Legends
Figure 1 . Phylogenomics of SARS-CoV-2 showing the
relevance of diversifying selection during the evolution of this
pathogen . A) Spatial dynamic of different phylogenetic clades during
the evolution of SARS-CoV-2 (Based on GISAID classification). B)
Circulation dynamic of diverse variants of concern (VOC) or variants of
interest (VOI) during the pandemic. C) Phylogenetic analysis conducted
by maximum likelihood using the general reversible model, showing
multiple clades predicted during the evolution of SARS-CoV-2 (GISAID
classification). Tree was constructed using 40 representative sequences.
Determination of branches under diversifying selection was conducted
using the algorithm aBSREL (p-<0.0001) (17) (blue branches
with black asterisk). Evidence of diversifying selection on the tree was
also confirmed by the algorithm BUSTED (p-<0.0001) (18). Sites
under positive selection were determined by the algorithm MEME
(p-<0.05) (19). The mapping of these sites at different
branches in the tree was conducted by BUSTED considering an empirical
bayes factor >10. Evidence of relaxation in the
diversifying selection during the evolution of distinct lineages was
produced by the comparison in the strength of the selection between
internal nodes and leaf nodes using the algorithm RELAX. D) Evidence of
intensified diversifying selection in the GRA clade (comprising the VOC
omicron) in relation with the rest of the clades was obtained by the
algorithm RELAX. Representative sequences and statistics about the
number sequences associated with multiple clades, and VOC and VOI were
obtained from the GISAID database (20).
Figure 2. Prevalence of SARS-CoV-2 phenotypes lacking ORF8
protein. A) to put in context the evolutionary dynamic of ORF8 in
comparison with the rest of the proteins present in SARS-CoV-2 during
the pandemic, the sequences used to develop the tree shown in figure 1C
were analyzed by the evolutionary algorithm SLAC (28). B) Using the
database of GISAID, the overall proportion of lineages lacking ORF8
protein was quantified. Based on the information shown in figures 1A and
1B, the proportion of lineages (C) and VOC or VOI (D) lacking ORF8
protein in each phylogenetic clade was estimated.