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. 2016 Mar 15;10(3):e0004511.
doi: 10.1371/journal.pntd.0004511. eCollection 2016 Mar.

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

Nazia Afreen  1 , Irshad H Naqvi  2 , Shobha Broor  3 , Anwar Ahmed  4 , Syed Naqui Kazim  1 , Ravins Dohare  1 , Manoj Kumar  5 , Shama Parveen  1
Affiliations

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

Nazia Afreen et al. PLoS Negl Trop Dis. .

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Maximum Likelihood Phylogenetic tree of DENV-2 strains.
Strains sequenced in the study are marked by shapes (2014 strains: diamonds; 2013 strains: circles; 2012 strains: rectangles; 2014 strains: triangles). Numbers on nodes indicate bootstrap support generated by 1000 replicates. Bootstrap values of >70 are shown.
Fig 2
Fig 2. Modelled structure of Envelope Protein (289–440) showing position of I322V & T404I mutations.
Fig 3
Fig 3. Maximum Clade Credibility tree of Dengue 2 virus.
Tree derived with the best fit model (relaxed uncorrelated lognormal clock & Bayesian skyline tree prior) showing node ages. Strains sequenced in the present study are coloured. Lineages showing Valine or Isoleucine at position 322 have been marked.
Fig 4
Fig 4. Bayesian skyline plots of Indian Cosmopolitan DENV-2 strains.
X axis: Time, Y axis: Relative genetic diversity (Neτ). Black solid line is the median estimate of Neτ. Blue shaded area shows 95% HPD.
See this image and copyright information in PMC

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