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Several prospective and retrospective studies have shown that genotypic testing for drug-resistant HIV-1 variants has helped health-care providers better understand patient responses to antiretroviral therapy (ART) and make wiser choices for both initial and salvage therapy. The standard approach to genotypic resistance testing begins with plasma HIV-1 RNA extraction, reverse transcription, and polymerase chain reaction (PCR) amplification, and it ends with the direct sequencing of PCR products by use of the standard dideoxynucleotide terminator sequencing method developed by Sanger 30 years ago. The high mutation rate of HIV-1 and the complex population genetics of HIV-1 in infected patients complicate the interpretation of standard genotypic tests for resistant variants because these tests are generally unable to detect minority or low-abundance drug-resistant mutations (DRMs) that are present at levels <20% of the virus quasispecies in a clinical sample.

Low-Abundance Drug-Resistant HIV-1 Variants: Finding Significance in an Era of Abundant Diagnostic and Therapeutic Options