How does phenotypic testing work? And is this kind of testing more recommended when you have multiple mutations and have been on lots of regimens?

Phenotypic resistance tests can be performed when a patients viral load is above 1,000 copies/ml.

The appropriate thresholds for the interpretation of phenotype results are still being determined for some drugs, thus the results may be more easily interpreted with some drugs compared to others.

As you suggest, many clinicians obtain a genotype test as their first resistance test due to quicker processing time, lower cost, and earlier changes of genotypes in response to viremia, at a time when relatively few mutations are likely to be found. Similarly, they reserve phenotype tests for more complex patients with multiple past treatment regimens, in whom multiple mutations are likely to be found. In those cases, a phenotype may more accurately reflect how the patient's virus will respond to individual ART drugs.