Strong evolutionary convergence of receptor-binding protein spike between COVID-19 and SARS-related coronaviruses

Yonghua Wu

Given their genome-level phylogenetic disparity, the high similarity of RBD protein sequences between SARS-related CoV and COVID-19-related CoV may suggest their evolutionary convergence in the spike protein. To test this possibility, we used an empirical Bayes approach in PAML 17 to reconstruct ancestral . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.975995 doi: bioRxiv preprint amino acid sequences along internal nodes, and our results showed there were up to 35 evolutionary convergent sites, including 3 convergent and 32 parallel amino acid substitutions that were shared by two ancestral branches leading to SARS-related CoV and COVID-19-related CoV, respectively (Fig. 1) . It should be noted that the 35 evolutionary convergent sites of spike protein were apparently underestimated, since those amino acid sites with alignment gaps were not considered by the approach used. Still, these 35 sites represented an unusually high incidence of evolutionary convergence sites, which have rarely been found in previous studies related to molecular convergent evolution 20-26 . This suggests a strong evolutionary convergence between SARS-related CoV and COVID-19-related CoV. On completion of our data analyses, one of the most recent studies showed that the RBD of the spike protein of Pangolin-CoV is nearly identical to that of 2019-nCoV, with only one amino acid difference 27 , suggesting that Pangolin-CoV also belongs to the clade of COVID-19-related CoV. It should be noted that the RBD sequences of two other coronavirus strains, BM48-31 (GU190215) and BtKY72 (KY352407), were grouped with SARS-related CoV and COVID-19-related CoV (Fig. 3, Fig. S4 ), suggesting an evolutionary convergence among them. In addition to these evolutionarily convergent coronavirus strains, intriguingly, we found the evidence of evolutionary convergence of the spike protein between the ancestral branch leading to SARS-related CoV and the ancestral branch of COVID-19-related CoV and its sister strains (CoVZC45 and CoVZXC21), which harbored 9 evolutionary convergent amino acid sites (Fig. S5) . These results suggest that the spike protein may have been subjected to a successive evolutionary convergence among ancestral coronavirus strains leading to SARS-related CoV, COVID-19related CoV and CoVZC45 and CoVZXC21.