Detection and Genomic Characterisation of Dengue Virus (DENV) from Clinical Isolates

Abstract

Dengue virus (DENV) infection presents a significant global health threat, especially in Indonesia. This study focuses on identification and genetic characterization of circulating DENV isolates in Timika and Jambi through serotyping, genotyping, and mutation analysis to understand genetic diversity and transmission dynamics. Samples from 119 and 115 suspected dengue patients in Timika and Jambi, respectively, were tested for NS1 antigen and IgM/IgG antibodies. The extracted RNA underwent qRT-PCR serotyping and whole genome sequencing for phylogenetic analysis. High seropositivity was observed in Timika (90%), whereas the seropositivity in Jambi still needs further investigation. Both regions were dominated by DENV-3. Interestingly, serotype shifting was observed in Jambi, which was previously dominated by DENV-1. Phylogenetic analysis revealed the circulation of genotype I, IV, and V (DENV-1), genotype Cosmopolitan (DENV-2), genotype I (DENV-3), and genotype II (DENV-4), all of which clustered with isolates in surrounding regions. Future studies should therefore focus on these genotypes, perform better surveillance for Timika patients, and perform ELISA IgG on Jambi samples for accurate seroprevalence determination. Nevertheless, this study highlights the importance of serotype identification, molecular surveillance, and seroprevalence determination, enhancing knowledge of DENV transmission patterns.