HIV-1 adaptation studies reveal a novel Env-mediated homeostasis mechanism for evading lethal hypermutation by APOBEC3G

HIV-1 replication normally requires Vif-mediated neutralization of APOBEC3 antiviral enzymes. Viruses lacking Vif succumb to deamination-dependent and -independent restriction processes. Here, HIV-1 adaptation studies were leveraged to ask whether viruses with an irreparable vif deletion could develop resistance to restrictive levels of APOBEC3G. Several resistant viruses were recovered with multiple amino acid substitutions in Env, and these changes alone are sufficient to protect Vif-null viruses from APOBEC3G-dependent restriction in T cell lines. Env adaptations cause decreased fusogenicity, which results in higher levels of Gag-Pol packaging. Increased concentrations of packaged Pol in turn enable faster virus DNA replication and protection from APOBEC3G-mediated hypermutation of viral replication intermediates. Taken together, these studies reveal that a moderate decrease in one essential viral activity, namely Env-mediated fusogenicity, enables the virus to change other activities, here, Gag-Pol packaging during particle production, and thereby escape restriction by the antiviral factor APOBEC3G. We propose a new paradigm in which alterations in viral homeostasis, through compensatory small changes, constitute a general mechanism used by HIV-1 and other viral pathogens to escape innate antiviral responses and other inhibitions including antiviral drugs.
Author summary APOBEC3G is a virus restriction factor that blocks the replication of Vif-deficient HIV-1 by deamination-dependent and -independent mechanisms. The HIV-1 accessary protein Vif counteracts APOBEC3G through a proteasome-mediated degradation pathway. However, viruses often possess multiple distinct mechanisms to evade innate immune responses, and it was unknown whether HIV-1 possesses alternative mechanisms for escaping restriction by APOBEC3G. To investigate this possibility, HIV-1 with a non-revertable vif deletion was adapted in stepwise cultures to increasing amounts of APOBEC3G. Three independent APOBEC3G resistant viral isolates acquired amino acid substitutions in Env. Mechanistic studies showed that these Env adaptations cause decreased fusogenicity, which re-optimizes viral homeostasis by allowing increased Gag-Pol packaging and higher rates of reverse transcription, which in turn protect viral DNA from lethal hypermutation by APOBEC3G. Thus, these results demonstrate a novel Env-dependent mechanism mediated by RT that HIV-1 can utilize to escape APOBEC3G-mediated restriction. Sequence comparisons suggest that transmitting isolates may also utilize this mechanism. More broadly, our results suggest a new paradigm in which relatively small changes in essential viral processes and overall viral homeostasis can have rather large phenotypic consequences such as enabling resistance to potent antiviral measures.