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

Due to the absence of temporal signal in the sarbecovirus data sets, we used informative prior distributions on the evolutionary rate to estimate divergence dates. We show that such prior calibration information can be obtained from other coronaviruses (SARS-CoV, MERS-CoV, and HCoV-OC43), but their rates vary with the time scale of sample collection. In the presence of time-dependent rate variation, a widely observed phenomenon for viruses (Duchene et al., 2014; Aiewsakun and Katzourakis, 2016; Membrebe et al., 2019) , the slower rates appear more appropriate for sarbecoviruses that currently encompass a sampling time range of about 18 years. We therefore centered the prior rate distributions on the mean HCoV-OC43 and MERS-CoV rate, but permitted the distributions a greater variance than the empirical rate estimates for these lineages. This approach resulted in similar posterior rates despite the different prior means, implying that the sarbecovirus data do inform the rate estimate even though root-to-top temporal signal was not apparent.