Could deer become the source of the next variant of the coronavirus? Many mammals can be infected with the virus responsible for Covid-19, hosts in which the virus can evolve and develop variants that can reinfect humans. But so far, transmission back to humans has only been observed in a small number of these animals, including mink and the hamster, which led to mass culling to prevent these transmissions. But a new group of mammals could be added to these potential sources of new variants, the deer.
The virus has accumulated dozens of mutations in deer
In August 2021, US authorities had highlighted that nearly half of deer in North America may have caught Covid, which was the first detection of massive exposure to the coronavirus in wild animals. This high rate of infection showed that the coronavirus appears to be very transmissible among deer (which do not develop serious illness after infection), but it was not yet certain that deer could relay the virus to humans. This uncertainty was raised on February 25, 2022, in a prepress (Scientific article not yet peer-reviewed) published by the Canadian Center for Animal Diseases. According to this study, the coronavirus has already passed from deer to humans at least once.
Canadian researchers analyzed samples from 300 white-tailed deer (Odocoileus virginianus) in the Canadian province of Ontario during the hunting season between November and December 2021. Among these deer, the presence of the coronavirus was confirmed in 21 samples (6% of the total deer in the study). Thanks to these samples, the researchers were able to reconstruct five entire genomes of the virus and two partial ones. Prior to this study, all sequences of the virus found in deer were very close to those present in humans at the same time, showing that the virus did not have time to evolve in its new hosts. But these five genomes, very similar to each other, were very distinct from the rest of the variants currently in circulation in humans, with 76 mutations compared to the sequence of the original coronavirus strain.
At least one transmission to humans
Their analysis also identified a genomic sequence of the virus very close to that found in deer (sharing the vast majority of these mutations) in a person living in Ontario. This person was infected in the fall of 2021 and had direct contact with deer shortly before the infection.
But no other human samples showed these mutations, and the closest genomic sequence had been detected a year earlier in Michigan (a US state bordering Canada), with less than half of these genetic variations. Therefore, it is likely that this new variant comes from a coronavirus that was transmitted to deer a year ago in North America, where it would have evolved for a year, accumulating 49 mutations, before being returned to humans.
But these mutations do not appear to pose a danger to humans.
Nine of the 76 mutations detected in deer and the infected person in Ontario are in the coronavirus’s Spike protein, six of which result in the change of at least one amino acid. This raised fears that this new variant could escape antibodies that recognize this protein. Fortunately, an analysis of plasma from vaccinated people showed that their antibodies have no problem recognizing and neutralizing this variant. These mutations therefore have no impact on the effectiveness of current vaccines.
In fact, the researchers found that the ratio of non-synonymous mutations (that change an amino acid) to synonymous mutations is very low, suggesting that there does not appear to have been any selection pressure for the coronavirus in deer. These mutations are therefore likely to be neutral, that is, they do not represent an advantage for the virus. This lack of selection pressure can be explained by weak (or even non-existent) acquired immunity to other coronaviruses in deer, which do not get very sick after infection, thus allowing the virus to be transmitted without difficulty, which accumulates neutral mutations between each passage. from one deer to another.
However, the authors caution that if a dangerous variant were to emerge in wild animals such as deer, it would be much more difficult to control than in cultivated species such as hamsters and mink. However, there is no further evidence of deer-to-human or human-to-human transmission of a deer variant of the coronavirus. So at the moment it seems unlikely that the next worrisome variant will come from these animals, but we will still have to remain vigilant.