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. 2021 Mar 12;19(3):e3001115. doi: 10.1371/journal.pbio.3001115

Fig 2. Schematic of the nonrecombinant ORF regions used for the nCoV clade selection analyses.

Fig 2

(A) Displays (top to bottom): Individual codon sites (N = 85), mapped to SARS-CoV-2 genomic coordinates, found to be under episodic positive selection in the nCoV clade (MEME p ≤ 0.05); brighter colours indicate that a larger fraction of lineages was subject to selection; sites (N = 3,388) subject to negative selection in the nCoV clade (FEL p ≤ 0.05); genome structure of SARS-CoV-2; ticks inside the genome structure indicate sites that are conserved in the nCoV clades (N = 8,184); nonrecombinant fragments (N = 20) found in the Boni and colleagues [6] analysis; colours show the coefficient of variation for the distribution of site-level synonymous rates. (B) The nCoV clade for 9/20 nonrecombinant segments that exhibit any evidence of branch-level selection according to the aBSREL method. Branches with significant tests (p ≤ 0.05) are shown in the orange-red colours; the colour is based on the average dN/dS estimate for these branches, thickness is proportional to the number of individual sites (genome-wide) that have evidence for positive selection along that branch. The list of GenBank and GISAID accessions for the Sarbecovirus sequences used are provided in S4 Table. aBSREL, adaptive branch-site random effects likelihood; dN, nonsynonymous substitution rate; dS, synonymous substitution rate; FEL, fixed effects likelihood; MEME, mixed effects model of evolution; nCoV, new coronavirus; ORF, open reading frame; SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2.