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Journal of Clinical Microbiology, April 2001, p. 1254-1257, Vol. 39, No. 4
0095-1137/01/$04.00+0   DOI: 10.1128/JCM.39.4.1254-1257.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

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,1 Bonnie Ank,2 Dan Lewis,3 Wei Lu,3 Michael Wantman,4 JoAnn Dileanis,5 J. Brooks Jackson,1 Paul Palumbo,3 Paul Krogstad,2 and Susan H. Eshleman1,*

Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland1; Department of Pediatrics, University of California at Los Angeles School of Medicine, Los Angeles,2 and Applied Biosystems, Foster City,5 California; Department of Pediatrics, University of Medicine and Dentistry of New Jersey, Newark, New Jersey3; and Statistical Data Analysis Center, Harvard School of Public Health, Boston, Massachusetts4

Received 6 November 2000/Returned for modification 18 December 2000/Accepted 15 January 2001

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.

* Corresponding author. Mailing address: Department of Pathology, The Johns Hopkins Medical Institutions, Ross Bldg. 646, 720 Rutland Ave., Baltimore, MD 21205. Phone: (410) 614-4734. Fax: (410) 614-3548. E-mail: seshlem{at}jhmi.edu.

Journal of Clinical Microbiology, April 2001, p. 1254-1257, Vol. 39, No. 4
0095-1137/01/$04.00+0   DOI: 10.1128/JCM.39.4.1254-1257.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


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Copyright © 2001 by the American Society for Microbiology. All rights reserved.