Dynamics of natural selection preceding human viral epidemics and pandemics

Using a phylogenetic framework to characterize natural selection, we investigate the hypothesis that zoonotic viruses require adaptation prior to zoonosis to sustain human-to-human transmission. Examining the zoonotic emergence of Ebola virus, Marburg virus, mpox virus, influenza A virus, and SARS-CoV-2, we find no evidence of a change in selection intensity immediately prior to outbreaks in humans compared with typical selection within reservoir hosts. We found a change in selection on SARS-CoV in an intermediate host. We conclude that extensive pre-zoonotic adaptation is not necessary for human-to-human transmission of zoonotic viruses. In contrast, the reemergence of H1N1 influenza A virus in 1977 was preceded by a shift in selection intensity, consistent with the hypothesis of passage in a laboratory setting. Holistic phylogenetic analysis of selection regimes can be used to detect evolutionary signals of host switching or laboratory passage, providing insight into the circumstances of past and future viral emergence.