Isolation and molecular characterization of dengue virus clinical isolates from pediatric patients in New Delhi

•Sixty-four dengue virus type 2 (DENV-2) isolates were amplified by blind passaging.•Twenty-five clinical isolates of DENV-2 from passage 3 were evaluated by growth kinetics in vitro.•Whole genome sequences of 21 clinical isolates were obtained.•Changes were observed in the B cell and CD8 T cell epitopes. To characterize the in vitro replication fitness, viral diversity, and phylogeny of dengue viruses (DENV) isolated from Indian patients. DENV was isolated from whole blood collected from patients by passaging in cell culture. Passage 3 viruses were used for growth kinetics in C6/36 mosquito cells. Parallel efforts also focused on the isolation of DENV RNA from plasma samples of the same patients, which were processed for next-generation sequencing. It was possible to isolate 64 clinical isolates of DENV, mostly DENV-2. Twenty-five of these were further used for growth curve analysis in vitro, which showed a wide range of replication kinetics. The highest viral titers were associated with isolates from patients with dengue with warning signs and severe dengue cases. Full genome sequences of 21 DENV isolates were obtained. Genome analysis mapped the circulating DENV-2 strains to the Cosmopolitan genotype. The replication kinetics of isolates from patients with mild or severe infection did not differ significantly, but the viral titers varied by two orders of magnitude between the isolates, suggesting differences in replication fitness among the circulating DENV-2.