Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Maciej F Boni; Philippe Lemey; Xiaowei Jiang; Tommy Tsan-Yuk Lam; Blair Perry; Todd Castoe; Andrew Rambaut; David L Robertson

The SARS-CoV divergence times are somewhat earlier than previously estimated dates (Hon et al., 2008) as previous estimates were obtained using a collection of SARS-CoV genomes from human and civet hosts (as well as a few closely related bat genomes) which implies that the evolutionary rates were predominantly informed by the short-term SARS outbreak scale and likely biased upwards for the time scale under investigation. Indeed, the rates reported by these studies are in line with the short-term SARS rates we estimate ( Figure 4) . The estimated divergence times for the pangolin virus most closely related to SARS-CoV-2/RaTG13 range from 1851 [1730, 1958] to 1877 [1746, 1986] , indicating that these pangolin lineages were acquired from bat viruses divergent to those that gave rise to SARS-CoV-2. Current sampling of pangolins does not implicate them as an intermediate host.