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Background:  Evidence is increasing that female genital tract represents a replication compartment for HIV-1. We compared the effect of HAART in the selection and evolution of variant forms of HIV-1 in cell-free and cell-associated virus from blood and vaginal samples and assessed the role of the vaginal tract as reservoir for drug resistant viruses.

Methods:  We collected blood and vaginal samples from 13 HIV-infected women. HIV-1 protease (Pro) and reverse transcriptase (RT) sequences from cell-free and cell-associated HIV-1 were obtained to determine presence of drug resistance mutations. Mutation patterns were used to assess evolution of HIV-1 in response to anti-retroviral drugs. Sequences were analyzed to determine whether the virus in each compartment represented a different evolutionary line.

Results:  We found 75% (9 of 12) of the women showed discordant mutation patterns between vaginal secretions and plasma virus. Treatment history showed resistant mutants remained detectable in the vaginal secretion virus for 2 to 4 years after cessation of drug. Analysis of plasma virus from a treatment-naïve patient showed no resistance mutations, however vaginal secretion virus showed M184V. Additionally, pol sequences from peripheral blood mononuclear cell (PBMC) HIV showed resistance mutations in 4 of 5 individuals whereas only 2 of 5 of the vaginal cell virus showed resistance mutations. Mutation pattern shown by plasma virus was different from PBMC virus. It was also observed that vaginal cell virus presents a different resistance pattern compared to vaginal secretion virus. Non-resistance associated mutations, many located at CTL epitopes suggest immune and drug selective pressure add to the differential evolution. Cell-associated compartments were less likely to show drug resistance compared to cell-free compartments suggesting delayed emergence of resistance mutations. Analysis of pol sequences of PBMC, vaginal cell, plasma, and vaginal secretion viruses showed that vaginal cell virus is genetically more related to PBMC virus than to vaginal secretion and plasma virus.

Conclusions:  This study provides further insight into the kinetics of drug-resistance-associated changes in protease and RT and the influence of HAART on the selection of certain viral forms. Drug-resistance mutants, detectable only in vaginal virus, suggests the genital tract may serve as a reservoir for drug-resistant viruses and that it may contribute to the transmission of drug resistance. Delayed emergence or elimination of resistance suggests differences in turnover rates among and within anatomical compartments.

Keywords: vaginal; resistance; discordance