Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis

Pillar 6
Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO)

Like other coronaviruses, SARS-CoV-2 can infect a broad range of animals. Since the beginning of the pandemic, there have been several reports of humans infecting animals (including pets like dogs and cats, and wild animals like deer) and a smaller number of transmissions in the other direction, from animals back to humans. Transmission among non-human species poses considerable risk for the establishment of SARS-CoV-2 reservoirs, makes eradication difficult, and provides the virus with opportunities for new evolutionary trajectories, including selection of adaptive mutations and emergence of new variants of concern. Here we use publicly available viral genome sequences to systematically investigate transmission of SARS-CoV-2 between cats, dogs, deer, mink, and humans, and to identify mutations associated with each species, which could help adapt the virus to these different hosts. Consistent with previous reports, for each animal species, we estimated several instances of human-to-animal transmission but a relatively smaller number of animal-to-human transmissions – effectively undetectable from dogs, cats, and deer to humans, but higher in minks, from which we estimated at least 12 separate transmission events. With ongoing sampling efforts of more viral sequences from humans, these estimates are likely to increase. We also identified three viral mutations that tend to be found predominantly in mink, but rarely in humans. These mutations all affect the sequence of different proteins encoded by the virus and might play a role in helping the virus adapt to infecting mink. While earlier studies have also identified several mink-associated mutations including those we report here, we provide strong statistical support for only these three. Finally, we identified 26 mutations associated with deer, but rarely seen in viral genomes sampled from humans. We hypothesize that such a high number of deer-associated mutations could be due to high rates of transmission among deer. These mutations are candidates for further experimental study to determine if and how they allow the virus to adapt to different animal species.

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