Figure 6. Between-taxa sliding window analysis of natural selection on overlapping frames of ORF3a.

Pairwise sliding window analysis (window size = 50 codons; step size = 1 codon) of selection across members of the species Severe acute respiratory syndrome-related coronavirus. OLG-appropriate d_N/d_S values were computed using OLGenie (Nelson et al., 2020a), a method that is conservative (non-conservative) for detecting purifying (positive) selection, and a Jukes-Cantor correction for multiple hits was employed. On the left-hand side, each genome is compared to SARS-CoV-2 in the ss12 reading frame of ORF3a, which contains ORF3d (Table 1 and Figure 2C). This frame shows evidence for purifying selection specific to the ORF3d region that is limited to the comparison with pangolin-CoV GX/P5L. On the right-hand side, this analysis is repeated for the ss13 reading frame of ORF3a, which contains ORF3c and ORF3b (Table 1 and Figure 2C), this time with respect to SARS-CoV, where full-length ORF3b is functional. This frame shows constraint across much of this gene and virus species, and ORF3c in particular is deeply conserved.

Figure 6—figure supplement 1. Between-taxa sliding window of genes overlapping N.

Pairwise OLGenie analysis of the N gene’s ss13 reading frame across members of the species Severe acute respiratory syndrome-related coronavirus. Details as in Figure 6, except only the ss13 frame is shown.