Background:  Extensive sequence diversity, a hallmark of HIV-1 infection, facilitates emergence of drug-resistant viral variants. The antiviral activity of APOBEC3 cytosine deaminases is a composite of editing and non-editing activities. We speculated that partial neutralization of these intracellular inhibitors may result in increased sequence diversity and be advantageous for viral escape from antiretroviral drugs.

Methods:  Single nucleotide mutations associated with partial APOBEC3G neutralization were introduced into the Vif region of full-length molecular clone NL4-3. Wild type and Vif mutant viral stocks were produced by transfection and used to infect peripheral mononuclear cells (PBMC) from HIV-1-negative donors. The spread of infection was monitored by measuring p24 antigen production in culture supernatants. Sequence diversity pertinent to each Vif mutant virus after PBMC propagation was assessed by cloning and sequencing. Drug-resistance selection experiments were conducted in T cell lines.

Results:  Vif mutants with suboptimal anti-APOBEC3G activity display mild to pronounced attenuation in PBMC. Vif mutant-associated sequence diversity was strongly biased towards G-to-A substitutions and surpassed the frequency of reverse transcriptase (RT) errors by an order of magnitude. Moreover, a third of all Vif mutant clones encoded lamivudine (3TC) -resistance-associated mutations. Propagation of Vif mutant quasispecies in the presence of high concentration of 3TC demonstrate a more rapid escape than wild type alone.

Conclusions:  Incomplete APOBEC3G neutralization reduces viral fitness, but also promotes the generation of highly diverse and skewed proviral reservoirs. The selection of drug resistance resulting from G-to-A substitutions is strongly favored by viruses with partially active Vif alleles and occurs prior to any drug exposure. This is the first report of HIV-1 exploiting a restriction mechanism as a means of escape.