Molecular epidemiology and evolutionary trends of dengue virus serotype-2 strains in Sri Lanka

Dengue virus (DENV) infections in Sri Lanka have intensified over the past 3 decades. Surveillance and characterization of different DENV lineages of different serotypes causing outbreaks is crucial for initiation of timely dengue control measures and for implementing dengue vaccines. Therefore, we characterized the DENV-2 strains in Sri Lanka from 2016, until end of 2023 and their evolutionary dynamics to understand the geographical spread and mutations arising with the DENV-2 serotypes in Sri Lanka. Sequencing was carried out on 80 DENV-2 samples collected from patients with acute dengue recruited in the years 2016 to 2018, and on 12 DENV-2 samples in patients recruited in years 2022 to 2023 using Oxford Nanopore Technology. Phylogenetic analysis was carried out using the IQ-TREE tool, and Galaxy to construct a phylogenetic tree from the aligned sequence data. The sequences were also analyzed for non-synonymous amino acid changes in the envelope and NS1 regions. The Sri Lankan DENV-2 sequences circulating from 2016 to end of 2023 belonged to genotype II.F.1.1 lineage. They were closely related to strains circulating in the same period in South Asia and Southeast Asia. We identified 15 non-synonymous mutations within the envelope region and 22 non-synonymous mutations within the NS1 region, with 7 non-synonymous mutations within the E region (M6I, Q52H, E71A, V129I, N390S, I484V, T478S) and 10 non-synonymous mutations within the NS1 region (S80T, T117A, Q131H, K174R, F178S, N222S, L247F, I264T, T265A, K272R) seen in all sequenced samples. Some of these mutations were previously shown to be associated with increase in viral replication, NS1 secretion and immune evasion, while some have not been reported elsewhere. Given the increase in dengue transmission in many countries, it is important to further strengthen DENV surveillance for studying the evolutionary patterns of the DENV to initiate timely and appropriate control measures.