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.