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Multiple-infection and recombination in HIV-1 within a longitudinal cohort of women

Alan R Templeton1*, Melissa G Kramer23, Joseph Jarvis2, Jeanne Kowalski4, Stephen Gange5, Michael F Schneider5, Qiujia Shao6, Guang Wen Zhang6, Mei-Fen Yeh4, Hua-Ling Tsai4, Hong Zhang6 and Richard B Markham6

Author Affiliations

1 Department of Biology, Washington University, St Louis, Missouri, USA

2 Division of Biological and Biomedical Sciences, Washington University, St Louis, Missouri, USA

3 US Environmental Protection Agency, Washington, DC, USA

4 Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

5 Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA

6 Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA

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Retrovirology 2009, 6:54  doi:10.1186/1742-4690-6-54

Published: 3 June 2009



Recombination between strains of HIV-1 only occurs in individuals with multiple infections, and the incidence of recombinant forms implies that multiple infection is common. Most direct studies indicate that multiple infection is rare. We determined the rate of multiple infection in a longitudinal study of 58 HIV-1 positive participants from The Women's Interagency HIV Study with a richer sampling design than previous direct studies, and we investigated the role of recombination and sampling design on estimating the multiple infection rate.


40% of our sample had multiple HIV-1 infections. This rate of multiple infection is statistically consistent with previous studies once differences in sampling design are taken into account. Injection drug use significantly increased the incidence of multiple infections. In general there was rapid elimination of secondary strains to undetectable levels, but in 3 cases a superinfecting strain displaced the initial infecting strain and in two cases the strains coexisted throughout the study. All but one secondary strain was detected as an inter- and/or intra-genic recombinant. Injection drug use significantly increased the rate of observed recombinants.


Our multiple infection rate is consistent with rates estimated from the frequency of recombinant forms of HIV-1. The fact that our results are also consistent with previous direct studies that had reported a much lower rate illustrates the critical role of sampling design in estimating this rate. Multiple infection and recombination significantly add to the genetic diversity of HIV-1 and its evolutionary potential, and injection drug use significantly increases both.