Evaluation of two human immunodeficiency virus-1 genotyping systems: ViroSeq™ 2.0 and an in-house method

S. Saravanan, M. Vidya, P. Balakrishanan, N. Kumarasamy, Sunil Solomon, S. Solomon, Rami Kantor, David Katzenstein, Bharat Ramratnam, Kenneth H. Mayer

Research output: Contribution to journalArticle

Abstract

Commercial HIV-1 genotypic resistance assays are very expensive, particularly for use in resource-constrained settings like India. Hence a cost effective in-house assay for drug resistance was validated against the standard ViroSeq™ HIV-1 Genotyping System 2.0 (Celera Diagnostics, CA, USA). A total of 50 samples were used for this evaluation (21 proficiency panels and 29 clinical isolates). Known resistance positions within HIV-1 protease (PR) region (1-99 codons) and HIV-1 reverse-transcriptase (RT) region (1-240 codons) were included. The results were analysed for each codon as follows: (i) concordant; (ii) partially concordant; (iii) indeterminate and (iv) discordant. A total of 2750 codons (55 codons per patient sample × 50 samples) associated with drug resistance (1050 PR and 1700 RT) were analysed. For PR, 99% of the codon results were concordant and 1% were partially concordant. For RT, 99% of the codon results were concordant, 0.9% were partially concordant and 0.1% were discordant. No indeterminate results were observed and the results were reproducible. Overall, the in-house assay provided comparable results to those of US FDA approved ViroSeq™, which costs about a half of the commercial assay ($ 100 vs. $ 230), making it suitable for resource-limited settings.

Original languageEnglish (US)
Pages (from-to)211-216
Number of pages6
JournalJournal of Virological Methods
Volume159
Issue number2
DOIs
StatePublished - Aug 2009
Externally publishedYes

Fingerprint

Codon
HIV-1
RNA-Directed DNA Polymerase
Drug Resistance
Peptide Hydrolases
Costs and Cost Analysis
India

Keywords

  • Concordance
  • HIV-1 genotyping evaluation
  • In-house HIV-1 drug resistance assay
  • Indeterminate rate
  • Mixtures
  • ViroSeq™ HIV-1 genotyping

ASJC Scopus subject areas

  • Virology

Cite this

Evaluation of two human immunodeficiency virus-1 genotyping systems : ViroSeq™ 2.0 and an in-house method. / Saravanan, S.; Vidya, M.; Balakrishanan, P.; Kumarasamy, N.; Solomon, Sunil; Solomon, S.; Kantor, Rami; Katzenstein, David; Ramratnam, Bharat; Mayer, Kenneth H.

In: Journal of Virological Methods, Vol. 159, No. 2, 08.2009, p. 211-216.

Research output: Contribution to journalArticle

Saravanan, S, Vidya, M, Balakrishanan, P, Kumarasamy, N, Solomon, S, Solomon, S, Kantor, R, Katzenstein, D, Ramratnam, B & Mayer, KH 2009, 'Evaluation of two human immunodeficiency virus-1 genotyping systems: ViroSeq™ 2.0 and an in-house method', Journal of Virological Methods, vol. 159, no. 2, pp. 211-216. https://doi.org/10.1016/j.jviromet.2009.03.021
Saravanan, S. ; Vidya, M. ; Balakrishanan, P. ; Kumarasamy, N. ; Solomon, Sunil ; Solomon, S. ; Kantor, Rami ; Katzenstein, David ; Ramratnam, Bharat ; Mayer, Kenneth H. / Evaluation of two human immunodeficiency virus-1 genotyping systems : ViroSeq™ 2.0 and an in-house method. In: Journal of Virological Methods. 2009 ; Vol. 159, No. 2. pp. 211-216.
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