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Journal of Clinical Microbiology, July 2003, p. 3265-3272, Vol. 41, No. 7
0095-1137/03/$08.00+0     DOI: 10.1128/JCM.41.7.3265-3272.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Evaluation of the Editing Process in Human Immunodeficiency Virus Type 1 Genotyping

Diana D. Huang,^1* Susan H. Eshleman,² Donald J. Brambilla,³ Paul E. Palumbo,⁴ and James W. Bremer¹

Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois,¹ Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland,² New England Research Institute, Inc., Watertown, Massachusetts,³ Pediatrics, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey⁴

Received 26 December 2002/ Returned for modification 20 February 2003/ Accepted 23 March 2003

Sequencing-based human immunodeficiency virus type 1 (HIV-1) genotyping assays require subjective interpretation (editing) of sequence data from multiple primers to form consensus sequences and identify antiretroviral drug resistance mutations. We assessed interlaboratory variations in editing and their impact on the recognition of resistance mutations. Six samples were analyzed in a central laboratory by using a research-use-only HIV-1 genotyping system previously produced by Applied Biosystems. The electronic files of individual primer sequences from the samples were sent to 10 laboratories to compare sequence editing strategies. Each sequence data set included sequences from seven primers spanning protease codons 1 to 99 and reverse transcriptase codons 1 to 320. Each laboratory generated a consensus sequence for each sample and completed a questionnaire about editing strategy. The amount of editing performed, the concordance of consensus sequences among the laboratories, and the identification of resistance mutations were evaluated. Sequence agreement was high among the laboratories despite wide variations in editing strategies. All laboratories identified 66 (88%) of 75 resistance mutations in the samples. Nonconcordant identifications were made for 9 (12%) of the 75 mutations, all of which required editing for identification. These results indicate a need for standardized editing guidelines in genotyping assays. Proficiency in editing should be assessed in training and included in quality control programs for HIV-1 genotyping.

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* Corresponding author. Mailing address: Department of Immunology/Microbiology, Rush Medical College, 1653 W. Congress Pkwy., Chicago, IL 60612. Phone: (312) 942-8737. Fax: (312) 942-2808. E-mail: diana_huang{at}rush.edu.

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Journal of Clinical Microbiology, July 2003, p. 3265-3272, Vol. 41, No. 7
0095-1137/03/$08.00+0     DOI: 10.1128/JCM.41.7.3265-3272.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

This article has been cited by other articles:

• Huang, D. D., Bremer, J. W., Brambilla, D. J., Palumbo, P. E., for the Pediatric ACTG Sequencing Working Group, (2005). Model for Assessment of Proficiency of Human Immunodeficiency Virus Type 1 Sequencing-Based Genotypic Antiretroviral Assays. J. Clin. Microbiol. 43: 3963-3970 [Abstract] [Full Text]