3.4. Substitution rates of the Spike, nsp12, nsp3, and
nsp5 genes of SARS-CoV-2 Delta and Omicron variants
We then determined the susbtitution rate for each gene of SARS-CoV-2
Delta and Omicron variants circulating in Yogyakarta and Central Java
provinces, Indonesia. In four genes studied, the substitution rates of
Omicron were higher than that of Delta variants, particularly in theSpike and nsp12 genes. The substitution rates for theSpike gene were 2.41 x 10-2 subs/site/yr (95%
HPD: 6.82 x 10-4 to 5.67 x 10-2) and
1.05 x 10-3 subs/site/yr (95% HPD: 3.65 x
10-6 to 3.92 x 10-3) for Omicron and
Delta variants, respectively. For nsp12 gene, the substitution
rates were 3.50 x 10-2 subs/site/yr (95% HPD: 3.36 x
10-7 to 1.24 x 10-1) and 3.44 x
10-3 subs/site/yr (95% HPD: 1.25 x
10-6 to 9.49 x 10-3) for Omicron and
Delta variants, respectively. Similar findings were found in thensp3 and nsp5 genes (Table 1) .