ABSTRACT:
In 2023, Nepal faced a big dengue outbreak, following a record-breaking number of dengue cases in 2022, characterized by expansion towards higher altitudes. However, the characteristics of the circulating dengue virus (DENV) and the vector remain poorly understood. Therefore, we performed DENV serotyping, genotyping, whole genome sequencing and entomological analysis of the outbreak in central Nepal. A total of 934 suspected dengue cases in different hospitals were enrolled, and blood samples were collected and tested by different techniques including RT-PCR. Of these, 679 (72.7%) had confirmed DENV infection. Three DENV serotypes (DENV-1, -2, and -3) were detected in both 2022 and 2023 with the majority of DENV-1 and -3 in 2022, and DENV-2 in 2023 and DENV-2 and 3 in 2024. DENV-2 re-emerged after six years in central Nepal while DENV-3 was identified for the first time indicating a serotype replacement phenomenon. DENV whole genome sequence analysis revealed that the circulating DENV strains belonged to Genotype V of DENV-1, Cosmopolitan Genotype of DENV-2 and Genotype III DENV-3. All of these strains showed a close similarity with DENV strains circulating in neighboring India. Aedes mosquitoes largely predominated (90.7%) with the majority being A. aegypti (60.7%). We also found high Aedes index (20.0%) and container index (16.7%). Interestingly the DENV serotypes we detected in Aedes mosquitoes correlated well with the dengue outbreaks suggesting the potential application of this One Health approach in outbreak prediction and preparedness. We confirmed multiple DENV serotype circulation with serotype re-emergence and new serotype introduction, and high vector density in central Nepal. DENV genotypes with a close relationship with Indian strains suggests for a regional and cross-border coordination. These findings call for urgent initiation of the one health approach and scaling up of DENV genomic surveillance in human and mosquito populations for dengue control and prevention in Nepal.