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Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis.
Naderi, Sana; Chen, Peter E; Murall, Carmen Lia; Poujol, Raphael; Kraemer, Susanne; Pickering, Bradley S; Sagan, Selena M; Shapiro, B Jesse.
  • Naderi S; Department of Microbiology & Immunology, McGill University, Montreal, Canada.
  • Chen PE; Department of Microbiology & Immunology, McGill University, Montreal, Canada.
  • Murall CL; Département de sciences biologiques, Université de Montréal, Montreal, Canada.
  • Poujol R; Department of Microbiology & Immunology, McGill University, Montreal, Canada.
  • Kraemer S; Public Health Agency of Canada, Winnipeg, Canada.
  • Pickering BS; Research Centre, Montreal Heart Institute, Montreal, Canada.
  • Sagan SM; Department of Microbiology & Immunology, McGill University, Montreal, Canada.
  • Shapiro BJ; National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada.
Elife ; 122023 04 04.
Article in English | MEDLINE | ID: covidwho-2273482
ABSTRACT
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a generalist virus, infecting and evolving in numerous mammals, including captive and companion animals, free-ranging wildlife, and humans. Transmission among non-human species poses a risk for the establishment of SARS-CoV-2 reservoirs, makes eradication difficult, and provides the virus with opportunities for new evolutionary trajectories, including the selection of adaptive mutations and the emergence of new variant lineages. Here, we use publicly available viral genome sequences and phylogenetic analysis to systematically investigate the transmission of SARS-CoV-2 between human and non-human species and to identify mutations associated with each species. We found the highest frequency of animal-to-human transmission from mink, compared with lower transmission from other sampled species (cat, dog, and deer). Although inferred transmission events could be limited by sampling biases, our results provide a useful baseline for further studies. Using genome-wide association studies, no single nucleotide variants (SNVs) were significantly associated with cats and dogs, potentially due to small sample sizes. However, we identified three SNVs statistically associated with mink and 26 with deer. Of these SNVs, ~⅔ were plausibly introduced into these animal species from local human populations, while the remaining ~⅓ were more likely derived in animal populations and are thus top candidates for experimental studies of species-specific adaptation. Together, our results highlight the importance of studying animal-associated SARS-CoV-2 mutations to assess their potential impact on human and animal health.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Deer / COVID-19 Type of study: Prognostic study / Randomized controlled trials Topics: Variants Limits: Animals Language: English Year: 2023 Document Type: Article Affiliation country: ELife.83685

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Deer / COVID-19 Type of study: Prognostic study / Randomized controlled trials Topics: Variants Limits: Animals Language: English Year: 2023 Document Type: Article Affiliation country: ELife.83685