Diversity in HIV-1 envelope V1-V3 sequences early in infection reflects sequence diversity throughout the HIV-1 genome but does not predict the extent of sequence diversity during chronic infection.

Differences in the extent of genetic diversity have been observed in human immunodeficiency virus type-1 (HIV-1) envelope sequences early in infection, and this has been linked to gender and to modifiable exogenous factors such as hormonal contraceptive use and genital tract infections. But it is unclear whether envelope diversity is indicative of diversity in other regions of the viral genome, and thus whether it adequately reflects whether multiple or a single virus initiated the infection. Here we show that six women with homogeneous envelope V1-V3 sequences during primary infection also had homogeneous gag and polymerase (pol) sequences at the same time. On the other hand, six women with multiple envelope sequences had diverse gag and pol genotypes during a similar interval after infection. This suggests that envelope sequences reflect sequence diversity throughout the viral genomes present early in infection and thus provide an indication of whether a single virus or multiple viruses initiated the infection. Analysis of HIV-1 sequences from about 3 years after infection revealed that the level of diversity and diversification was similar between the women in the two groups.