Evaluations of an in-house drug resistance method for HIV-1 drug resistance using ViroSeq™ 2.0 genotyping system as a gold standard.
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.
National AIDS Research Institute, Plot 73, 'G' Block, M.I.D.C., Bhosari, Pune 411 026, India. chaturbhujdn@gmail.com
Devidas N
DN
Chaturbhuj
Pravin S
PS
Deshmukh
Nitin K
NK
Hingankar
K
K
Siddhaarth
Sohan N
SN
Deshpande
Sourav
S
Sen
Sandhya
S
Kabra
Ramesh S
RS
Paranjape
Srikanth P
SP
Tripathy
D019380:Anti-HIV Agents / Q000494:pharmacology; D001483:Base Sequence; D024882:Drug Resistance, Viral / Q000235:genetics*; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics*; D006801:Humans; D009154:Mutation; D010447:Peptide Hydrolases / Q000235:genetics; D017422:Sequence Analysis, DNA
D019380:Anti-HIV Agents; D054303:HIV Reverse Transcriptase; D010447:Peptide Hydrolases