Hypermutation, the introduction of excessive G-to-A substitutions by host proteins in the APOBEC family, can impair replication of the human immunodeficiency virus (HIV). Because hypermutation represents a potential antiviral strategy, it is important to determine whether greater hypermutation is associated with slower disease progression in natural infection. We examined the level of HIV-1 hypermutation among 28 antiretroviral-naive Kenyan women at two times during infection. By examining single-copy gag sequences from proviral DNA, hypermutation was detected in 16 of 28 individuals. Among individuals with any hypermutation, a median of 15% of gag sequences were hypermutated (range, 5 to 43%). However, there was no association between the level of gag hypermutation and the viral load or CD4 count. Thus, we observed no overall relationship between hypermutation and markers of disease progression among individuals with low to moderate levels of hypermutation. In addition, one individual sustained a typical viral load despite having a high level of hypermutation. This individual had 43% of gag sequences hypermutated and harbored a partially defective Vif, which was found to permit hypermutation in a peripheral blood mononuclear cell culture. Overall, our results suggest that a potential antiviral therapy based on hypermutation may need to achieve a substantially higher level of hypermutation than is naturally seen in most individuals to impair virus replication and subsequent disease progression.Interactions between the human immunodeficiency virus type 1 (HIV-1) protein Vif (for viral infectivity factor) and antiviral host factors in the APOBEC family (for apolipoprotein B mRNA editing enzyme, catalytic polypeptide) have recently attracted interest as potential targets for antiviral therapy (10,13,16,26,28,40). One of the mechanisms by which APOBEC3G, a cytidine deaminase, may impair HIV-1 replication is through the introduction of C-to-U lesions in the negative-sense DNA strand during reverse transcription (RT). This process, known as hypermutation, results in excessive G-to-A changes in the HIV-1 coding strand, leading to premature stop codons and other potentially disruptive mutations (24). APOBEC3G activity is typically counteracted by the HIV-1 protein Vif, which targets it for degradation by the proteasome (38). This prevents APOBEC from being incorporated into nascent virions and causing hypermutation. However, Vif activity in vivo is imperfect, as demonstrated by the observation of hypermutated sequences in HIV-infected individuals (9,17,18,31,42). Because hypermutation is expected to impair virus replication, recent efforts have focused on characterizing hypermutation in HIV-infected individuals and examining its relationship with disease progression.The relationship between hypermutation and markers of disease progression has been addressed in two different ways. In three studies, markers of disease progression were compared between individuals with or without hypermutation detected by population sequen...