Wildlife reservoirs of broad-host-range viruses have the potential to enable evolution of viral variants that can emerge to infect humans. In North America, there is phylogenomic evidence of continual transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (Odocoileus virginianus) through unknown means, but no evidence of transmission from deer to humans. We carried out an observational surveillance study in Ontario, Canada during November and December 2021 (n = 300 deer) and identified a highly divergent lineage of SARS-CoV-2 in white-tailed deer (B.1.641). This lineage is one of the most divergent SARS-CoV-2 lineages identified so far, with 76 mutations (including 37 previously associated with non-human mammalian hosts). From a set of five complete and two partial deer-derived viral genomes we applied phylogenomic, recombination, selection and mutation spectrum analyses, which provided evidence for evolution and transmission in deer and a shared ancestry with mink-derived virus. Our analysis also revealed an epidemiologically linked human infection. Taken together, our findings provide evidence for sustained evolution of SARS-CoV-2 in white-tailed deer and of deer-to-human transmission.

Wildlife reservoirs of SARS-CoV-2 can lead to viral adaptation and spillback from wildlife to humans (Oude Munnink et al., 2021). In North America, there is evidence of spillover of SARS-CoV-2 from humans to white-tailed deer (Odocoileus virginianus), but no evidence of transmission from deer to humans (Hale et al., 2021; Kotwa et al., 2022; Kuchipudi et al., 2021). Through a multidisciplinary research collaboration for SARS-CoV-2 surveillance in Canadian wildlife, we identified a new and highly divergent lineage of SARS-CoV-2. This lineage has 76 consensus mutations including 37 previously associated with non-human animal hosts, 23 of which were not previously reported in deer. There were also mutational signatures of host adaptation under neutral selection. Phylogenetic analysis revealed an epidemiologically linked human case from the same geographic region and sampling period. Together, our findings represent the first evidence of a highly divergent lineage of SARS-CoV-2 in white-tailed deer and of deer-to-human transmission.

ABSTRACT:During August 2006 and 2007, baits containing oral rabies vaccine, live adenovirus vector, known as ONRABH, were aerially distributed in SW Ontario, Canada. Bait acceptance during 2006 was 62 and 74% in raccoons (Procyon lotor) in areas baited at 150 baits/km 2 and 75 and 77% in plots baited at 300 baits/km 2 . During 2007, bait acceptance for raccoons ranged between 59% and 80%, and 83% and 87%, in areas baited at 75 and 400 baits/km 2 , respectively. Bait acceptance by skunks varied among plots (5-24%). Rabies virus-specific seroconversion during 2006 averaged 66 and 81% in raccoons in areas baited at 150 and 300 baits/km 2 , respectively. During 2007, seroconversion by raccoons was 76 and 84% in areas baited at 75 and 400 baits/km 2 , respectively. Seroconversion by skunks varied among plots (17-51%). Vaccine efficacy, as judged by the percentage of animals that consumed a bait and seroconverted, averaged 79 and 87% during 2006 for raccoons in areas baited at 150 and 300 baits/km 2 , respectively, and 81 and 90% in areas baited during 2007 at 75 and 400 baits/km 2 , respectively. Because tetracycline marking was poor in skunks, an estimate of vaccine efficacy was not possible. Aerial distribution of ONRABH vaccine baits seems to be a feasible tactic for controlling rabies in skunks and raccoons.

ABSTRACT:Proactive and reactive tactics have been utilized in Ontario, Canada, to prevent raccoon rabies from becoming established. A total of 96,621 raccoons (Procyon lotor) and 7,967 striped skunks (Mephitis mephitis) were live captured using 1,221,044 trap nights, vaccinated against rabies by injection, and released, during proactive Trap-Vaccinate-Release (TVR) programs in southern Ontario during 1994-2007. During those years, on average, 43% to 83% of the raccoon populations were vaccinated against rabies. In addition, 20,129 raccoons and 2,735 skunks were vaccinated against rabies, and 8,311 raccoons and 1,449 skunks were euthanized, using 576,359 trap nights, during reactive Point Infection Control (PIC) operations in eastern Ontario during 1999-2005. A significant correlation was detected between trapping effort and the percentage of the raccoon population that was vaccinated. Between 1999 and 2007, 132 cases of raccoon variant rabies (130 raccoons, two striped skunks) were reported in eastern Ontario. The last case occurred on 23 September 2005 with Ontario being free of reported raccoon rabies to 10 November 2008, proving that TVR and PIC are effective tactics for the control of this disease.