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).