There is an ever-increasing volume of data on host genes that are modulated during HIV infection, influence disease susceptibility or carry genetic variants that impact HIV infection. This public resource supports queries on genome-wide genetic variation and gene expression profile across multiple phenotypes relevant to HIV biology.

Query gene, marker or region
Enter gene name, rs number or a region in the format of chr:start-stop (max 5Mb range).
Filter for study. For details of each study refer to the table below. Some of the datasets are not yet published, if you want to access them, we kindly ask you to contact us (contact at guavah.org) .

HIV Acquisition

HIV-1 susceptibility is partially dependent on host genetics. In this GWAS of resistance against HIV-1 infection 431 hemophilia patients highly exposed to potentially contaminated factor VIII transfusions were compared to 765 HIV-infected controls.
Study name Sample Count Reference Technology Public
HESN 1196 Lane et al. Hum. Mol. Genet. (2013) 22 (9): 1903-1910. Illumina, HapMap3 imputed. Additive tests. Yes
HESN (Additive, 1KG imputed) 1380 Lane et al. Hum. Mol. Genet. (2013) 22 (9): 1903-1910. Illumina, imputed into 1000 Genomes haplotypes Yes

HIV set point viral load

HIV-1 viral load at set point is a strong correlate of disease progression. GWAS and exome sequencing were performed in carefully selected subsets of the Swiss HIV Cohort Study (http://www.shcs.ch).
Study name Sample Count Reference Technology Public
ICGH2 6315 http://www.pnas.org/content/112/47/14658 Illumina, 1kg imputed Yes
SHCS (Exome) 392 Unpublished Illumina HiSeq2000 w/ Truseq 65Mb No
SHCS (GWAS) 815 Fellay et al. PLoS Genet 5(12): e1000791 Illumina, 1kg imputed Yes

Durable control of HIV infection

A small number of people demonstrate sustained ability to control HIV replication at low levels without therapy. These HIV controllers maintain stable CD4+ T cell counts, do not develop clinical disease, and are less likely to transmit HIV to others. A GWAS was performed comparing 516 HIV controllers to 1196 individuals with progressive infection as part of the International HIV Controllers Study.
Study name Sample Count Reference Technology Public
IHCS (gene based tests) 1712 Unpublished Illumina, 1KG imputed. SKAT. No
IHCS (GWAS) 1712 Pereyra et al. Science 2010 Illumina GWAS chips. 1KG imputed Yes

Host genetic pressure on HIV Sequence Variation

Selection pressures arising from host genomic factors affect HIV-1 sequence diversity. Amino acid variants of HIV-1 were used as phenotypes in 1071 individuals with paired host/viral genetic data. This strategy allowed a global assessment of host-pathogen interactions at the genome level and revealed sites of genomic conflict between the HLA region and the HIV-1 proteome.
Study name Sample Count Reference Technology Public
G2G 1071 Bartha et al. eLife 2013;2:e01123 Illumina / Affymetrix GWAS chips. 1KG imputed Yes

Gene-level genetic variation in the general population

Every individual harbors ~20,000 unique coding variants, including potentially severe premature stop codons or frameshifts. Publicly available data from the <a href="http://evs.gs.washington.edu/EVS">NHLBI Exome Sequencing Project</a> provides a population level survey of genetic variants within genes in >6000 individuals of European ancestry and >2000 African Americans. This detailed level of protein sequence variation information allows for visualization and first-pass estimation of the level of conservation or variation of a given gene.
Study name Sample Count Reference Technology Public
ESP 8706 Fu et al. Nature (2013) 493 (7431): 216-20 see the Exome Variant Server Yes

Gene expression

Transcriptome analysis are revealing of the biological process during HIV infection. Gene expression in CD4+ T cells isolated from HIV-infected individuals representing the full spectrum of disease and viral load were investigated (CD4_Expression). In vitro analysis captured the dynamic process of the viral cycle in a permissive cell line (SupT1) over 24 hours (Viral_Cycle), and the process of latency and reactivation upon pharmacological or immunological stimuli in a primary CD4+ T cell model (Latency).
Study name Sample Count Reference Technology Public
CD4 Expression 127 Rotger et al. PLoS Pathog 6(2): e1000781 Illumina HumanWG-6 v3.0 expression beadchip Yes
Latency 36 Mohammadi et al PLoS Pathog 10(5): e1004156 TruSeq, Illumina HiSeq2000 Yes
Viral Lifecycle 24 Plos Pathog 2013 Mohammadi et al SAGE-seq,Solid3 Yes

Gene-level genetic variation in HIV positive population

Every individual harbors ~20,000 unique coding variants, including potentially severe premature stop codons or frameshifts. These data represents exome sequencing results from HIV-infected population. This detailed level of protein sequence variation information allows for visualization and first-pass estimation of functional variants of interest for HIV biology.
Study name Sample Count Reference Technology Public
SHCS (Exome variations) 392 Unpublished Illumina HiSeq2000 w/ Truseq 65Mb No