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.