Performance of the Applied Biosystems ViroSeq Human Immunodeficiency Virus Type 1 (HIV-1) Genotyping System for Sequence-Based Analysis of HIV-1 in Pediatric Plasma Samples

Shawn Cunningham; Bonnie Ank; Dan Lewis; Wei Lu; Michael Wantman; JoAnn Dileanis; J. Brooks Jackson; Paul Palumbo; Paul Krogstad; Susan H Eshleman

doi:10.1128/JCM.39.4.1254-1257.2001

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Performance of the Applied Biosystems ViroSeq Human Immunodeficiency Virus Type 1 (HIV-1) Genotyping System for Sequence-Based Analysis of HIV-1 in Pediatric Plasma Samples

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Performance of the Applied Biosystems ViroSeq Human Immunodeficiency Virus Type 1 (HIV-1) Genotyping System for Sequence-Based Analysis of HIV-1 in Pediatric Plasma Samples

Shawn Cunningham, Bonnie Ank, Dan Lewis, Wei Lu, Michael Wantman, JoAnn Dileanis, J. Brooks Jackson, Paul Palumbo, Paul Krogstad and Susan H Eshleman

Journal of clinical microbiology, Vol.39(4), pp.1254-1257

04/2001

DOI: 10.1128/JCM.39.4.1254-1257.2001

PMCID: PMC87920

PMID: 11283037

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Abstract

The ViroSeq HIV-1 Genotyping System is a commercially available, integrated sequence-based system for analysis of human immunodeficiency virus type 1 (HIV-1) drug resistance. We evaluated the performance of this system by analyzing HIV-1 in pediatric plasma samples. Plasma samples from children 4 months to 17 years of age were obtained from a clinical trial protocol (PACTG 377). Children in PACTG 377 were randomized to four treatment arms, including different combinations of antiretroviral drugs. HIV-1 genotyping was performed using samples collected prior to antiretroviral therapy (baseline) and at the time of virologic failure. Performance of the genotyping system was compared in three university laboratories. A total of 196 samples were analyzed, including 135 baseline and 61 failure samples. Plasma volumes ranged from 0.05 to 0.5 ml, and viral loads ranged from 1,084 to 3,484,991 copies/ml. PCR products suitable for sequencing were obtained for 192 of the 196 samples. Complete sequences for protease and reverse transcriptase were obtained for all of these 192 samples. For 180 samples, data were obtained from both DNA strands for the entire region analyzed. There was no evidence of sample cross-contamination based on phylogenetic analysis of HIV-1 sequences. Performance of the genotyping system was similar in three laboratories. This genotyping system performs well for analysis of HIV-1 in pediatric plasma samples, including those with low volume and low viral load. The availability of this system should facilitate studies of HIV-1 drug resistance.

Virology

Details

Title: Subtitle: Performance of the Applied Biosystems ViroSeq Human Immunodeficiency Virus Type 1 (HIV-1) Genotyping System for Sequence-Based Analysis of HIV-1 in Pediatric Plasma Samples
Creators: Shawn Cunningham - Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
Bonnie Ank - Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
Dan Lewis - Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
Wei Lu - Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
Michael Wantman - Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
JoAnn Dileanis - Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
J. Brooks Jackson - Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
Paul Palumbo - Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
Paul Krogstad - Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
Susan H Eshleman - Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
Resource Type: Journal article
Publication Details: Journal of clinical microbiology, Vol.39(4), pp.1254-1257
DOI: 10.1128/JCM.39.4.1254-1257.2001
PMID: 11283037
PMCID: PMC87920
NLM abbreviation: J Clin Microbiol
ISSN: 0095-1137
eISSN: 1098-660X
Publisher: American Society for Microbiology
Language: English
Date published: 04/2001
Academic Unit: Pathology; VPMA - Administration
Record Identifier: 9984046811702771

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