1. APOBEC3H Haplotypes and HIV-1 Pro-Viral vif DNA Sequence Diversity in Early Untreated HIV-1 Infection
- Author
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Gourraud, PA, Karaouni, A, Woo, JM, Schmidt, T, Oksenberg, JR, Hecht, FM, Liegler, TJ, and Barbour, JD
- Subjects
Adult ,Genes, vif ,Male ,Base Sequence ,viruses ,Chromosomes, Human, Pair 22 ,virus diseases ,Genetic Variation ,HIV Infections ,Sequence Analysis, DNA ,Polymorphism, Single Nucleotide ,Article ,Immunity, Innate ,Linkage Disequilibrium ,Cytosine Deaminase ,Haplotypes ,Proviruses ,Aminohydrolases ,DNA, Viral ,HIV-1 ,Leukocytes, Mononuclear ,vif Gene Products, Human Immunodeficiency Virus ,Humans ,RNA, Viral ,Female - Abstract
We examined single nucleotide polymorphisms (SNP) in the APOBEC3 locus on chromosome 22, paired to population sequences of pro-viral HIV-1 vif of peripheral blood mononuclear cells (PBMC), from 96 recently HIV-1 infected treatment naïve adults. We found evidence for the existence of an APOBEC3H linkage disequilibrium (LD) block associated with variation in GA->AA, or APOBEC3F signature, sequence changes in pro-viral HIV-1 vif sequence (top significant 10 SNPs with a top-significant p=4.8×10−3). We identified a common 5 position risk haplotype distal to APOBEC3H (A3Hrh). These markers were in high LD (D′ = 1; r2=0.98) to a previously described A3H ‘RED’ haplotype containing a variant (E121) with enhanced susceptibility to HIV-1 Vif (Zhen et al 2009 [1]). This association is confirmed by a haplotype analysis: Homozygote carriers of the A3Hrh had lower GA->AA (A3F) sequence editing on pro-viral HIV-1 vif sequence (p = 0.01), and lower HIV-1 RNA levels over time during early, untreated HIV-1 infection, (p = 0.015 mixed effects model). This effect may be due to enhanced susceptibility of A3H forms to HIV-1 Vif mediated viral suppression of sequence editing activity, slowing viral diversification and escape from immune responses.
- Published
- 2010