Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood: Compartmentalization and intrapatient recombination

Sean Philpott, Harold Burger, Christos Tsoukas, Brian Foley, Kathryn Anastos, Christina Kitchen, Barbara Weiser

Research output: Contribution to journalArticle

74 Citations (Scopus)

Abstract

Investigation of human immunodeficiency virus type 1 (HIV-1) in the genital tract of women is crucial to the development of vaccines and therapies. Previous analyses of HIV-1 in various anatomic sites have documented compartmentalization, with viral sequences from each location that were distinct yet phylogenetically related. Full-length RNA genomes derived from different compartments in the same individual, however, have not yet been studied. Furthermore, although there is evidence that intrapatient recombination may occur frequently, recombinants comprising viruses from different sites within one individual have rarely been documented. We compared full-length HIV-1 RNA sequences in the plasma and female genital tract, focusing on a woman with high HIV-1 RNA loads in each compartment who had been infected heterosexually and then transmitted HIV-1 by the same route. We cloned and sequenced 10 full-length HIV-1 RNA genomes from her genital tract and 10 from her plasma. We also compared viral genomes from the genital tract and plasma of four additional heterosexually infected women, sequencing 164 env and gag clones obtained from the two sites. Four of five women, including the one whose complete viral sequences were determined, displayed compartmentalized HIV-1 genomes. Analyses of full-length, compartmentalized sequences made it possible to document complex intrapatient HIV-1 recombinants that were composed of alternating viral sequences characteristic of each site. These findings demonstrate that the genital tract and blood harbor genetically distinct populations of replicating HIV-1 and provide evidence that recombination between strains from the two compartments contributes to rapid evolution of viral sequence variation in infected individuals.

Original languageEnglish (US)
Pages (from-to)353-363
Number of pages11
JournalJournal of Virology
Volume79
Issue number1
DOIs
StatePublished - Jan 2005
Externally publishedYes

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female genitalia
Human immunodeficiency virus 1
Genetic Recombination
HIV-1
genomics
nucleotide sequences
blood
genitalia
genome
Genome
RNA
Active Immunotherapy
Viral Genome
vaccine development
Clone Cells
clones
Viruses
viruses
therapeutics

ASJC Scopus subject areas

  • Immunology

Cite this

Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood : Compartmentalization and intrapatient recombination. / Philpott, Sean; Burger, Harold; Tsoukas, Christos; Foley, Brian; Anastos, Kathryn; Kitchen, Christina; Weiser, Barbara.

In: Journal of Virology, Vol. 79, No. 1, 01.2005, p. 353-363.

Research output: Contribution to journalArticle

Philpott, Sean ; Burger, Harold ; Tsoukas, Christos ; Foley, Brian ; Anastos, Kathryn ; Kitchen, Christina ; Weiser, Barbara. / Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood : Compartmentalization and intrapatient recombination. In: Journal of Virology. 2005 ; Vol. 79, No. 1. pp. 353-363.
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