Advantages and disadvantages to phenotypic and genotypic resistance testing
What are the advantages and disadvantages to phenotypic resistance testing and genotypic resistance testing and what's a virtual phenotype? What do you use and why? Thanks!
Are all these tests still in use?
Genotype Tests TrueGene HIV-1 Genotyping Kit, Visible Genetics Inc. VircoGEN, Virco, processed in US by LabCorp INNO-LiPA HIV-1 RT (Line Probe Assay), Innogenetics HIV-1 GentypR, Specialty Laboratories
Phenotype Tests PhenoSense HIV, ViroLogic, Inc. Antivirogram, Virco
Genotypic resistance testing generates a list of mutations that are known to confer resistance to anti-HIV drugs. From this, an expert can infer the presence or absence of resistance to individual drugs or drug classes. Phenotypic resistance actually takes a virus (or part of a virus) and measures how each of the drugs work on an individual basis against the virus that is actually present in the blood. The "Virtual Phenotype" is simply a method of interpreting the genotypic result in a systematic way (a type of "computer expert", if you will).
Some limitations of the tests must be pointed out. They cannot predict the efficacy of drug combinations, nor can they evaluate the effect of viral strains that constitute a minority of the isolates that are present in the blood or in cells. The genotypic tests, by their nature, cannot evaluate new mutations that have not yet been described.
In cases where an individual has never been treated or has limited drug exposure, a genotypic test is cheaper and can usually be interpreted appropriately. Once drug exposure is more extensive and the genotype more complex, a phenotypic test may be particularly helpful.
All of the tests you mention are still in use, and have their relative advantages and disadvantages. Each center tends to have access to a single test in each of the genotype and phenotype categories, usually by contract. You can understand that the VircoGEN and Antivirogram are often used together. There is little advantage of one genotypic test over the other, and the same can be said of the phenotypic tests. Overall, however, the latter are significantly more expensive.