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The copyright holder for this preprint (which was not peer-reviewed) is the .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 CoV-2, RaTG13, and Pan_SL-CoV viruses at the 3'-end of the S gene (after the furin cleavage site) is 0.013, compared to w =0.05 in the S region preceding the furin cleavage site, and to w =0.04 after the site for all other CoVs. The much lower w value at the 3'-end of the S gene among the SARS-CoV-2, RaTG13, and Pan_SL-CoV viruses indicates that this region is under strong purifying selection within these sequences ( fig. 3A) . A plot of synonymous and nonsynonymous substitutions relative to Wuhan-Hu-1 highlights the regional differences across the region before and after the RBM and the furin cleavage site ( We observe similar patterns of purifying selection pressure in other parts of the genome, including the E and M genes, as well as the partial ORF1a and ORF1b genes ( fig. 4) . Interestingly, the purifying selection pressure varies among different viruses depending on which genes are analyzed. The broadest group includes SARS-CoV-2, RaTG13, all Pan_SL-CoV and the two bat CoVs (ZXC21 and ZC45) for both E and M genes (figs. 4 and S5). The second group includes SARS-CoV-2, RaTG13, and all Pan_SL-CoV only for the 3' end of the S gene. The narrowest selection group only contains SARS-CoV-2, RaTG13, and pangolin CoVs from Guangdong for the partial regions of ORF1a and ORF1b (figs. 4 and S6). Consistently low ω values and strong purifying selection pressure on SARS-CoV-2, RaTG13 and Pan_SL-CoV_GD viruses suggest that these complete and partial genes are under similar functional/structural constraints among the different host species. In two extreme cases, amino acid sequences of the E gene and the 3' end of ORF1a are identical among the compared CoV sequences, although genetic distances are quite large among these viruses at the nucleic acid level. Such evolutionary constraints across viral genomes, especially at functional domains in the S gene, which plays an important role in cross-species transmission (5, 17) , coupled with frequent recombination, may facilitate cross-species transmissions between RaTG13-like bat and/or Pan_SL-CoV_GD-like viruses.