Impact of Suboptimal APOBEC3G Neutralization on the Emergence of HIV Drug Resistance in Humanized Mice

Abstract

HIV diversification facilitates immune escape and complicates antiretroviral therapy. In this study, we take advantage of a humanized-mouse model to probe the contribution of APOBEC3 mutagenesis to viral evolution. Humanized mice were infected with isogenic HIV molecular clones (HIV-WT, HIV-45G, and HIV-ΔSLQ) that differ in their abilities to counteract APOBEC3G (A3G). Infected mice remained naive or were treated with the reverse transcriptase (RT) inhibitor lamivudine (3TC). Viremia, emergence of drug-resistant variants, and quasispecies diversification in the plasma compartment were determined throughout infection. While both HIV-WT and HIV-45G achieved robust infection, over time, HIV-45G replication was significantly reduced compared to that of HIV-WT in the absence of 3TC treatment. In contrast, treatment responses differed significantly between HIV-45G- and HIV-WT-infected mice. Antiretroviral treatment failed in 91% of HIV-45G-infected mice, while only 36% of HIV-WT-infected mice displayed a similar negative outcome. Emergence of 3TC-resistant variants and nucleotide diversity were determined by analyzing 155,462 single HIV reverse transcriptase gene (RT) and 6,985 vif sequences from 33 mice. Prior to treatment, variants with genotypic 3TC resistance (RT-M184I/V) were detected at low levels in over a third of all the animals. Upon treatment, the composition of the plasma quasispecies rapidly changed, leading to a majority of circulating viral variants encoding RT-184I. Interestingly, increased viral diversity prior to treatment initiation correlated with higher plasma viremia in HIV-45G-infected animals, but not in HIV-WT-infected animals. Taken together, HIV variants with suboptimal anti-A3G activity were attenuated in the absence of selection but displayed a fitness advantage in the presence of antiretroviral treatment. IMPORTANCE Both viral (e.g., RT) and host (e.g., A3G) factors can contribute to HIV sequence diversity. This study shows that suboptimal anti-A3G activity shapes viral fitness and drives viral evolution in the plasma compartment in humanized mice.

Human APOBEC3 Variations and Viral Infection

“…On the other hand, the targeting of the HIV-1 genome by less mutagenic enzymes, such as APOBEC3D and APOBEC3F, or by partially neutralized APOBEC3G or APOBEC3H haplotype II, can generate sub-lethally mutated viruses. APOBEC3-induced sub-lethal mutagenesis can contribute to HIV-1 diversification [35][36][37][38][39], evolution [37,40,41], immune escape [42][43][44], and drug resistance [42,[45][46][47][48][49][50].…”

Effects of APOBEC3G's Cytidine Deaminase Activity on Retroviral Evolution

“…However, when they started the treatment with the drug, they found that the mutant strain was less susceptible to the antiretroviral drug's effect because of its defectiveness. In other words, because the mutant HIV strain is less fit, the drug has a decreased effect on it compared to the wild type, hence the mutant strains become resistant to the drug [12]. Thus, these studies show that sublethal mutations caused by A3G, increase viral diversification which could make the virus gain resistance to certain drugs.…”

“…However, lower expression of A3 proteins in cells could also lead to viral evolution [3,5,6]. When A3 proteins such as A3G and A3F are expressed at lower levels, they are likely to introduce missense mutations in the virus, which instead of inhibiting the virus, helps it ob-tain beneficial mutations that allow it to become more fit and able to evade the cells' immune response [10,13] and develop drug resistance [6,11,12]. Also, many studies show that HIV can evolve to overcome A3's cytidine deaminase activity by encoding Vif's variants that more effectively target A3 for proteasomal degradation [1,3,5,14].…”

“…In a similar study by Hernandez et al, it was found that sublethal mutations induced by A3G could lead to viral diversification. They infected humanized mice with different variants of HIV (that were mutated via A3-independent means), and they found that the wild type HIV strain had a higher fitness compared to the mutant strains prior to its treatment with 3TC [12]. However, when they started the treatment with the drug, they found that the mutant strain was less susceptible to the antiretroviral drug's effect because of its defectiveness.…”

Structural Insights into APOBEC3-Mediated Lentiviral Restriction

“…It has been proposed that hypermutation by A3 proteins can increase genetic variation in HIV-1 populations and can promote viral evolution [ 73 , 74 , 75 , 76 , 77 ]. In support of this notion, several studies have suggested that resistance to antiviral drugs is increased when A3 proteins are present and can induce G-to-A mutations in the viral genome [ 78 , 79 , 80 , 81 , 82 ]. However, other studies have suggested that A3G-induced hypermutation is an “all or nothing” phenomenon; virion incorporation of A3G and A3F leads to hypermutation and lethal mutational loads which inactivate the provirus and hence do not significantly contribute to viral genetic diversification [ 80 , 83 , 84 , 85 ].…”