Fig. 1

Phylogenetic analysis of Omicron and Delta variants of SARS-CoV-2 virus collected from Central Java and Yogyakarta regions from 2021–2022. Phylogenetic trees are displayed in rectangular (a) and polar (b) layouts. The evolutionary history was inferred using the Neighbor-Joining method [19, 20] and computed using the Kimura 2-parameter [21] method with 1000 bootstrap replication in MEGA X [23]. The number of base substitutions per site (0.0001) is shown on the left of the rectangular tree, where the rate variation among sites was modeled with a gamma distribution. This analysis involved 392 nucleotide sequences, a total of 29.409 positions in the final dataset. Moreover, all ambiguous positions were removed for each sequence pair (pairwise deletion option). Samples from our study were color-coded as follows: the Delta variant taxa are indicated in red, followed by Omicron-BA.1-like in blue, Omicron-BA.2-like in green, Omicron-BA.3-like in purple, and other variants previously circulating in Indonesia that are involved in this analysis are indicated in black