News Scan for Feb 28, 2022

New lineage of SARS-CoV-2 detected in Canadian deerAn investigation led by Canadian Food Inspection Agency scientists has identified a new and highly divergent lineage of SARS-CoV-2, the virus that causes COVID-19 in white-tailed deer (WTD) in that country.

The findings, which are not peer-reviewed, are published as a preprint study on bioRxiv.The divergent strain was seen in samples from Ontario deer that were collected from Nov 1 to Dec 31, 2021, during the annual hunting season.

The researchers collected 213 nasal swabs and tissue from 294 retropharyngeal lymph nodes. Overall, the authors said, SARS-CoV-2 RNA was detected in 21 samples representing 6% (17/298) of hunter-harvested deer.

All positive deer from were from southwestern Ontario.Using nasal swab samples, the researchers produced 5 high-quality genomes and 3 partial genomes of the virus, and they identified a highly divergent strain that most closely resembled sequences seen in human and mink samples from Michigan collected in September and October 2020; southwestern Ontario borders Michigan."This high degree of divergence (and consequent long branch in the phylogenetic analyses) is indicative of a period of unsampled viral evolution leading to 49 mutations compared to the closest genomes," the authors said.  "This is reminiscent of the long branch and viral evolution that led to the Omicron variant, which has recently been linked to a possible mouse reservoir."The authors say there was no evidence of animal-to-human spillover with this strain but say it could be possible."At this time, there is no evidence of recurrent deer to human or sustained human to human transmission of the Ontario WTD SARS-CoV-2 clade," the authors wrote. "However, the emergence of