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 December 2019, a cluster of pneumonia cases epidemiologically linked to an open-air wet market in city of Wuhan (Hubei Province), China Zhou et al., 2020b) led local health officials to issue an epidemiological alert to the Chinese Center for Disease Control and Prevention (China CDC) and the World Health Organization's (WHO) China Country Office. In early January, the etiological agent of the pneumonia cases was found to be a coronavirus (World Health Organization, 2020a) , subsequently named SARS-CoV-2 by an International Committee on Taxonomy of Viruses (ICTV) Study Group (Gorbalenya et al., 2020) , (also named hCoV-19 by (Wu et al., 2020b) ). The first available sequence data placed this novel human pathogen in the Sarbecovirus subgenus of Coronaviridae (Lu et al., 2020) , the same sub-genus as the SARS virus that caused a global outbreak of nearly 8000 cases in [2002] [2003] . By mid-January, the virus was spreading widely inside Hubei province and by early March SARS-CoV-2 reached pandemic status (World Health Organization, 2020b) .