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Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning.

Philippe Lemey1, Martin Lott, Darren P Martin

  • 1Rega Institute, Katholieke Universiteit Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium. philippe.lemey@gmail.com

BMC Bioinformatics
|April 29, 2009
PubMed
Summary

This study introduces quartet scanning, a novel method for detecting viral recombination patterns in molecular sequences. Quartet scanning effectively identifies recombinant sequences and offers an advancement over existing triplet-based methods.

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Area of Science:

  • Virology
  • Molecular Evolution
  • Bioinformatics

Background:

  • Viral recombination significantly impacts evolution but remains challenging to characterize.
  • Identifying recombinant sequences is less emphasized in current detection frameworks.
  • Existing methods often require prior specification of query and reference sequences.

Purpose of the Study:

  • To develop and evaluate a novel quartet-mapping based method for identifying recombinant sequences.
  • To compare the performance of the quartet approach with existing triplet-based methods.
  • To analyze complex viral datasets, including HIV-1 and SIV, to demonstrate the method's utility.

Main Methods:

  • Extension of a quartet-mapping based recombination detection method.
  • Evaluation of recombinant identification statistics and significance tests through simulations.
  • Comparison with triplet-based methods using heuristic tests.

Main Results:

  • Quartet scanning performs well in identifying descendants of old recombination events, outperforming triplet-based methods.
  • Analysis of HIV-1 strains provides evidence for the recombinant origin of subtype G and the 'pure' lineage of CRF02_AG.
  • Demonstrated HIV-1 intrasubtype recombination, confirmed SIV hybrid origins in chimpanzees, and clarified SIV lineage histories.

Conclusions:

  • Quartet scanning is a valuable addition to existing triplet-based methods for identifying recombinant sequences without prior sequence specifications.
  • The new method enhances the ability to detect and characterize viral recombination patterns.
  • The quartet scanning method is available in the VisRD v.3.0 package.