Within-host genetic diversity of SARS-CoV-2 across animal species

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

Infectious disease transmission to different host species makes eradication very challenging and expands the diversity of evolutionary trajectories taken by the pathogen. Since the beginning of the ongoing COVID-19 pandemic, SARS-CoV-2 has been transmitted from humans to many different animal species, and viral variants of concern could potentially evolve in a non-human animal. The ultimate source of genetic variation in a virus is mutation that occurs within individual infections. Here we quantify within-host genetic diversity of SARS-CoV-2 across animal species and show that deer harbour more diversity than other animals, providing a larger pool of genetic diversity for natural selection to act upon. Within-host diversity is particularly high in deer lymph nodes compared to nasopharyngeal samples, suggesting tissue-specific differences in viral population sizes or selective pressures. Neither mixed infections involving more than one viral lineage nor large changes in the strength of natural selection are likely to explain the higher diversity within deer. Rather, deer are more likely to contain larger viral population sizes, to be infected for longer periods of time, or to be systematically sampled at later stages of infections. Combined with extensive deer-to-deer transmission documented in previous studies, the high levels of within-deer viral diversity help explain the apparent rapid adaptation of SARS-CoV-2 to deer.

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