3.3. Mutation analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 Delta and Omicron variants
The complete mutational analysis was shown in Supplementary Table 5. High frequency (hotspot) mutations (>10%)44 identified in either Delta and Omicron variants were shown in Figure 3, while visualization of these mutations were depicted in Figure 4. Mutational events highly occurred in the Spike gene. The most frequent amino acid substitutions in the Spike protein of Delta variant were T19R, G142D, A222V, L452R, T478K, Q613H, D614G, P681R, D950N, and V1264L. While the Omicron variant had more mutations than the Delta variant. The amino acid mutations T478K, D614G, D950N, and N969K were found in Delta and Omicron variants. However, the frequency of D950N mutation in the Omicron and N969K mutation in the Delta was low (<10%).
The Delta variant had more frequent amino acid substitutions than the Omicron in the nsp12 gene. Several mutations found in Delta variant were V42V, R249M, P323L, G671S, and N600N. While in Omicron variant, the prevalent mutations were P323L, N600N, and L758L. Interestingly, Delta and Omicron variants had similar amino acid substitutions P323L with a frequency of 100%. The amino acid substitution in the nsp5 gene only occurred in the Omicron variant. There are three amino acid changes with >10% frequency, including L27L, R131R, and P132H. In the nsp5 gene, the amino acid substitutions occurred in both variants. However, Omicron had more prevalent mutations than Delta, with nine amino acid substitutions identified within this gene. F106F mutation occurred in both variants with a high frequency (>95%). For P1228L mutation, the frequency was higher in the Delta (85,9%) than in Omicron (2,9%) variants.