SARS-CoV-2 has caused a worldwide pandemic since January 2020. Through the huge amounts of genomic data generated by the sequencing of SARS-CoV-2, we are seeing several astonishing and puzzling evolutionary phenomena, including the continual replacement of dominant variants. This phenomenon hints at a new pattern of evolution that we have not been able to see in traditional evolutionary studies due to sample size limitations, namely, that a set of mutations which has been successful in the past can eventually fail. But the prevalence of variants prior to Omicron was low (Delta was about 1%), why can't the population accommodate more than one variants at the same time? Given the consistency of this pattern throughout the evolution of SARS-CoV-2, a general driving force is likely to exist.
We focus on population exposure, a factor inherent in the spread of the virus, and model the transmission dynamics. We assume two variants with different infectivities circulating in a naive population. We find that when the number of exposures of susceptible population is greater than 1, these two variants compete with each other and cause substitution to occur. Though outnumbered, the strong variant may eventually beat the increasing dominant weak variant due to its high probability of infection in a single exposure. The exposure times of susceptible individuals actually reflect the overlap of the two transmission chains in the population. As exposure increases, person-to-person contact increases, the two variants become more disruptive to each other's transmission, and competition between them becomes more intense. The overall low prevalence is only indication of the number of people infected, in this scenario, many uninfected individuals have also been exposed to the virus and provide an implicit platform for virus substitution. The results suggest that the exposure process shapes the current evolutionary pattern of SARS-CoV-2 in some way. Different sets of mutations lead to the gap in the selection advantage of different variants, and variants with greater transmission advantages are constantly selected. Understanding this fundamental phenomenon of variants substitution can give us insight into other doubts about the evolution of SARS-CoV-2 and other species. Beyond that, an emphasis on viral exposure allows us to better optimize our public health policy to respond to such serious emergencies in future.
An epidemiological model of SARS-CoV-2 give us insight into a previously unseen pattern of evolution