Characterization of novel recombinant HIV-1 genomes using the branching index

Karin Wilbe, Mika Salminen, Tiina Laukkanen, Francine McCutchan, Stuart C. Ray, Jan Albert, Thomas Leitner

Research output: Contribution to journalArticlepeer-review

Abstract

We have characterized six novel genomes of human immunodeficiency virus type 1 (HIV-1) sampled from individuals infected in Uganda and former Zaire. Four isolates (SE6954, SE8603, UG035, and UG266) had clear recombination patterns that included subtypes A1, D and C. The two remaining strains (SE8646 and SE9010) also appeared to be recombinant but had a more complex pattern. To facilitate the classification of these two genomes we developed a metric, the branching index, for characterization of "problematic" sequence fragments that associate to a subtype cluster with a high bootstrap value but are only distantly related to the reference sequences. The branching index is able to signal when parental representatives may be missing and a subtype classification thus is not meaningful. Several fragments of SE8646 and SE9010 had a branching index below the subtype defining cutoff value (0.55) and, therefore, these genomes could not be unequivocally classified. The branching index, with a cutoff value defined from analyses of HIV-1 reference sequences, may be a useful approach not only for more conservative classifications of HIV-1 subtypes but also for analyzing relationships among other types of sequences.

Original languageEnglish (US)
Pages (from-to)116-125
Number of pages10
JournalVirology
Volume316
Issue number1
DOIs
StatePublished - Nov 10 2003

Keywords

  • HIV-1
  • Molecular evolution
  • Recombination
  • Subtype classification

ASJC Scopus subject areas

  • Virology

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