Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1

• Published in: Journal of virological methods Vol. 163; no. 2; pp. 505 - 508
• Main Authors: Wallis, Carole L., Papathanasopoulos, Maria A., Lakhi, Shabir, Karita, Etienne, Kamali, Anatoli, Kaleebu, Pontiano, Sanders, Eduard, Anzala, Omu, Bekker, Linda-Gail, Stevens, Gwynn, Wit, Tobias F. Rinke de, Stevens, Wendy
• Format: Journal Article
• Language: English
• Published: Kidlington Elsevier B.V 01.02.2010; Elsevier
• Subjects: Affordable; Anti-Retroviral Agents - pharmacology; Antiretroviral drug resistance; Antiviral agents; Automation; Biological and medical sciences; DNA Primers - genetics; Drug Resistance, Viral; Fundamental and applied biological sciences. Psychology; Genes, Viral; Genotype; HIV-1 - drug effects; HIV-1 - genetics; HIV-1 - isolation & purification; HIV-1 subtype C; Human immunodeficiency virus 1; Humans; Microbial Sensitivity Tests - economics; Microbial Sensitivity Tests - methods; Microbiology; Mutation profile; Reverse Transcriptase Polymerase Chain Reaction - methods; RNA, Viral - genetics; RNA, Viral - isolation & purification; Sensitivity and Specificity; South Africa; Techniques used in virology; Virology; South Africa; Antiretroviral drug resistance; HIV-1 subtype C; Affordable; Mutation profile; Antiretroviral agent; HIV-1 virus; Retroviridae; Method; Lentivirus; Virus; Resistance; Antiviral; Human immunodeficiency virus; Mutation; Subtype
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2009.11.011

The introduction of antiretroviral (ARV) therapy in resource-poor settings is effective in suppressing HIV-1 replication and prolonging life of infected individuals. This has led to a demand for affordable HIV-1 drug resistance assays, since treatment failure due to development of drug resistance is common. This study developed and evaluated an affordable “in–house” genotyping assay to monitor HIV-1 drug resistance in Africa, particularly South Africa. An “in-house” assay using automated RNA extraction, and subtype C specific PCR and sequencing primers was developed and successfully evaluated 396 patient samples (viral load ranges 1000–1.6 million RNA copies/ml). The “in-house” assay was validated by comparing sequence data and drug resistance profiles from 90 patient and 10 external quality control samples to data from the ViroSeq™ HIV-1 Genotyping kit. The “in-house” assay was more efficient, amplifying all 100 samples, compared to 91 samples using Viroseq. The “in house” sequences were 99.2% homologous to the ViroSeq sequences, and identical drug resistance mutation profiles were observed in 96 samples. Furthermore, the “in-house” assay genotyped 260 of 295 samples from seven African sites, where 47% were non-subtype C. Overall, the newly validated “in-house” drug resistance assay is suited for use in Africa as it overcomes the obstacle of subtype diversity.