Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings

Commercially available HIV-1 drug resistance (HIVDR) genotyping assays are expensive and have limitations in detecting non-B subtypes and circulating recombinant forms that are co-circulating in resource-limited settings (RLS). This study aimed to optimize a low cost and broadly sensitive in-house a...

Full description

Saved in:
Bibliographic Details
Published in:PloS one 2011-11, Vol.6 (11), p.e28184-e28184
Main Authors: Zhou, Zhiyong, Wagar, Nick, DeVos, Joshua R, Rottinghaus, Erin, Diallo, Karidia, Nguyen, Duc B, Bassey, Orji, Ugbena, Richard, Wadonda-Kabondo, Nellie, McConnell, Michelle S, Zulu, Isaac, Chilima, Benson, Nkengasong, John, Yang, Chunfu
Format: Article
Language:English
Subjects:
Acquired immune deficiency syndrome
AIDS
Amino Acids - genetics
Antiretroviral drugs
Assaying
Base Sequence
Biological Assay - economics
Biology
Cladistic analysis
Comparative analysis
Costs and Cost Analysis
Developing Countries - economics
Disease control
Disease transmission
DNA polymerases
Dried Blood Spot Testing
Drug resistance
Drug Resistance, Viral - genetics
Economic aspects
Genotyping
Genotyping Techniques - economics
Genotyping Techniques - methods
GLP-1 receptor agonists
Health Resources - economics
HIV
HIV Infections - blood
HIV Infections - virology
HIV-1 - classification
HIV-1 - genetics
Human immunodeficiency virus
Humans
Indicators and Reagents - economics
Low cost
Medicine
Molecular Sequence Data
Mutation
Mutation - genetics
Nucleotide sequence
Optimization
Phylogeny
Plasmas
Plasmas (physics)
Pol gene
Polls & surveys
Population Surveillance
Proteases
Reproducibility of Results
RNA-directed DNA polymerase
Sensitivity
Sequence Homology, Nucleic Acid
Spots
Surveillance
Surveys
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Commercially available HIV-1 drug resistance (HIVDR) genotyping assays are expensive and have limitations in detecting non-B subtypes and circulating recombinant forms that are co-circulating in resource-limited settings (RLS). This study aimed to optimize a low cost and broadly sensitive in-house assay in detecting HIVDR mutations in the protease (PR) and reverse transcriptase (RT) regions of pol gene. The overall plasma genotyping sensitivity was 95.8% (N = 96). Compared to the original in-house assay and two commercially available genotyping systems, TRUGENE® and ViroSeq®, the optimized in-house assay showed a nucleotide sequence concordance of 99.3%, 99.6% and 99.1%, respectively. The optimized in-house assay was more sensitive in detecting mixture bases than the original in-house (N = 87, P
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0028184