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Given the presumed zoonotic origin of SARS-CoV-2, the human-animal-environment interface of the COVID-19 pandemic is an area of great scientific and public and animal health interest. Identification of animal species that are susceptible to infection by SARS-CoV-2 may help to elucidate the potential origin of the virus, identify potential reservoirs or intermediate hosts, and define the mechanisms underlying cross-species transmission to humans., The origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing the global coronavirus disease 2019 (COVID-19) pandemic, remains a mystery. Current evidence suggests a likely spillover into humans from an animal reservoir. Understanding the host range and identifying animal species that are susceptible to SARS-CoV-2 infection may help to elucidate the origin of the virus and the mechanisms underlying cross-species transmission to humans. Here, we demonstrated that white-tailed deer (Odocoileus virginianus), an animal species in which the angiotensin-converting enzyme 2 (ACE2)—the SARS-CoV-2 receptor—shares a high degree of similarity to that of humans, are highly susceptible to infection. Intranasal inoculation of deer fawns with SARS-CoV-2 resulted in established subclinical viral infection and shedding of infectious virus in nasal secretions. Notably, infected animals transmitted the virus to noninoculated contact deer. Viral RNA was detected in multiple tissues 21 days postinoculation (p.i.). All inoculated and indirect contact animals seroconverted and developed neutralizing antibodies as early as day 7 p.i. The work provides important insights into the animal host range of SARS-CoV-2 and identifies white-tailed deer as a wild animal species susceptible to the virus. IMPORTANCE Given the presumed zoonotic origin of SARS-CoV-2, the human-animal-environment interface of the COVID-19 pandemic is an area of great scientific and public and animal health interest. Identification of animal species that are susceptible to infection by SARS-CoV-2 may help to elucidate the potential origin of the virus, identify potential reservoirs or intermediate hosts, and define the mechanisms underlying cross-species transmission to humans. Additionally, it may also provide information and help to prevent potential reverse zoonosis that could lead to the establishment of new wildlife hosts. Our data shows that upon intranasal inoculation, white-tailed deer became subclinically infected and shed infectious SARS-CoV-2 in nasal secretions and feces. Importantly, indirect contact animals were infected and shed infectious virus, indicating efficient SARS-CoV-2 transmission from inoculated animals. These findings support the inclusion of wild cervid species in investigations conducted to assess potential reservoirs or sources of SARS-CoV-2 infection.

Significant pathogens of domestic livestock and public-health related pathogens, such as bovine viral diarrhea virus (BVDV) and Coxiella burnetii, are commonly diagnosed in some wildlife species. BVDV is an economically important pathogen of domestic bovids and Coxiella burnetii is a highly infectious zoonotic bacterium. As a result of recent shifting patterns of disease, it is critical that baseline information regarding the status of both significant pathogens of domestic livestock and public-health related pathogens are established for commonly encountered wildlife such as white-tailed deer (Odocoileus virginianus). White-tailed deer are susceptible to both BVDV and C. burnetii infection, and the purpose of this study was to investigate for the presence of antibodies to these two pathogens in New York and Pennsylvania white-tailed deer. Exposure to BVDV and C. burnetii was determined using sera collected from 333 (219 males and 114 females) wild white-tailed deer in New York and 291 (130 males and 161 females) wild white-tailed deer from Pennsylvania. Samples were collected from hunter-harvested deer in central New York State in 2009 and live-captured deer in Pennsylvania in 2010. Sera were screened for anti-BVDV antibodies via a commercial blocking BVDV enzyme-linked immunosorbent assay. Coxiella burnetii phase II whole-cell antigen-coated slides were used to screen sera via an indirect microimmunofluorescence assay. Antibody prevalence was compared by sex class and location of collection. Deer in New York had higher antibody prevalence to BVDV (6.01%) than did deer in Pennsylvania (0.34%). Conversely, C. burnetii phase II antibodies were more common in Pennsylvania (20.96%) than in New York (14.41%). No statistically significant difference between locations was observed in either BVDV or C. burnetii antibody prevalence when data were analyzed by sex-class. Overall, C. burnetii seroprevalence was not significantly higher in Pennsylvania than in New York.

A previously unrecognized virus belonging to the subfamily Pneumovirinae and most closely related to murine pneumovirus (MPV) was identified in domestic dogs in 2 related animal shelters. Additional diagnostic testing yielded 3 new viral isolates and identified 6 additional PCR positive dogs from other USA locations indicating that its distribution is not geographically limited. Nucleotide sequences encompassing 9 of the 10 genes were compared to the only 2 available MPV strains, 15 and J3666. Several features distinguished the canine pneumovirus (CnPnV) from the murine strains. Two regions of diversity were identified in the amino-proximal region of P and the overlapping P2 ORF was only 54 amino acids (aa) compared to 137aa in MPV. The G protein had an amino-terminal cytoplasmic tail 18aa longer than in the MPV strains. The CnPnV SH protein showed the highest divergence with only 90.2% aa identity when compared to MPV strain 15. Like strain 15, the CnPnV SH ORF coded for a protein of 92aa while J3666 has a 114aa variant. Comparison of CnPnV isolates at culture passages 4 and 17 revealed 7nt differences within the 8598nt sequenced. Of note was a substitution at nt 364 in G resulting in a termination codon that would produce a truncated G protein of 122aa. Analysis of early passage and ex vivo samples showed the termination codon in G to be predominant after 6 days in culture indicating rapid selection of the mutation in A72 cells.

The objective of the current study was to determine the capability of 3 recently described one-step TaqMan real-time reverse transcription polymerase chain reaction (real-time RT-PCR) assays targeting the nucleoprotein (NP), matrix (M), and hemagglutinin (HA) genes of H3N8 Equine influenza virus (EIV NP, EIV M, and EIV HA3 assays, respectively) to detect Canine influenza virus (CIV). The assays were initially evaluated with nucleic acid extracted from tissue culture fluid (TCF) containing the A/canine/FL/43/04 strain of Influenza A virus associated with the 2004 canine influenza outbreak in Florida. The EIV NP, EIV M, and EIV HA3 assays could detect CIV nucleic acid at threshold cycle (Ct) values of 16.31, 23.71, and 15.28, respectively. Three assays using TCF or allantoic fluid (AF) samples containing CIV ( n = 13) and archived canine nasal swab samples ( n = 20) originally submitted for laboratory diagnosis of CIV were further evaluated. All TCF and AF samples, together with 10 nasal swab samples that previously tested positive for virus by attempted isolation in embryonated hens' eggs or Madin–Darby canine kidney cells, were positive in all 3 real-time RT-PCR assays. None of the 3 assays detected the H1N1 Swine influenza virus strain in current circulation. These findings demonstrate that previously described real-time RT-PCR assays targeting NP, M, and H3 HA gene segments of H3N8 EIV are also valuable for the diagnosis of CIV infection in dogs. The assays could expedite the detection and identification of CIV.

To determine which respiratory viruses circulate among confined dogs, we analyzed nasal and pharyngeal swab specimens from shelter dogs with acute respiratory disease. An unknown virus was isolated. Monoclonal antibody testing indicated that it was probably a pneumovirus. PCR and sequence analysis indicated that it was closely related to murine pneumovirus.

Over a three-year period, 2004-2007, greater than 12,000 alpacas in the United States were screened by real-time RT-PCR to identify alpacas persistently infected (PI) with bovine viral diarrhea virus (BVDV). A total of 46 BVD viruses were isolated from PI alpacas or diagnostic samples from alpacas. Forty-three US alpaca BVDV isolates and 3 Canadian isolates were analyzed by comparison of nucleotide sequences of two viral genomic regions, the 5'-UTR and the N(pro) gene to determine their genetic relatedness. All 46 alpaca BVDV isolates from 8 different states of the US and Canada were genotype 1b with > or =99% nt identity in the 290-base 5'-UTR region with the exception of one Canadian isolate. In contrast, 21 bovine BVDV isolates collected during the same period were grouped into the typical 3 genotypes, 1a, 1b, and 2, respectively. Forty five alpaca BVDV isolates formed a distinctive cluster separated from closely related bovine genotype 1b isolates by phylogenetic analysis of the 5'-UTR region. Comparison of the 504-base N(pro) gene sequences of 32 alpaca isolates also assigned them all to type 1b in a similar fashion as observed with the 5'-UTR region. The results suggest that unique genotypes of bovine BVDV 1b may be maintained in the alpaca population even though camelids are susceptible to infection by other genotypes. Further studies are needed to address why alpacas were predominantly infected with genotype 1b BVDV isolates and how bovine BVD viruses evolved to infect alpacas.