Fitness Landscapes of APOBEC3G Antagonism by HIV-1 Vif proteins

Host immune factors shape viral evolution. The HIV-1 Vif protein counteracts viral hypermutation caused by the host cytidine deaminase APOBEC3G (A3G), ensuring productive infection. Using deep mutational scanning (DMS) across two divergent HIV-1 clade B Vif proteins, we systematically mapped the mutational landscape governing their antagonism of A3G. These high-resolution fitness maps define conserved and adaptable regions of Vif, illuminating core principles of host–virus coevolution. Most missense mutations were strongly deleterious, reflecting pervasive purifying selection. Yet several highly conserved residues at binding interfaces with A3G, RNA, and CBFβ exhibited unexpected mutational tolerance, revealing structural flexibility at these sites. Comparative analysis revealed shared constraints and striking differences between HIV-1 strains, shaped by epistatic interactions and additional selective pressures, including Vif antagonism of A3H and PP2A. By pinpointing evolutionary vulnerabilities and adaptive mechanisms, this study provides a framework for understanding viral plasticity and developing targeted strategies to disrupt Vif-mediated immune evasion.