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

Yonghua Wu

Evolutionary convergence may occur by chance or by Darwinian selection. Our results showed that the evolutionary convergent sites found in this study were mainly restricted to two genes (S and ORF3a, Fig. 1 ), and in particular, they were centered within the RBD of the S gene. This biased distribution of evolutionary convergent sites is difficult to explain according to chance; rather, Darwinian selection would be favored as a plausible explanation. In support of this, we used CONVERG2 31 to evaluate the probability of the occurrence of our observed convergent sites of spike protein between the two ancestral branches leading to SARS-related CoV and COVID-19-related CoV, and the results showed high statistical significance (p = 0.000000), regardless of whether the JTT model or Poisson model was used. This result apparently rejects chance or neutral evolution as a possible explanation; rather, it indicates a . 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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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 predominately strong Darwinian selection. Moreover, we observed an apparently accelerated evolution of RBD of SARS-related CoV and COVID-19-related CoV related to their phylogenetic intermediates (Fig. 3) , and we detected a significant Darwinian selection of the S gene along two branches (branches C and K) of SARS-related CoV and COVID-19-related CoV (Fig. 1 , Table 1 ). These lines of evidence may strongly support the evolutionary convergence found in this study as a result of adaptive evolution. Regarding the possible adaptive evolutionary convergence, previously proposed causes, such as gene duplication and horizontal gene transfer 21,32,33 , are less likely because only single-copy S genes were found in all 35 genomes examined and evolutionary convergent sites presented an apparently biased distribution pattern. Parallel and/convergent evolution, which occur through point mutation, could contribute to our observed evolutionary convergence, but it could not account for the unusually high incidence of convergent sites observed in this study, representing a rare finding in previous studies 20- 26 . Recent studies have shown a relatively high likelihood of occurrence of homologous recombination in spike protein 7,34,35 , and especially, it is considered that the RBD of 2019-nCov may be derived from a recombination event between that of human SARS-CoV and another (unsampled) SARS-like CoV 35 . If this is the case, the homologous recombination, if any, may have occurred between the ancestors (branches C and K) of SARS-related CoV and COVID-19-related CoV, accounting for their unusually high incidence of convergent sites observed in this study.