Performance of the Celera Diagnostics ViroSeq HIV-1 genotyping system for sequence-based analysis of diverse human immunodeficiency virus type 1 strains

Susan Eshleman, John Hackett, Priscilla Swanson, Shawn P. Cunningham, Birgit Drews, Catherine Brennan, Sushil G. Devare, Léopold Zekeng, Lazare Kaptué, Natalia Marlowe

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2711-2717
Number of pages7
JournalJournal of Clinical Microbiology
Volume42
Issue number6
DOIs
StatePublished - Jun 2004

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Sequence Analysis
HIV-1
Drug Resistance
Peptide Hydrolases
Cercopithecine Herpesvirus 1
Amino Acids
Cameroon
Uganda
RNA-Directed DNA Polymerase
Argentina
Thailand
United States Food and Drug Administration
Systems Analysis
South Africa
Viral Load
varespladib methyl
Brazil
Genotype
Polymerase Chain Reaction
Mutation

ASJC Scopus subject areas

  • Microbiology (medical)
  • Microbiology

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Performance of the Celera Diagnostics ViroSeq HIV-1 genotyping system for sequence-based analysis of diverse human immunodeficiency virus type 1 strains. / Eshleman, Susan; Hackett, John; Swanson, Priscilla; Cunningham, Shawn P.; Drews, Birgit; Brennan, Catherine; Devare, Sushil G.; Zekeng, Léopold; Kaptué, Lazare; Marlowe, Natalia.

In: Journal of Clinical Microbiology, Vol. 42, No. 6, 06.2004, p. 2711-2717.

Research output: Contribution to journalArticle

Eshleman, Susan ; Hackett, John ; Swanson, Priscilla ; Cunningham, Shawn P. ; Drews, Birgit ; Brennan, Catherine ; Devare, Sushil G. ; Zekeng, Léopold ; Kaptué, Lazare ; Marlowe, Natalia. / Performance of the Celera Diagnostics ViroSeq HIV-1 genotyping system for sequence-based analysis of diverse human immunodeficiency virus type 1 strains. In: Journal of Clinical Microbiology. 2004 ; Vol. 42, No. 6. pp. 2711-2717.
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