Evolutionary dynamics and impact of genetic diversity of co-circulating multiple dengue serotypes among severe and non-severe cases in Kolkata, Eastern India during 2020-2022.

India being within global dengue-endemic region faces frequent dengue outbreaks in different parts with Kolkata in eastern India reporting frequent serotype switching. Thus, present study deals with evolutionary perspective of circulating DENV serotypes/genotypes, their association with development of disease severity among infected patients in Kolkata during 2020–2022. DENV envelope-(E)-gene of 58 samples isolated from 718 symptomatic patients was PCR-amplified, sequenced, subjected to molecular phylogenetic analysis using maximum likelihood method and evolutionary time clock analysis using TamuraNei 93 model. Co-circulation of four serotypes (DENV1:DENV2:DENV3:DENV4 = 1:3.3:2.5:1.4) with significantly increased infectivity from 2020 to 2022 was noted (p = 0.0009). DENV3 (42.42%) and DENV1 (30.30%) were predominant in 2020, whereas, DENV2 (43.85% to 46.42%) in 2021–2022. Approximately, 15% of patients were hospitalized, with significant predominance of DENV2 (55.55%) (p < 0.05). Phylogenetic analyses revealed circulation of DENV1 genotypes I and V, DENV2 cosmopolitan genotype lineages I-III, DENV3 genotype III, and DENV4 genotype I clades-A, C. Nucleotide-substitution-rate of DENV2 (7.17 × 10−4 substitutions/site/year) was highest, indicating greater immunological pressure driving divergence of DENV2. Nucleotide-substitution rate and antigenic score of E-gene was higher among severe patients than non-severe ones. Only severe patients harboured uncommon substitutions. DENV2 of severe patients harboured mutation at K123R and Q52H, I322V. One DHF strain harboured amino acid substitutions at M183T, D192B, E338V, I339T, D341L, G349S, of which E338V, D341L were under positive selection. Overall, shift in most dominant serotype from DENV3 to DENV2, DENV1 genotypic shift, DENV4 clade-replacement, DENV2 lineages-II, III introduction among Kolkata patients might be responsible for larger outbreak with increased disease severity in 2022.