Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection

Xiaojun Li; Elena E. Giorgi; Manukumar Honnayakanahalli Marichann; Brian Foley; Chuan Xiao; Xiang-peng Kong; Yue Chen; Bette Korber; Feng Gao

Previous studies using more limited sequence sets found that SARS-CoVs originated through multiple recombination events between different bat-CoVs (10, 17, 19, 28, 29) . Our phylogenetic analyses of individual genes show that SARS-CoV sequences tend to cluster with YN2018B, Rs9401, Rs7327, WIV16 and Rs4231 (group A) for some genes and Rf4092, YN2013, Anlong-112 and GX2013 (group B) for others ( fig. S7 ). SimPlot analysis using both groups of bat_SL-CoVs and the closely related bat CoV YNLF-34C (29) shows that SARS-CoV GZ02 shifts in similarity across different bat SL-CoVs at various regions of the genome ( fig. 5A ). In particular, phylogenetic reconstruction of the beginning of ORF1a (region 1) confirms that SARS-CoVs cluster with YNLF-34C (29) , and this region is distinctive comparing to all other CoVs ( fig. 5B ). YNLF-34C is more divergent from SARS-CoV than other bat-CoV viruses before and after this region, confirming the previously reported complex recombinant nature of YNLF-34C (29) ( fig. 5A ). At the end of the S gene (region 2), SARS-CoVs cluster with group A CoVs, forming a highly divergent clade ( fig. 5C ). In region 3 (ORF8), SARS-CoVs and group B CoVs, together author/funder. All rights reserved. No reuse allowed without permission.