• Vol. 41 No. 12, 553–558
  • 15 December 2012

Clinical Evaluation of an In-House Human Immunodeficiency Virus (HIV) Genotyping Assay for the Detection of Drug Resistance Mutations in HIV-1 Infected Patients in Singapore



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Introduction: Human immunodeficiency virus type 1 (HIV-1) genotyping resistance test (GRT) is essential for monitoring HIV-1 drug resistance mutations (DRMs). High cost and HIV-1 genetic variability are challenges to assay availability in Singapore. An in-house Sanger sequencing-based GRT method was developed at the Communicable Disease Centre (CDC), Singapore’s HIV national treatment reference centre for both subtype B and non-subtype B HIV-1.

Materials and Methods: The in-house GRT sequenced the first 99 codons of protease (PR) and 244 codons of reverse transcriptase (RT) in the pol gene. The results were compared with the Food and Drug Administration (FDA)-approved ViroSeqTM HIV-1 Genotyping System.

Results: Subtype assignment for the 46 samples were as follows: 31 (67.4%) CRF01_AE, 14 (30.5%) subtype B and 1 (2.1%) subtype C. All 46 samples had viral load of ≥500 copies/mL, and were successfully amplified by the in-house primer sets. Compared to the ViroSeqTM test, our in-house assay showed drug-resistance conferring codon concordance of 99.9% at PR and 98.9% at RT, and partial concordance of 0.1% at PR and 1.1% at RT. No discordant result was observed.

Conclusion: The assay successfully identified DRMs in both subtype AE and B, making it suitable for the efficient treatment monitoring in genetically diverse population. At less than half of the running cost compared to the ViroSeqTM assay, the broadly sensitive in-house assay could serve as a useful addition to the currently limited HIV genotyping assay options for resource-limited settings, thereby enhancing the DRM surveillance and monitoring in the region.

Human immunodeficiency virus (HIV) drug resistance testing is a standard of care test recommended for HIV-infected patients prior to initiation of antiretroviral therapy (treatment-naïve), and prior to treatment switch (treatment-experienced). For treatment-naïve patients, HIV drug resistance testing detects transmitted resistance and enables selection of an optimal first regimen. For treatment-experienced patients, drug resistance testing facilitates selection of an optimal next regimen with the highest number of effective agents.

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