Abstract
Methods To precisely quantify frequencies of low abundance variants, we characterized a large number of viral genomes from three HIV-1 infected individuals using a newly developed parallel allele-specific sequencing (PASS) assay that can simultaneously analyze thousands of viral genomes at multiple nucleoside positions and perform linkage analysis for those sites. Several unique positions (8–15) on each genome were analyzed among hundreds or thousands of viral genomes from each sample to determine minority viral populations.
Highlights
Minority viral populations present in very low abundance (
To precisely quantify frequencies of low abundance variants, we characterized a large number of viral genomes from three HIV-1 infected individuals using a newly developed parallel allele-specific sequencing (PASS) assay that can simultaneously analyze thousands of viral genomes at multiple nucleoside positions and perform linkage analysis for those sites
The PASS assay may serve as a useful method to detect low frequencies of T cell escape mutants, recombinant genomes, and minority transmitted viruses in HIV-1 infected individuals
Summary
Identification of low frequency genetic variants during acute and early infection by parallel-allele specific sequencing. Address: Duke Human Vaccine Institute, Duke University, Durham, NC, USA * Corresponding author from AIDS Vaccine 2009 Paris, France. Published: 22 October 2009 Retrovirology 2009, 6(Suppl 3):P373 doi:10.1186/1742-4690-6-S3-P373. AIDS Vaccine 2009 Anna Laura Ross Meeting abstracts – A single PDF containing all abstracts in this Supplement is available here. http://www.biomedcentral.com/content/pdf/1471-2105-10-S12-info.pdf
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