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

Abstract

The introduction of antiretroviral 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 1,000->1.6million 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 ViroSeqTM 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. Keywords HIV-1 subtype C; antiretroviral drug resistance; mutation profile; affordable The introduction of highly active antiretroviral therapy (HAART) in patients with AIDS is effective in suppressing HIV viral replication and prolonging life (Fauci et al., 1996). However, failure of antiretroviral (ARV) treatment may arise as a result of drug toxicity, lack of adherence *Corresponding