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

Yonghua Wu

We used likelihood ratio tests based on the branch and branch-site models implemented in the codeml program of PAML 17 to examine the possible Darwinian selection of all 11 genes annotated in the 2019-nCoV genome (NC_045512). Positively selected genes (PSGs) were found by the branch-site model ( Table 1) , independent of the initial value variation of parameters (kappa and ω). Specifically, for the branches leading to 2019-nCoV and SARS-CoV, no PSGs were found, nor were PSGs found along the branches leading to their sister coronaviruses. However, we detected PSGs along the ancestral branch (branch C) of 2019-nCoV and its sister taxon, RaTG13, as well as along the ancestral branch (branch K) of SARS-CoV and its sister taxa, WIV16 and Rs4231 (Table 1 , Fig. 1 ). For branch C, three PSGs (S, Orf1ab and N) were found, and for branch K, only one gene (S) was found to be under positive selection (Table 1) . Orf1ab encodes replicase and N encodes nucleocapsid 18 . Intriguingly, the S gene was subject to Darwinian selection in both branches, C and K. This gene encodes the spike protein, which mediates receptor binding and membrane fusion 6 . The finding of Darwinian selection on the spike protein may suggest its adaptive evolution to the host receptors. To further examine the possible adaptive evolution of 2019-nCoV and SARS-CoV to a human host, we used RELAX 19 to analyze the relative selection intensity change of the 11 genes along the branches leading to 2019-nCoV and SARS-CoV compared with their most recent ancestors, branches C and K, respectively (Tables S1-2). Among the 11 genes examined, gene S along the 2019-nCoV branch exhibited a significant selection intensification signal (K = 30.54, p = 0.000, Table S1, Fig. S1 ), and this remained robust in four independent runs. We also found that the ORF6 gene showed slight selection intensification (K = 1.81, p = 0.000) along the SARS-CoV branch (Table S2) , while its statistical significance only received two supports among five independent runs. For the selectively intensified gene S along the 2019-nCoV branch, 0.46% of the amino acid sites (about five amino acids) were under positive selection, while most sites (86.63%) were under purification selection (Table S1 ). This may suggest that 2019-nCoV was subject to an adaptive evolution during its adaption to possible intermediate and/or human hosts.