Resistance assays

Excerpt

This chapter describes the different methods used to measure HIV-1 resistance against antiretroviral drugs. There are essentially three approaches to detecting antiretroviral resistance in routine clinical practice. The most direct method measures the virus phenotypic susceptibility to drugs directly by culturing virus in the presence of increasing concentrations of the drug of interest. The concentration of drug required to inhibit virus replication by either 50% (IC₅₀) or 90% (IC₉₀) relative to a control virus is then taken as a measure of resistance. These assays are similar to those that have been used by bacteriologists for more than a century, although methods employed to measure antiretroviral drug resistance have become more sophisticated. An alternative method for measuring drug resistance is to determine the sequence of the gene (or parts thereof) targeted by the drug of interest and use this information to deduce drug susceptibility (i.e. the likely virus phenotype). This method is the basis of genotyping assays, which are most commonly used in clinical practice because they are generally less expensive, laborious and time-consuming than phenotyping assays. A third approach, the virtual phenotyping assay, is a mixture of the first two methods, whereby the virus under investigation is sequenced and identified changes are matched to a large dataset of genotype–phenotype pairs of previously sequenced viruses for which the phenotype is known.