Abstract
During the Covid-19 pandemic, the
resurgence of SARS-CoV-2 was due to the development of novel variants of
concern (VOC). Thus, genomic surveillance is essential to monitor
continuing evolution of SARS-CoV-2 and to track the emergence of novel
variants. In this study, we performed phylogenetic, mutation, and
selection pressure analyses of the Spike, nsp12, nsp3, andnsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and
Central Java provinces, Indonesia from May 2021 to February 2022.
Various bioinformatics tools were employed to investigate the
evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study
period, 213 and 139 isolates of Omicron and Delta variants were
identified, respectively. Particularly in the Spike gene,
mutations were significantly more abundant in Omicron than in Delta
variants. Consistently, in all of four genes studied, the substitution
rates of Omicron were higher than that of Delta variants, especially in
the Spike and nsp12 genes. In addition, selective pressure
analysis revealed several sites that were positively selected in
particular genes, implying that these sites were functionally essential
for virus evolution. In conclusion, our study demonstrated a distinct
evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta
and Central Java provinces, Indonesia.