Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1.
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.
Wallis
Carole L
CL
Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa. cwallis@mweb.co.za
Papathanasopoulos
Maria A
MA
Lakhi
Shabir
S
Karita
Etienne
E
Kamali
Anatoli
A
Kaleebu
Pontiano
P
Sanders
Eduard
E
Anzala
Omu
O
Bekker
Linda-Gail
LG
Stevens
Gwynn
G
de Wit
Tobias F Rinke
TF
Stevens
Wendy
W
D044966:Anti-Retroviral Agents / Q000494:pharmacology*; D001331:Automation; D017931:DNA Primers / Q000235:genetics; D024882:Drug Resistance, Viral; D005814:Genes, Viral; D005838:Genotype; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000191:economics* / Q000379:methods*; D012367:RNA, Viral / Q000235:genetics* / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D013019:South Africa
D044966:Anti-Retroviral Agents; D017931:DNA Primers; D012367:RNA, Viral