The precise immunological role played by CD4⁺T cells in retroviral infections is poorly defined. Here, we describe a new function of these cells, the elimination of retrovirus-infected macrophages. After experimental CD8⁺cell depletion, elite controlling macaques with set-point viral loads ≤500 viral RNA copies/mL mounted robust Gag- and Nef-specific CD4⁺T cell responses during reestablishment of control with ≥54% of all virus-specific CD4⁺T cells targeting these 2 proteins. Ex vivo, these simian immunodeficiency virus (SIV)-specific CD4⁺T cells neither recognized nor suppressed viral replication in SIV-infected CD4⁺T cells. In contrast, they recognized SIV-infected macrophages as early as 2 h postinfection because of presentation of epitopes derived from virion-associated Gag and Nef proteins. Furthermore, virus-specific CD4⁺T cells displayed direct effector function and eliminated SIV-infected macrophages. These results suggest that retrovirus-specific CD4⁺T cells may contribute directly to elite control by inhibiting viral replication in macrophages.

It is generally accepted that CD8⁺ T cell responses play an important role in control of immunodeficiency virus replication. The association of HLA-B27 and -B57 with control of viremia supports this conclusion. However, specific correlates of viral control in individuals expressing these alleles have been difficult to define. We recently reported that transient in vivo CD8⁺ cell depletion in simian immunodeficiency virus (SIV)-infected elite controller (EC) macaques resulted in a brief period of viral recrudescence. SIV replication was rapidly controlled with the reappearance of CD8⁺ cells, implicating that these cells actively suppress viral replication in ECs. Here we show that three ECs in that study made at least seven robust CD8⁺ T cell responses directed against novel epitopes in Vif, Rev, and Nef restricted by the MHC class I molecule Mamu-B*08. Two of these Mamu-B*08-positive animals subsequently lost control of SIV replication. Their breakthrough virus harbored substitutions in multiple Mamu-B*08-restricted epitopes. Indeed, we found evidence for selection pressure mediated by Mamu-B*08-restricted CD8⁺ T cells in all of the newly identified epitopes in a cohort of chronically infected macaques. Together, our data suggest that Mamu-B*08-restricted CD8⁺ T cell responses effectively control replication of pathogenic SIV_mac239. All seven regions encoding Mamu-B*08-restricted CD8⁺ T cell epitopes also exhibit amino acid replacements typically seen only in the presence of Mamu-B*08, suggesting that the variation we observe is indeed selected by CD8⁺ T cell responses. SIV_mac239 infection of Indian rhesus macaques expressing Mamu-B*08 may therefore provide an animal model for understanding CD8⁺ T cell-mediated control of HIV replication in humans.

Vaccines that elicit CD8⁺T-cell responses are routinely tested for immunogenicity in nonhuman primates before advancement to clinical trials. Unfortunately, the magnitude and specificity of vaccine-elicited T-cell responses are variable in currently utilized nonhuman primate populations, owing to heterogeneity in major histocompatibility (MHC) class I genetics. We recently showed that Mauritian cynomolgus macaques (MCM) have unusually simple MHC genetics, with three common haplotypes encoding a shared pair of MHC class IA alleles,Mafa-A*25andMafa-A*29. Based on haplotype frequency, we hypothesized that CD8⁺T-cell responses restricted by these MHC class I alleles would be detected in nearly all MCM. We examine here the frequency and functionality of these two alleles, showing that 88% of MCM expressMafa-A*25andMafa-A*29and that animals carrying these alleles mount three newly defined simian immunodeficiency virus-specific CD8⁺T-cell responses. The epitopes recognized by each of these responses accumulated substitutions consistent with immunologic escape, suggesting these responses exert antiviral selective pressure. The demonstration thatMafa-A*25andMafa-A*29restrict CD8⁺T-cell responses that are shared among nearly all MCM indicates that these animals are an advantageous nonhuman primate model for comparing the immunogenicity of vaccines that elicit CD8⁺T-cell responses.

The role of CD4⁺T cells in the control of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication is not well understood. Even though strong HIV- and SIV-specific CD4⁺T-cell responses have been detected in individuals that control viral replication, major histocompatibility complex class II (MHC-II) molecules have not been definitively linked with slow disease progression. In a cohort of 196 SIVmac239-infected Indian rhesus macaques, a group of macaques controlled viral replication to less than 1,000 viral RNA copies/ml. These elite controllers (ECs) mounted a broad SIV-specific CD4⁺T-cell response. Here, we describe five macaque MHC-II alleles (Mamu-DRB*w606, -DRB*w2104, -DRB1*0306, -DRB1*1003, and -DPB1*06) that restricted six SIV-specific CD4⁺T-cell epitopes in ECs and report the first association between specific MHC-II alleles and elite control. Interestingly, the macaque MHC-II alleles,Mamu-DRB1*1003and -DRB1*0306, were enriched in this EC group (Pvalues of 0.02 and 0.05, respectively). Additionally,Mamu-B*17-positive SIV-infected rhesus macaques that also expressed these two MHC-II alleles had significantly lower viral loads thanMamu-B*17-positive animals that did not expressMamu-DRB1*1003and -DRB1*0306(Pvalue of <0.0001). The study of MHC-II alleles in macaques that control viral replication could improve our understanding of the role of CD4⁺T cells in suppressing HIV/SIV replication and further our understanding of HIV vaccine design.

Two hundred forty-six snap bean genotypes and 49 dry beans representing both centers of domestication and six bean races with materials from Europe, Asia, and the Americas were genotyped using a single nucleotide polymorphism (SNP) array. The data was analyzed for expected heterozygosity, K-means clustering, principal components, phylogenetic relationships, and population substructure. When all gene pools of snap bean were assembled, the expected heterozygosity was roughly equivalent to a carefully chosen panel of dry beans representing all bean races and centers of domestication demonstrating the genetic richness of snap materials in total. K-means clustering and K = 2 structure analysis showed significant mixing of gene pools in the European and American commercial snap materials and the dominance of the Andean center of domestication among commercial contemporary snap beans. Conversely, the same analysis showed that Chinese, Iberian, and heirloom materials were underrepresented in contemporary materials. Further, Structure analysis revealed eight distinct groups within snap beans. Two showed strong kinship to the Middle American center of domestication, three to the Andean center of domestication, and three showed admixture between the two centers. Snap beans may have been independently derived from dry beans more than once and from both centers. Overall, we identified eight potential germplasm pools for snap bean.

Snap beans are a significant source of micronutrients in the human diet. Among the micronutrients present in snap beans are phenolic compounds with known beneficial effects on human health, potentially via their metabolism by the gut-associated microbiome. The genetic pathways leading to the production of phenolics in snap bean pods remain uncertain. In this study, we quantified the level of total phenolic content (TPC) in the Bean Coordinated Agriculture Program (CAP) snap bean diversity panel of 149 accessions. The panel was characterized spectrophotometrically for phenolic content with a Folin–Ciocalteu colorimetric assay. Flower, seed and pod color were also quantified, as red, purple, yellow and brown colors are associated with anthocyanins and flavonols in common bean. Genotyping was performed through an Illumina Infinium Genechip BARCBEAN6K_3 single nucleotide polymorphism (SNP) array. Genome-Wide Association Studies (GWAS) analysis identified 11 quantitative trait nucleotides (QTN) associated with TPC. An SNP was identified for TPC on Pv07 located near the P gene, which is a major switch in the flavonoid biosynthetic pathway. Candidate genes were identified for seven of the 11 TPC QTN. Five regulatory genes were identified and represent novel sources of variation for exploitation in developing snap beans with higher phenolic levels for greater health benefits to the consumer.