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Journal of Clinical Microbiology, October 2005, p. 5263-5271, Vol. 43, No. 10
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.10.5263-5271.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Use of Sequence Data Generated in the Bayer TruGene Genotyping Assay To Recognize and Characterize Non-Subtype-B Human Immunodeficiency Virus Type 1 Strains

Diane L. Hirigoyen1 and Charles P. Cartwright1,2*

Department of Laboratory Medicine and Pathology, Hennepin County Medical Center, Minneapolis, Minnesota 55415,1 Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota 554552

Received 21 April 2005/ Returned for modification 5 July 2005/ Accepted 11 July 2005

Human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) gene sequences obtained during antiretroviral resistance testing with a commercial genotyping assay (TruGene; Bayer Corp.) were analyzed to assess the utility of these data for detecting and characterizing non-subtype-B HIV-1 strains. A total of 125 viral sequences obtained from patients believed to have acquired their HIV-1 infection in Africa were analyzed, of which 121 were determined to belong to non-B subtypes. Utilizing TruGene sequence data alone, 92 (76%) of these viruses could be subtyped by conventional phylogenetic analysis. The addition of supplemental RT sequence data enabled a further 28 (23.1%) viruses to be classified, while one (0.9%) sample could not be classified conclusively. Two internet-accessible databases that generate HIV-1 subtypes from PR and RT sequences (HIV-SEQ and Geno2Pheno) were also evaluated, and both achieved 88% concordance (106/120) with phylogenetic analysis. Non-subtype-B and B-subtype HIV-1 sequences could be readily discriminated by tallying silent polymorphisms listed on the TruGene research report. The mean number of silent polymorphisms in the non-B HIV-1 sequences identified in this study was 58.3 (95% confidence interval [CI], 41.1 to 75.5), compared with 20.7 (95% CI, 9.9 to 31.5) for the four subtype B viruses in the study cohort and 118 case-matched B-subtype controls. Sequence data generated in the TruGene HIV-1 genotyping assay could, therefore, provide a ready means of tracking the prevalence and identity of non-B subtypes in HIV-1-infected populations undergoing routine antiretroviral resistance testing.

* Corresponding author. Mailing address: Clinical Laboratories P4, Hennepin County Medical Center, 701 Park Ave., Minneapolis, MN 55415. Phone: (612) 873-3026. Fax: (612) 904-4229. E-mail: charles.cartwright{at}co.hennepin.mn.us.

Journal of Clinical Microbiology, October 2005, p. 5263-5271, Vol. 43, No. 10
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.10.5263-5271.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.





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