Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population

AIDS. 2011 Feb 20;25(4):513-8. doi: 10.1097/QAD.0b013e328343817b.

Abstract

Objective: To date, CCR5 variants remain the only human genetic factors to be confirmed to impact HIV-1 acquisition. However, protective CCR5 variants are largely absent in African populations, in which sporadic resistance to HIV-1 infection is still unexplained. We investigated whether common genetic variants associate with HIV-1 susceptibility in Africans.

Methods: We performed a genome-wide association study (GWAS) in a population of 1532 individuals from Malawi, a country with high prevalence of HIV-1 infection. Using single-nucleotide polymorphisms (SNPs) present on the genome-wide chip, we also investigated previously reported associations with HIV-1 susceptibility or acquisition. Recruitment was coordinated by the Center for HIV/AIDS Vaccine Immunology at two sexually transmitted infection clinics. HIV status was determined by HIV rapid tests and nucleic acid testing.

Results: After quality control, the population consisted of 848 high-risk seronegative and 531 HIV-1 seropositive individuals. Logistic regression testing in an additive genetic model was performed for SNPs that passed quality control. No single SNP yielded a significant P value after correction for multiple testing. The study was sufficiently powered to detect markers with genotype relative risk 2.0 or more and minor allele frequencies 12% or more.

Conclusion: This is the first GWAS of host determinants of HIV-1 susceptibility, performed in an African population. The absence of any significant association can have many possible explanations: rarer genetic variants or common variants with weaker effect could be responsible for the resistance phenotype; alternatively, resistance to HIV-1 infection might be due to nongenetic parameters or to complex interactions between genes, immunity and environment.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adolescent
  • Adult
  • African Continental Ancestry Group / genetics*
  • Female
  • Genetic Predisposition to Disease*
  • Genome-Wide Association Study
  • HIV Infections / epidemiology
  • HIV Infections / genetics*
  • HIV-1*
  • Humans
  • Malawi / epidemiology
  • Male
  • Middle Aged
  • Phenotype
  • Receptors, CCR5 / genetics*
  • Young Adult

Substances

  • Receptors, CCR5