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

In outbreaks of zoonotic pathogens, identification of the infection source is crucial, as this may allow health authorities to separate human populations from the wild-life or domestic-animal reservoirs posing the zoonotic risk (Stegeman et al., 2004; Yu et al., 2013) . If controlling an outbreak in its early stages is not possible -as was the case for the COVID-19 epidemic in Hubei province -identification of origins and point sources is nevertheless important for containment purposes in other provinces and prevention of future outbreaks. When the first genome sequence of SARS-CoV-2, Wuhan-Hu-1, was released on January 10 2020 on Virological.org by a consortium led by Yong-Zhen Zhang it enabled the immediate analyses of its ancestry. Across a large region of its genome, corresponding approximately to ORF1b , it did not cluster with any of the known bat coronaviruses indicating that recombination likely played a role in the evolutionary history of these viruses (Lu et al., 2020; Wu et al. 2020b ). Subsequently, a bat sarbecovirus -RaTG13 sampled from a Rhinolophus affinis horseshoe bat in 2013 in Yunnan province -was reported that clusters with SARS-CoV-2 in almost all genomic regions with approximately 96% genome sequence identity (Zhou et al., 2020b) . Zhou et al. (2020b) concluded from the genetic proximity of SARS-CoV-2 to a bat virus that a bat origin for the current COVID-19 outbreak is probable. Recent evidence has also identified pangolins as potential intermediate species for SARS-CoV-2 emergence or as a potential reservoir species themselves (Lam et al., 2020; Xiao et al., 2020) .