Use of a short fragment of the C-terminal E gene for detection and characterization of two new lineages of dengue virus 1 in India

J Clin Microbiol. 2006 Apr;44(4):1519-29. doi: 10.1128/JCM.44.4.1519-1529.2006.


Here we propose the use of a 216-nucleotide fragment located in the carboxyl terminus of the E gene (E-COOH) and a pairwise-based comparison method for genotyping of dengue virus 1 (DENV-1) strains. We have applied this method to the detection and characterization of DENV-1 in serum samples from travelers returning from the tropics. The results obtained with the typing system correlate with the results obtained by comparison of the sequences of the entire E gene of the strains. The approach demonstrates utility in plotting the distribution and circulation of different genotypes of DENV-1 and also suggests the presence of two new clades of Indian strains. The integration of the method with an online database and a typing characterization tool enhances its strength. Additionally, the analysis of the complete E gene of DENV-1 strains suggested the occurrence of a nondescribed recombination event in the China GD23-95 strain. We propose the use of this methodology as a tool for real-time epidemiological surveillance of dengue virus infections and their pathogenesis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Viral / analysis*
  • Dengue / epidemiology
  • Dengue / virology*
  • Dengue Virus / classification*
  • Dengue Virus / genetics
  • Dengue Virus / pathogenicity
  • Genome, Viral*
  • Humans
  • India / epidemiology
  • Molecular Epidemiology / methods*
  • Phylogeny


  • DNA, Viral