, and CRF12-13) and displaying a viral load range of 200 to >500,000 RNA copies/ml was 97%. The drug susceptibility measurements, based on discrimination between infected and noninfected cells on a single-cell level by flow cytometry, were reproducible, with coefficients of variation for resistance ranging from 7% to 31%, and were consistent with scientific literature in terms of magnitude and specificity.Despite continued improvements in treatment of human immunodeficiency virus type 1 (HIV-1)-infected patients, therapy failure still occurs, often leading to drug resistance development, which necessitates a change in regimen. At this moment, clinicians have at their disposal 22 drugs, targeting the viral protease (PR), the reverse transcriptase (RT), the integrase (IN), the transmembrane glycoprotein (gp41), or the interaction between the surface glycoprotein (gp120) and the cellular coreceptor CCR5. The choice of which drugs to include in the next regimen is based upon the likelihood of the drugs being active against the mutant virus present in the patient with incomplete suppression of replication (11).Currently, genotypic drug resistance testing is used more frequently within the clinical setting of patient follow-up due to practical reasons, such as a shorter turnaround time, easier implementation within laboratories, and lower cost, but also due to the fact that no clinical trial has yet provided sufficient evidence for supporting phenotypic over genotypic drug resistance testing. Nevertheless, the interpretation of genotypic drug resistance testing can be very complex, which makes phenotypic drug resistance testing in certain settings very useful and even necessary (48).Increasing numbers of drug resistance mutations have been identified within gag, pol, and env, reflecting the genetic flexibility of HIV-1. These mutations can directly boost the ability of the virus to specifically replicate in the presence of the drug (major mutations) or indirectly aid the virus by increasing its replication capacity in general, whether in the presence or absence of the drug (minor or compensatory mutations). In general, the major mutations are found at the drug binding sites within the targeted protein (or the viral protein that interacts with the cellular target), whereas the others can be found at distinct sites within the target protein or even other proteins. In this respect, PR inhibitor (PI) mutations have been observed not only within the PR but also at several sites within its Gag substrate (13,28).The use of genotypic data to determine if certain drugs are still active against patient-derived virus is further complicated by the presence of natural polymorphisms in non-B strains and by baseline subtype-dependent combinations of mutations that occur during treatment, leading to discordances between different interpretation algorithms (43,51). Several studies have revealed novel mutations or differences in the prevalence of known mutations in non-B subtypes (1, 3). Others have demonstrated the impact of the genet...