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

Yonghua Wu

We used the amino acid-based marginal reconstruction implemented in the empirical Bayes approach in PAML 17 for ancestral sequence reconstruction. In the analyses, the character was assigned to a single interior node and the character with the highest posterior probability was used as the best reconstruction. We used two different amino acid substitution models, JTT and Poisson, to examine the consistency of our results. The JTT model assumes different substitution rates of different amino acids, while the Poisson model assumes the same substitution rate of all amino acids. For the analyses, we obtained the full-length spike protein sequences of our focal coronavirus strains and used their phylogeny, as given in Fig. 1 . The amino acid substitutions along our focal branches were analyzed. The results based on the JTT and Poisson models were generally identical; for convenience, only the results based on the JTT model are shown.