Strain-specific epistasis shapes fitness landscapes of APOBEC3G antagonism by HIV-1 Vif proteins

Host immune factors shape viral evolution. The HIV-1 viral infectivity factor (Vif) protein counteracts host Apolipoprotein B Messenger RNA Editing Enzyme Catalytic Polypeptide-like 3 (A3G) to ensure productive infection. Using deep mutational scanning across two divergent HIV-1 Vif proteins, we systematically mapped and compared the mutational landscapes governing Vif antagonism of A3G. These high-resolution fitness maps reveal core principles of host-virus coevolution. Most missense mutations were strongly deleterious, reflecting pervasive purifying selection. However, several highly conserved Vif residues at binding interfaces with A3G, RNA, and core-binding factor β exhibited unexpected mutational tolerance, indicating structural flexibility at these sites. Comparative analysis revealed that strain-specific epistasis dictates Vif-A3G interactions, including adaptive changes at the Vif-A3G interface. Further analysis uncovered notable temporal epistasis, whereby initially adaptive Vif mutations critical for antagonizing hominoid A3G subsequently exhibited reduced fitness. Thus, structural robustness permits adaptation, while epistasis imposes constraints on Vif's ability to maintain A3G antagonism while remaining responsive to new evolutionary pressures.