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

J Virol Methods. 2010 Feb;163(2):505-8. doi: 10.1016/j.jviromet.2009.11.011. Epub 2009 Nov 14.


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.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Anti-Retroviral Agents / pharmacology*
  • Automation
  • DNA Primers / genetics
  • Drug Resistance, Viral*
  • Genes, Viral*
  • Genotype
  • HIV-1 / drug effects*
  • HIV-1 / genetics
  • HIV-1 / isolation & purification
  • Humans
  • Microbial Sensitivity Tests / economics*
  • Microbial Sensitivity Tests / methods*
  • RNA, Viral / genetics*
  • RNA, Viral / isolation & purification
  • Reverse Transcriptase Polymerase Chain Reaction / methods
  • Sensitivity and Specificity
  • South Africa


  • Anti-Retroviral Agents
  • DNA Primers
  • RNA, Viral