2.3. Phylogenetic analysis
A total of 213 and 139 cleaned sequences of SARS-CoV-2 Delta and Omicron
variants and five reference sequences of each VOC (Alpha, Beta, Delta,
Gamma, and Omicron variants, listed in Supplementary Table 2) were used
to construct four different Maximum Likelihood (ML) trees based on theSpike, nsp12, nsp3, and nsp5 genes.
All reference sequences were
selected based on the earliest submission on GISAID databases and
identified as the respective variants. All ML trees were generated usingRaxmlGUI v2.0 with 1,000 bootstraps using the GTR-Gamma model as
the substitution model.41 The ML trees were visualized
and annotated using MEGA11 .42