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

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.20.000885 doi: bioRxiv preprint with YNLF-34C, form a very divergent and distinctive cluster ( fig. 5D ). To further explore the recombinant nature of SARS-CoVs, we compared GZ02 to representative bat CoV sequences using the RIP recombination detection tool (16) . We identified four significant breakpoints (at 99% confidence) between the two parental lineages ( fig. S8A ), further supported by phylogenetic analysis ( fig. S8B-S8D ). In addition, the two aforementioned groups of bat CoVs (shown in light brown and light blue in the trees) show similar cluster changes across the five recombinant regions, suggesting multiple events of historic recombination among bat SL-CoVs. These results demonstrate that SARS-CoV shares a recombinant history with at least three different groups of bat-CoVs and confirms the major role of recombination in the evolution of these viruses.