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. 2020 Oct 23;11:550674. doi: 10.3389/fmicb.2020.550674

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Copyright © 2020 Velazquez-Salinas, Zarate, Eberl, Gladue, Novella and Borca.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Diversifying and purifying selection on SARS-CoV-2. (A) General overview obtained by SLAC analysis, showing the evolutionary rate (dN-dS or dN/dS) along the genome and at individual genes of SARS-CoV-2. Statistically significant codons were inferred by multiple evolutionary tests used in this study. Red asterisks represent codons with significant evidence for selection. Codons evolving at (B) purifying (negative) or (C) diversifying (positive) selection are shown numbers in red represent evolutionary tests with significant values according to the analysis: SLAC, FEL, MEME (p = 0.1), and FUBAR (posterior probability = 0.9). The criteria for considering a site positively or negatively selected was based on their identification by at least one of the tests. The phylogenetic group column (assigned according with Figure 2A) shows also the isolates carrying the substitutions. LP, leader protein; 3LP, 3C-like proteinase; n9, nsp9; 3'-5' exo, 3' to 5' exonuclease; EN, endoRNAse; and 2'M, 2'-O-ribose methyltransferase.