3.2. Phylogenetic analyses of SARS-CoV-2 circulating in
Yogyakarta and Central Java provinces based on the Spike, nsp12, nsp3,
and nsp5 genes
The Maximum likelihood (ML) phylogenetic tree of the Spike gene
of our original isolates (n=352) is shown in Figure 1. Based on theSpike gene, all original viral isolates collected from Yogyakarta
and Central Java provinces were clustered in two main lineages of the
Delta and Omicron variants, while the previous VOCs (Alpha, Beta, and
Gamma) were separated in distinct clusters. Similarly, the ML tree based
on nsp12 (Figure 2A) and nsp5 genes (Figure 2C) also
showed that our isolates were segregrated into two independent clusters
of Delta and Omicron variants. While in nsp3 gene, the Delta and
Omicron variants did not form specific clusters, but more diverse
segregation was observed (Figure 2B).