Infection with SARS-CoV-2 lineage B.1.1.7 in Three Malayan Tigers at the Virginia Zoological Park

Patrick K. Mitchell Cornell University Mathias Martins Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University Tara Reilly Virginia Zoo Leonardo C. Caserta Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University Renee Anderson Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University Brittany D. Cronk Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech Julia Murphy VA Department of Health Erin L. Goodrich Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University Diego G. Diel (  dgdiel@cornell.edu ) Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University https://orcid.org/0000-0003-3237-8940

cough on April 10 and clear nasal discharge was observed on April 13. Clinical signs in all three tigers resolved by April 15.
Nasal swabs and fecal samples were collected from the two tigers on April 9 and from the ten year old on April 13 and submitted to the Cornell Animal Health Diagnostic Center for testing. Samples were tested for common feline respiratory pathogens including Bordetella sp., Chlamydia felis, Mycoplasma cynos, Mycoplasma felis, Streptococcus equi. ssp zooepidemicus, In uenza virus, pneumovirus, feline calicivirus and feline herpesvirus, all of which were not detected. All samples tested positive for SARS-CoV-2 using the EZ-SARS-CoV-2 RT-PCR assay and SARS-CoV-2 was isolated from respiratory and fecal specimens from the rst tiger. Con rmatory SARS-CoV-2 testing performed by U.S. Department of Agriculture National Veterinary Services Laboratories was positive as well. Screening of the samples with the ThermoFisher COVID-19 TaqPath kit revealed a spike gene dropout, with only the N and Orf1ab gene targets being detected, suggesting potential infection with a B.1.1.7 variant.
Whole genome sequencing of all samples was run using an Oxford Nanopore Technologies MinION as previously described (1). Reads were assembled using the ARTIC ncov-2019 protocol using Medaka for The source of infection is unknown. While the zoo has been open to the public, the setup of the tiger exhibit makes transmission from a visitor unlikely as all areas of the tiger exhibit are either enclosed by glass or are separated from the public by distances of at least 9 meters. Given the potential for close contact with the infected animals, the most plausible explanation is that one or more of the tigers acquired the virus from a zoo employee, though no employees had a positive SARS-CoV-2 test nor presented symptoms consistent with COVID-19 in the four weeks prior to symptom onset in the tigers. It is possible that all three tigers were infected by a person or that transmission occurred between the tigers. Two of the tigers were kept in the same enclosure and while the third had no direct contact with the others all three rotated through common spaces in their enclosures.
After the tiger infections were identi ed, four additional animals from the zoo were tested for SARS-CoV-2: one lion (Panthera leo) with lethargy and hyporexia starting approximately one week after the diagnosis in the tigers, a second lion that was asymptomatic but tested because of age and proximity to the rst lion, and two degus (Octodon degus) that died in late March and had interstitial pneumonia found on necropsy. These four animals were negative for SARS-CoV-2.
This report underscores the susceptibility of felids to SARS-CoV-2. Infections have previously been identi ed in captive lions, tigers, snow leopards, and pumas, as well as in domestic cats. Other nonhuman animal species including gorillas, dogs, minks, ferrets have also acquired SARS-CoV-2 and additional species have been shown to be susceptible in laboratory settings(5-7). B.1.1.7 lineage infections have been reported in several domestic cats and dogs in the United Kingdom and United States, suggesting that the Spike protein mutations that characterize this lineage have not constrained its host range (8,9). Monitoring for SARS-CoV-2 infection in animals is critical to understanding potential host range of the pathogen, particularly new variants emerge and proliferate. Figure 1 Subset of phylogenetic tree showing parent (G23236T) and grandparent (C4900T) nodes of the tiger sequences, with tips labeled as United States or Australian state of origin. Tiger samples are numbered in order of symptom onset.