Emergence of new genotypes and lineages of dengue viruses during the 2012–15 epidemics in southern India

Syed Fazil Ahamed, V. Rosario, Carl Britto, Mary Dias, Kaustuv Nayak, A. Chandele, Murali Krishna Kaja, A. Shet

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Objectives: To genotypically characterize dengue virus (DENV) isolates among dengue-infected children from 2012–13/2014–15 outbreaks in southern India. Methods: Children hospitalized with suspected dengue were tested for dengue RT-PCR targeting Capsid-preMembrane (C-prM) and Envelope (Env) regions. Following virologic confirmation (n = 612), a representative selection of DENV isolates (n = 99) were sequenced for C-prM, aligned using ClustalW and subjected to phylogenetic analysis by maximum-likelihood method in MEGA6. Results: In 2012–13 (n = 113), DENV-3 (44, 38.9%) and DENV-2 (43, 38.1%) predominated; DENV-1 (22, 19.5%) and DENV-4 (1, 0.9%) were less common. The pattern changed in 2014–15 (n = 499), when DENV-1 (329, 65.7%) predominated, followed by DENV-2 (97, 21.2%), DENV-3 (36, 6.7%) and DENV-4 (10, 2.0%). Multiple-serotype co-infections occurred in 2.7% and 5.4% in 2012–13 and 2014–15, respectively. Genotype III (GIII) of DENV-1 predominated (85.7%) in 2012–13, ceding to GI predominance (80.8%) in 2014–15. Among DENV-2, 71.9% (23/32) showed distinct clustering suggesting a new lineage, ‘GIVc’. All tested DENV-4 were GIC, whose clustering pattern showed the emergence of two distinct clades. Conclusions: New genotypic/lineage variations in DENV-1 and DENV-2 may have influenced the magnitude and severity of dengue epidemics in southern India during this period. These findings emphasize the role of active surveillance of DENV serotypes/genotypes in aiding outbreak control and vaccine studies.

Original languageEnglish (US)
Pages (from-to)S34-S43
JournalInternational Journal of Infectious Diseases
StatePublished - Jul 2019


  • Dengue virus
  • Genotypes
  • Lineages
  • Phylogenetics
  • Sequencing
  • Serotyping

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases


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