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 extent of the sarbecoviruses' recombination history can be demonstrated by five phylogenetic trees inferred from BFRs or concatenated adjacent BFRs (Figure 1, bottom) . BFRs were concatenated if no . CC-BY-NC 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.30.015008 doi: bioRxiv preprint 6 / 25 phylogenetic incongruence signal could be identified between them. When viewing the last 7kb of the genome a clade of viruses from northeast (NE) China appears to cluster with sequences from south-central (SC) Chinese provinces, but when inspecting trees from different parts of ORF1ab the NE China clade is phylogenetically separated from the SC China clade. Individual sequences such as RpShaanxi2011, Guangxi GX2013, and two sequences from Zhejiang province (CoVZXC21/CoVZC45), as previously shown Zhou et al., 2020a) , show strong phylogenetic recombination signals, as they fall on different evolutionary lineages (with bootstrap support > 80%) depending what region of the genome is being examined.