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Estimating the rate of intersubtype recombination in early HIV-1 group M strains

Melissa J Ward1, Samantha J Lycett, Marcia L Kalish

  • 1University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom.

Journal of Virology
|December 14, 2012
PubMed

Insights

Intersubtype recombination significantly contributes to HIV-1 diversity in West Central Africa. This process, involving recombination between different human immunodeficiency virus type 1 (HIV-1) subtypes, was found in approximately 20% of lineages over 30 years.

Area of Science:

  • Virology
  • Molecular Epidemiology
  • Genetics

Background:

  • West Central Africa is the epicenter of the HIV-1 epidemic, with diverse group M subtypes present.
  • Early HIV-1 group M sequences from Kinshasa show evidence of intersubtype recombination.
  • Recombination between different subtypes can lead to viruses occupying different phylogenetic positions.

Purpose of the Study:

  • To develop a method for quantifying HIV-1 group M intersubtype recombination.
  • To apply this method to early HIV-1 sequences from Kinshasa.
  • To estimate the rate and impact of intersubtype recombination on HIV-1 diversity.

Main Methods:

  • Discrete ancestral trait mapping was used to quantify recombination.
  • gag (p17) and env (gp41) subtypes were analyzed.
  • The number of excess ancestral subtype transitions (NEST) was calculated.

Main Results:

  • Nine different gag/env intersubtype recombinant combinations were identified.
  • Excess subtype transitions occurred at a rate of approximately 7-8 × 10(-3) per lineage per year.
  • Intersubtype recombination was present in approximately 20% of lineages over 30 years.

Conclusions:

  • Intersubtype recombination is a substantial force in generating HIV-1 group M diversity.
  • The developed method provides a way to quantify intersubtype recombination.
  • Understanding recombination is crucial for tracking HIV-1 evolution and diversity.

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