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

Jesse Taylor, Bette T. Korber

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

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
Volume5
Issue number1
DOIs
StatePublished - Jan 2005
Externally publishedYes

Fingerprint

Superinfection
human immunodeficiency virus
Human immunodeficiency virus 1
Genetic Recombination
recombination
HIV-1
Viral Genome
genome
Population
Viruses
Genealogy and Heraldry
viruses
urban population
Urban Population
virus
genealogy
rate
superinfection
Infection
infection

Keywords

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

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Microbiology
  • Infectious Diseases

Cite this

HIV-1 intra-subtype superinfection rates : Estimates using a structured coalescent with recombination. / Taylor, Jesse; Korber, Bette T.

In: Infection, Genetics and Evolution, Vol. 5, No. 1, 01.2005, p. 85-95.

Research output: Contribution to journalArticle

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