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Journal of Clinical Microbiology, June 2004, p. 2711-2717, Vol. 42, No. 6
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.6.2711-2717.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Performance of the Celera Diagnostics ViroSeq HIV-1 Genotyping System for Sequence-Based Analysis of Diverse Human Immunodeficiency Virus Type 1 Strains

Susan H. Eshleman,1* John Hackett Jr.,2 Priscilla Swanson,2 Shawn P. Cunningham,1 Birgit Drews,3 Catherine Brennan,2 Sushil G. Devare,2 Léopold Zekeng,4 Lazare Kaptué,5 and Natalia Marlowe3

Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland,1 AIDS Research and Retrovirus Discovery, Abbott Laboratories, Abbott Park, Illinois,2 Laboratoire de Santé Hygiène Mobile,4 Université de Yaoundé, Yaoundé, Cameroon,5 Celera Diagnostics, Alameda, California3

Received 24 September 2003/ Returned for modification 8 January 2004/ Accepted 1 March 2004

The Celera Diagnostics ViroSeq HIV-1 Genotyping System is a Food and Drug Administration-cleared, integrated system for sequence-based analysis of drug resistance mutations in subtype B human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase (RT). We evaluated the performance of this system for the analysis of diverse HIV-1 strains. Plasma samples were obtained from 126 individuals from Uganda, Cameroon, South Africa, Argentina, Brazil, and Thailand with viral loads ranging from 2.92 to >6.0 log10 copies/ml. HIV-1 genotyping was performed with the ViroSeq system. HIV-1 subtyping was performed by using phylogenetic methods. PCR products suitable for sequencing were obtained for 125 (99%) of the 126 samples. Genotypes including protease (amino acids 1 to 99) and RT (amino acids 1 to 321) were obtained for 124 (98%) of the samples. Full bidirectional sequence data were obtained for 95 of those samples. The sequences were categorized into the following subtypes: A1/A2 (16 samples), B (12 samples), C (13 samples), D (11 samples), CRF01_AE (9 samples), F/F2 (9 samples), G (7 samples), CRF02_AG (32 samples), H (1 sample), and intersubtype recombinant (14 samples). The performances of the individual sequencing primers were examined. Genotyping of duplicate samples in a second laboratory was successful for 124 of the 126 samples. The identity level for the sequence data from two laboratories ranged from 98 to 100% (median, 99.8%). The ViroSeq system performs well for the analysis of plasma samples with diverse non-B subtypes. The availability of this genotyping system should facilitate studies of HIV-1 drug resistance in non-subtype B strains of HIV-1.

* 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, June 2004, p. 2711-2717, Vol. 42, No. 6
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.6.2711-2717.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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