Background:  Retroviruses have devised a number of strategies to evade cellular defenses. For example, HIV-1 expresses Vif, a protein that counteracts the antiviral activity of cytidine deaminases APOBEC3G and APOBEC3F. The anti-APOBEC3 activity of Vif variants in infected persons remains uncharacterized.

Methods:  We tested a panel of 40 distinct Vif variants derived from 2 different sources:  uncultured material from 3 long-term non-progressors (LTNP, no detectable virus in the plasma without therapy > 20 years of asymptomatic HIV-1 infection), and viruses from 1 chronically and 3 newly infected individuals following short-term culture. The infectivity of viral particles generated in the presence of APOBEC3G or APOBEC3F and each patient-derived Vif variant was measured. In addition, Gag-pol sequences from the uncultured LTNP samples were analyzed to detect G-to-A mutations.

Results:  The majority of Vif variants tested counteract APOBEC3G activity with potency similar to that of NL4-3 Vif. However, 20% of the vif genes were inactive or only weakly active. By comparing functional and non-functional Vif variants, we identified specific missense mutations that do not significantly affect protein expression but alter APOBEC3G or APOBEC3F neutralization activity. The loss of function in these Vif variants was recapitulated by introduction of the changes into NL4-3 vif. Some of the mutants that displayed no activity against APOBEC3G retained, however, activity against APOBEC3F and vice versa. Thus, Vif may display discordant activity against APOBEC3G vs APOBEC3F, which could, in principle, affect the extent and direction of cytidine deamination-driven HIV-1 evolution. Indeed, evidence of multiple, independently hypermutated proviruses with G-to-A transitions in a GA or GG dinucleotide context was found in proviruses of 2 LTNP in whom Vif variants that were inactive against both APOBEC3G/3F or only APOBEC3G were detected.

Conclusions:  Vif variants that do not neutralize APOBEC3G or APOBEC3F activity can be found rather frequently in vivo. Sporadic and selective inactivation of Vif’s anti-cytidine deaminase activities may result in selective APOBEC3-driven mutagenesis and thereby exert a major effect on viral evolution in HIV-1-infected individuals.

Keywords: APOBEC3G/3F; Patient derived Vif variants; G to A hypermutation