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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
immunology and microbiology
Automated sequence analysis and editing software for HIV drug resistance testing
Journal of Clinical Virology, Volume 54, No. 1, Year 2012
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Description
Background: Access to antiretroviral treatment in resource-limited-settings is inevitably paralleled by the emergence of HIV drug resistance. Monitoring treatment efficacy and HIV drugs resistance testing are therefore of increasing importance in resource-limited settings. Yet low-cost technologies and procedures suited to the particular context and constraints of such settings are still lacking. The ART-A (Affordable Resistance Testing for Africa) consortium brought together public and private partners to address this issue. Objectives: To develop an automated sequence analysis and editing software to support high throughput automated sequencing. Study design: The ART-A Software was designed to automatically process and edit ABI chromatograms or FASTA files from HIV-1 isolates. Results: The ART-A Software performs the basecalling, assigns quality values, aligns query sequences against a set reference, infers a consensus sequence, identifies the HIV type and subtype, translates the nucleotide sequence to amino acids and reports insertions/deletions, premature stop codons, ambiguities and mixed calls. The results can be automatically exported to Excel to identify mutations. Automated analysis was compared to manual analysis using a panel of 1624 PR-RT sequences generated in 3 different laboratories. Discrepancies between manual and automated sequence analysis were 0.69% at the nucleotide level and 0.57% at the amino acid level (668,047 AA analyzed), and discordances at major resistance mutations were recorded in 62 cases (4.83% of differences, 0.04% of all AA) for PR and 171 (6.18% of differences, 0.03% of all AA) cases for RT. Conclusions: The ART-A Software is a time-sparing tool for pre-analyzing HIV and viral quasispecies sequences in high throughput laboratories and highlighting positions requiring attention. © 2012 Elsevier B.V.
Authors & Co-Authors
Struck, Daniel
Luxembourg, Strassen
Luxembourg Institute of Health
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
South Africa, Johannesburg
University of the Witwatersrand
Wallis, Carole Lorraine
South Africa, Johannesburg
University of the Witwatersrand
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Luxembourg, Strassen
Luxembourg Institute of Health
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
Denisov, Gennady
United States, Rockville
J. Craig Venter Institute
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Luxembourg, Strassen
Luxembourg Institute of Health
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
South Africa, Johannesburg
University of the Witwatersrand
Lambert, Christine
Luxembourg, Strassen
Luxembourg Institute of Health
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
South Africa, Johannesburg
University of the Witwatersrand
Servais, Jean Yeves
Luxembourg, Strassen
Luxembourg Institute of Health
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
South Africa, Johannesburg
University of the Witwatersrand
Viana, Raquel V.
South Africa, Johannesburg
University of the Witwatersrand
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Luxembourg, Strassen
Luxembourg Institute of Health
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
Letsoalo, Esrom
South Africa, Johannesburg
University of the Witwatersrand
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Luxembourg, Strassen
Luxembourg Institute of Health
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
Bronze, Michelle
South Africa, Johannesburg
University of the Witwatersrand
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Luxembourg, Strassen
Luxembourg Institute of Health
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
Aitken, Susan C.
South Africa, Johannesburg
University of the Witwatersrand
Netherlands, Utrecht
University Medical Center Utrecht
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Luxembourg, Strassen
Luxembourg Institute of Health
Netherlands, Amsterdam
Pharmaccess Foundation
Belgium, Mechelen
Virco Bvba
Schuurman, Rob J.
Netherlands, Utrecht
University Medical Center Utrecht
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Luxembourg, Strassen
Luxembourg Institute of Health
Netherlands, Amsterdam
Pharmaccess Foundation
Belgium, Mechelen
Virco Bvba
South Africa, Johannesburg
University of the Witwatersrand
Stevens, Wendy Susan
South Africa, Johannesburg
University of the Witwatersrand
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Luxembourg, Strassen
Luxembourg Institute of Health
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
Schmit, Jean Claude
Luxembourg, Strassen
Luxembourg Institute of Health
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
South Africa, Johannesburg
University of the Witwatersrand
Rinke de Wit, Tobias Floris
Netherlands, Amsterdam
Universiteit Van Amsterdam
South Africa, Johannesburg
Contract Laboratory Services
Luxembourg, Strassen
Luxembourg Institute of Health
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
South Africa, Johannesburg
University of the Witwatersrand
Perez-Bercoff, Danielle
Luxembourg, Strassen
Luxembourg Institute of Health
South Africa, Johannesburg
Contract Laboratory Services
Netherlands, Amsterdam
Universiteit Van Amsterdam
Netherlands, Amsterdam
Pharmaccess Foundation
Netherlands, Utrecht
University Medical Center Utrecht
Belgium, Mechelen
Virco Bvba
South Africa, Johannesburg
University of the Witwatersrand
Statistics
Citations: 14
Authors: 14
Affiliations: 8
Identifiers
Doi:
10.1016/j.jcv.2012.01.018
ISSN:
13866532
e-ISSN:
18735967
Research Areas
Health System And Policy
Infectious Diseases
Maternal And Child Health