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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
immunology and microbiology
Development and evaluation of an assay for HIV-1 protease and reverse transcriptase drug resistance genotyping of all major group-M subtypes
Journal of Clinical Virology, Volume 54, No. 1, Year 2012
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Description
Background: High cost and varying sensitivity for non-B HIV-1 subtypes limits application of current commercial kits for HIV-1 drug resistance genotyping of all major HIV-1 group-M subtypes. Objectives: Our research aimed to develop and validate an assay specific for all major HIV-1 group-M subtypes for use as an alternative to commercial assays for HIV-1 protease (PR) and reverse transcriptase (RT) drug resistance genotyping. Study design: A nested RT-PCR encompassing the entire PR and RT up to amino acid 321 of HIV-1 was designed to detect HIV-1 group-M subtypes. Primers compatible with group-M subtypes were defined and analytical sensitivity of the assay evaluated using a panel of reference viruses for subtypes A-H and CRF01_AE. The assay was subsequently evaluated on 246 plasma samples from HIV-1 infected individuals harboring various group-M subtypes and viral loads (VLs). Results: All major group-M HIV-1 subtypes were detected with an overall analytical sensitivity of 1.00E+03 RNA copies/ml. Application of the genotyping assay on 246 primarily African clinical samples comprising subtypes A (n= 52; 21.7%), B (n= 12; 5.0%), C (n= 127; 52.9%), D (n= 25; 10.4%), CRF01_AE (n= 10; 4.2%), and CRF02_AG (n= 10; 4.2%), and unassigned variants (n= 10; 4.2%), VL range 4.32E+02-8.63E+06 (median 2.66E+04) RNA copies/ml, was ∼98% successful. Conclusions: A group-M subtype-independent genotyping assay for detection of HIV-1 drug resistance was developed. The described assay can serve as an alternative to commercial assays for HIV-1 drug resistance genotyping in routine diagnostics, and for surveillance and monitoring of drug resistance in resource-limited settings (RLS). © 2012 Elsevier B.V.
Authors & Co-Authors
Aitken, Susan C.
Netherlands, Utrecht
University Medical Center Utrecht
South Africa, Johannesburg
University of the Witwatersrand
Kliphuis, Aletta
Netherlands, Utrecht
University Medical Center Utrecht
Netherlands, Amsterdam
Pharmaccess International
Wallis, Carole Lorraine
South Africa, Johannesburg
University of the Witwatersrand
Chu, Mei Ling J.N.
Netherlands, Utrecht
University Medical Center Utrecht
Fillekes, Quirine
Netherlands, Nijmegen
Radboud University Medical Center
Barth, Roos E.
Netherlands, Utrecht
University Medical Center Utrecht
Stevens, Wendy Susan
South Africa, Johannesburg
University of the Witwatersrand
South Africa, Johannesburg
National Health Laboratory Service
Rinke de Wit, Tobias Floris
Netherlands, Amsterdam
Pharmaccess International
Netherlands, Amsterdam
Amsterdam Institute for Global Health and Development
Schuurman, Rob J.
Netherlands, Utrecht
University Medical Center Utrecht
Statistics
Citations: 16
Authors: 9
Affiliations: 6
Identifiers
Doi:
10.1016/j.jcv.2012.01.010
ISSN:
13866532
e-ISSN:
18735967
Research Areas
Infectious Diseases