HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays.

ABSTRACT:

Background

HIV-1 infected patients for whom standard gp160 phenotypic tropism testing failed are currently excluded from co-receptor antagonist treatment. To provide patients with maximal treatment options, massively parallel sequencing of the envelope V3 domain, in combination with tropism prediction tools, was evaluated as an alternative tropism determination strategy. Plasma samples from twelve HIV-1 infected individuals with failing phenotyping results were available. The samples were submitted to massive parallel sequencing and to confirmatory recombinant phenotyping using a fraction of the gp120 domain.

Results

A cut-off for sequence reads interpretation of 5 to10 times the sequencing error rate (0.2%) was implemented. On average, each sample contained 7 different V3 h

SUBMITTER: Vandenbroucke I 

PROVIDER: S-EPMC2834596 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature