A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

István Bartha, Jonathan M. Carlson, Chanson J. Brumme, Paul J. McLaren, Zabrina L. Brumme, Mina John, David W. Haas, Javier Martinez-Picado, Judith Dalmau, Cecilio López-Galíndez, Concepción Casado, Andri Rauch, Huldrych F. Günthard, Enos Bernasconi, Pietro Vernazza, Thomas Klimkait, Sabine Yerly, Stephen J. O'Brien, Jennifer Listgarten, Nico PfeiferChristoph Lippert, Nicolo Fusi, Zoltán Kutalik, Todd M. Allen, Viktor Müller, P. Richard Harrigan, David Heckerman, Amalio Telenti, Jacques Fellay

Research output: Contribution to journalArticle

66 Citations (Scopus)

Abstract

HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p<2.4 × 10-12). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the 'intermediate phenotype' nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host-pathogen interaction.

Original languageEnglish
Article numbere01123
JournaleLife
Volume2013
Issue number2
DOIs
Publication statusPublished - Oct 29 2013

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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    Bartha, I., Carlson, J. M., Brumme, C. J., McLaren, P. J., Brumme, Z. L., John, M., Haas, D. W., Martinez-Picado, J., Dalmau, J., López-Galíndez, C., Casado, C., Rauch, A., Günthard, H. F., Bernasconi, E., Vernazza, P., Klimkait, T., Yerly, S., O'Brien, S. J., Listgarten, J., ... Fellay, J. (2013). A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. eLife, 2013(2), [e01123]. https://doi.org/10.7554/eLife.01123