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

Phylogenetic analysis of 43 complete genome sequences from three clades (SARS-CoVs and bat_SL-CoVs; SARS-CoV-2, bat_SL-CoVs and pan_SL-CoVs; and two divergent bat_SL-CoVs) within the Sarbecovirus group (9) confirms that RaTG13 is overall the closest sequence to SARS-CoV-2 (fig. S1). It is followed by Pan_SL-CoV_GD viruses next, and then Pan_SL-CoV_GX. Among the bat-CoV sequences in clade 2 ( fig. S1 ), ZXC21 and ZC45, sampled from bats in 2005 in Zhoushan, Zhejiang, China, are the most divergent, with the exception of the beginning of the ORF1a gene (region 1, fig. 1A ). All other Bat_SL-CoV and SARS-CoV sequences form a separate clade 3, while clade 1 comprises BtKY72 and BM48-31, the two most divergent Bat_SL-CoV sequences, in the Sarbecovirus group ( fig. S1 ). Recombination in the first SARS-CoV-2 sequence (Wuhan-Hu-1) with other divergent CoVs has been previously observed (3) . Here, to better understand the role of recombination in the origin of SARS-CoV-2 among these genetically similar CoVs, we compare Wuhan-Hu-1 to six representative Bat_SL-CoVs, one SARS-CoV, and the two Pan_SL-CoV_GD sequences using SimPlot analysis (14) . RaTG13 has the highest similarity across the genome (8) , with two notable exceptions where a switch occurs ( fig. 1A ). In phylogenetic reconstructions, SARS-CoV-2 clusters closer to ZXC21 and ZC45 than RaTG13 at the beginning of the ORF1a gene (region 1, fig. 1B) , and, as reported (10, 15) , to a Pan_SL-CoV_GD in region 2 (fig.s 1C and S2), which spans the receptor angiotensinconverting enzyme 2 (ACE2) binding site in the spike (S) glycoprotein gene. Comparing Wuhan-Hu-1 to Pan_SL-CoV_GD and RaTG13, as representative of distinct host-species branches in the evolutionary history of SARS-CoV-2, using the recombination detection tool RIP (16) , we find significant recombination breakpoints before and after the ACE2 binding site ( fig. S2A ), suggesting that SARS-CoV-2 carries a history of cross-species recombination between the bat and the pangolin CoVs.