Resistance of human immunodeficiency virus type 1 to reverse transcriptase and protease inhibitors: genotypic and phenotypic testing.

Treatment of HIV-1-infected persons with antiretroviral drugs including reverse transcriptase (RT) and protease inhibitors has significantly reduced the rate of HIV and AIDS-related morbidity and mortality. However, these treatments can select for drug-resistant viruses which are associated with poor virologic responses to the antiretroviral therapies and loss of clinical benefit. Drug resistance is conferred by single or several amino acid changes in the pol gene. These mutations can be classified as primary when they directly confer reduced drug susceptibility, or secondary when their influence is primarily on replication capabilities of resistant viruses. Both genotypic and phenotypic methods are used for drug resistance testing. Genotypic assays detect resistance-related mutations by sequence analysis or point mutations assays. Phenotypic testing measures drug susceptibility of patient-derived viruses in culture assays. Viruses can be conventionally isolated from peripheral blood lymphocytes, or generated more rapidly through recombination of plasma-derived RT/protease sequences and modified HIV-1 vectors. Phenotypic testing provides direct evidence of resistance, is easy to interpret, but is laborious and expensive. In contrast, genotypic testing provides indirect evidence of resistance, is relatively faster and cheaper, but some complex mutation patterns may be difficult to interpret. Non-culture based phenotypic assays that measure susceptibility of RT activity in plasma to RT inhibitors have been described recently, and provide new tools for rapid phenotypic testing. Resistance testing is currently recommended to help guide the choice of new regimens after treatment failure and for guiding therapy in pregnant women.