Plasticity, Paralogy, and Pseudogenization: Rhabdoviruses of Freshwater Mussels Elucidate Mechanisms of Viral Genome Diversification and the Evolution of the Finfish-Infecting Rhabdoviral Genera.

Viruses in the family Rhabdoviridae display remarkable genomic variation and ecological diversity. This plasticity occurs despite the fact that, as negative sense RNA viruses, rhabdoviruses rarely if ever recombine. Here, we describe nonrecombinatorial evolutionary processes leading to genomic diversification in the Rhabdoviridae inferred from two novel rhabdoviruses of freshwater mussels (Mollusca: Bivalvia: Unionida). Killamcar virus 1 (KILLV-1) from a plain pocketbook (Lampsilis cardium) is closely related phylogenetically and transcriptionally to finfish-infecting viruses in the subfamily Alpharhabdovirinae. KILLV-1 offers a novel example of glycoprotein gene duplication, differing from previous examples in that the paralogs overlap. Evolutionary analyses reveal a clear pattern of relaxed selection due to subfunctionalization in rhabdoviral glycoprotein paralogs, which has not previously been described in RNA viruses. Chemarfal virus 1 (CHMFV-1) from a western pearlshell (Margaritifera falcata) is closely related phylogenetically and transcriptionally to viruses in the genus Novirhabdovirus, the sole recognized genus in the subfamily Gammarhabdovirinae, representing the first known gammarhabdovirus of a host other than finfish. The CHMFV-1 G-L noncoding region contains a nontranscribed remnant gene of precisely the same length as the NV gene of most novirhabdoviruses, offering a compelling example of pseudogenization. The unique reproductive strategy of freshwater mussels involves an obligate parasitic stage in which larvae encyst in the tissues of finfish, offering a plausible ecological mechanism for viral host-switching. IMPORTANCE Viruses in the family Rhabdoviridae infect a variety of hosts, including vertebrates, invertebrates, plants and fungi, with important consequences for health and agriculture. This study describes two newly discovered viruses of freshwater mussels from the United States. One virus from a plain pocketbook (Lampsilis cardium) is closely related to fish-infecting viruses in the subfamily Alpharhabdovirinae. The other virus from a western pearlshell (Margaritifera falcata) is closely related to viruses in the subfamily Gammarhabdovirinae, which until now were only known to infect finfish. Genome features of both viruses provide new evidence of how rhabdoviruses evolved their extraordinary variability. Freshwater mussel larvae attach to fish and feed on tissues and blood, which may explain how rhabdoviruses originally jumped between mussels and fish. The significance of this research is that it improves our understanding of rhabdovirus ecology and evolution, shedding new light on these important viruses and the diseases they cause.

Novel Aquareovirus isolated from channel catfish (Ictalurus punctatus) used in mussel restoration efforts in Wisconsin.

Channel catfish (Ictalurus punctatus) are a food fish extensively reared in aquaculture facilities throughout the world and are also among the most abundant wild catfish species in North America, making them a popular target of anglers. Furthermore, channel catfish are important members of aquatic ecosystems; for example, they serve as a glochidial host for the endangered winged mapleleaf mussel (Quadrula fragosa), making them critical for conserving this species through hatchery-based restoration efforts. During a routine health inspection, a novel aquareovirus was isolated from channel catfish used in mussel propagation efforts at a fish hatchery in Wisconsin. This virus was isolated on brown bullhead cells (ATCC CCL-59) and identified through metagenomic sequencing as a novel member of the family Spinareoviridae, genus Aquareovirus. The virus genome consists of 11 segments, as is typical of the aquareoviruses, with phylogenetic relationships based on RNA-dependent RNA polymerase and major outer capsid protein amino acid sequences showing it to be most closely related to golden shiner virus (aquareovirus C) and aquareovirus C/American grass carp reovirus (aquareovirus G) respectively. The potential of the new virus, which we name genictpun virus 1 (GNIPV-1), to cause disease in channel catfish or other species remains unknown.

Octomacrum spinum (Monogenoidea: Polyopisthocotylea: Octomacridae) from highland stoneroller, Campostoma spidaceum (Cypriniformes: Leuciscidae) from Arkansas and Oklahoma, USA, with a summary of the genus from North American and European fishes.

Octomacrum spinum Dansby & Shoemaker, 1973, is reported for the first time from 23 of 146 (16%) highland stonerollers, Campostoma spadiceum collected from central and western Arkansas and southeastern Oklahoma, USA. Analysis of molecular data revealed that the SSU rRNA gene of specimens of O. spinum from Arkansas was identical to a number of Octomacrum spp. and the LSU rRNA gene was 97.46% similar to Octomacrum europaeum. We also provide a summary of the species of Octomacrum reported from North American and European fishes.

Pathology and infectious agents of unionid mussels: A primer for pathologists in disease surveillance and investigation of mortality events.

Freshwater mussels are one of the most imperiled groups of organisms in the world, and more than 30 species have gone extinct in the last century. While habitat alteration and destruction have contributed to the declines, the role of disease in mortality events is unclear. In an effort to involve veterinary pathologists in disease surveillance and the investigation of freshwater mussel mortality events, we provide information on the conservation status of unionids, sample collection and processing techniques, and unique and confounding anatomical and physiological differences. We review the published accounts of pathology and infectious agents described in freshwater mussels including neoplasms, viruses, bacteria, fungi, fungal-like agents, ciliated protists, Aspidogastrea, Digenea, Nematoda, Acari, Diptera, and Odonata. Of the identified infectious agents, a single viral disease, Hyriopsis cumingii plague disease, that occurs only in cultured mussels is known to cause high mortality. Parasites including ciliates, trematodes, nematodes, mites, and insects may decrease host fitness, but are not known to cause mortality. Many of the published reports identify infectious agents at the light or ultrastructural microscopy level with no lesion or molecular characterization. Although metagenomic analyses provide sequence information for infectious agents, studies often fail to link the agents to tissue changes at the light or ultrastructural level or confirm their role in disease. Pathologists can bridge this gap between identification of infectious agents and confirmation of disease, participate in disease surveillance to ensure successful propagation programs necessary to restore decimated populations, and investigate mussel mortality events to document pathology and identify causality.

Efficacy of hydrogen peroxide to reduce Gyrodactylus species infestation density on four fish species.

OBJECTIVE: The ability to effectively treat parasitic infestations of fish is of high importance for fish culture facilities. However, tools or approved therapies for treating infestations on fish are limited. This paper summarizes results from four separate clinical field studies that evaluated the efficacy of hydrogen peroxide (H2 O2 ; 35% PEROX-AID) for reducing Gyrodactylus spp. infestation density. METHODS: Three species of Gyrodactylus were studied (G. salmonis, hosts: Brook Trout Salvelinus fontinalis and Lake Trout S. namaycush; G. freemani, host: Yellow Perch Perca flavescens; G. hoffmani, host: Fathead Minnow Pimephales promelas) before and after the application of immersion H2 O2 therapy. RESULT: Parasite density was significantly reduced for each parasite × host combination to which H2 O2 therapy was applied. Two clinical field studies in salmonids were found to demonstrate substantial effectiveness that enabled 35% PEROX-AID approval. CONCLUSION: Further assessments of Gyrodactylus spp. could expand the use of H2 O2 for controlling these parasites in aquaculture. Specifically, H2 O2 was effective at all levels tested (50 or 75 mg H2 O2 /L for 60 min for the Yellow Perch and Fathead Minnow clinical field studies; 100 or 150 mg H2 O2 /L for 30 min regardless of salt pre-treatment for the Brook Trout study; and 100 mg H2 O2 /L for 30 min or 50 mg H2 O2 /L for 60 min for the Lake Trout study).

A new Myxobolus (Cnidaria: Myxosporea: Myxobolidae) from the gills of the southern striped shiner, Luxilus chrysocephalus isolepis (Cypriniformes: Leuciscidae), from southwestern Arkansas, USA.

The southern striped shiner, Luxilus chrysocephalus isolepis (Hubbs & Brown) is a relatively large minnow belonging to the true minnow family Leuciscidae Bonaparte. Between May 2020 and January 2022, 55 L. c. isolepis were collected from watersheds in Montgomery (n = 6), Polk (n = 17) and Sevier (n = 32) counties, Arkansas, USA, and their gills, gallbladders, urinary bladders, fins, integument, other major organs, and musculature were examined for myxozoans. Gills of 11 (34%) individual southern striped shiners from Sevier County were infected with a new myxozoan, Myxobolus carlhubbsi n. sp. A qualitative and quantitative morphological description was based on formalin-fixed preserved myxospores, and molecular data consisted of a 1,970 base pair sequence of the partial small subunit rRNA gene from ethanol-preserved specimens. Histologically, plasmodia filled and expanded interlamellar troughs. Hyperplastic epithelial and goblet cells filled interlamellar troughs adjacent to plasmodia, but inflammatory response was limited to scattered lymphocytes. Phylogenetic analysis revealed that M. carlhubbsi n. sp. is a member of a clade of species with pyriform myxospores parasitizing North American Pogonichthyinae Girard and North American and Eurasian Leuciscinae Bonaparte. This is the first report of a myxozoan from L. c. isolepis. This article was registered in the Official Register of Zoological Nomenclature (ZooBank) as urn:lsid:zoobank.org:pub:D10D71C2-2C75-4A1C-80ED-B98FF36CB509.

Pseudomurraytrema fergusoni n. sp. (Monogenea: Dactylogyridae) from gills of Pealip Redhorse, Moxostoma pisolabrum (Catostomidae) from Arkansas, USA, with a description of gill pathology.

Pseudomurraytrema fergusoni n. sp. is described from the Pealip Redhorse, Moxostoma pisolabrum from the Black River (White River drainage), Lawrence County, Arkansas, USA. This represents the second monogenean described from M. pisolabrum as well as the second species of Pseudomurraytrema reported from an Arkansas catostomid. The description includes partial 18S rRNA and 28S rRNA gene sequences (732 bp and 851 bp, respectively), helping fill a void in sequence data from North American monogeneans, particularly those in the genus Pseudomurraytrema. In addition, histopathologic changes associated with the infection resulted in severe localized pathologic lesions in gills of the host, suggesting compromise of respiratory surfaces within affected areas adjacent to the worms.

Development of duplex qPCR targeting Carnobacterium maltaromaticum and Vagococcus salmoninarum.

In November 2018, Vagococcus salmoninarum was identified as the causative agent of a chronic coldwater streptococcosis epizootic in broodstock brook trout (Salvelinus fontinalis) at the Iron River National Fish Hatchery in Wisconsin, USA. By February 2019, the epizootic spread to adjacent raceways containing broodstock lake trout (Salvelinus namaycush), whereby fish were found to be coinfected with Carnobacterium maltaromaticum and V. salmoninarum. To differentiate these two pathogens and determine the primary cause of the lake trout morbidity, a quantitative real-time PCR (qPCR) was developed targeting the C. maltaromaticum phenylalanyl-tRNA synthase alpha subunit (pheS) gene. The qPCR was combined with a V. salmoninarum qPCR, creating a duplex qPCR assay that simultaneously quantitates C. maltaromaticum and V. salmoninarum concentrations in individual lake trout tissues, and screens presumptive isolates from hatchery inspections and wild fish from national fish hatchery source waters throughout the Great Lakes basin. Vagococcus salmoninarum and C. maltaromaticum were co-detected in broodstock brook trout from two tribal hatcheries and C. maltaromaticum was present in wild fish in source waters of several national fish hatcheries. This study provides a powerful new tool to differentiate and diagnose two emerging Gram-positive bacterial pathogens.

Isolations of the Spring Viremia of Carp Virus in the Upper Mississippi River (USA), Including a New Host, the Quillback.

In July of 2018 and 2019, wild fish health surveys were conducted along the Wisconsin and Minnesota portions of the upper Mississippi River. Spring viremia of carp virus (SVCV) was isolated from Common Carp Cyprinus carpio as well as a newly identified host species, the Quillback Carpiodes cyprinus. Sanger sequencing of the gene encoding for the G protein revealed a high similarity of the Quillback isolate to various SVCV isolates identified from Common Carp that were collected during earlier wild fish health surveys and mortality events in the USA. Despite annual monitoring, this virus has been infrequently identified. The speculative role of native fish and invertebrates in allowing the virus to persist for long periods without detection is discussed.

A new species of Myxidium (Cnidaria: Myxosporea: Myxidiidae) from the gallbladder of pickerels, Esox spp. (Esociformes: Esocidae), from southwestern Arkansas, USA.

During April 2016 and again in November 2021, four Chain Pickerels, Esox niger were collected from Union (n = 3) and Nevada (n = 1) counties, Arkansas, USA, and 65 Grass Pickerels, Esox americanus vermiculatus were collected between January 2015 and December 2021 from four counties of Arkansas (n = 31) and McCurtain County, Oklahoma, USA (n = 34), and examined for myxozoans. Gallbladders of an individual E. niger from Nevada County, Arkansas, as well as a single individual of E. a. vermiculatus from Sevier County, Arkansas, were infected with a new myxozoan, Myxidium whippsi n. sp. Qualitative and quantitative morphological data were from formalin-fixed preserved myxospores while molecular data (SSU rRNA gene) consisted of 2031bp (host: E. niger) and 1723 bp (host: E. a. vermiculatus) partial sequences of the small subunit ribosomal RNA gene. Phylogenetic analysis placed M. whippsi n. sp. in a clade with two other myxozoans, Zschokkella nova and Myxidium truttae, previously reported from cyprinids and salmonids, respectively. We document the first report of a myxozoan from E. a. vermiculatus. This article was registered in the Official Register of Zoological Nomenclature (ZooBank) as urn:lsid:zoobank.org:pub:A50FCEB3-68C3-428E-A04E-37A16790F1EB.

Nephroblastoma in a Common Mudpuppy Necturus maculosus simultaneously Present with a Mollicute Bacterium of the Genus Acholeplasma.

In March 2017, a wild-caught female common mudpuppy Necturus maculosus from Iowa, USA, with an enlarged posterior abdomen was submitted for diagnostic assessment. The cause of the abdominal distension was a large fluid-filled abdominal mass, diagnosed as a nephroblastoma. Parasites and numerous bacteria were isolated and identified from the mudpuppy but were determined to be incidental. Samples of the neoplasm inoculated onto an American toad Anaxyrus americanus cell line (BufoTad) yielded cytopathic effect during several passages. However, standard molecular testing of the cell culture supernatant failed to identify any viruses. Next-generation sequencing identified the replicating agent as a bacterium of the genus Acholeplasma. Immunohistochemistry confirmed the presence of Acholeplasma within the nephroblastoma, including within tumor cells. This is the first report of nephroblastoma and the second report of neoplasia in this species. The results also suggest that certain bacteria of the genus Acholeplasma might be oncogenic.

A variant of Gyrodactylus mediotorus King, Marcogliese, Forest, McLaughlin and Bentzen, 2013 (Monogenea) identified from weed shiner (Notropis texanus) in Wisconsin portions of the upper Mississippi River.

Gyrodactylus mediotorus King, Marcogliese, Forest, McLaughlin and Bentzen, 2013, previously described from the spottail shiner Notropis hudsonius (Clinton) in the St. Lawrence River, Quebec, was identified from weed shiner Notropis texanus (Girard) in Wisconsin. The parasite was primarily observed to infect the fins and, to a lesser extent, the skin. BLASTn searches of a 436 bp partial 18S rRNA gene and 1066 bp targeting the ITS region were highly similar (100%; 98.75%, respectively) to Canadian specimens of G. mediotorus. The slight genetic difference coupled with nearly identical morphology led us to conclude the Wisconsin specimens on weed shiner were a variant of G. mediotorus. This species also shares a prominent anteromedial knob on the ventral bar (and noticeable similarity in overall form of the haptoral hard parts and male copulatory organ) with G. campostomae Wellborn, 1967, G. laruei Kritsky and Mizelle, 1968, G. protuberus Rogers and Wellborn, 1965, G. rhinichthius Wood and Mizelle, 1957, G. spathulatus Mueller, 1936 and G. stunkardi Kritsky and Mizelle, 1968. It seems likely these knob-bearing species are members of a gyrodactylid lineage that has radiated among leuciscid and catostomid host fishes endemic to North America, although whether this knob is a shared or independent character remains unsolved.

Morphometric and genetic evidence for cryptic diversity in Gyrodactylus (Monogenea) infecting non-native European populations of Ameiurus nebulosus and A. melas.

Gyrodactylid parasites were observed on non-native populations of North-American freshwater catfishes, Ameiurus nebulosus and Ameiurus melas (Siluriformes: Ictaluridae), at several sites in the Elbe River basin, Czech Republic, Europe. Using a combination of morphological and genetic analyses, the parasites infecting A. nebulosus were determined to be Gyrodactylus nebulosus, a North American parasite co-introduced to Europe along with its Ameiurus fish hosts. Subtle morphometrical differences, as well as seasonal variations, were observed among parasites collected from A. nebulosus and A. melas. The host-related variation was further supported through genetic analysis of the partial 18S rDNA, ITS1-5.8S-ITS2 and COI, showing 0.2, 3.0 and 4.8% divergence, respectively. Consistent genetic differences indicated there were two distinct genotypes. Subtle morphological differences associated with the shape of sickle toe, anchor root and ventral bar membrane, according to host species, also supported the description of a new cryptic species, Gyrodactylus melas n. sp., infecting A. melas. Multivariate morphometrical analysis of haptoral hard parts showed significant differences between the anchor lengths of G. nebulosus and G. melas n. sp. However, the measurements of the haptoral hard structures partially overlapped between species, limiting the usage of these parameters for species delineation.

Vagococcus salmoninarum II-qPCR, tropism and egg-associated transmission.

Vagococcus salmoninarum was identified as the causative agent of a chronic epizootic in broodstock "coaster" brook trout (Salvelinus fontinalis) at the Iron River National Fish Hatchery. The epizootic spanned more than a year, was unresponsive to multiple florfenicol treatments, and resulted in >50% mortality of the affected fish. The decision was made to cull the remaining fish during spawning, which presented an opportunity to more thoroughly examine V. salmoninarum sampling methods, organ tropism and vertical transmission. A newly developed qPCR targeting the pheS gene was used in concert with bacterial culture to show that V. salmoninarum indeed disproportionately affects females and has a tropism for female reproductive tissues. The study demonstrates that some female reproductive tissues (e.g. ovarian fluid, unfertilized eggs) are also an effective option for non-lethal detection. Despite the widespread presence of V. salmoninarum in ovarian fluid and on egg surfaces, we found no evidence of intra-ova transmission.

Vagococcus salmoninarum I-A chronic coldwater streptococcosis in broodstock brook trout (Salvelinus fontinalis) in Wisconsin, USA.

In 2018, Vagococcus salmoninarum was isolated from two lots of broodstock "coaster" brook trout (Salvelinus fontinalis) containing ~1,500 fish at the Iron River National Fish Hatchery, at which time it was identified as the causative agent of a chronic coldwater streptococcosis epizootic. Clinical signs included exophthalmia, lethargy, erratic swimming and loss of equilibrium. Female fish experienced disproportionately higher morbidity and mortality than male co-inhabitants, and routinely retained eggs following spawning. The most consistent gross clinical sign was heart pallor and turbid pericardial effusion. An attempted treatment using florfenicol was ineffective at halting the epizootic, which spanned more than a year and resulted in >50% mortality before remaining fish were culled. As there is no previous documentation of V. salmoninarum at this hatchery or in this species, it is still unclear what circumstances led to this epizootic. The inability to treat this chronic disease led to the loss of valuable broodstock, hampering ongoing fishery conservation efforts in the Great Lakes Basin.

Supplemental diagnosis of Gyrodactylus nebulosus Kritsky and Mizelle, 1968 (Monogenea) on 0+ age Ameiurus nebulosus (Siluriformes) considered for commercial grow-out in Southwestern Nova Scotia, Canada.

Gyrodactylus nebulosus Kritsky and Mizelle, 1968 is reported for the first time from brown bullhead Ameiurus nebulosus (Siluriformes; Ictaluridae) in Nova Scotia. The study results from a screening of parasites with the potential to disrupt commercial rearing of wild-caught young-of-the-year (YOY) brown bullhead. Infected YOY were collected July 30, 2018 and estimated to be 3 weeks old. Eight of 10 fish were infected. Mean intensity was 3.1 ± 3.5 with a range of 1-10. The parasite occurred all over the body surface, but particularly on the ventral regions of the head including the base of the maxillary barbels. Diagnostically important features of the anchors, ventral bar/shield, marginal hooks, and male copulatory organ are described. A partial sequence of the 18S rRNA gene (432 bp) is included and represents the first confirmed molecular data for this species. Molecular analysis revealed a high similarity (99.3%) to a Gyrodactylus sp. reported from the same host, A. nebulosus, in Ontario and the next closest similarity (96.9%) to Gyrodactylus fairporti Van Cleave, 1921 from Ameiurus melas in Wisconsin. The report extends the known distribution of G. nebulosus from North Dakota, Iowa, and Ontario to Nova Scotia. The study concludes that any commercial venture to harvest local YOY brown bullhead from the wild for intense grow-out in captivity should include appropriate quarantine and therapeutic treatments for G. nebulosus as part of the operation.

In vitro transcribed dsRNA limits viral hemorrhagic septicemia virus (VHSV)-IVb infection in a novel fathead minnow (Pimephales promelas) skin cell line.

The farming of baitfish, fish used by anglers to catch predatory species, is of economic and ecological importance in North America. Baitfish, including the fathead minnow (Pimephales promelas), are susceptible to infection from aquatic viruses, such as viral hemorrhagic septicemia virus (VHSV). VHSV infections can cause mass mortality events and have the potential to be spread to novel water bodies through baitfish as a vector. In this study, a novel skin cell line derived from fathead minnow (FHMskin) is described and its use as a tool to study innate antiviral immune responses and possible therapies is introduced. FHMskin grows optimally in 10% fetal bovine serum and at warmer temperatures, 25-30 °C. FHMskin is susceptible and permissive to VHSV-IVb infection, producing high viral titres of 7.35 × 107 TCID50/mL after only 2 days. FHMskin cells do not experience significant dsRNA-induced death after treatment with 50-500 ng/mL of in vitro transcribed dsRNA for 48 h and respond to dsRNA treatment by expressing high levels of three innate immune genes, viperin, ISG15, and Mx1. Pretreatment with dsRNA for 24 h significantly protected cells from VHSV-induced cell death, 500 ng/mL of dsRNA reduced cell death from 70% to less than 15% at a multiplicity of infection of 0.1. Thus, the novel cell line, FHMskin, represents a new method for producing high tires of VHSV-IVb in culture, and for studying dsRNA-induced innate antiviral responses, with future applications in dsRNA-based antiviral therapeutics.

Bluegill Picornavirus isolated from a mortality event involving Bluegill (Lepomis macrochirus) in the upper Mississippi River.

A mortality event involving an estimated 1,000 adult bluegills (Lepomis macrochirus) was observed in an ice-covered backwater lake of the upper Mississippi River near Alma, Wisconsin, in December of 2017. Macroscopic signs of disease included abdominal distension due to fluid accumulation within the internal organs as well as external and internal haemorrhaging. Histological evaluation revealed chronic peritonitis with peritoneal adhesions in all fish examined. Kidney, spleen and ascites fluid samples were collected from diseased bluegills and examined for the presence of pathogens. Bluegill picornavirus (BGPV) was isolated using tissue cell culture methods utilizing a recently developed, uncharacterized bluegill fry cell line (BF-4), and the presence of this virus was confirmed through molecular identification. The current geographic range, known susceptible hosts as well as historical epizootics associated with BPGV is discussed. The ability of BGPV to cause significant mortality in wild fish further emphasizes the importance of monitoring both wild and hatchery populations for this pathogen.

Yersinia ruckeri Isolated from Common Mudpuppy Necturus maculosus.

During a routine health inspection of apparently healthy wild-caught common mudpuppies Necturus maculosus, the bacteria Yersinia ruckeri was isolated and the identity confirmed using biochemical and molecular methods. This represents the first isolation of Y. ruckeri from an amphibian. This finding increases the known host range capable of harboring this important fish pathogen and could have serious management implications for aquaculture. Furthermore, addressing wild amphibians in fish hatchery biosecurity plans is discussed.

Optimizing, validating, and field testing a multiplex qPCR for the detection of amphibian pathogens.

Amphibian populations worldwide are facing numerous threats, including the emergence and spread of infectious diseases. In the past 2 decades, Batrachochytrium dendrobatidis (Bd), a parasitic fungus, and a group of viruses comprising the genus Ranavirus have become widespread and resulted in mass mortality events and extirpations worldwide. In 2013, another novel fungus, B. salamandrivorans (Bsal), was attributed to dramatic declines in populations of fire salamander Salamandra salamandra in the Netherlands. Experimental infections demonstrated that Bsal is highly pathogenic to numerous salamander genera. In an effort to prevent the introduction of Bsal to North America, the US Fish and Wildlife Service (USFWS) listed 201 salamander species as injurious wildlife under the Lacey Act. To determine infection status and accurately assess amphibian health, the development of a sensitive and specific diagnostic assay was needed. We describe the optimization and validation of a multiplex quantitative polymerase chain reaction (qPCR) protocol for the simultaneous detection of Bd, Bsal, and frog virus 3-like ranaviruses. A synthetic genome template (gBlock®) containing the target genes from all 3 pathogens served as the positive control and allowed accurate quantification of pathogen genes. The assay was validated in the field using an established non-lethal swabbing technique to survey local amphibian populations throughout a range of habitats. This multiplex qPCR demonstrates high reproducibility, sensitivity, and was capable of detecting both Bd and ranavirus in numerous locations, species, and life stages. Bsal was not detected at any point during these sampling efforts.