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

S. Cunningham, B. Ank, D. Lewis, W. Lu, M. Wantman, J. Dileanis, J. B. Jackson, P. Palumbo, P. Krogstad, Susan Eshleman

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1254-1257
Number of pages4
JournalJournal of Clinical Microbiology
Volume39
Issue number4
DOIs
StatePublished - 2001

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Sequence Analysis
HIV-1
Pediatrics
Clinical Protocols
Viral Load
Drug Resistance
Plasma Volume
RNA-Directed DNA Polymerase
Drug Combinations
Systems Analysis
Peptide Hydrolases
Clinical Trials
Polymerase Chain Reaction
DNA
Therapeutics

ASJC Scopus subject areas

  • Microbiology (medical)
  • Microbiology

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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. / Cunningham, S.; Ank, B.; Lewis, D.; Lu, W.; Wantman, M.; Dileanis, J.; Jackson, J. B.; Palumbo, P.; Krogstad, P.; Eshleman, Susan.

In: Journal of Clinical Microbiology, Vol. 39, No. 4, 2001, p. 1254-1257.

Research output: Contribution to journalArticle

Cunningham, S. ; Ank, B. ; Lewis, D. ; Lu, W. ; Wantman, M. ; Dileanis, J. ; Jackson, J. B. ; Palumbo, P. ; Krogstad, P. ; Eshleman, Susan. / 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. In: Journal of Clinical Microbiology. 2001 ; Vol. 39, No. 4. pp. 1254-1257.
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