HIV-1 intra-subtype superinfection rates: Estimates using a structured coalescent with recombination

Jesse E. Taylor, Bette T. Korber

Research output: Contribution to journalArticlepeer-review

18 Scopus citations


Because recombination between a pair of viral genomes can occur only when both viruses are present in the same host, genealogical evidence of recombination is influenced by the rate of viral migration between infected hosts. If superinfection is rare, then recombining viral genomes will usually be more closely related to each other than to viral genomes present in other hosts and the impact of recombination on the genealogy of a sample of viruses from different hosts may be weak. We used this relationship to estimate the relative rate of intra-subtype HIV-1 superinfection in six urban populations. Comparisons of the population recombination rates estimated from the HIV-1 sequence data with population recombination rates estimated for sets of sequences simulated using a structured coalescent process suggest that intra-subtype superinfection rates in all but one of these populations may be as high as 15% of the corresponding infection rate. However, we caution that these estimates might be upwardly biased if variation in contact and mixing rates between infected hosts causes viral lineages to be concentrated in groups with higher than average superinfection rates.

Original languageEnglish (US)
Pages (from-to)85-95
Number of pages11
JournalInfection, Genetics and Evolution
Issue number1
StatePublished - Jan 2005
Externally publishedYes


  • Coalescent process
  • HIV-1
  • Population structure
  • Recombination
  • Superinfection
  • Vaccines

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Microbiology (medical)
  • Infectious Diseases


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