BACKGROUND: The integrin alpha4beta7 mediates the trafficking of immune cells to the gut associated lymphoid tissue (GALT) and is an attachment factor for the HIV gp120 envelope glycoprotein. We developed a viral replication inhibition assay to more clearly evaluate the role of alpha4beta7 in HIV infection and the contribution of viral and host factors. RESULTS: Replication of 60 HIV-1 subtype C viruses collected over time from 11 individuals in the CAPRISA cohort were partially inhibited by antibodies targeting alpha4beta7. However, dependence on alpha4beta7 for replication varied substantially among viral isolates from different individuals as well as over time in some individuals. Among 8 transmitted/founder (T/F) viruses, alpha4beta7 reactivity was highest for viruses having P/SDI/V tri-peptide binding motifs. Mutation of T/F viruses that had LDI/L motifs to P/SDI/V resulted in greater alpha4beta7 reactivity, whereas mutating P/SDI/V to LDI/L motifs was associated with reduced alpha4beta7 binding. P/SDI/V motifs were more common among South African HIV subtype C viruses (35%) compared to subtype C viruses from other regions of Africa (<8%) and to other subtypes, due in part to a founder effect. In addition, individuals with bacterial vaginosis (BV) and who had higher concentrations of IL-7, IL-8 and IL-1alpha in the genital tract had T/F viruses with higher alpha4beta7 dependence for replication, suggesting that viruses with P/SDI/V motifs may be preferentially transmitted in the presence of BV in this population. CONCLUSIONS: Collectively, these data suggest a role for alpha4beta7 in HIV infection that is influenced by both viral and host factors including the sequence of the alpha4beta7 binding motif, the cytokine milieu and BV in the genital tract. The higher frequency of P/SDI/V sequences among South African HIV-1 subtype C viruses may have particular significance for the role of alpha4beta7 in this geographical region.