Genomic recombination events may reveal the evolution of coronavirus and the origin of SARS-CoV-2

To trace the evolution of coronaviruses and reveal the possible origin of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19, we collected and thoroughly analyzed 29,452 publicly available coronavirus genomes, including 26,312 SARS-CoV-2 genomes. We observed coronavirus recombination events among different hosts, including 3 independent recombination events with statistical significance between isolates from humans, bats and pangolins. Consistent with previous records, we detected putative recombination between strains similar or related to Bat-CoV-RaTG13 and Pangolin-CoV-2019. The putative recombination region is located inside the receptor-binding domain (RBD) of the spike glycoprotein (S protein), which may represent the origin of SARS-CoV-2. Population genetic analyses suggest that the putatively introduced genetic sequence within the RBD is undergoing directional evolution, potentially resulting in adaptation to hosts. We found that the putative recombination region in S protein was highly diverse among bat strains. Bats harbor numerous coronavirus subclades that frequently participate in recombination with human coronaviruses and may therefore provide a pool of genetic diversity for the origin of SARS-CoV-2.