Evaluations of an in-house drug resistance method for HIV-1 drug resistance using ViroSeq™ 2.0 genotyping system as a gold standard
| Autor: | Nitin K. Hingankar, K. Siddhaarth, P. S. Deshmukh, Devidas N. Chaturbhuj, Sandhya Kabra, Ramesh S. Paranjape, Srikanth Tripathy, Sourav Sen, Sohan N. Deshpande |
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| Rok vydání: | 2012 |
| Předmět: |
Plasma samples
Base Sequence Genotype Anti-HIV Agents Concordance Human immunodeficiency virus (HIV) Positive control HIV Infections Drug resistance Gold standard (test) Sequence Analysis DNA Biology medicine.disease_cause Molecular biology Reverse transcriptase HIV Reverse Transcriptase Virology Drug Resistance Viral Mutation medicine HIV-1 Humans Genotyping Peptide Hydrolases |
| Zdroj: | Journal of virological methods. 189(1) |
| ISSN: | 1879-0984 |
| Popis: | An in-house method was evaluated for its efficiency to detect the HIV-1 drug resistance mutations. This method was compared with the ViroSeq™ Genotyping System 2.0 (Celera Diagnostics, US) a gold standard. Sixty-five stored plasma samples, previously tested for HIV-1 drug resistance using the ViroSeq™ method were used to evaluate the in-house method. Out of the sixty five plasma samples, sixty were HIV-1 positive clinical samples; four samples from the Virology Quality Assessment (VQA) program and one positive control from the ViroSeq™ kit were used in this study. The sequences generated by the ViroSeq™ and an in-house method showed 99.5 ± 0.5% and 99.7 ± 0.4% (mean ± SD) nucleotide and amino acid identity, respectively. Out of 214 Stanford HIVdb listed HIV-1 drug resistance mutations in the protease and reverse transcriptase regions, concordance was observed in 203 (94.9%), partial discordance in 11 (5.1%) and complete discordance was absent. The in-house primers are broadly sensitive in genotyping multiple HIV-1 group M subtypes. The amplification sensitivity of the in-house method was 1000 copies/ml. The evaluation of the in-house method provides results comparable with that of ViroSeq™ method thus, making the in-house method suitable for HIV-1 drug resistance testing in the developing countries. |
| Databáze: | OpenAIRE |
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