ANALYSIS OF CIRCULATING DENGUE VIRUS SEROTYPE 1 (DENV 1) STRAINS IN INDONESIA BASED ON THE ENVELOPE GENE: A BIOINFORMATIC STUDY

Abstract

Dengue virus serotype 1 (DENV 1) is a major contributor to dengue burden in Indonesia, where all four serotypes co-circulate and cause recurrent outbreaks, but comprehensive mapping of DENV 1 genetic diversity at the national level remains limited. The envelope (E) gene is a key molecular marker for genotyping and phylogenetic analysis because it encodes critical antigenic determinants and shows high sequence variability that reflects viral evolution and geographic spread. DENV 1 sequences were retrieved from international public databases using predefined keywords and country filters. Envelope gene regions were extracted, curated to remove duplicates, low-quality sequences, and obvious recombinants, then aligned to estimate nucleotide and amino acid diversity. Phylogenetic trees were inferred with Maximum Likelihood, and genotypes/lineages were assigned by clustering with published global DENV 1 reference sequences, followed by spatiotemporal mapping based on location and year of isolation. Most Indonesian DENV 1 strains formed a highly homogeneous endemic lineage within Genotype I, with intra-Indonesia nucleotide identity of approximately 98-100% and very low genetic distances among strains from multiple cities and years. Travel-associated strains (Taiwan/Indonesia, Korea/Indonesia, Australia/Bali) showed similarly high homology to Indonesian strains, whereas Indian Ocean strains (Réunion, Seychelles) clustered into a distinct, more divergent lineage. DENV 1 circulation in Indonesia is dominated by a genetically stable Genotype I lineage that also underlies many travel-associated cases, while remaining clearly separated from Indian Ocean lineages, highlighting regional structuring and the importance of continuous genomic surveillance.