Use of drug resistance sequence data for the systematic detection of non-B human immunodeficiency virus type 1 (HIV-1) subtypes: how to create a sentinel site for monitoring the genetic diversity of HIV-1 at a country scale

J Infect Dis. 2001 May 1;183(9):1311-7. doi: 10.1086/319859. Epub 2001 Mar 27.

Abstract

To assess the molecular epidemiology of human immunodeficiency virus type 1 (HIV-1), a screening method was developed for identification of non-B subtypes from sequence data obtained for resistance testing. The method is based on the evaluation of the percentage of divergence of a given sequence from the reference B subtype HXB2. Analysis of 1720 reverse-transcriptase (RT) and 1824 protease sequences stored in a database allowed for the determination of a threshold level of divergence from HXB2 above which a non-B subtype could be unambiguously characterized regardless of the pattern of resistance mutations (>8.6% for RT; >10.8% for protease). This conclusion was validated by phylogenetic analysis of RT, protease, and env genes. Overall, 72 (4.2%) and 73 (4.0%) non-B sequences were identified in the RT and protease coding regions, respectively. This method allows for the rapid detection of non-B subtypes among retrospective, recent, and future RT and/or protease sequence databases.

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Cluster Analysis
  • Cohort Studies
  • Drug Resistance / genetics
  • Female
  • France / epidemiology
  • Genes, env / genetics
  • Genetic Variation*
  • HIV Infections / epidemiology
  • HIV Infections / virology*
  • HIV Protease / analysis
  • HIV Protease / genetics*
  • HIV Reverse Transcriptase / analysis
  • HIV Reverse Transcriptase / genetics*
  • HIV-1* / classification
  • HIV-1* / enzymology
  • HIV-1* / genetics
  • Humans
  • Immunophenotyping
  • Male
  • Middle Aged
  • Mutation
  • Phylogeny
  • Polymerase Chain Reaction
  • Reproducibility of Results
  • Sequence Analysis

Substances

  • HIV Reverse Transcriptase
  • HIV Protease