3.5. Selective pressure analysis
Selective pressure analysis was performed for each gene to comprehend
which sites that evolve under selective pressure, implying that the
sites are functionally essential for virus evolution. Selective pressure
analysis on Spike gene revealed that several sites were under
positive selection, including 95 (T), 142 (G), 222 (A), 452 (L), 614
(D), 1264 (V) in Delta and 213 (V), 339 (G), 375 (S), 417 (K), and 440
(N) in Omicron variants. In nsp12 gene, only one site (249
[R]) was under positive selection in Delta variant. Nsp3 gene
revealed 1183 (A), 1206 (S), 1228 (P), and 1733 (E) that were under
positive selection in Delta variant. No sites in nsp5 gene that
were under positive selection. Thus, in Omicron variant, we only
identified positively selected sites in the Spike gene.