Deer found carrying old Covid variants no longer in human circulation

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White-tailed deer — the most abundant large mammal in North America — have been found harbouring old Covid variants that are no longer seen in human circulation. It is estimated that there are some 30 million white-tailed deer across the United States. The animals became infected with coronavirus during the pandemic thanks to ongoing contact with humans, experts explained, likely via the feeding of wild animals, hunting, contact with water or wastewater sources or wildlife rehabilitation.

Paper author and virologist Professor Diego Diel of Cornell University said: “One of the most striking findings of this study was the detection of co-circulation of three variants of concern — alpha, gamma and delta — in this wild animal population.

“A virus that emerged in humans in Asia, most likely after a spillover event from an animal reservoir into humans […] potentially has found a new wildlife reservoir in North America.”

In their study, Prof. Diel and his team analysed some 5,700 samples collected from white-tailed deer in New York in the period from 2020–22.

They compared the genomic sequences of the Covid variants found in the deer with the sequences of the same variants in New York’s human population.

The analysis revealed that the viruses had mutated in the deer — a fact that suggests the variants had been circulating within the animals for several months.

For example, by the time that the alpha and gamma variants were first found in the deer, there was no evidence that they were still circulating in humans in the area.

In fact, at the time, neither variant had been detected in New York in 4–6 months.

Prof. Diel said: “When we did sequence comparisons between those viruses recovered from white-tailed deer with the human sequences, we observed a significant number of mutations across the virus genome.”

Some of the viruses sequenced in the study, Prof. Diel added, had as many as 80 mutations from the human sequences.

These mutations have likely helped the virus adapt to the deer, potentially making it easier to transmit between the animals.

The findings build on previous work by Prof. Diel and his colleagues published last year, which found that — across five US states — Covid was found in up to 40 percent of all white-tailed deer.

And the present work, the team have said, is one of the most comprehensive studies to date on the prevalence, genetic diversity and evolution of SARS-CoV-2 in white-tailed deer.

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According to the researchers, more work is needed to confirm whether these variants will also disappear from the deer over time — or whether there is a risk that Covid might spread to other wildlife, including the animal’s predators.

Prof. Diel explained: “Because of the evidence obtained in our study, it is very important to continue to monitor the virus in these animal populations.”

Only this way, he added, will we be able to “really understand and track changes that could lead to spill back into humans and other wildlife.”

The full findings of the study were published in the journal Proceedings of the National Academy of Sciences.

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