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.
Anzala, O.; Bekker, L.G.; Kaleebu, P.; Kamali, A.; Karita, E.; Lakhi, S.; Papathanasopoulos, M.A.; Sanders, E.; Stevens, G.; Stevens, W.; Wallis, C.L.; de Wit, T.F.R. Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1. Journal of Virological Methods (2010) 163 (2) 505-508. [DOI: 10.1016/j.jviromet.2009.11.011]