SARS-CoV-2 wildlife surveillance in Ontario and Québec, Canada

Greenhorn, Janet E.; Kotwa, Jonathon D.; Bowman, Jeff; Bruce, Laura L.; Buchanan, Tore; Buck, Peter; Dibernardo, Antonia; Flockhart, Logan; Gagnier, Marianne; Hou, Aaron; Jardine, Claire M.; Lair, Stéphane; Lindsay, L. Robbin; Massé, Ariane; Muchaal, Pia K.; Nituch, Larissa A.; Sotto, A.; Stevens, Brian; Yip, Lily; Mubareka, Samira

doi:10.1101/2021.12.02.470924

Cited by 3 publications

(1 citation statement)

References 30 publications

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“…In this study, we highlight the power of the extensive whole genome sequencing of SARS-CoV-2 isolates collected during the 2020 outbreaks in mink farms and recommend that this remains a high priority for future zoonotic spillover events of SARS-CoV-2. For the future, we encourage applying a One Health approach to zoonotic SARS-CoV-2 surveillance ( Greenhorn et al 2021 ), focusing on the intersections of ecological, animal, and public health. Lastly, we highlight that the continuation of sampling, sequencing, and sharing data is critical for our ability to monitor the evolutionary dynamics of zoonotic SARS-CoV-2.…”

Section: Resultsmentioning

confidence: 99%

Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink

et al. 2023

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To investigate genetic signatures of adaptation to the mink host, we characterised the evolutionary rate heterogeneity in mink-associated SARS-CoV-2. In 2020, the first detected anthropozoonotic spillover event of SARS-CoV-2 occurred in mink farms throughout Europe and North America. Both spill-back of mink-associated lineages into the human population and spread into surrounding wildlife was reported, highlighting the potential formation of a zoonotic reservoir. Our findings suggest the evolutionary rate of SARS-CoV-2 underwent an episodic increase upon introduction to the mink host before returning to the normal range observed in humans. Furthermore, SARS-CoV-2 lineages could have circulated in the mink population for a month before detection, and during this period, evolutionary rate estimates reached 6.59 x 10-3, a 9-fold increase compared to that in humans. As there is evidence for unique mutational patterns within mink-associated lineages, we explored the emergence of 4 mink-specific mutations Y486F, S1147L, F486L and Q314K. We found that mutation Y486F emerged early in multiple mink outbreaks, and that mutations F486L and Q314K may co-occur. We suggest that SARS-CoV-2 undergoes a brief, but considerable, increase in evolutionary rate in response to greater selective pressures during species jumps, which may lead to the occurrence of mink-specific mutations. These findings emphasise the necessity of ongoing surveillance of zoonotic SARS-CoV-2 infections in the future.

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Section: Resultsmentioning

confidence: 99%

Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink

et al. 2023

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Genomic and transcriptomic characterization of Delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)

Kotwa

Massé

Gagnier

et al. 2022

Preprint

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White-tailed deer are susceptible to SARS-CoV-2 and represent a relevant species for surveillance. We investigated SARS-CoV-2 infection in white-tailed deer in Québec, Canada. In November 2021, 251 nasal swabs and 104 retropharyngeal lymph nodes from 258 deer were analyzed for SARS-CoV-2 RNA, whole genome sequencing and virus isolation and 251 thoracic cavity fluid samples were tested for neutralizing antibodies. We detected SARS-CoV-2 RNA in three nasal swabs from the Estrie region and virus was isolated from two samples; evidence of past exposure was detected among deer from the same region. Viral sequences were assigned to lineage AY.44, a sublineage of B.1.617.2. All deer sequences clustered with human GISAID sequences collected in October 2021 from Vermont USA, which borders the Estrie region. Mutations in the S-gene and a deletion in ORF8 encoding a truncated protein were detected. These findings underscore the importance of ongoing surveillance of key wildlife species for SARS-CoV-2.

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Surveillance for SARS-CoV-2 in Norway Rats (Rattus norvegicus) from Southern Ontario

Robinson

Kotwa

Jeeves

et al. 2023

Transboundary and Emerging Diseases

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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from wildlife has raised concerns about spillover from humans to animals, the establishment of novel wildlife reservoirs, and the potential for future outbreaks caused by variants of wildlife origin. Norway rats (Rattus norvegicus) are abundant in urban areas and live in close proximity to humans, providing the opportunity for spillover of SARS-CoV-2. Evidence of SARS-CoV-2 infection and exposure has been reported in Norway rats. We investigated SARS-CoV-2 infection and exposure in Norway rats from Southern Ontario, Canada. From October 2019 to June 2021, 224 rats were submitted by collaborating pest control companies. The majority of samples were collected in Windsor (79.9%; n = 179), Hamilton (13.8%; n = 31), and the Greater Toronto Area (5.8%; n = 13). Overall, 50.0% (n = 112) were female and most rats were sexually mature (55.8%; n = 125). Notably, 202 samples were collected prior to the emergence of variants of concern (VOC) and 22 were collected while the Alpha variant (B.1.1.7) was the predominant circulating VOC in humans. Nasal turbinate (n = 164) and small intestinal (n = 213) tissue samples were analyzed for SARS-CoV-2 RNA by RT-PCR. Thoracic cavity fluid samples (n = 213) were tested for neutralizing antibodies using a surrogate virus neutralization test (sVNT) (GenScript cPass); confirmatory plaque reduction neutralization test (PRNT) was conducted on presumptive positive samples. We did not detect SARS-CoV-2 RNA in any samples tested. Two out of eleven samples positive on sVNT had neutralizing antibodies confirmed positive by PRNT (1 : 40 and 1 : 320 PRNT70); both were collected prior to the emergence of VOC. It is imperative that efforts to control and monitor SARS-CoV-2 include surveillance of rats and other relevant wildlife species as novel variants continue to emerge.

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SARS-CoV-2 wildlife surveillance in Ontario and Québec, Canada

Cited by 3 publications

References 30 publications

Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink

Evolutionary rate of SARS-CoV-2 increases during zoonotic infection of farmed mink

Genomic and transcriptomic characterization of Delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)

Surveillance for SARS-CoV-2 in Norway Rats (Rattus norvegicus) from Southern Ontario

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