Genotypic Resistance Testing Most genotypic antiretroviral DR testing (GART) methods are based on polymerase chain reaction (PCR) amplification of the target gene followed by sequencing by automated capillary electrophoresis. For the purpose of this dissertation, unless otherwise specified, genotypic resistance refers to resistance detected by PCR and sequencing. GART was also used at an early stage of ARV development: Mutations associated with AZT resistance in culture, namely D67N, K70R, T215Y/F and K219Q, were identified using PCR and sequencing or selective PCR which paved the way for genotypic resistance testing (Larder et al., 1991). Many more mutations were subsequently discovered that are associated with resistance to particular…show more content… Phenotypes are more expensive than genotypes but have more limited availability and also a problem of interpretation exists, the values (or “cutoffs”) that define resistance phenotypically have been based on the technical variability of the assay or, more recently, the biologic variability of wild type strains. Two companies have developed standardized assays amenable to high-throughput performance (Virco, Mechelen, Belgium and ViroLogic, South San Francisco, CA, USA) (Hertogs et al., 1998; Petropoulos et al., 2000). Both assays amplify the entire PR, much of RT and some of gag from HIV-1 RNA extracted from patient plasma.
2.13.3 Virtual Phenotypic Resistance Testing Virtual phenotyping is actually a genotype test that uses a database of phenotypes to enhance the genotype results. After determining the genotype, the results are compared to a database of resistance results. This database is made up of resistance test results where both genotyping and phenotyping were performed on each patient. If a person's virus has a genotype that matches a genotype in the database, it is assumed that the phenotype matched to the genotype in the database will be the same for the person being tested. Although virtual phenotyping is a type of genotypic testing, it is generally considered to be advancement over standard genotypic testing. However, virtual