US scientists detect Omicron variant for first time in deer

Some white-tailed deer living in the US are actively infected with the Omicron variant of SARS-CoV-2, the virus that causes COVID-19, according to a study.

The yet-to-be peer-reviewed study, posted recently on the preprint repository bioRxiv, also found neutralising antibodies to SARS-CoV-2 in one of the Omicron-infected deer, suggesting that, like humans, these animals can be reinfected with the virus.

“Our finding that some of these animals harbour SARS-CoV-2 suggests the presence of another potential threat,” said Kurt Vandegrift, associate research professor at Penn State, and lead author of the paper.

Last year, the team found that up to 80 per cent of white-tailed deer sampled across Iowa in the US tested positive for SARS-CoV-2.

The finding was the first direct evidence of SARS-CoV-2 virus in any free-living species.

The latest research highlights that many urgent steps are needed to monitor the spread of the virus in deer and prevent potential spillback to humans.

“While there is no indication so far of any of the SARS-CoV-2 variants spilling back into humans from deer, such an outcome is possible,” said Suresh Kuchipudi, a clinical professor of veterinary and biomedical sciences, Penn State.

“The longer the virus circulates in these animals and the greater the number of individuals it infects, the more likely the virus is to evolve and potentially lead to the emergence of a completely novel variant that may be resistant to our current vaccines,” Kuchipudi said.

The study may reveal whether spillover of the virus back to humans from deer is possible, the researchers said.

The researchers analysed blood samples from 131 individual deer collected between December 12, 2021, and January 31, 2022, and found that 19 were positive for SARS-CoV-2-specific antibodies. They also detected SARS-CoV-2 nucleic acid in nasal swabs from seven of 68 of the sampled deer, indicating that these deer were actively infected with the virus.

“Our previous research in Iowa examined the lymph nodes of deer that had already been killed during hunting, but we were not able to confirm an active infection from these samples,” said Vivek Kapur, from Penn State,and co-lead author of the study.

“In our new study, we were able to obtain nasal swabs, which revealed live virus in the animals’ noses,” he added.
Whole-genome sequencing identified that the virus circulating among the white-tailed deer on Staten Island in New York was Omicron.

Phylogenetic analyses, which examine the evolutionary history among groups of organisms, revealed that the Omicron sequences in the deer were related to those recovered from infected humans in New York City and elsewhere, suggesting the virus spilled over from humans to deer.

“Importantly, one individual deer was both positive for viral RNA and had a high level of neutralising antibodies, suggesting that neutralising antibodies developed rapidly during an ongoing infection or that a breakthrough infection occurred,” said Kuchipudi.

“If this animal had a reinfection, then this suggests that white-tailed deer can serve as a reservoir for the virus to continue to mutate, potentially producing new variants that are more dangerous,” he added.