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

All authors contributed to analyses and interpretations. DLR and XJ performed recombination and phylogenetic analysis, and annotated the virus names with geographical and sampling dates. AR performed the S recombination analysis. PB and TC performed the codon-usage analysis. MFB performed the . 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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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 recombination analysis for non-recombining regions 1 and 2, breakpoint analysis, and phylogenetic inference on recombinant segments. PL performed recombination analysis for non-recombining alignment 3, calibration of rate of evolution, and phylogenetic reconstruction and dating. TT-YL collected SARS-CoV data. PL, MFB, and DLR wrote the first draft of the manuscript, and all authors contributed to manuscript editing.