Wallis C.L., Mahomed I., Morris L., Chidarikire T., Stevens G., Rekhviashvili N., Stevens W.
Dept. of Molec. Med. and Haematology, School of Pathology, Univ. of the Witwatersrand Med. Sch., South Africa; National Health Laboratory Services, South Africa
Wallis, C.L., Dept. of Molec. Med. and Haematology, School of Pathology, Univ. of the Witwatersrand Med. Sch., South Africa; Mahomed, I., Dept. of Molec. Med. and Haematology, School of Pathology, Univ. of the Witwatersrand Med. Sch., South Africa; Morris, L., National Health Laboratory Services, South Africa; Chidarikire, T., National Health Laboratory Services, South Africa; Stevens, G., National Health Laboratory Services, South Africa; Rekhviashvili, N., National Health Laboratory Services, South Africa; Stevens, W., Dept. of Molec. Med. and Haematology, School of Pathology, Univ. of the Witwatersrand Med. Sch., South Africa
The oligonucleotide ligation assay (OLA) has been proposed as an affordable alternative to sequence-based HIV-1 drug resistance testing in resource poor settings. The aim was to evaluate OLA for detecting mutations K103N, Y181C, K65R, Q151M, M184V and T215Y/F in subtype C. Forty-four subtype C and 8 subtype B HIV-1 positive individuals were analysed using the ViroSeq™ HIV-1 genotyping assay (Applied Biosystems, Foster City, CA). A one-step RT-PCR and nested PCR were performed using subtype B specific primers from the OLA kit (NIH AIDS Research and Reference Reagent Program). Seventy-eight subtype C sequences were used to design subtype C specific primers. Ligation and detection steps were followed according to OLA kit protocol. For codons, K103N, Y181C, K65R, Q151M, M184V and T215Y/F, four or more mismatches compared to the probe or mismatches less than four bases from the ligation site were not tolerated. Results revealed accurate identification of mutations in 2/10, 4/9 3/9, 6/7, 2/7 and 6/7 VQA samples and 5/20, 4/17 0/20, 18/24, 5/24 and 13/24 subtype C positive individuals, respectively. It was concluded that the probes and primers in the NIH reference kit would need modification to optimize detection of mutations in subtype C individuals. © 2005 Elsevier B.V. All rights reserved.
RNA directed DNA polymerase inhibitor; article; codon; genotype; human; Human immunodeficiency virus 1; Human immunodeficiency virus infection; nonhuman; oligonucleotide ligation assay; polymerase chain reaction; priority journal; reverse transcription polymerase chain reaction; serotype; virus mutation; Anti-HIV Agents; Drug Resistance, Multiple, Viral; HIV-1; Humans; Molecular Biology; Mutation; Oligodeoxyribonucleotides; Oligonucleotide Probes; Oligonucleotides; Reverse Transcriptase Inhibitors; Sensitivity and Specificity; Sequence Analysis, DNA; Human immunodeficiency virus 1