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Journal of Clinical Microbiology, August 1999, p. 2533-2537, Vol. 37, No. 8
0095-1137/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Performance of the Affymetrix GeneChip HIV PRT 440 Platform for Antiretroviral Drug Resistance Genotyping of Human Immunodeficiency Virus Type 1 Clades and Viral Isolates with Length Polymorphisms

Maryanne Vahey,1,* Martin E. Nau,2 Sandra Barrick,2 John D. Cooley,2 Robert Sawyer,2 Alex A. Sleeker,2 Peter Vickerman,2 Stuart Bloor,3 Brendan Larder,3 Nelson L. Michael,1 and Scott A. Wegner1

Division of Retrovirology, Walter Reed Army Institute of Research,1 and The Henry M. Jackson Foundation for the Advancement of Military Medicine,2 Rockville, Maryland, and Virco UK, Cambridge, United Kingdom3

Received 30 November 1998/Returned for modification 2 February 1999/Accepted 10 May 1999

The performance of a silica chip-based resequencing method, the Affymetrix HIV PRT 440 assay (hereafter referred to as the Affymetrix assay), was evaluated on a panel of well-characterized nonclade B viral isolates and on isolates exhibiting length polymorphisms. Sequencing of human immunodeficiency virus type 1 (HIV-1) pol cDNAs from clades A, C, D, E, and F resulted in clade-specific regions of base-calling ambiguities in regions not known to be associated with resistance polymorphisms, as well as a small number of spurious resistance polymorphisms. The Affymetrix assay failed to detect the presence of additional serine codons distal to reverse transcriptase (RT) codon 68 that are associated with multinucleoside RT inhibitor resistance. The increasing prevalence of non-clade B HIV-1 strains in the United States and Europe and the identification of clinically relevant pol gene length polymorphisms will impact the generalizability of the Affymetrix assay, emphasizing the need to accommodate this expanding pool of pol genotypes in future assay versions.

* Corresponding author. Mailing address: Division of Retrovirology, Walter Reed Army Institute of Research, 1600 E. Gude Dr., Rockville, MD 20850. Phone: (301) 294-1887, ext. 1044. Fax: (301) 762-7460. E-mail: mvahey{at}pasteur.hjf.org.

Journal of Clinical Microbiology, August 1999, p. 2533-2537, Vol. 37, No. 8
0095-1137/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


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