious diseases threaten amphibian species across the globe. In Brazil, the American bullfrog (Aquarana catesbeiana) is a highly invasive species that can potentially transmit parasites and pathogens to native amphibians. This is the first assessment of co-infection of Ranavirus and helminth macroparasites in invasive populations of bullfrogs in South America. We collected, measured, and euthanized 65 specimens of A. catesbeiana sampled from 9 sites across three states of Brazil in the Atlantic Forest biome. We collected and identified helminth macroparasites and sampled host liver tissue to test for the presence and load of Ranavirus with quantitative PCR. We documented patterns of prevalence, parasite load, and co-infection with generalized linear mixed models, generalized logistic regressions, and randomization tests. Most individual bullfrogs did not exhibit clinical signs of infection, but the overall Ranavirus prevalence was 27% (95% confidence interval, [CI 17-38]). Bullfrogs were infected with helminth macroparasites from 5 taxa. Co-infection of helminth macroparasites and Ranavirus was also common (21% CI [12-31]). Bullfrog size was positively correlated with total macroparasite abundance and richness, and the best-fitting model included a significant interaction between bullfrog size and Ranavirus infection status. We observed a negative correlation between Ranavirus viral load and nematode abundance (slope = -0.22, P = 0.03). Invasive bullfrogs (A. catesbeiana) in Brazil were frequently infected with both Ranavirus and helminth macroparasites, so adult bullfrogs could serve as reservoir hosts for both pathogens and parasites. However, many macroparasites collected were encysted and not developing. Coinfection patterns suggest a potential interaction between Ranavirus and macroparasites because helminth abundance increased with bullfrog size but was lower in Ranavirus infected individuals. Future studies of bullfrogs in the Atlantic Forest should investigate their potential role in pathogen and parasite transmission to native anurans.

Unexpected thermal stability of two enveloped megaviruses, Emiliania huxleyi virus and African swine fever virus, as measured by viability PCR

BACKGROUND

The particle structure of Emiliania huxleyi virus (EhV), an algal infecting member of nucleocytoplasmic large DNA viruses (NCLDVs), contains an outer lipid membrane envelope similar to that found in animal viruses such as African swine fever virus (ASFV). Despite both being enveloped NCLDVs, EhV and ASFV are known for their stability outside their host environment.

METHOD

Here we report for the first time, the application of a viability qPCR (V-qPCR) method to describe the unprecedented and similar virion thermal stability of both EhV and ASFV. This result contradicts the cell culture-based assay method that suggests that virus "infectivity" is lost in a matter of seconds (for EhV) and minutes (for ASFV) at temperature greater than 50 °C. Confocal microscopy and analytical flow cytometry methods was used to validate the V-qPCR data for EhV.

RESULTS

We observed that both EhV and ASFV particles has unprecedented thermal tolerances. These two NCLDVs are exceptions to the rule that having an enveloped virion anatomy is a predicted weakness, as is often observed in enveloped RNA viruses (i.e., the viruses causing Porcine Reproductive and Respiratory Syndrome (PRRS), COVID-19, Ebola, or seasonal influenza). Using the V-qPCR method, we confirm that no PRRSV particles were detectable after 20 min of exposure to temperatures up to 100 °C. We also show that the EhV particles that remain after 50 °C 20 min exposure was in fact still infectious only after the three blind passages in bioassay experiments.

CONCLUSIONS

This study raises the possibility that ASFV is not always eliminated or contained after applying time and temperature inactivation treatments in current decontamination or biosecurity protocols. This observation has practical implications for industries involved in animal health and food security. Finally, we propose that EhV could be used as a surrogate for ASFV under certain circumstances.

Ranavirus (Frog Virus 3) Infection in Free-Living Three-Toed Box Turtles (Terrapene mexicana triunguis) in Missouri, USA

Frog virus 3 (FV3) and related ranaviruses are emerging infectious disease threats to ectothermic vertebrate species globally. Although the impact of these viruses on amphibian health is relatively well studied, less is understood about their effects on reptile health. We report two cases of FV3 infection, 11 mo apart, in three-toed box turtles (Terrapene mexicana triunguis) from a wildlife rehabilitation center. Case 1 had upper respiratory signs upon intake but had no clinical signs at the time of euthanasia 1 mo later. Case 2 presented for vehicular trauma, had ulcerative pharyngitis and glossitis, and died overnight. In case 1, we detected FV3 nucleic acid with qPCR in oral swabs, kidney, liver, spleen, and tongue. In case 2, we detected FV3 in an oral swab, an oral plaque, heart, kidney, lung, liver, spleen, and tongue. We also detected FV3 nucleic acid with in situ hybridization for case 2. For both cases, FV3 was isolated in cell culture and identified with DNA sequencing. Histopathologic examination of postmortem tissue from case 1 was unremarkable, whereas acute hemorrhagic pneumonia and splenic necrosis were noted in case 2. The difference in clinical signs between the two cases may have been due to differences in the temporal course of FV3 disease at the time of necropsy. Failure to detect this infection previously in Missouri reptiles may be due to lack of surveillance, although cases may also represent a novel spillover to box turtles in Missouri. Our findings reiterate previous suggestions that the range of FV3 infection may be greater than previously documented and that infection may occur in host species yet to be tested.

Critical review of the phytohemagglutinin assay for assessing amphibian immunity

Infectious diseases are a major driver of the global amphibian decline. In addition, many factors, including genetics, stress, pollution, and climate change can influence the response to pathogens. Therefore, it is important to be able to evaluate amphibian immunity in the laboratory and in the field. The phytohemagglutinin (PHA) assay is an inexpensive and relatively non-invasive tool that has been used extensively to assess immunocompetence, especially in birds, and more recently in amphibians. However, there is substantial variation in experimental methodology among amphibian PHA studies in terms of species and life stages, PHA doses and injection sites, and use of experimental controls. Here, we compile and compare all known PHA studies in amphibians to identify knowledge gaps and develop best practices for future work. We found that research has only been conducted on a limited number of species, which may not reflect the diversity of amphibians. There is also a lack of validation studies in most species, so that doses and timing of PHA injection and subsequent swelling measurements may not effectively evaluate immunocompetence. Based on these and other findings, we put forward a set of recommendations to make future PHA studies more consistent and improve the ability to utilize this assay in wild populations, where immune surveillance is greatly needed.

Widespread amphibian Perkinsea infections associated with Ranidae hosts, cooler months and Ranavirus co-infection

Amphibians suffer from large-scale population declines globally, and emerging infectious diseases contribute heavily to these declines. Amphibian Perkinsea (Pr) is a worldwide anuran pathogen associated with mass mortality events, yet little is known about its epidemiological patterns, especially in comparison to the body of literature on amphibian chytridiomycosis and ranavirosis. Here, we establish Pr infection patterns in natural anuran populations and identify important covariates including climate, host attributes and co-infection with Ranavirus (Rv). We used quantitative (q)PCR to determine the presence and intensity of Pr and Rv across 1234 individuals sampled throughout central Florida in 2017-2019. We then implemented random forest ensemble learning models to predict infection with both pathogens based on physiological and environmental characteristics. Perkinsea infected 32% of all sampled anurans, and Pr prevalence was significantly elevated in Ranidae frogs, cooler months, metamorphosed individuals and frogs co-infected with Rv, while Pr intensity was significantly higher in ranid frogs and individuals collected dead. Ranavirus prevalence was 17% overall and was significantly higher in Ranidae frogs, metamorphosed individuals, locations with higher average temperatures, and individuals co-infected with Pr. Perkinsea prevalence was significantly higher than Rv prevalence across months, regions, life stages and species. Among locations, Pr prevalence was negatively associated with crayfish prevalence and positively associated with relative abundance of microhylids, but Rv prevalence did not associate with any tested co-variates. Co-infections were significantly more common than single infections for both pathogens, and we propose that Pr infections may propel Rv infections because seasonal Rv infection peaks followed Pr infection peaks and random forest models found Pr intensity was a leading factor explaining Rv infections. Our study elucidates epidemiological patterns of Pr in Florida and suggests that Pr may be under-recognized as a cause of anuran declines, especially in the context of pathogen co-infection.

Diet- and salinity-induced modifications of the gut microbiota are associated with differential physiological responses to ranavirus infection in Rana sylvatica

Greater knowledge of how host-microbiome interactions vary with anthropogenic environmental change and influence pathogenic infections is needed to better understand stress-mediated disease outcomes. We investigated how increasing salinization in freshwaters (e.g. due to road de-icing salt runoff) and associated increases in growth of nutritional algae influenced gut bacterial assembly, host physiology and responses to ranavirus exposure in larval wood frogs (Rana sylvatica). Elevating salinity and supplementing a basic larval diet with algae increased larval growth and also increased ranavirus loads. However, larvae given algae did not exhibit elevated kidney corticosterone levels, accelerated development or weight loss post-infection, whereas larvae fed a basic diet did. Thus, algal supplementation reversed a potentially maladaptive stress response to infection observed in prior studies in this system. Algae supplementation also reduced gut bacterial diversity. Notably, we observed higher relative abundances of Firmicutes in treatments with algae-a pattern consistent with increased growth and fat deposition in mammals-that may contribute to the diminished stress responses to infection via regulation of host metabolism and endocrine function. Our study informs mechanistic hypotheses about the role of microbiome mediation of host responses to infection that can be tested in future experiments in this host-pathogen system. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.

Amphibian Dermatology

Amphibians are susceptible to a multitude of skin disorders, many of which can appear grossly similar. The most common clinical presentations include hyperemia, discoloration, dermal mass, ulceration, and necrosis. Many amphibian skin diseases are related to captive husbandry. The diagnostic process starts with environmental evaluations, a full history, physical examination and sampling for direct observation, histology, polymerase chain reaction testing, and bacterial and fungal culture. This review emphasizes the main conditions encountered in amphibian dermatology.

Renal protein reabsorption impairment related to a myxosporean infection in the grass frog (Rana temporaria L.)

A morphophysiological study of tubular reabsorption and mechanisms of protein endocytosis in the kidney of frogs (Rana temporaria L.) during parasitic infection was carried out. Pseudoplasmodia and spores of myxosporidia, beforehand assigned to the genus Sphaerospora, were detected in Bowman's capsules and in the lumen of individual renal tubules by light and electron microscopy. Remarkable morphological alteration and any signs of pathology in kidney tissue related to this myxosporean infection have not been noted. At the same time, significant changes in protein reabsorption and distribution of molecular markers of endocytosis in the proximal tubule (PT) cells in infected animals were detected by immunofluorescence confocal microscopy. In lysozyme injection experiments, the endocytosed protein and megalin expression in the infected PTs were not revealed. Tubular expression of cubilin and clathrin decreased, but endosomal recycling marker Rab11 increased or remained unchanged. Thus, myxosporean infection resulted in the alterations in lysozyme uptake and expression of the main molecular determinants of endocytosis. The inhibition of receptor-mediated clathrin-dependent protein endocytosis in amphibian kidneys due to myxosporidiosis was shown for the first time. Established impairment of the endocytic process is a clear marker of tubular cell dysfunction that can be used to assess the functioning of amphibian kidneys during adaptation to adverse environmental factors.

Molecular diversity and functional implication of amphibian interferon complex: Remarking immune adaptation in vertebrate evolution

Cross-species comparison of vertebrate genomes has unraveled previously unknown complexities of interferon (IFN) systems in amphibian species. Recent genomic curation revealed that amphibian species have evolved expanded repertoires of four types of intron-containing IFN genes akin to those seen in jawed fish, intronless type I IFNs and intron-containing type III IFNs akin to those seen in amniotes, as well as uniquely intronless type III IFNs. This appears to be the case with at least ten analyzed amphibian species; with distinct species encoding diverse repertoires of these respective IFN gene subsets. Amphibians represent a key stage in vertebrate evolution, and in this context offer a unique perspective into the divergent and converged pathways leading to the emergence of distinct IFN families and groups. Recent studies have begun to unravel the roles of amphibian IFNs during these animals' immune responses in general and during their antiviral responses, in particular. However, the pleiotropic potentials of these highly expanded amphibian IFN repertoires warrant further studies. Based on recent reports and our omics analyses using Xenopus models, we posit that amphibian IFN complex may have evolved novel functions, as indicated by their extensive molecular diversity. Here, we provide an overview and an update of the present understanding of the amphibian IFN complex in the context of the evolution of vertebrate immune systems. A greater understanding of the amphibian IFN complex will grant new perspectives on the evolution of vertebrate immunity and may yield new measures by which to counteract the global amphibian declines.

Numerous uncertainties in the multifaceted global trade in frogs’ legs with the EU as the major consumer

The commercial trade in frogs and their body parts is global, dynamic and occurs in extremely large volumes (in the thousands of tonnes/yr or billions of frogs/yr). The European Union (EU) remains the single largest importer of frogs’ legs, with most frogs still caught from the wild. Amongst the many drivers of species extinction or population decline (e.g. due to habitat loss, climate change, disease etc.), overexploitation is becoming increasingly more prominent. Due to global declines and extinctions, new attention is being focused on these markets, in part to try to ensure sustainability. While the trade is plagued by daunting realities of data deficiency and uncertainty and the conflicts of commercial interests associated with these data, it is clear is that EU countries are most responsible for the largest portion of the international trade in frogs’ legs of wild species. Over decades of exploitation, the EU imports have contributed to a decline in wild frog populations in an increasing number of supplying countries, such as India and Bangladesh, as well as Indonesia, Turkey and Albania more recently. However, there have been no concerted attempts by the EU and present export countries to ensure sustainability of this trade. Further work is needed to validate species identities, secure data on wild frog populations, establish reasonable monitored harvest/export quotas and disease surveillance and ensure data integrity, quality and security standards for frog farms. Herein, we call upon those countries and their representative governments to assume responsibility for the sustainability of the trade. The EU should take immediate action to channel all imports through a single centralised database and list sensitive species in the Annexes of the EU Wildlife Trade Regulation. Further, listing in CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora) can enforce international trade restrictions. More joint efforts are needed to improve regional monitoring schemes before the commercial trade causes irreversible extinctions of populations and species of frogs.

Experimental evidence that host species composition alters host-pathogen dynamics in a ranavirus-amphibian assemblage

Losses in biodiversity can alter disease risk through changes in host species composition. Host species vary in pathogen susceptibility and competence, yet how changes in diversity alter host-pathogen dynamics remains unclear in many systems, particularly with respect to generalist pathogens. Amphibians are experiencing worldwide population declines linked to generalist pathogens, such as ranavirus, and thus represent an ideal group to investigate how host species composition affects disease risk. We conducted experiments in which amphibian larvae of three native species (Pacific tree frogs, Pseudacris regilla; Cascades frogs, Rana cascadae; and Western toads, Anaxyrus boreas) were exposed to ranavirus individually (in the laboratory) or as assemblages (in outdoor mesocosms). In a laboratory experiment, we observed low survival and high viral loads in P. regilla compared to the other species, suggesting that this species was highly susceptible to the pathogen. In the mesocosm experiment, we observed 41% A. boreas mortality when alone and 98% mortality when maintained with P. regilla and R. cascadae. Our results suggest that the presence of highly susceptible species can alter disease dynamics across multiple species, potentially increasing infection risk and mortality in co-occurring species.

Is Xenopus laevis introduction linked with Ranavirus incursion, persistence and spread in Chile?

Ranaviruses have been associated with amphibian, fish and reptile mortality events worldwide and with amphibian population declines in parts of Europe. Xenopus laevis is a widespread invasive amphibian species in Chile. Recently, Frog virus 3 (FV3), the type species of the Ranavirus genus, was detected in two wild populations of this frog near Santiago in Chile, however, the extent of ranavirus infection in this country remains unknown. To obtain more information about the origin of ranavirus in Chile, its distribution, species affected, and the role of invasive amphibians and freshwater fish in the epidemiology of ranavirus, a surveillance study comprising wild and farmed amphibians and wild fish over a large latitudinal gradient (2,500 km) was carried out in 2015-2017. In total, 1,752 amphibians and 496 fish were tested using a ranavirus-specific qPCR assay, and positive samples were analyzed for virus characterization through whole genome sequencing of viral DNA obtained from infected tissue. Ranavirus was detected at low viral loads in nine of 1,011 X. laevis from four populations in central Chile. No other amphibian or fish species tested were positive for ranavirus, suggesting ranavirus is not threatening native Chilean species yet. Phylogenetic analysis of partial ranavirus sequences showed 100% similarity with FV3. Our results show a restricted range of ranavirus infection in central Chile, coinciding with X. laevis presence, and suggest that FV3 may have entered the country through infected X. laevis, which appears to act as a competent reservoir host, and may contribute to the spread the virus locally as it invades new areas, and globally through the pet trade.

Over 25 Years of Partnering to Conserve Chiricahua Leopard Frogs (Rana chiricahuensis) in Arizona, Combining Ex Situ and In Situ Strategies

The Phoenix Zoo has partnered with US Fish and Wildlife Service, Arizona Game and Fish Department, US Forest Service, and other organizations for more than 25 years to help recover Chiricahua leopard frogs (Rana [=Lithobates] chiricahuensis) in Arizona, USA. This federally threatened species faces declines due to habitat loss and degradation, long-term drought, disease, and invasive species. Over 26,000 larvae, froglets, and adults, as well as 26 egg masses produced by adults held at the Phoenix Zoo have been released to the wild, augmenting and/or re-establishing wild populations. Chiricahua leopard frog-occupied sites in Arizona have increased from 38 in 2007, when the species’ recovery plan was published, to a high of 155 in the last five years, as a result of ex situ and in situ conservation efforts. As one of the longest-running programs of its kind in the United States, communication among partners has been key to sustaining it. Recovery strategies and complex decisions are made as a team and we have worked through numerous management challenges together. Though Chiricahua leopard frogs still face significant threats and a long road to recovery, this program serves as a strong example of the positive effects of conservation partnerships for native wildlife.

Ranavirus infection-induced avoidance behaviour in wood frog juveniles: do amphibians socially distance?

Hosts may limit exposure to pathogens through changes in behaviour, such as avoiding infected individuals or contaminated areas. Here, we tested for a behavioural response to ranavirus infection in juvenile wood frogs (Rana sylvatica) because the majority of dispersal between populations occurs during this life stage. We hypothesized that if infections are transmissible and detectable at this life stage, then susceptibles would display avoidance behaviours when introduced to an infected conspecific. Despite no apparent signs of infection, we observed a greater distance between susceptible-infected pairs, compared to pairs of either two infected or two susceptible animals. Further, distances between susceptible-infected pairs were positively related to the infection intensity of the focal exposed frog, suggesting the cue to avoid infected conspecifics may become more detectable with more intense infections. Although we did not quantify whether the transmission was affected by their distancing, our findings suggest that juvenile frogs have the potential to reduce terrestrial transmission of ranaviruses through avoidance behaviours.

Sustained Ranavirus Outbreak Causes Mass Mortality and Morbidity of Imperiled Amphibians in Florida

A persistent 2-month long outbreak of Ranavirus in a natural community of amphibians contributed to a mass die-off of gopher frog tadpoles (Lithobates capito) and severe disease in striped newts (Notophthalmus perstriatus) in Florida. Ongoing mortality in L. capito and disease signs in N. perstriatus continued for 5 weeks after the first observation. Hemorrhagic disease and necrosis were diagnosed from pathological examination of L. capito tadpoles. We confirmed detection of a frog virus 3 (FV3)-like Ranavirus via quantitative PCR in all species. Our findings highlight the susceptibility of these species to Rv and the need for long-term disease surveillance during epizootics.

Prior induction of cellular antiviral pathways limits frog virus 3 replication in two permissive Xenopus laevis skin epithelial-like cell lines

Frog virus 3 (FV3) causes mortality in a range of amphibian species. Despite the importance of the skin epithelium as a first line of defence against FV3, the interaction between amphibian skin epithelial cells and FV3 remains largely uncharacterized. Here, we used newly established Xenopus laevis skin epithelial-like cell lines, Xela DS2 and Xela VS2, to study the susceptibility and permissiveness of frog skin epithelial cells to FV3, and the innate immune antiviral and proinflammatory gene regulatory responses of these cells to FV3. Both cell lines are susceptible and permissive to FV3, yet do not exhibit appreciable transcript levels of scavenger receptors thought to be used by FV3 for cellular entry. Xela DS2 and Xela VS2 upregulate antiviral and proinflammatory cytokine transcripts in response to poly(I:C) but not to FV3 or UV-inactivated FV3. Poly(I:C) pretreatment limits FV3 replication and FV3-induced cytopathic effects in both cell lines. Thus, Xela DS2 and Xela VS2 can support FV3 replication, represent in vitro systems to investigate antiviral responses of frog skin epithelial cells, and can serve as novel tools for screening compounds that initiate effective antiviral programs to limit FV3 replication.

Molecular Confirmation of Ranavirus Infection in Amphibians From Chad, Africa

Ranaviruses are DNA viruses (Family Iridoviridae; Subfamily Alphairidovirinae) and ranaviral disease is considered an emerging infectious disease of ectothermic vertebrates. Ranavirus infection can have varying pathological effects on infected amphibians, reptiles, and fish, most notably causing significant mortality events and population declines. Despite having a broad global range with reports from six continents, only a single incidental finding in Xenopus longipes from mainland Africa (Cameroon) is known and lacks molecular confirmation. Thus, there is a considerable knowledge gap concerning ranaviruses in Africa. We opportunistically obtained tissue samples from 160 amphibians representing five genera (Hoplobatrachus, Hylarana, Ptychadena, Pyxicephalus, and Xenopus) and two turtles (Pelomedusa sp.) from Chad, Africa. Samples were tested for ranavirus infection using a conventional PCR assay targeting the major capsid protein (MCP). A total of 25/160 (16%) frogs tested positive including 15/87 (17%) Hoplobatrachus occipitalis, 10/58 (17%) Ptychadena spp., 0/3 Pyxicephalus spp., 0/9 Xenopus spp., and 0/3 Hylarana spp. One of two turtles tested positive. Partial MCP gene sequences indicated all samples were >98% similar to several frog virus 3 (FV3)-like sequences. Additional gene targets (DNA polymerase [DNApol], ribonucleotide reductase alpha [RNR- α], ribonucleotide reductase beta subunit [RNR- β]) were sequenced to provide further detailed classification of the virus. Sequences of individual gene targets indicate that the ranavirus detected in frogs in Chad is most similar to tiger frog virus (TFV), a FV3-like virus previously isolated from diseased amphibians cultured in China and Thailand. Full genome sequencing of one sample indicates that the Chad frog virus (CFV) is a well-supported sister group to the TFVs previously determined from Asia. This work represents the first molecular confirmation of ranaviruses from Africa and is a first step in comparing ranavirus phylogeography on a local and global scale.

Expanded collectin family in bullfrog (Rana catesbeiana): Identification and characterization of plasma collectins

BLAST searches against databases for the bullfrog (Rana catesbeiana), using the collectin sequence previously identified in tadpoles, revealed the presence of at least 20 members of the collectin gene family. Phylogenetic analysis demonstrated that the bullfrog possesses expanded gene subfamilies encoding mannose-binding lectin (MBL) and pulmonary surfactant-associated protein D (PSAPD). Two collectins, of 20 kDa (PSAPD1) and 25 kDa (PSAPD6), were purified as a mixture from adult bullfrog plasma using affinity chromatography. These collectins were present as an oligomer of ~400 kDa in their native state, and showed Ca²⁺-dependent carbohydrate binding with different sugar preferences. Affinity-purified collectins showed weak E. coli agglutination and bactericidal activities, compared with those of plasma. Although both PSAPD1 and PSAPD6 genes were predominantly expressed in the liver, PSAPD1 transcripts were abundant in adults whereas PSAPD6 transcripts were abundant in tadpoles. The findings indicate that two gene subfamilies in the collectin family have diverged structurally, functionally and transcriptionally in the bullfrog. Rapid expansion of the collectin family in bullfrogs may reflect the onset of sub-functionalization of the prototype MBL gene towards tetrapod MBL and PSAPDs, and may be one means of natural adaptation in the innate immune system to various pathogens in both aquatic and terrestrial environments.

Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction with Host Interferon Response in Frog Virus 3-Infected Frog Tissues

Ranaviruses (Iridoviridae), including Frog Virus 3 (FV3), are large dsDNA viruses that cause devastating infections globally in amphibians, fish, and reptiles, and contribute to catastrophic amphibian declines. FV3’s large genome (~105 kb) contains at least 98 putative open reading frames (ORFs) as annotated in its reference genome. Previous studies have classified these coding genes into temporal classes as immediate early, delayed early, and late viral transcripts based on their sequential expression during FV3 infection. To establish a high-throughput characterization of ranaviral gene expression at the genome scale, we performed a whole transcriptomic analysis (RNA-Seq) using total RNA samples containing both viral and cellular transcripts from FV3-infected Xenopus laevis adult tissues using two FV3 strains, a wild type (FV3-WT) and an ORF64R-deleted recombinant (FV3-∆64R). In samples from the infected intestine, liver, spleen, lung, and especially kidney, an FV3-targeted transcriptomic analysis mapped reads spanning the full-genome coverage at ~10× depth on both positive and negative strands. By contrast, reads were only mapped to partial genomic regions in samples from the infected thymus, skin, and muscle. Extensive analyses validated the expression of almost all of the 98 annotated ORFs and profiled their differential expression in a tissue-, virus-, and temporal class-dependent manner. Further studies identified several putative ORFs that encode hypothetical proteins containing viral mimicking conserved domains found in host interferon (IFN) regulatory factors (IRFs) and IFN receptors. This study provides the first comprehensive genome-wide viral transcriptome profiling during infection and across multiple amphibian host tissues that will serve as an instrumental reference. Our findings imply that Ranaviruses like FV3 have acquired previously unknown molecular mimics, interfering with host IFN signaling during evolution.

Thermal Performance Curves of Multiple Isolates of Batrachochytrium dendrobatidis, a Lethal Pathogen of Amphibians

Emerging infectious disease is a key factor in the loss of amphibian diversity. In particular, the disease chytridiomycosis has caused severe declines around the world. The lethal fungal pathogen that causes chytridiomycosis, Batrachochytrium dendrobatidis (Bd), has affected amphibians in many different environments. One primary question for researchers grappling with disease-induced losses of amphibian biodiversity is what abiotic factors drive Bd pathogenicity in different environments. To study environmental influences on Bd pathogenicity, we quantified responses of Bd phenotypic traits (e.g., viability, zoospore densities, growth rates, and carrying capacities) over a range of environmental temperatures to generate thermal performance curves. We selected multiple Bd isolates that belong to a single genetic lineage but that were collected across a latitudinal gradient. For the population viability, we found that the isolates had similar thermal optima at 21°C, but there was considerable variation among the isolates in maximum viability at that temperature. Additionally, we found the densities of infectious zoospores varied among isolates across all temperatures. Our results suggest that temperatures across geographic point of origin (latitude) may explain some of the variation in Bd viability through vertical shifts in maximal performance. However, the same pattern was not evident for other reproductive parameters (zoospore densities, growth rates, fecundity), underscoring the importance of measuring multiple traits to understand variation in pathogen responses to environmental conditions. We suggest that variation among Bd genetic variants due to environmental factors may be an important determinant of disease dynamics for amphibians across a range of diverse environments.

Targeted Transcriptomics of Frog Virus 3 in Infected Frog Tissues Reveal Non-Coding Regulatory Elements and microRNAs in the Ranaviral Genome and Their Potential Interaction with Host Immune Response

Background

Frog Virus 3 (FV3) is a large dsDNA virus belonging to Ranaviruses of family Iridoviridae. Ranaviruses infect cold-blood vertebrates including amphibians, fish and reptiles, and contribute to catastrophic amphibian declines. FV3 has a genome at ~105 kb that contains nearly 100 coding genes and 50 intergenic regions as annotated in its reference genome. Previous studies have mainly focused on coding genes and rarely addressed potential non-coding regulatory role of intergenic regions.

Results

Using a whole transcriptomic analysis of total RNA samples containing both the viral and cellular transcripts from FV3-infected frog tissues, we detected virus-specific reads mapping in non-coding intergenic regions, in addition to reads from coding genes. Further analyses identified multiple cis-regulatory elements (CREs) in intergenic regions neighboring highly transcribed coding genes. These CREs include not only a virus TATA-Box present in FV3 core promoters as in eukaryotic genes, but also viral mimics of CREs interacting with several transcription factors including CEBPs, CREBs, IRFs, NF-κB, and STATs, which are critical for regulation of cellular immunity and cytokine responses. Our study suggests that intergenic regions immediately upstream of highly expressed FV3 genes have evolved to bind IRFs, NF-κB, and STATs more efficiently. Moreover, we found an enrichment of putative microRNA (miRNA) sequences in more than five intergenic regions of the FV3 genome. Our sequence analysis indicates that a fraction of these viral miRNAs is targeting the 3'-UTR regions of Xenopus genes involved in interferon (IFN)-dependent responses, including particularly those encoding IFN receptor subunits and IFN-regulatory factors (IRFs).

Conclusions

Using the FV3 model, this study provides a first genome-wide analysis of non-coding regulatory mechanisms adopted by ranaviruses to epigenetically regulate both viral and host gene expressions, which have co-evolved to interact especially with the host IFN response.

GEOGRAPHIC AND INDIVIDUAL DETERMINANTS OF IMPORTANT AMPHIBIAN PATHOGENS IN HELLBENDERS (CRYPTOBRANCHUS ALLEGANIENSIS) IN TENNESSEE AND ARKANSAS, USA

Wildlife diseases are a major threat for species conservation and there is a growing need to implement disease surveillance programs to protect species of concern. Globally, amphibian populations have suffered considerable losses from disease, particularly from chytrid fungi (Batrachochytrium dendrobatidis [Bd] and Batrachochytrium salamandrivorans [Bsal]) and ranavirus. Hellbenders (Cryptobranchus alleganiensis) are large riverine salamanders historically found throughout several watersheds of the eastern and midwestern US. Populations of both subspecies (Ozark hellbender, Cryptobranchus alleganiensis bishopi; eastern hellbender, Cryptobranchus alleganiensis alleganiensis) have experienced precipitous declines over at least the past five decades, and emerging pathogens are hypothesized to play a role. We surveyed Ozark hellbender populations in Arkansas (AR) and eastern hellbender populations in Middle Tennessee (MTN) and East Tennessee (ETN) for both chytrid fungi and ranavirus from swabs and tail tissue, respectively, from 2011 to 2017. Overall, we detected Bd on hellbenders from nine out of 15 rivers, with total prevalence of 26.7% (54/ 202) that varied regionally (AR: 33%, 28/86; MTN: 11%, 4/36; ETN: 28%, 22/80). Ranavirus prevalence (9.0%, 18/200) was comparatively lower than Bd, with less regional variation in prevalence (AR: 6%, 5/ 85; MTN: 11%, 4/36; ETN: 10%, 8/79). We did not detect Bsal in any hellbender populations. We detected a significant negative correlation between body condition score and probability of ranavirus infection (β=-0.13, SE=0.06, 95% confidence interval: -0.24, -0.02). Evaluation of infection load of positive individuals revealed different trends than prevalence alone for both ranavirus and Bd, with MTN having a significantly greater average ranaviral load than both other regions. We documented a variety of lesions that likely have multiple etiologies on hellbenders located within all geographic regions. Our data represent a multiyear pathogen dataset across several regions of C. alleganiensis, and we emphasize the need for continued pathogen surveillance.

The application of community ecology theory to co-infections in wildlife hosts

Priority effect theory, a foundational concept from community ecology, states that the order and timing of species arrival during species assembly can affect species composition. Although this theory has been applied to co-infecting parasite species, it has almost always been with a single time lag between co-infecting parasites. Thus, how the timing of parasite species arrival affects co-infections and disease remains poorly understood. To address this gap in the literature, we exposed postmetamorphic Cuban tree frogs (Osteopilus septentrionalis) to Ranavirus, the fungus Batrachochytrium dendrobatidis (Bd), a nematode Aplectana hamatospicula, or pairs of these parasites either simultaneously or sequentially at a range of time lags and quantified load of the secondary parasite and host growth, survival, and parasite tolerance. Prior exposure to Bd or A. hamatospicula significantly increased viral loads relative to hosts singly infected with Ranavirus, whereas A. hamatospicula loads in hosts were higher when coexposed to Bd than when coexposed to Ranavirus. There was a significant positive relationship between time since Ranavirus infection and Bd load, and prior exposure to A. hamatospicula decreased Bd loads compared to simultaneous co-infection with these parasites. Infections with Bd and Ranavirus either singly or in co-infections decreased host growth and survival. This research reveals that time lags between co-infections can affect parasite loads, in line with priority effects theory. As co-infections in the field are unlikely to be simultaneous, an understanding of when co-infections are impacted by time lags between parasite exposures may play a major role in controlling problematic co-infections.

Ten years of ranavirus research (2010–2019): an analysis of global research trends

Ranaviruses are large nucleocytoplasmic DNA viruses that infect ectothermic vertebrates. Here we report the results of a scientometric analysis of the field of ranavirology for the last 10 years. Using bibliometric tools we analyse trends, identify top publications and journals, and visualise the ranavirus collaboration landscape. The Web of Science core collection contains 545 ranavirus-related publications from 2010 to 2019, with more publications produced every year and a total of 6830 citations. Research output is primarily driven by the United States and People’s Republic of China, who together account for more than 60% of ranavirus publications. We also observed a positive correlation between the average number of co-authors on ranavirus publications and the year of publication, indicating that overall collaboration is increasing. A keyword analysis of ranavirus publications from 2010 to 2019 reveals several areas of research interest including; ecology, immunology, virology/molecular biology, genetics, ichthyology, and herpetology. While ranavirus research is conducted globally, relatively few publications have co-authors from both European and Asian countries, possibly because closer countries (geographical distance) are more likely to share co-authors. To this end, efforts should be made to foster collaborations across geopolitical and cultural boundaries, especially between countries with shared research interests as ultimately, understanding global pathogens, like ranaviruses, will require global collaboration.

Genomic analysis of Ranavirus and exploring alternative genes for phylogenetics

Ranaviruses can infect both captive and wild cold-blooded vertebrates, leading to significant economic and environmental losses. With the cases of ranavirus infection increasing, many ranavirus genomic sequences were published, but little is known about ranavirus taxonomy on a whole-genome level. In this study, 44 ranaviruses core genes were identified in 32 ranaviruses genome sequences by using PanX. The neighbour-joining phylogenetic trees (NJ-tree) based on 44 ranaviruses core genes and 24 iridoviridae core genes and composition vector phylogenetic tree (CV-Tree) based on whole genome were constructed. The three of phylogenetic trees showed that 32 ranavirus isolates can be divided into 4 different subgroups including SGIV-like, EHNV-like, FV3-like and CMTV-like, and subgroups taxonomic position of three phylogenetic trees were consistent. However, the phylogenetic position of ToRV could not be determined if it belongs to FV3-like or CMTV-like group. Subsequently, we carried out dot plot analysis and confirmed that ToRV should belong to CMTV-like group. Based on dot plot analysis and phylogenetic trees, the taxonomic classification of ranaviruses was confirmed. Finally, four genes which are suitable for the construction of phylogenetic tree were selected from ranavirus core genes by recombination analysis, substitution saturation analysis and single-gene phylogenetic analysis. Phylogenetic tree based on concatenated sequences of the four selected genes showed that the classification of subgroups was identical with three of the phylogenetic trees. Conclusion: Our results confirmed taxonomic identification of ranaviruses; the four selected genes used in phylogenetic analysis will make taxonomic identification more convenient and accurate.

Selected Emerging Infectious Diseases of Amphibians

This article updates the understanding of two extirpation-driving infectious diseases, Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans, and Ranavirus. Experimental studies and dynamic, multifactorial population modeling have outlined the epidemiology and future population impacts of B dendrobatidis, B salamandrivorans, and Ranavirus. New genomic findings on divergent fungal and viral pathogens can help optimize control and disease management strategies. Although there have been major advances in knowledge of amphibian pathogens, controlled studies are needed to guide population recovery to elucidate and evaluate transmission routes for several pathogens, examine environmental control, and validate new diagnostic tools to confirm the presence of disease.

Risky Business: Live Non-CITES Wildlife UK Imports and the Potential for Infectious Diseases

International wildlife trade is recognised as a major transmission pathway for the movement of pathogenic organisms around the world. The UK is an active consumer of non-native live wild animals and is therefore subject to the risks posed by pathogen pollution from imported wildlife. Here, we characterise a key yet overlooked portion of the UK wildlife import market. We evaluate the trade in live non-CITES (Convention on International Trade in Endangered Species) wild terrestrial animals entering the UK over a 5-year period using data reported by the Animal and Plant Health Agency (APHA). Between 2014 and 2018, over 48 million individual animals, across five taxonomic classes and 24 taxonomic orders, were imported into the UK from 90 countries across nine global regions. The largest volumes of wild animals were imported from North America and Asia, and most of the import records were from Europe and Africa. Excluding Columbiformes (pigeons) and Galliformes ('game birds'), amphibians were the most imported taxonomic class (73%), followed by reptiles (17%), mammals (4%), birds (3%), and arachnids (<1%). The records described herein provide insight into the scope and scale of non-CITES listed wildlife imported in to the UK. We describe the potential for pathogen pollution from these vast and varied wildlife imports and highlight the potential threats they pose to public health. We also draw attention to the lack of detail in the UK wildlife import records, which limits its ability to help prevent and manage introduced infectious diseases. We recommend that improved record keeping and reporting could prove beneficial in this regard.

Salinity stress increases the severity of ranavirus epidemics in amphibian populations

The stress-induced susceptibility hypothesis, which predicts chronic stress weakens immune defences, was proposed to explain increasing infectious disease-related mass mortality and population declines. Previous work characterized wetland salinization as a chronic stressor to larval amphibian populations. Thus, we combined field observations with experimental exposures quantifying epidemiological parameters to test the role of salinity stress in the occurrence of ranavirus-associated mass mortality events. Despite ubiquitous pathogen presence (94%), populations exposed to salt runoff had slightly more frequent ranavirus related mass mortality events, more lethal infections, and 117-times greater pathogen environmental DNA. Experimental exposure to chronic elevated salinity (0.8-1.6 g l^-1 Cl^-) reduced tolerance to infection, causing greater mortality at lower doses. We found a strong negative relationship between splenocyte proliferation and corticosterone in ranavirus-infected larvae at a moderate elevation of salinity, supporting glucocorticoid-medicated immunosuppression, but not at high salinity. Salinity alone reduced proliferation further at similar corticosterone levels and infection intensities. Finally, larvae raised in elevated salinity had 10 times more intense infections and shed five times as much virus with similar viral decay rates, suggesting increased transmission. Our findings illustrate how a small change in habitat quality leads to more lethal infections and potentially greater transmission efficiency, increasing the severity of ranavirus epidemics.

Depauperate major histocompatibility complex variation in the endangered reticulated flatwoods salamander (Ambystoma bishopi)

Reticulated flatwoods salamander (Ambystoma bishopi) populations began decreasing dramatically in the 1900s. Contemporary populations are small, isolated, and may be susceptible to inbreeding and reduced adaptive potential because of low genetic variation. Genetic variation at immune genes is especially important as it influences disease susceptibility and adaptation to emerging infectious pathogens, a central conservation concern for declining amphibians. We collected samples from across the extant range of this salamander to examine genetic variation at major histocompatibility complex (MHC) class Iα and IIβ exons as well as the mitochondrial control region. We screened tail or toe tissue for ranavirus, a pathogen associated with amphibian declines worldwide. Overall, we found low MHC variation when compared to other amphibian species and did not detect ranavirus at any site. MHC class Iα sequencing revealed only three alleles with a nucleotide diversity of 0.001, while MHC class IIβ had five alleles with a with nucleotide diversity of 0.004. However, unique variation still exists across this species' range with private alleles at three sites. Unlike MHC diversity, mitochondrial variation was comparable to levels estimated for other amphibians with nine haplotypes observed, including one haplotype shared across all sites. We hypothesize that a combination of a historic disease outbreak and a population bottleneck may have contributed to low MHC diversity while maintaining higher levels of mitochondrial DNA variation. Ultimately, MHC data indicated that the reticulated flatwoods salamander may be at an elevated risk from infectious diseases due to low levels of immunogenetic variation necessary to combat novel pathogens.

Ranaviruses in captive and wild Australian lizards

Ranaviral infections have been associated with mass mortality events in captive and wild amphibian, fish, and reptile populations globally. In Australia, two distinct types of ranaviruses have been isolated: epizootic haematopoietic necrosis virus in fish and a Frog virus 3-like ranavirus in amphibians. Experimental studies and serum surveys have demonstrated that several Australian native fish, amphibian, and reptile species are susceptible to infection and supported the theory that ranavirus is naturally circulating in Australian herpetofauna. However, ranaviral infections have not been detected in captive or wild lizards in Australia. Oral-cloacal swabs were collected from 42 wild lizards from northern Queensland and 83 captive lizards from private collections held across three states/territories. Samples were tested for ranaviral DNA using a quantitative PCR assay. This assay detected ranaviral DNA in 30/83 (36.1%) captive and 33/42 (78.6%) wild lizard samples. This is the first time molecular evidence of ranavirus has been reported in Australian lizards.

Phylogenomic characterization of ranaviruses isolated from cultured fish and amphibians in Thailand

Ranaviruses are emerging pathogens associated with worldwide epizootics in farmed and wild ectothermic vertebrates. In this study, we determined the full genomes of eight ranaviruses isolated from marbled sleeper goby ( Oxyeleotris marmorata), goldfish ( Carassius auratus), guppy ( Poecilia reticulata), tiger frog ( Hoplobatrachus tigerinus), Asian grass frog ( Fejervarya limnocharis), and East Asian bullfrog ( H. rugulosus) cultured or imported into Thailand. These ranaviral isolates induced the same cytopathic effects (i.e., progression of coalescing round plaques) in epithelioma papulosum cyprini (EPC) cell cultures. Transmission electron microscopy of infected EPC cells revealed cytoplasmic viral particles with ultrastructural features typical for ranaviruses. Pairwise genetic comparisons of the complete major capsid protein coding sequences from the Thai ranaviruses displayed the highest identity (99.8%–100%) to a ranavirus (tiger frog virus; TFV) isolated from diseased tiger frogs cultured in China, a slightly lower identity (99.3%–99.4%) to a ranavirus (Wamena virus; WV) isolated from diseased green tree pythons ( Morelia viridis) illegally exported from Papua New Guinea, and a lower identity to 35 other ranaviruses (93.7%–98.6%). Phylogenomic analyses supported the eight Thai ranaviruses, Chinese TFV, and WV as a subclade within a larger frog virus 3 clade. Our findings confirm the spread of TFV among cultured fish and amphibians in Asia and likely in reptiles in Oceania. Biosecurity measures are needed to ensure TFV does not continue to spread throughout Southeast Asia and to other parts of the world via international trade.

Xenopus Interferon Complex: Inscribing the Amphibiotic Adaption and Species-Specific Pathogenic Pressure in Vertebrate Evolution?

Several recent studies have revealed previously unknown complexity of the amphibian interferon (IFN) system. Being unique in vertebrate animals, amphibians not only conserve and multiply the fish-like intron-containing IFN genes, but also rapidly evolve amniote-like intronless IFN genes in each tested species. We postulate that the amphibian IFN system confers an essential model to study vertebrate immune evolution in molecular and functional diversity to cope with unprecedented pathophysiological requirement during terrestrial adaption. Studies so far have ascribed a potential role of these IFNs in immune regulation against intracellular pathogens, particularly viruses; however, many knowledge gaps remain elusive. Based on recent reports about IFN's multifunctional properties in regulation of animal physiological and defense responses, we interpret that amphibian IFNs may evolve novel function pertinent to their superior molecular diversity. Such new function revealed by the emerging studies about antifungal and developmental regulation of amphibian IFNs will certainly promote our understanding of immune evolution in vertebrates to address current pathogenic threats causing amphibian decline.

Detecting Amphibians in Agricultural Landscapes Using Environmental DNA Reveals the Importance of Wetland Condition

Amphibians are declining worldwide, in part because of large-scale degradation of habitat from agriculture and pervasive pathogens. Yet a common North American amphibian, the wood frog (Lithobates sylvaticus), ranges widely and persists in agricultural landscapes. Conventional survey techniques rely on visual encounters and dip-netting efforts, but detectability limits the ability to test for the effects of environmental variables on amphibian habitat suitability. We used environmental DNA to determine the presence of wood frogs and an amphibian pathogen (ranavirus) in Prairie Pothole wetlands and investigated the effects of 32 water quality, wetland habitat, and landscape-level variables on frog presence at sites representing different degrees of agricultural intensity. Several wetland variables influenced wood frog presence, the most influential being those associated with wetland productivity (i.e., nutrients), vegetation buffer width, and proportion of the surrounding landscape that is comprised of other water bodies. Wood frog presence was positively associated with higher dissolved phosphorus (>0.4 mg/L), moderate dissolved nitrogen (0.1-0.2 mg/L), lower chlorophyll a (≤15 µg/L), wider vegetation buffers (≥10 m), and more water on the landscape (≥0.25). These results highlight the effects of environmental factors at multiple scales on the presence of amphibians in this highly modified landscape-namely the importance of maintaining wetland water quality, vegetation buffers, and surrounding habitat heterogeneity. Environ Toxicol Chem 2019;38:2750-2763. © 2019 SETAC.

Pathogen vs. predator: ranavirus exposure dampens tadpole responses to perceived predation risk

There is increasing interest in how animals respond to multiple stressors, including potential synergistic or antagonistic interaction between pathogens and perceived predation risk (PPR). For prey that exhibit phenotypic plasticity, it is unclear whether infection and PPR affect behaviour and morphology independently, or in an antagonistic or synergistic manner. Using a 2 × 2 factorial experiment involving green frog (Lithobates clamitans) tadpoles exposed to ranavirus (FV3) and larval dragonflies (Anax spp.), we assessed whether anti-predator responses were affected by infection. We found that activity and feeding were reduced additively by both stressors. Body mass of tadpoles from FV3-exposed tanks was lighter relative to control and PPR-only tanks, while metabolism was comparable across treatments. We found that FV3 exposure compromised morphometric responses to PPR in an antagonistic manner: tadpoles exposed to both treatments had restricted changes in tail depth compared to those receiving singular treatment. We conclude that multiple stressors can have complex and substantive effects on organisms, and that interactions between stressors may yield a range of responses depending on the level of exposure and sensitivity of the organism. Additional work should more fully determine mechanisms underlying the complex interplay between infection and predation risk, across a range of environmental conditions.

Ranavirus infection dynamics and shedding in American bullfrogs: consequences for spread and detection in trade

American bullfrogs Lithobates catesbeianus are thought to be important in the global spread of ranaviruses-often lethal viruses of cold-blooded vertebrates-because they are commonly farmed, dominate international trade, and may be 'carriers' of ranavirus infections. However, whether American bullfrogs are easily infected and maintain long-lasting ranavirus infections, or are refractory to or rapidly clear infections, remains unknown. We tracked the dynamics of ranavirus in American bullfrogs through time and with temperature in multiple types of samples and also screened shipments from commercial suppliers to determine whether we could detect subclinical infections. Collectively, we found that tadpoles and juveniles were commonly infected at moderate doses, and while some died, others controlled and appeared to clear their infections. Some individuals, however, harbored subclinical infections for up to 49 d, suggesting that American bullfrogs may be important carriers. Indeed, tadpoles and metamorphosed frogs from 2 of 5 commercial suppliers harbored subclinicial infections. Juveniles at warmer temperatures had less intense but still persistent infections. Because diagnostic performance was strongly related to infection intensity, non-lethal samples (i.e. tail or toe clips, swabs, and environmental DNA) had only a moderate chance of detecting subclinical infections. Even internal tissues may fail to detect subclinical infections. However, viral shedding was correlated with the intensity of infection, so while subclinically infected tadpoles shed virus for 35-49 d, the low levels might lead to little transmission. We suggest that a quantitative focus on virus dynamics within hosts can provide a more nuanced view of ranavirus infections and the risk presented by American bullfrogs in trade.

Behavioural fever reduces ranaviral infection in toads

1. Host behaviour is known to influence disease dynamics. Additionally, hosts often change their behaviours in response to pathogen detection to resist and avoid disease. The capacity of wildlife populations to respond to pathogens using behavioural plasticity is critical for reducing the impacts of disease outbreaks. However, there is limited information regarding the ability of ectothermic vertebrates to resist diseases via behavioural plasticity. 2. Here, we experimentally examine the effect of host behaviour on ranaviral infections, which affect at least 175 species of ectothermic vertebrates. We placed metamorphic (temporal block 1) or adult (block 2) Southern toads (Anaxyrus terrestris) in thermal gradients, tested their temperature preferences before and after oral inoculation by measuring individual-level body temperature over time, and measured ranaviral loads of viral-exposed individuals. 3. We found significant individual-level variation in temperature preference and evidence for behavioural fever in both metamorph and adult A. terrestris during the first two days after exposure. Additionally, we found that individual-level change in temperature preference was negatively correlated with ranaviral load and a better predictor of load than average temperature preference or maximum temperature reached by an individual. In other words, an increase in baseline temperature preference was more important than simply reaching an absolute temperature. 4. These results suggest that behavioural fever is an effective mechanism for resisting ranaviral infections.

Outbreaks of an Emerging Viral Disease Covary With Differences in the Composition of the Skin Microbiome of a Wild United Kingdom Amphibian

There is growing appreciation of the important role of commensal microbes in ensuring the normal function and health of their hosts, including determining how hosts respond to pathogens. A range of infectious diseases are threatening amphibians worldwide, and evidence is accumulating that the host-associated bacteria that comprise the microbiome may be key in mediating interactions between amphibian hosts and infectious pathogens. We used 16S rRNA amplicon sequencing to quantify the skin microbial community structure of over 200 individual wild adult European common frogs (Rana temporaria), from ten populations with contrasting history of the lethal disease ranavirosis, caused by emerging viral pathogens belonging to the genus Ranavirus. All populations had similar species richness irrespective of disease history, but populations that have experienced historical outbreaks of ranavirosis have a distinct skin microbiome structure (beta diversity) when compared to sites where no outbreaks of the disease have occurred. At the individual level, neither age, body length, nor sex of the frog could predict the structure of the skin microbiota. Our data potentially support the hypothesis that variation among individuals in skin microbiome structure drive differences in susceptibility to infection and lethal outbreaks of disease. More generally, our results suggest that population-level processes are more important for driving differences in microbiome structure than variation among individuals within populations in key life history traits such as age and body size.

eDNA Increases the Detectability of Ranavirus Infection in an Alpine Amphibian Population

The early detection and identification of pathogenic microorganisms is essential in order to deploy appropriate mitigation measures. Viruses in the Iridoviridae family, such as those in the Ranavirus genus, can infect amphibian species without resulting in mortality or clinical signs, and they can also infect other hosts than amphibian species. Diagnostic techniques allowing the detection of the pathogen outside the period of host die-off would thus be of particular use. In this study, we tested a method using environmental DNA (eDNA) on a population of common frogs (Rana temporaria) known to be affected by a Ranavirus in the southern Alps in France. In six sampling sessions between June and September (the species' activity period), we collected tissue samples from dead and live frogs (adults and tadpoles), as well as insects (aquatic and terrestrial), sediment, and water. At the beginning of the breeding season in June, one adult was found dead; at the end of July, a mass mortality of tadpoles was observed. The viral DNA was detected in both adults and tadpoles (dead or alive) and in water samples, but it was not detected in insects or sediment. In live frog specimens, the virus was detected from June to September and in water samples from August to September. Dead tadpoles that tested positive for Ranavirus were observed only on one date (at the end of July). Our results indicate that eDNA can be an effective alternative to tissue/specimen sampling and can detect Ranavirus presence outside die-offs. Another advantage is that the collection of water samples can be performed by most field technicians. This study confirms that the use of eDNA can increase the performance and accuracy of wildlife health status monitoring and thus contribute to more effective surveillance programs.

Pathogen Dynamics in an Invasive Frog Compared to Native Species

Emerging infectious diseases threaten the survival of wildlife populations and species around the world. In particular, amphibians are experiencing population declines and species extinctions primarily in response to two pathogens, the fungus Batrachochytrium dendrobatidis (Bd) and the iridovirus Ranavirus (Rv). Here, we use field surveys and quantitative (q)PCR to compare infection intensity and prevalence of Bd and Rv across species and seasons on Jekyll Island, a barrier island off the coast of Georgia, USA. We collected oral and skin swabs for 1 year from four anuran species and three families, including two native hylids (Hyla cinerea and Hyla squirella), a native ranid (Rana sphenocephala), and the invasive rain frog Eleutherodactylus planirostris. Bd infection dynamics did not vary significantly over sampling months, but Rv prevalence and intensity were significantly higher in fall 2014 compared to spring 2015. Additionally, Rv prevalence and intensity were significantly higher in E. planirostris than in the other three species. Our study highlights the potential role of invasive amphibians as drivers of disease dynamics and demonstrates the importance of pathogen surveillance across multiple time periods and species to accurately capture the infectious disease landscape.

Evaluating observer bias and seasonal detection rates in amphibian pathogen eDNA collections by citizen scientists

We trained volunteers from conservation organizations to collect environmental DNA (eDNA) from 21 ponds with amphibian communities that had a history of Batrachochytrium dendrobatidis (Bd) and ranavirus (Rv) infections. Volunteers were given sampling kits to filter pond water and preserve eDNA on filter paper, as were the principal investigators (PIs), who made independent collections within 48 h of volunteer collections. Using multi-scale occupancy modeling, we found no evidence to suggest the observer who collected the water sample (volunteer or PI) influenced either the probability of capturing eDNA on a filter or the probability of detecting extracted eDNA in a quantitative PCR (qPCR) reaction. The cumulative detection probability of Bd eDNA at a pond decreased from May through July 2017 because there was a decrease in the probability of detecting eDNA in qPCR reactions. In contrast, cumulative detection probability increased from May to July for Rv due to a higher probability of capturing eDNA on filters later in the year. Our models estimate that both pathogens could be detected with 95% confidence in as few as 5 water samples taken in June or July tested with either 4 or 3 qPCR reactions, respectively. Our eDNA protocols appeared to detect pathogens with 95% confidence using considerably fewer samples than protocols which typically recommend sampling ≥30 individual animals. In addition, eDNA sampling could reduce some biosecurity concerns, jurisdictional and institutional permitting, and stress to biota at ponds.