Finally, we found that the global distribution of stable/unstable APOBEC3H haplotypes correlates with the distribution a critical hyper/hypo-functional Vif amino acid residue. Figure S3: Stable APOBEC3H inhibits HIV-1 replication in primary T lymphocytes. A) HIV-1 replication kinetics of the hyper-, lab-, and hypo-Vif variants in CD4+ T lymphocytes from 5 healthy donors encoding the unstable A3H haplotype indicated (donors 1, 5, 8, 12, and 18). B) HIV-1 replication kinetics of the hyper-, lab-, and hypo-Vif variants in CD4+ T lymphocytes from 2 healthy donors heterozygous for the indicated allele of stable A3H (donors 10 and 11). We were not able to identify a second haplotype V donor and therefore have not been able to determine whether the lab-Vif phenotype of donor 11 is reproducible.(TIF) pgen.1004761.s003.tif (560K) GUID:?62BB1663-FBA4-49EF-93A0-482B8C11731C Figure S4: Stable APOBEC3H alleles inflict GA-to-AA hypermutations in viruses encoding hypo-Vif variants. HIV-1 G-to-A mutation profiles of the hyper-, lab-, and hypo-Vif proviruses originating from primary T lymphocytes with the indicated A3H haplotype (donors 2, 4, and 12). GA-to-AA mutations characteristic of A3H activity are shown in red.(TIF) pgen.1004761.s004.tif (397K) GUID:?EEEE805B-79DD-495C-B7E9-66C675DA8B12 Table S1: Selected donor genotyping results.(TIF) pgen.1004761.s005.tif (97K) GUID:?3EC48920-0DE0-4135-B29E-25DD0F84BFEA Table S2: Worldwide allele frequencies.(TIF) pgen.1004761.s006.tif (43K) GUID:?98240AD0-54EB-4518-AABF-1DC6DDD6BD5C Table S3: Worldwide haplotype frequencies.(TIF) pgen.1004761.s007.tif (44K) GUID:?288CBDCD-D541-4AEA-9D3C-CDD0F6EF2B39 Data Availability StatementThe authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files. Abstract The Vif protein of HIV-1 allows virus replication by degrading several members of the host-encoded APOBEC3 family of DNA cytosine deaminases. Polymorphisms in both host genes and the viral gene have the potential to impact the extent of virus replication among individuals. The most genetically diverse of the seven human genes is with seven known haplotypes. Overexpression studies have shown that a subset of these variants express stable and active proteins, whereas the others encode proteins with a short half-life and little, if any, antiviral activity. We demonstrate that these stable/unstable phenotypes are an intrinsic property of endogenous APOBEC3H proteins in primary CD4+ T lymphocytes and confer differential resistance to HIV-1 infection in a manner BIO-5192 that depends on natural variation in Cdh5 the Vif protein of the infecting virus. HIV-1 with a Vif protein hypo-functional for APOBEC3H degradation, yet fully able to counteract APOBEC3D, APOBEC3F, and APOBEC3G, was susceptible to restriction and hypermutation in stable APOBEC3H expressing lymphocytes, but not in unstable APOBEC3H expressing lymphocytes. In contrast, HIV-1 with hyper-functional Vif counteracted stable APOBEC3H proteins as well as all BIO-5192 other endogenous APOBEC3s and replicated to high levels. We also found that APOBEC3H protein levels are induced over 10-fold by infection. Finally, we found that the global distribution of stable/unstable APOBEC3H haplotypes correlates with the distribution a critical hyper/hypo-functional Vif amino acid residue. These data combine to strongly suggest that stable APOBEC3H haplotypes present as barriers to HIV-1 replication, that Vif is capable of adapting to these restrictive pressures, and that an evolutionary equilibrium has yet to be reached. Author Summary The APOBEC3 enzymes protect BIO-5192 cells by inhibiting the spread of retroelements, including HIV-1, by blocking reverse transcription and mutating cytosines in single-stranded DNA replication intermediates. HIV-1 Vif counteracts restriction by marking APOBEC3 proteins for proteasomal degradation. APOBEC3H is the most diverse member of this protein family. Humans have seven distinct haplotypes with three producing stable and four producing unstable proteins upon forced overexpression. Here, we examine the stability phenotype of endogenous APOBEC3H in donors with different haplotypes and address how these stability differences, as well as natural viral diversity, combine to determine HIV-1 infectivity. We found that endogenous haplotypes yield stable or unstable proteins and that stable APOBEC3H is induced during viral infection and.