Evolutionary Analysis of Dengue Serotype 2 Viruses Using Phylogenetic and Bayesian Methods from New Delhi, India

Citation: Afreen N, Naqvi IH, Broor S, Ahmed A, Kazim SN, Dohare R, et al. (2016) Evolutionary Analysis of Dengue Serotype 2 Viruses Using Phylogenetic and Bayesian Methods from New Delhi, India. PLoS Negl Trop Dis 10(3): e0004511. doi:10.1371/journal.pntd.0004511
Published: March 15, 2016

Abstract
Dengue fever is the most important arboviral disease in the tropical and sub-tropical countries of the world. Delhi, the metropolitan capital state of India, has reported many dengue outbreaks, with the last outbreak occurring in 2013. We have recently reported predominance of dengue virus serotype 2 during 2011–2014 in Delhi. In the present study, we report molecular characterization and evolutionary analysis of dengue serotype 2 viruses which were detected in 2011–2014 in Delhi. Envelope genes of 42 DENV-2 strains were sequenced in the study. All DENV-2 strains grouped within the Cosmopolitan genotype and further clustered into three lineages; Lineage I, II and III. Lineage III replaced lineage I during dengue fever outbreak of 2013. Further, a novel mutation Thr404Ile was detected in the stem region of the envelope protein of a single DENV-2 strain in 2014. Nucleotide substitution rate and time to the most recent common ancestor were determined by molecular clock analysis using Bayesian methods. A change in effective population size of Indian DENV-2 viruses was investigated through Bayesian skyline plot. The study will be a vital road map for investigation of epidemiology and evolutionary pattern of dengue viruses in India.

Author Summary: Dengue is a mosquito borne disease prevalent in more than 100 tropical and sub-tropical countries. In this study, we carried out phylogenetic and molecular clock analysis of dengue serotype 2 strains found to be circulating in Delhi, India, in 2011–2014. All the study strains were found to belong to the Cosmopolitan genotype of dengue 2 viruses. Further we also detected a lineage replacement event in the 2013 dengue fever outbreak. We identified a novel mutation in the stem region of the Envelope protein. We also determined nucleotide substitution rate and time to the most recent common ancestor of dengue 2 viruses. Further a change in the population size of dengue 2 viruses in India as depicted by Bayesian Skyline plot is reported.

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