PMID- 19490976 OWN - NLM STAT- MEDLINE DCOM- 20090716 LR - 20211020 IS - 1879-0984 (Electronic) IS - 0166-0934 (Print) IS - 0166-0934 (Linking) VI - 159 IP - 2 DP - 2009 Aug TI - Evaluation of two human immunodeficiency virus-1 genotyping systems: ViroSeq 2.0 and an in-house method. PG - 211-6 LID - 10.1016/j.jviromet.2009.03.021 [doi] AB - 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 samplex50 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. FAU - Saravanan, S AU - Saravanan S AD - YRG Centre for AIDS Research and Education, Chennai 600 113, India. FAU - Vidya, M AU - Vidya M FAU - Balakrishnan, P AU - Balakrishnan P FAU - Kumarasamy, N AU - Kumarasamy N FAU - Solomon, Sunil S AU - Solomon SS FAU - Solomon, S AU - Solomon S FAU - Kantor, Rami AU - Kantor R FAU - Katzenstein, David AU - Katzenstein D FAU - Ramratnam, Bharat AU - Ramratnam B FAU - Mayer, Kenneth H AU - Mayer KH LA - eng GR - R01 AI066922/AI/NIAID NIH HHS/United States GR - R01 AI066922-03/AI/NIAID NIH HHS/United States PT - Comparative Study PT - Evaluation Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090402 PL - Netherlands TA - J Virol Methods JT - Journal of virological methods JID - 8005839 RN - 0 (RNA, Viral) SB - IM EIN - J Virol Methods. 2010 Feb;163(2):513. Balakrishanan, P [corrected to Balakrishnan, P] MH - Genotype MH - HIV Infections/*virology MH - HIV-1/*drug effects/*genetics MH - Humans MH - India MH - Microbial Sensitivity Tests/economics/*methods MH - RNA, Viral/*genetics MH - Sensitivity and Specificity PMC - PMC2923210 MID - NIHMS226626 COIS- Conflict of interest None declared. EDAT- 2009/06/06 09:00 MHDA- 2009/07/17 09:00 PMCR- 2010/08/17 CRDT- 2009/06/04 09:00 PHST- 2008/12/30 00:00 [received] PHST- 2009/03/21 00:00 [revised] PHST- 2009/03/24 00:00 [accepted] PHST- 2009/06/04 09:00 [entrez] PHST- 2009/06/06 09:00 [pubmed] PHST- 2009/07/17 09:00 [medline] PHST- 2010/08/17 00:00 [pmc-release] AID - S0166-0934(09)00158-X [pii] AID - 10.1016/j.jviromet.2009.03.021 [doi] PST - ppublish SO - J Virol Methods. 2009 Aug;159(2):211-6. doi: 10.1016/j.jviromet.2009.03.021. Epub 2009 Apr 2.