Abstract
Common single-nucleotide variation in the host accounts for 25% of the variability in the plasma levels of HIV during the clinical latency stage (viral load set point). However, the role of rare variants and copy number variants remains relatively unexplored. Previous work has suggested copy number variation of a cluster of β-defensin genes affects HIV load in treatment-naïve sub-Saharan Africans and rate of response to antiretroviral treatment. Here we analyse a total of 1827 individuals from two cohorts of HIV-infected individuals from Europe and sub-Saharan Africa to investigate the role of β-defensin copy number variation on HIV load at set point. We find no evidence for association of copy number with viral load. We also compare distribution of β-defensin copy number between European cases and controls and find no differences, arguing against a role of β-defensin copy number in HIV acquisition. Taken together, our data argue against an effect of copy number variation of the β-defensin region in the spontaneous control of HIV infection.
Highlights
Rates of HIV acquisition and progression, and levels of viral control during the clinical latency period, show differences between individuals, which are in part due to genetic variation (Shea et al, 2013).The role of gene copy number variation, where the number of copies of the same gene differs between individuals, in affecting clinical parameters of HIV infection is of interest (Hollox & Hoh, 2014)
Using the weighted mean raw copy number values generated by paralogue ratio test (PRT), we tested for association with log(spVL) using a generalised linear model, with sex, age, and the first three principal components of genomewide SNP genotype data as covariates
We found no association with β-defensin genomic copy number (β=0.007, 95%CI -0.064 to 0.077, p=0.853, table 3)
Summary
Rates of HIV acquisition and progression, and levels of viral control during the clinical latency period, show differences between individuals, which are in part due to genetic variation (Shea et al, 2013).The role of gene copy number variation, where the number of copies of the same gene differs between individuals, in affecting clinical parameters of HIV infection is of interest (Hollox & Hoh, 2014). Both differ from the initial study in that the viral load at set point (spVL) is the primary clinical variable tested for genetic association, rather than VL immediately prior to HAART or response to HAART (follow up of CD4 count). All participants from the International AIDS Vaccine Initiative (IAVI) and SHCS cohorts were HIV-1 infected adults.
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