Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.

ABSTRACT:

Background

Ultra-deep pyrosequencing (UDPS) allows identification of rare HIV-1 variants and minority drug resistance mutations, which are not detectable by standard sequencing.

Principal findings

Here, UDPS was used to analyze the dynamics of HIV-1 genetic variation in reverse transcriptase (RT) (amino acids 180-220) in six individuals consecutively sampled before, during and after failing 3TC and AZT containing antiretroviral treatment. Optimized UDPS protocols and bioinformatic software were developed to generate, clean and analyze the data. The data cleaning strategy reduced the error rate of UDPS to an average of 0.05%, which is lower than previously reported. Consequently, the cut-off for detection of resistance mutations was very low. A median of 16,016 (range 2,406-3

SUBMITTER: Hedskog C 

PROVIDER: S-EPMC2898805 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature