Host Variation in Type I Interferon Signaling Genes (MX1), CCR5Δ32, and MHC Class I Alleles in Treated HIV+ Non-Controllers Predict Viral Reservoir Size

Prior genomewide association studies have identified variation in MHC Class I alleles and CCR5Δ32 as genetic predictors of viral control, especially in “elite” controllers, individuals who remain virally suppressed in the absence of therapy. We analyzed custom host whole exome sequencing and direct HLA typing from 202 ART-suppressed HIV+ non-controllers in relation to four measures of the peripheral CD4+ T cell reservoir: HIV intact DNA, total (t)DNA, unspliced (us)RNA, and RNA/DNA. Linear mixed models were adjusted for potential covariates including age, sex, nadir CD4+ T cell count, pre-ART HIV RNA, timing of ART initiation from date of detected HIV infection, and duration of ART suppression. Previously reported HLA “protective” B*57:01 (in untreated elite controllers) was significantly associated with lower usRNA (p=4.2×10−4, Benjamini-Hochberg false discovery rate [FDR] q=3.3×10−3). The favorable CCR5Δ32 mutation was also associated with lower tDNA and usRNA, primarily in Europeans (p=4.3×10−3 and 8.7×10−3). Several SNPs in interferon stimulated gene, MX1, were associated with HIV total DNA (p=1.3×10−7; q=0.02), and the direction of these associations paralleled predicted eQTL (expression quantitative trait) MX1 gene expression. Among Europeans, gene set enrichment analysis identified genes involved in “negative regulation of host cell viral entry” to be significantly associated with usRNA (q=0.03). These findings suggest a potential role for interferon signaling, MHC class I alleles, and CCR5Δ32 in maintaining the reservoir size in HIV non-controllers. These data need to be further validated in functional studies and replication cohorts.