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Epidemics of H3N8 and H3N2 influenza A viruses (IAVs) in dogs, along with recognition of spillover infections from IAV strains typically found in humans or other animals, have emphasized the importance of efficient laboratory testing. Given the lack of active IAV surveillance or immunization requirements for dogs, cats, or horses imported into the United States, serotype prediction and whole-genome sequencing of positive specimens detected at veterinary diagnostic laboratories are also needed. The conserved sequences at the ends of the viral genome segments facilitate universal amplification of all segments of viral genomes directly from respiratory specimens. Although several methods for genomic analysis have been reported, no optimization focusing on companion animal strains has been described, to our knowledge. We compared 2 sets of published universal amplification primers using 26 IAV-positive specimens from dogs, horses, and a cat. Libraries prepared from the resulting amplicons were sequenced using Illumina chemistry, and reference-based assemblies were generated from the data produced by both methods. Although both methods produced high-quality data, coverage profiles and base calling differed between the 2 methods. The sequence data were also used to identify the subtype of the IAV strains sequenced and then compared to standard PCR assays for neuraminidase types N2 and N8.

The outcome of pathogen spillover from a reservoir to a novel host population can range from a “dead‐end” when there is no onward transmission in the recipient population, to epidemic spread and even establishment in new hosts. Understanding the evolutionary epidemiology of spillover events leading to discrete outcomes in novel hosts is key to predicting risk and can lead to a better understanding of mechanisms of emergence. Here we use a Bayesian phylodynamic approach to examine cross‐species transmission and evolutionary dynamics during a canine distemper virus spillover event causing clinical disease and population decline in an African lion population (Panthera leo) in the Serengeti Ecological Region between 1993 and 1994. Using 21 near‐complete viral genomes from four species we found that this large‐scale outbreak was likely ignited by a single cross‐species spillover event from a canid reservoir to non‐canid hosts less than one year before disease detection and explosive spread of CDV in lions. Cross‐species transmission from other non‐canid species likely fueled the high prevalence of CDV across spatially structured lion prides. Multiple lines of evidence suggest that spotted hyenas (Crocuta crocuta) could have acted as the proximate source of CDV exposure in lions. We report thirteen nucleotide substitutions segregating CDV strains found in canids and non‐canids. Our results are consistent with the hypothesis that virus evolution played a role in CDV emergence in non‐canid hosts following spillover during the outbreak, and suggests that host barriers to clinical infection can limit outcomes of CDV spillover in novel host species.

Background Equine parvovirus-hepatitis (EqPV-H) has been proposed as the aetiological cause of Theiler's disease, also known as serum hepatitis. EqPV-H-associated Theiler's disease has not been previously reported in Europe. Objectives To determine whether EqPV-H infection was associated with a 2018-2019 outbreak of Theiler's disease in four horses on a studfarm. Study design Descriptive case series. Methods The medical records of four horses from the same farm diagnosed with fatal Theiler's disease were examined retrospectively. Information collected included a clinical history, physical examination findings, tetanus antitoxin exposure, serum biochemistry and necropsy reports. Liver tissue from all four horses was tested for EqPV-H using PCR and in situ hybridisation (ISH) assays. Results Three of the horses had a history of recent (7-11 weeks) tetanus antitoxin administration. Liver tissue from all four horses tested positive for EqPV-H with PCR. In situ hybridisation revealed a widespread distribution of viral nucleic acid in hepatocytes in one case, and a more sporadic distribution in the remaining three cases. Main limitations Case controls were not available from the farm in question given the retrospective nature of analysis. Conclusions This case series documents the first reported EqPV-H-associated Theiler's disease in Europe and the first use of ISH to visualise the viral nucleic acid in liver tissues of horses with Theiler's disease.

An outbreak of canine distemper virus in a private zoo in eastern Tennessee in July 2016 led to fatal clinical disease in 5 adult, wild-caught Linnaeus’s 2-toed sloths ( Choloepus didactylus). Clinical signs included hyporexia, lethargy, mucopurulent nasal discharge, and oral and facial ulcers. At necropsy, affected animals had crusts and ulcers on the lips, nose, tongue, and oral cavity. Microscopically, all sloths had widespread, random, hepatic necrosis; lymphoid depletion; and bronchointerstitial pneumonia. The central nervous system did not contain gross or histopathologic lesions in any of the 5 sloths, although immunoreactivity for viral antigen was present within vessel walls. Epithelial cells and histiocytes within numerous organs contained intranuclear and intracytoplasmic inclusions and occasional syncytial cells. Canine distemper virus was confirmed with immunohistochemistry and virus isolation. Viral sequencing identified the novel American-4 strain prevalent in eastern Tennessee wildlife. This is the first pathologic characterization of canine distemper virus infection in sloths (family Choloepodidae, order Pilosa) and emphasizes the significant morbidity and mortality in this species.

Equine parvovirus-hepatitis (EqPV-H) has recently been associated with cases of Theiler's disease, a form of fulminant hepatic necrosis in horses. To assess whether EqPV-H is the cause of Theiler's disease, we first demonstrated hepatotropism by PCR on tissues from acutely infected horses. We then experimentally inoculated horses with EqPV-H and 8 of 10 horses developed hepatitis. One horse showed clinical signs of liver failure. The onset of hepatitis was temporally associated with seroconversion and a decline in viremia. Liver histology and in situ hybridization showed lymphocytic infiltrates and necrotic EqPV-H-infected hepatocytes. We next investigated potential modes of transmission. Iatrogenic transmission via allogeneic stem cell therapy for orthopedic injuries was previously suggested in a case series of Theiler's disease, and was demonstrated here for the first time. Vertical transmission and mechanical vectoring by horse fly bites could not be demonstrated in this study, potentially due to limited sample size. We found EqPV-H shedding in oral and nasal secretions, and in feces. Importantly, we could demonstrate EqPV-H transmission via oral inoculation with viremic serum. Together, our findings provide additional information that EqPV-H is the likely cause of Theiler's disease and that transmission of EqPV-H occurs via both iatrogenic and natural routes.

Feline herpesvirus type 1 (FHV-1) is endemic in captive cheetahs and sporadically causes devastating disease. Modified live vaccines (MLV), intended for use in domestic cats, are used in some captive cheetah populations and have been anecdotally linked to disease in certain subpopulations. Ten FHV-1 isolates from ten captive cheetahs and one isolate from an MLV used to inoculate four of the host animals were analyzed. Viral DNA was extracted for full-genome sequencing by Illumina MiSeq with viral genomes then used for phylogenomic and recombinational analyses. The FHV-1 shed by vaccinated cheetahs were almost identical to the MLV, with few variants among viral genomes. Eight cheetah FHV-1 isolates and the MLV were grouped in a clade along with FHV-1 isolates from domestic cats in the USA. The remaining two cheetah FHV-1 isolates (unknown host vaccine status) were not associated with a clade. The likely ancestral origin of these two isolates involves recombination events between Australian domestic cat and cheetah FHV-1 isolates. Collectively, these data suggest that the MLV is capable of causing clinical disease and viral shedding in some cheetahs and represents evidence of interspecies transmission of virus between domestic and wild cats.

A concurrent outbreak of infection by canine parvovirus 2b (CPV-2b) and Clostridium difficile producing A and/or B toxins occurred in Asian small-clawed otters ( Amblonyx cinereus). The 5 clinically affected otters were 6- to 24-mo-old intact females that had severe diarrhea, dehydration, were acutely comatose, and died 1–4 d after the onset of clinical signs. Postmortem examination was performed in 3 of 7 otters. Macroscopically, the small intestine was diffusely reddened and contained red-to-brown, malodorous, watery digesta without formed feces (3 of 3). Histologic examination identified loss of enterocytes and necrosis of crypt epithelial cells. Denuded villi were often covered by mixed bacterial colonies with a predominance of gram-positive cocci to short rods in addition to larger gram-positive and -negative rods. There was also splenic lymphoid follicle depletion (2 of 3). Immunofluorescence assay revealed CPV antigen in enterocytes (2 of 3), mesenteric lymph nodes (3 of 3), and spleen (1 of 3). Immunohistochemistry revealed CPV antigen in enterocytes, lymphocytes, and dendritic cells of the Peyer patches and spleen (3 of 3), and lingual epithelial cells (1 of 2). CPV was isolated from tissues from 2 of 3 otters, and DNA sequencing identified CPV-2b for the 1 isolate tested. C. difficile producing A and/or B toxins were identified in the intestinal content by ELISA (3 of 3). To our knowledge, an outbreak of CPV-2b infection and C. difficile with clinically significant gastrointestinal disease has not been described previously in otters. The source of the viral infections remains unknown; however, these agents should be considered in otters and other mesocarnivores with similar clinical and pathologic findings.

The Cooper and Los Angeles (LA) strains were the two original respiratory strains of bovine herpesvirus type 1.1 (BoHV-1.1) isolated in the 1950s from cattle with infectious bovine rhinotracheitis. We report the complete genome sequence for the BoHV-1.1 LA strain and compare it to the prototype Cooper strain and six wild-type BoHV-1.1 isolates. A nucleotide sequence divergence of 0.74% was noted across the two complete genomes, caused by 19 single-nucleotide polymorphisms (SNPs) involving 12 genes and insertions/deletions that primarily affected the number of repeats within reiterated repeat regions of the genome. Phylogenetic analysis revealed that Cooper and LA strains are genetically the most ancient strains from which all of the more-recently isolated field strains of BoHV-1.1 evolved.

Latent canine herpesvirus-1 (CaHV-1) infections are common in domestic dogs, but viral shedding patterns in dogs are poorly understood. Previous research failed to detect spontaneous subclinical ocular CaHV-1 shedding in dogs following ocular infection, a situation that is fundamentally distinct from many of the alphaherpesviruses closely related to CaHV-1. One possible explanation for this finding is that the sampling interval in the prior studies evaluating ocular shedding patterns was too infrequent to detect rapidly cleared, brief ocular viral shedding episodes. To evaluate for this potential viral shedding scenario, 10 laboratory beagles recovered from experimental primary ocular CaHV-1 infection and with latent CaHV-1infection were intensively monitored for viral reactivation and shedding for 28 days. Clinical ophthalmic examinations were performed daily. Ocular swab samples were collected for CaHV-1 polymerase chain reaction 3 times daily and CaHV-1 virus neutralizing antibody assays were evaluated at 2-week intervals. No abnormalities suggestive of recurrent CaHV-1 ocular disease were observed during clinical ophthalmic examination in the dogs during the study. Ocular CaHV-1 shedding was not detected by polymerase chain reaction and CaHV-1 virus neutralizing antibody titers remained stable in all dogs for the study duration. In the present study utilizing frequent multiple daily sample collections, no evidence of subclinical ocular CaHV-1 shedding was detected in mature dogs with experimentally-induced latent CaHV-1 infection.

Pegiviruses frequently cause persistent infection (as defined by >6 months), but unlike most other Flaviviridae members, no apparent clinical disease. Human pegivirus (HPgV, previously GBV-C) is detectable in 1–4% of healthy individuals and another 5–13% are seropositive. Some evidence for infection of bone marrow and spleen exists. Equine pegivirus 1 (EPgV-1) is not linked to disease, whereas another pegivirus, Theiler’s disease-associated virus (TDAV), was identified in an outbreak of acute serum hepatitis (Theiler’s disease) in horses. Although no subsequent reports link TDAV to disease, any association with hepatitis has not been formally examined. Here, we characterized EPgV-1 and TDAV tropism, sequence diversity, persistence and association with liver disease in horses. Among more than 20 tissue types, we consistently detected high viral loads only in serum, bone marrow and spleen, and viral RNA replication was consistently identified in bone marrow. PBMCs and lymph nodes, but not liver, were sporadically positive. To exclude potential effects of co-infecting agents in experimental infections, we constructed full-length consensus cDNA clones; this was enabled by determination of the complete viral genomes, including a novel TDAV 3’ terminus. Clone derived RNA transcripts were used for direct intrasplenic inoculation of healthy horses. This led to productive infection detectable from week 2–3 and persisting beyond the 28 weeks of study. We did not observe any clinical signs of illness or elevation of circulating liver enzymes. The polyprotein consensus sequences did not change, suggesting that both clones were fully functional. To our knowledge, this is the first successful extrahepatic viral RNA launch and the first robust reverse genetics system for a pegivirus. In conclusion, equine pegiviruses are bone marrow tropic, cause persistent infection in horses, and are not associated with hepatitis. Based on these findings, it may be appropriate to rename the group of TDAV and related viruses as EPgV-2., Author summary Transmissible hepatitis in horses (Theiler’s disease) has been known for 100 years without knowledge of causative infectious agents. Recently, two novel equine pegiviruses (EPgV) were discovered. Whereas EPgV-1 was not associated to disease, the other was identified in an outbreak of acute serum hepatitis and therefore named Theiler’s disease-associated virus (TDAV). This finding was surprising since human and monkey pegiviruses typically cause long-term infection without associated clinical disease. Whereas no subsequent reports link TDAV to disease, the original association to hepatitis has not been formally examined. Here, we studied EPgV-1 and TDAV and found that their natural history of infection in horses were remarkably similar. Examination of various tissues identified the bone marrow as the primary site of replication for both viruses with no evidence of replication in the liver. To exclude potential effects of other infectious agents, we developed molecular full-length clones for EPgV-1 and TDAV and were able to initiate infection in horses using derived synthetic viral genetic material. This demonstrated long-term infection, but no association with hepatitis. These findings call into question the connection between TDAV, liver infection, and hepatitis in horses.

Island fox (Urocyon littoralis) populations on four California Channel Islands have declined severely since 1994. Canine distemper (CDV) was suspected to be responsible for the decline of the Santa Catalina Island fox, so knowledge of infectious disease exposure in the remaining island fox populations was urgently needed. This study reviewed previous pathogen exposure in island foxes and investigated the current threat by conducting a serologic survey of foxes on all islands and sympatric feral cats on three islands from 2001 to 2003 for antibodies against canid pathogens. Before the decline, foxes had evidence of exposure to CDV, canine adenovirus (CAV), canine parvovirus (CPV), and Toxoplasma, with exposure to these five pathogens differing greatly by island. Exposure to canine coronavirus (CCV), canine herpesvirus (CHV), and Leptospira was rare. In 2001–2003, wild-born foxes had evidence of exposure to CDV (5.2–32.8%) on 5 of 6 islands, CPV (28–100%) and CAV (4.7–100%) on five islands, and Toxoplasma gondii (2.3–15.4%) on four islands. Exposure to CCV, CHV and Leptospira was less common. Sharing of infectious agents between sympatric foxes and feral cats appeared minimal, but CDV exposure was detected in two cats on Santa Catalina Island. Domestic dogs have historically been present on the islands, but it is not known if canine diseases can be maintained in fox populations without the continual presence of dogs. Targeted vaccination programs against the most virulent pathogens and continued intensive disease surveillance may help protect the critically small remaining fox populations from disease outbreaks that could threaten the success of ongoing conservation efforts.

Serum samples of 11 Bengal tigers (Panthera tigris tigris) from Chitwan National Park in Nepal, collected between 2011-17, were evaluated for the presence of antibodies to eight diseases commonly investigated in large felids. This initial serologic survey was done to establish baseline information to understand the exposure of Nepal's free-ranging tiger population to these diseases. Tiger serum samples collected opportunistically during encounters such as translocation, human conflict, and injury were placed in cold storage for later use. Frozen serum samples were assessed for feline coronavirus (FCoV), feline immunodeficiency virus, feline leukemia virus, feline herpesvirus (FHV), canine distemper virus, canine parvovirus-2 (CPV-2), leptospirosis (LEP; seven serovars), and toxoplasmosis (TOX). Six tigers were found to be positive for LEP, eight for CPV-2, five for FHV, one for FCoV, and 10 for TOX. Tigers, like other wild felids, have been exposed to these common pathogens, but further research is needed to determine the significance of these pathogens to the Nepali population.

As part of the national recovery effort, endangered black-footed ferrets (Mustela nigripes) were reintroduced to the Cheyenne River Sioux Reservation in South Dakota, US in 2000. Despite an encouraging start, numbers of ferrets at the site have declined. In an effort to determine possible causes of the population decline, we undertook a pathogen survey in 2012 to detect exposure to West Nile virus (WNV), canine distemper virus (CDV), plague (Yersinia pestis), tularemia (Francisella tularensis), and heartworm (Dirofilaria immitis) using coyotes (Canis latrans) as a sentinel animal. The highest seroprevalence was for WNV with 71% (20/28) of coyotes testing antibody-positive. Seroprevalence of CDV and plague were lower, 27% and 13%, respectively. No evidence of active infection with tularemia or heartworm was seen in the coyotes sampled. As this study did not sample black-footed ferrets themselves, the definitive cause for the decline of this population cannot be determined. However, the presence of coyotes seropositive for two diseases, plague and CDV, lethal to black-footed ferrets, indicated the potential for exposure and infection. The high seroprevalence of WNV in the coyotes indicated a wide exposure to the virus; therefore, exposure of black-footed ferrets to the virus is also likely. Due to the ability of WNV to cause fatal disease in other species, studies may be useful to elucidate the impact that WNV could have on the success of reintroduced black-footed ferrets as well as factors influencing the spread and incidence of the disease in a prairie ecosystem.

Background A novel equine parvovirus (EqPV-H) was recently discovered in the equine liver with Theiler's disease. Objectives To determine the prevalence of EqPV-H infection in naturally occurring Theiler's disease cases and in-contact horses in the absence of historical equine biologic product administration. Animals Ten cases of Theiler's disease from 6 separate properties were included in the study, based on the criteria of acute onset of clinical signs of liver failure with laboratory or histopathologic findings characteristic of Theiler's disease and no history of receiving an equine biologic product within the preceding 4 months. In addition, 37 in-contact horses from 4 of the 6 properties were screened for EqPV-H infection and hepatitis. Methods In prospective case series, cases were diagnosed with Theiler's disease by the attending veterinarian and were tested for EqPV-H by PCR of liver or serum. In-contact horses were assessed via serum chemistry and PCR at the attending veterinarian's discretion. Hepatitis was defined as serum gamma-glutamyltransferase activity above reference interval. The association of EqPV-H with hepatitis was determined by Fisher's exact test. Results Nine of 10 (90%) Theiler's disease cases and 54% of tested in-contact horses were EqPV-H positive. Hepatitis was significantly associated with EqPV-H infection (P = .036). Conclusions and clinical importance Although further study is required to identify EqPV-H as the causative agent of Theiler's disease, EqPV-H appears strongly associated with cases of fatal Theiler's disease and subclinical hepatitis in horses in contact with those cases. The prevalence of EqPV-H infection on affected properties can be high.

Equine serum hepatitis (i.e., Theiler’s disease) is a serious and often life-threatening disease of unknown etiology that affects horses. A horse in Nebraska, USA, with serum hepatitis died 65 days after treatment with equine-origin tetanus antitoxin. We identified an unknown parvovirus in serum and liver of the dead horse and in the administered antitoxin. The equine parvovirus-hepatitis (EqPV-H) shares

A canine influenza A(H3N2) virus emerged in the United States in February-March 2015, causing respiratory disease in dogs. The virus had previously been circulating among dogs in Asia, where it originated through the transfer of an avian-origin influenza virus around 2005 and continues to circulate. Sequence analysis suggests the US outbreak was initiated by a single introduction, in Chicago, of an H3N2 canine influenza virus circulating among dogs in South Korea in 2015. Despite local control measures, the virus has continued circulating among dogs in and around Chicago and has spread to several other areas of the country, particularly Georgia and North Carolina, although these secondary outbreaks appear to have ended within a few months. Some genetic variation has accumulated among the US viruses, with the appearance of regional-temporal lineages. The potential for interspecies transmission and zoonotic events involving this newly emerged influenza A virus is currently unknown.

The Galapagos sea lion ( Zalophus wollebaeki ), an endangered species, experiences high pup mortality (up to 100%) in years when El Niño events reduce food supply in the Galapagos Islands. Mortality of pups in non-El Niño years is estimated to be 5% in undisturbed colonies. From 2009 to 2012 we observed high pup mortality (up to 67%) in colonies close to the Galapagos capital, Puerto Baquerizo Moreno, where contact with humans, domestic animals, and rats is frequent. Gross postmortem findings from 54 pups included hemorrhagic lesions in liver and congestion in lungs; histopathology suggested a possible association with infectious diseases. Evidence of Leptospira infection was found in five out of seven samples collected in 2010. Canine distemper viral (CDV) RNA was detected in tissues from six sea lions (in 2011-12), four of which were confirmed by nucleotide sequencing. The absence of CDV antibodies in 109 juvenile animals tested in 2014 at urban and remote colonies could indicate that the CDV infection observed in 2011 was likely confined to a few animals. Our results indicated that Galapagos sea lions have been exposed at least to two pathogens, Leptospira and CDV; however, the impact of these infections on the sea lions is unclear.

West Nile virus (genus Flavivirus) outbreaks and mortality events have been documented in both wild and captive avian species, including penguins. Serologic response to vaccination in avian species has varied and appears to be largely species dependent; however, Humboldt penguins ( Spheniscus humboldti ) previously showed excellent rates of seroconversion. The goal of this study was to determine virus neutralization titers of 17 Humboldt penguin hens and their subsequent eggs, chicks, or both following vaccination with a killed West Nile vaccine. Chicks were also vaccinated at 56, 70, and 84 days old. Titers were measured from 10-346 days prior to lay as well as serially in seven chicks. Data collected showed positive rank correlation between maternal titers and yolk titers (ρ = 0.90, P0.0001, n = 14) but no association between booster vaccination and yolk titers. All seven chicks had detectable antibody on days 14 and 28, and antibody levels had increased (relative to day 56) in 3 of 6 chicks (50%; 95% confidence interval 14-86%) by day 112. Further information is provided on a suggested vaccination schedule for Humboldt penguin chicks based on a time-dependent decline in maternal antibody titers. Cell-mediated immunity and experimental challenge following vaccination have not yet been investigated in this species.

No evidence of exposure to canine distemper virus (CDV) was detected in 70 samples corresponding to 58 wild-trapped Darwin's foxes (

The aim of this study of serpentovirus infection in captive snakes was to assess the susceptibility of different types of snakes to infection and disease, to survey viral genetic diversity, and to evaluate management practices that may limit infection and disease. Antemortem oral swabs were collected from 639 snakes from 12 US collections, including 62 species, 28 genera, and 6 families: Pythonidae (N = 414 snakes; pythons were overrepresented in the sample population), Boidae (79), Colubridae (116), Lamprophiidae (4), Elapidae (12), and Viperidae (14). Infection was more common in pythons (38%; 95% CI: 33.1–42.4%), and in boas (10%; 95% CI: 5.2–18.7%) than in colubrids (0.9%, 95% CI

A concurrent outbreak of infection by canine parvovirus 2b (CPV-2b) and Clostridium difficile producing A and/or B toxins occurred in Asian small-clawed otters (Amblonyx cinereus). The 5 clinically affected otters were 6- to 24-mo-old intact females that had severe diarrhea, dehydration, were acutely comatose, and died 1–4 d after the onset of clinical signs. Postmortem examination was performed in 3 of 7 otters. Macroscopically, the small intestine was diffusely reddened and contained red-to-brown, malodorous, watery digesta without formed feces (3 of 3). Histologic examination identified loss of enterocytes and necrosis of crypt epithelial cells. Denuded villi were often covered by mixed bacterial colonies with a predominance of gram-positive cocci to short rods in addition to larger gram-positive and -negative rods. There was also splenic lymphoid follicle depletion (2 of 3). Immunofluorescence assay revealed CPV antigen in enterocytes (2 of 3), mesenteric lymph nodes (3 of 3), and spleen (1 of 3). Immunohistochemistry revealed CPV antigen in enterocytes, lymphocytes, and dendritic cells of the Peyer patches and spleen (3 of 3), and lingual epithelial cells (1 of 2). CPV was isolated from tissues from 2 of 3 otters, and DNA sequencing identified CPV-2b for the 1 isolate tested. C. difficile producing A and/or B toxins were identified in the intestinal content by ELISA (3 of 3). To our knowledge, an outbreak of CPV-2b infection and C. difficile with clinically significant gastrointestinal disease has not been described previously in otters. The source of the viral infections remains unknown; however, these agents should be considered in otters and other mesocarnivores with similar clinical and pathologic findings.

Canine parvovirus (CPV) is a highly successful pathogen that has sustained pandemic circulation in dogs for more than 40 years. Here, integrating full-genome and deep sequencing analyses, structural information, andin vitroexperimentation, we describe the macro- and micro-scale features that have accompanied CPV’s evolutionary success. Despite 40 years of viral evolution, all CPV variants are >∼99% identical in nucleotide sequence, with only a limited number (IMPORTANCERapid mutation rates and correspondingly high levels of standing intra-host diversity and accumulated inter-host diversity over epidemic scales are often cited as key features of viruses with the capacity for emergence and sustained transmission in a new host species. However, most of this information comes from studies of RNA viruses, with relatively little being known about that evolutionary processes that occur for viruses with DNA genomes. Here we provide a unique model of virus evolution, integrating both long-term global-scale and short-term intra-host evolutionary processes of a virus in a new host animal. Our analysis reveals that successful host jumping and sustained onward transmission does not necessarily depend on a high level of intra-host diversity or result in the continued accumulation of high levels of long-term evolution change. These findings indicate that all aspects of a virus’s biology and ecology are relevant when considering their adaptability.

Epizootic mortalities in American Crows (

Three fishers ( Martes pennanti), 2 gray foxes ( Urocyon cinereoargenteus), 1 mink ( Neovison vison), 1 skunk ( Mephitis mephitis), and 1 raccoon ( Procyon lotor), from Vermont and New Hampshire, had lesions on autopsy consistent with canine distemper virus (CDV) infections diagnosed in a 12-mo period in 2016–2017. Lesions of CDV infection were most commonly noted in the lungs (8 of 8 animals), urothelium (5 of 8), biliary tract (5 of 8), gastrointestinal tract (4 of 7), and brain (4 of 6). Splenic lesions were seen in 3 animals. The diagnosis was confirmed via immunohistochemistry and virus isolation. Viral genotyping indicated that all 8 animals were infected with a distinct clade of CDV that has only been reported in wildlife in New England, and this clade of viruses is distinct from vaccine strains. During the 12 mo when these cases occurred, no other CDV clade was identified in any other wildlife or domesticated animal submitted from the 2 states.

Bovine herpesvirus type 1 (BoHV-1) causes various disease syndromes in cattle including respiratory disease and abortions. During an investigation into the potential role of BoHV-1 modified-live vaccines (MLV) causing diseases in cattle, we performed whole genome sequencing on six BoHV-1 field strains isolated at Cornell Animal Health Diagnostic Center in the late 1970s. Three isolates (two respiratory and a fetal) were identified as vaccine-derived isolates, having SNP patterns identical to that of a previously sequenced MLV virus that exhibited a deleted US2 and truncated US1.67 genes. Two other isolates (a respiratory and a fetal) were categorized as wild-type (WT) viruses based on their unique SNP pattern that is distinct from MLV viruses. The sixth isolate from an aborted fetus was a recombinant virus with 62% of its genome exhibiting SNPs identical to one of the above-mentioned WT viruses also recovered from an aborted fetus. The remaining 38% consisted of two blocks of sequences derived from the MLV virus. The first block replaced the UL9-UL19 region, and the second vaccine-derived sequence block encompassed all the genes within the unique short region and the internal/terminal repeats containing the regulatory genes BICP4 and BICP22. This is confirmatory evidence that recombination between BoHV-1 MLV and WT viruses can occur under natural conditions and cause disease. It is important in that it underscores the potential for the glycoprotein E negative (gE-) marker vaccine used to eradicate BoHV-1 in some countries, to recombine with virulent field strains allowing them to capture the gE- marker, thereby endangering the control and eradication programs.

Understanding multi-host pathogen maintenance and transmission dynamics is critical for\ud disease control. However, transmission dynamics remain enigmatic largely because they are\ud difficult to observe directly, particularly in wildlife. Here, we investigate the transmission\ud dynamics of canine parvovirus (CPV) using state-space modelling of 20-years of CPV serology\ud data from domestic dogs and African lions in the Serengeti ecosystem. We show that, although\ud vaccination reduces the probability of infection in dogs, and despite indirect enhancement of\ud population seropositivity as a result of vaccine shedding, the vaccination coverage achieved\ud has been insufficient to prevent CPV from becoming widespread. CPV is maintained by the\ud dog population and has become endemic with ~3.5-year cycles and prevalence reaching ~80%.\ud While the estimated prevalence in lions is lower, peaks of infection consistently follow those\ud in dogs. Dogs exposed to CPV are also more likely to become infected with a second multihost\ud pathogen, canine distemper virus. However, vaccination can weaken this coupling raising\ud questions about the value of monovalent versus polyvalent vaccines against these two\ud pathogens. Our findings highlight the need to consider both pathogen- and host-level\ud community interactions when seeking to understand the dynamics of multi-host pathogens and\ud their implications for conservation, disease surveillance and control programmes.

Parapoxviruses (PaPVs) cause widespread infections in ruminants worldwide. All PaPVs are zoonotic and may infect humans after direct or indirect contact with infected animals. Herein we report the development and validation of a highly sensitive real-time PCR assay for rapid detection of PaPVs. The new assay (referred to as the RVSS assay) was specific for PaPVs only and had no cross-reactivity against other pox viruses. Using a recombinant plasmid as positive control, the analytical sensitivity of the assay was determined to be 16 genome copies of PaPV per assay. The amplification efficiency estimate (91–99%), the intra- and interassay variability estimate (standard deviation [SD]: 0.28–1.06 and 0.01–0.14, respectively), and the operator variability estimate (SD: 0.78 between laboratories and 0.28 between operators within a laboratory) were within the acceptable range. The diagnostic specificity was assessed on 100 specimens from healthy normal animals and all but 1 tested negative (99%). The diagnostic sensitivity (DSe) was assessed on 77 clinical specimens (skin/scab) from infected sheep, goats, and cattle, and all tested positive (100%). The assay was multiplexed with beta-actin as an internal positive control, and the multiplex assay exhibited the same DSe as the singleplex assay. Further characterization of the PaPV specimens by species-specific real-time PCR and nucleotide sequencing of the PCR products following conventional PCR showed the presence of Orf virus not only in sheep and goats but also in 1 bovid. The validated RVSS assay demonstrated high specificity, sensitivity, reproducibility, and ruggedness, which are critical for laboratory detection of PaPVs.

Was the 1993/1994 fatal canine distemper virus (CDV) epidemic in lions and spotted hyaenas in the Serengeti ecosystem caused by the recent spillover of a virulent domestic dog strain or one well adapted to these noncanids? We examine this question using sequence data from 13 ‘Serengeti’ strains including five complete genomes obtained between 1993 and 2011. Phylogenetic and haplotype network analyses reveal that strains from noncanids during the epidemic were more closely related to each other than to those from domestic or wild canids. All noncanid ‘Serengeti’ strains during the epidemic encoded: (1) one novel substitution G134S in the CDV‐V protein; and (2) the rare amino acid combination 519I/549H at two sites under positive selection in the region of the CDV‐H protein that binds to SLAM (CD 150) host cell receptors. Worldwide, only a few noncanid strains in the America II lineage encode CDV‐H 519I/549H. All canid ‘Serengeti’ strains during the epidemic coded CDV‐V 134G, and CDV‐H 519R/549Y, or 519R/549H. A functional assay of cell entry revealed the highest performance by CDV‐H proteins encoding 519I/549H in cells expressing lion SLAM receptors, and the highest performance by proteins encoding 519R/549Y, typical of dog strains worldwide, in cells expressing dog SLAM receptors. Our findings are consistent with an epidemic in lions and hyaenas caused by CDV variants better adapted to noncanids than canids, but not with the recent spillover of a dog strain. Our study reveals a greater complexity of CDV molecular epidemiology in multihost environments than previously thought.

Bovine herpesvirus-1 (BoHV-1) causes disease in cattle with varied clinical forms. In the U.S. there are two BoHV1 subtypes, BoHV-1.1 and BoHV-1.2b. Control programs in North America incorporate modified live (MLV) or killed (KV) viral vaccines. However, BoHV-1 strains continue to be isolated from diseased animals or fetuses after vaccination. It is possible to differentiate BoHV-1 wild-type from MLV vaccine strains by determining their single nucleotide polymorphism (SNP) patterns through either whole-genome sequencing or PCR sequencing of genomic regions containing vaccine-defining SNPs. To determine the BoHV-1 subtype in clinical isolates and their relationship to MLV strains, 8 isolates from varied clinical disease at three different laboratories in the U.S. were sequenced and phylogenetically analyzed. Five samples were isolated within the past 5 years from New York and 3 were archived samples recovered 35 years prior from Oklahoma and Louisiana. Based on phylogenetic analysis, four of the cases appeared to be due to an MLV vaccine: 3 cases of aborted fetuses and one neonate with systemic BoHV-1 disease. One aborted fetus was from a herd with no reported history of MLV vaccination in two years. The remaining four isolates did not group with any MLV vaccines: two were associated with bovine respiratory disease, one with vulvovaginitis, and a fourth was determined to be a BoHV-1.2b respiratory isolate. Recovery of BoHV-1.1 that is very closely related to an MLV vaccine virus from a herd not receiving vaccines in an extended period prior to its isolation suggests that MLV viruses may remain latent or circulate within herds for long periods.

Introduced animals impact endemic populations through predation, competition, and disease transmission. Populations of endemic carnivores in Madagascar are declining, and pathogens transmitted from introduced species may further endanger these unique species. We assessed the exposure of introduced and endemic carnivores to common viral and parasitic pathogens in two national parks of Madagascar (Kirindy Mitea National Park and Ankarafantsika National Park) and their neighboring villages. We also identified variables associated with the presence of antibodies to these pathogens in fosa ( Cryptoprocta ferox ). Introduced and endemic species were exposed to canine parvovirus, canine herpesvirus, feline calicivirus, and Toxoplasma gondii . Domestic dogs ( Canis familiaris ) and cats ( Felis catus ) may be sources of infection for these pathogens. Prevalence of antibodies to Toxoplasma in captured fosa was93%, and adults were more likely to be exposed than immature individuals. Our data provide a basis upon which to evaluate and manage risks of pathogen transmission between species.

No evidence of exposure to canine distemper virus (CDV) was detected in 70 samples corresponding to 58 wild-trapped Darwin's foxes (Lycalopex fulvipes) in Chile. Given its current endangered status and it being immunologically naive, in the event of a CDV spillover from dogs to foxes, high population mortality is expected.

Adenoviruses have been reported to affect a broad range of host species, tend to be species specific, and often affect the respiratory system. This report describes the isolation of an adenovirus from deep nasal swabs of two wild North American porcupines (Erethizon dorsatum) with respiratory diseases that presented to a wildlife hospital. Partial sequences of the deoxyribonucleic acid polymerase gene of the isolated virus were identical to skunk adenovirus (SkAdV-1), also known as pygmy marmoset adenovirus. Both porcupines survived and were released back to the wild after successful medical treatment and rehabilitation. The significance of the adenovirus isolated from these porcupines is unknown; however, this is the first report of an adenovirus in porcupines, and the first report of SkAdV-1 in a rodent.

Canine influenza virus (CIV) subtypes H3N8 and H3N2 are endemic among domestic dog ( Canis lupus familiaris ) populations in the northeastern US. Infection of free-ranging carnivores with influenza virus has been sporadically reported. Generalist mesocarnivores that exploit anthropogenic, peri-urban habitats share a wide interface with domestic dogs that allows for the transmission of infectious disease. To investigate the potential exposure of free-ranging canids to CIV in Pennsylvania, US, serum samples were obtained from freshly killed coyotes ( Canis latrans, n=67), grey foxes ( Urocyon cinereoargenteus, n=8), and red foxes ( Vulpes vulpes, n=5) from 24 counties. Animals were harvested during the January-February 2017 hunting season. We failed to detect antibodies to CIV subtypes H3N2 and H3N8 by using hemagglutination inhibition assays validated for domestic dogs. Results suggest CIV was not endemic in free-ranging canid populations in Pennsylvania or that prevalence was too low to be detected by our limited sample size.

Background Three flaviviruses (equine pegivirus [EPgV]; Theiler's disease-associated virus [TDAV]; non-primate hepacivirus [NPHV]) and equine parvovirus (EqPV-H) are present in equine blood products; the TDAV, NPHV, and EqPV-H have been suggested as potential causes of serum hepatitis. Objective To determine the prevalence of these viruses in horses with equine serum hepatitis. Animals Eighteen horses diagnosed with serum hepatitis, enrolled from US referral hospitals. Methods In the prospective case study, liver, serum, or both samples were tested for EPgV, TDAV, NPHV, and EqPV-H by PCR. Results Both liver tissue and serum were tested for 6 cases, serum only for 8 cases, and liver only for 4 cases. Twelve horses received tetanus antitoxin (TAT) 4-12.7 weeks (median = 8 weeks), 3 horses received commercial equine plasma 6-8.6 weeks, and 3 horses received allogenic stem cells 6.4-7.6 weeks before the onset of hepatic failure. All samples were TDAV negative. Two of 14 serum samples were NPHV-positive. Six of 14 serum samples were EPgV-positive. All liver samples were NPHV-negative and EPgV-negative. EqPV-H was detected in the serum (N = 8), liver (N = 4), or both samples (N = 6) of all 18 cases. The TAT of the same lot number was available for virologic testing in 10 of 12 TAT-associated cases, and all 10 samples were EqPV-H positive. Conclusions and clinical importance We demonstrated EqPV-H in 18 consecutive cases of serum hepatitis. EPgV, TDAV, and NPHV were not consistently present. This information should encourage blood product manufacturers to test for EqPV-H and eliminate EqPV-H-infected horses from their donor herds.

Avian-origin H3N2 canine influenza virus (CIV) transferred to dogs in Asia around 2005, becoming enzootic throughout China and South Korea before reaching the United States in early 2015. To understand the posttransfer evolution and epidemiology of this virus, particularly the cause of recent and ongoing increases in incidence in the United States, we performed an integrated analysis of whole-genome sequence data from 64 newly sequenced viruses and comprehensive surveillance data. This revealed that the circulation of H3N2 CIV within the United States is typified by recurrent epidemic burst–fade-out dynamics driven by multiple introductions of virus from Asia. Although all major viral lineages displayed similar rates of genomic sequence evolution, H3N2 CIV consistently exhibited proportionally more nonsynonymous substitutions per site than those in avian reservoir viruses, which is indicative of a large-scale change in selection pressures. Despite these genotypic differences, we found no evidence of adaptive evolution or increased viral transmission, with epidemiological models indicating a basic reproductive number, R0, of between 1 and 1.5 across nearly all U.S. outbreaks, consistent with maintained but heterogeneous circulation. We propose that CIV9s mode of viral circulation may have resulted in evolutionary cul-de-sacs, in which there is little opportunity for the selection of the more transmissible H3N2 CIV phenotypes necessary to enable circulation through a general dog population characterized by widespread contact heterogeneity. CIV must therefore rely on metapopulations of high host density (such as animal shelters and kennels) within the greater dog population and reintroduction from other populations or face complete epidemic extinction. IMPORTANCE The relatively recent appearance of influenza A virus (IAV) epidemics in dogs expands our understanding of IAV host range and ecology, providing useful and relevant models for understanding critical factors involved in viral emergence. Here we integrate viral whole-genome sequence analysis and comprehensive surveillance data to examine the evolution of the emerging avian-origin H3N2 canine influenza virus (CIV), particularly the factors driving ongoing circulation and recent increases in incidence of the virus within the United States. Our results provide a detailed understanding of how H3N2 CIV achieves sustained circulation within the United States despite widespread host contact heterogeneity and recurrent epidemic fade-out. Moreover, our findings suggest that the types and intensities of selection pressures an emerging virus experiences are highly dependent on host population structure and ecology and may inhibit an emerging virus from acquiring sustained epidemic or pandemic circulation.

Carnivores of Madagascar are at increased risk of extinction due to anthropogenic loss of habitat, hunting, and interactions with introduced carnivores. Interactions between introduced and native animals also present the potential for introduction of pathogens into new geographic areas or host species. Here, we provide serologic data regarding pathogen exposure of domestic and native carnivores from the Betampona Natural Reserve Landscape, a protected area in eastern Madagascar. For the Eupleridae, we found limited evidence of exposure to viruses from domestic animals but greater prevalence for Toxoplasma gondii (39%) and Leptospira interrogans (40%). We also evaluated the associations between the presence of antibodies to selected pathogens and the demographic and spatial variables. We showed that individual characteristics such as sex and species were associated with exposure to T. gondii but not to L. interrogans or canine parvovirus (CPV). Finally, we investigated the spatial structure of pathogen exposure in Betampona and found no evidence of spatial structuring, indicating the absence of hotspots and agent-free refugia for T. gondii, L. interrogans, and CPV in the protected area. Our results may be useful for assessing and monitoring disease risk and for formulating control strategies to minimize the negative impact of exotic species on the endemic carnivores of Madagascar.

Canine distemper virus (CDV) affects many wild and captive, nondomestic species worldwide but has not been previously reported in Xenarthra. Paucity of information on vaccination safety and efficacy presents challenges for disease prevention in captive collections. CDV infections and subsequent mortalities in five captive Linnaeus's two-toed sloths ( Choloepus didactylus) in eastern Tennessee are reported. Clinical signs included oculonasal discharge, oral ulcerations, and diarrhea, and the diagnosis was confirmed by necropsy, histopathology, immunohistochemistry, virus isolation, and polymerase chain reaction. Viral sequencing identified the strain to be consistent with a new CDV lineage currently affecting domestic dogs and wildlife in Tennessee. Seven sloths were examined and vaccinated using a recombinant CDV vaccine on days 0 and 21. Subsequent blood samples showed increased titers in 3/4 sloths. Based on the outbreak and serologic findings postvaccination without adverse effects, the authors recommend recombinant CDV vaccination in sloths exposed to known carriers of CDV.

Bluetongue virus (BTV) is a vector-transmitted pathogen that typically infects and causes disease in domestic and wild ruminants. BTV is also known to infect domestic canines as discovered when dogs were vaccinated with a BTV-contaminated vaccine. Canine BTV infections have been documented through serological surveys, and natural infection by the Culicoides vector has been suggested. The report of isolation of BTV serotype 11 (BTV-11) from 2 separate domestic canine abortion cases in the states of Texas in 2011 and Kansas in 2012, were apparently unrelated to BTV-contaminated vaccination or consumption of BTV-contaminated raw meat as had been previously speculated. To elucidate the origin and relationship of these 2 domestic canine BTV-11 isolates, whole genome sequencing was performed. Six additional BTV-11 field isolates from Texas, Florida, and Washington, submitted for diagnostic investigation during 2011 and 2013, were also fully sequenced and analyzed. The phylogenetic analysis indicates that the BTV-11 domestic canine isolates are virtually identical, and both share high identity with 2 BTV-11 isolates identified from white-tailed deer in Texas in 2011. The results of the current study further support the hypothesis that a BTV-11 strain circulating in the Midwestern states could have been transmitted to the dogs by the infected Culicoides vector. Our study also expands the short list of available BTV-11 sequences, which may aid BTV surveillance and epidemiology.