interpreting Resistance Tests


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Interpreting Resistance Tests

Various systems for interpreting HIV-1 genotypes have been developed. Most interpretations use a "rules-based" approach. That is, a group of experts determine which mutations or combination of mutations are associated with resistance to specific drugs, and establish an algorithm for interpreting the genotype. These algorithms are used as the basis of automated computer-generated reports, as in the TruGene assay. Such algorithms require periodic updating as new information becomes available. Alternatively, clinicians may refer to one of a number of on-line databases, some of which now offer genotype interpretation (Table 2). Genotype reports from diagnostic laboratories usually come with some form of rules-based interpretation indicating to which drugs the virus has developed resistance.

Although results of phenotypic assays seem to be straightforward, interpreting phenotypes in fact may be more complicated than originally believed. For example, an important issue is how to define "cut-offs" for susceptible and resistant viruses. Both the PhenoSense and AntiVirogram assays use laboratory strains of HIV-1 as controls. Until recently, cut-offs were defined solely on the basis of interassay variation. For example, if the IC50 of wild-type control viruses varied by 4-fold, then viruses with IC50's that were more than 4-fold greater than the control were considered to be resistant; those with IC50's that were less than 4-fold above the control were considered to be susceptible. This approach has two short-comings: first, the natural variation in susceptibility of wild-type isolates might be greater than the interassay variation for the laboratory control strain, and second, these cut-offs were not based on clinical response data.

These shortcomings have been addressed by modifications in reporting for both the AntiVirogram and PhenoSense assays. Virco has defined new ranges for "sensitive" and "resistant" based on the distribution of susceptibility of isolates from 1000 treatment-naïve patients (11). This change has narrowed the range of IC50 values that fall within the sensitive category for the nucleoside RT inhibitors, but considerably widened the range of IC50's included under the susceptible category for NNRTIs. ViroLogic has re-defined resistance to d4T and ddI as a >1.7-fold increase in IC50 for these drugs as compared to control based on data that suggest a reduced response to these drugs in viruses with only modest reductions in susceptibility. Similarly, clinical response data resulted in redefinition of resistance to abacavir as an IC50 >4.5-fold above control (12).

Even the concept of "cut-offs" presents certain difficulties, however. For example, the cutoff for lopinavir has been defined as a >10-fold increase in IC50 above control. However, clinical trials show that there is a continuous relationship between lopinavir susceptibility and virologic response (13). Two-thirds of patients with virus that had 20- to 40-fold resistance to lopinavir still achieved virologic suppression on lopinavir-containing regimens. Data suggest that even NRTI's may have residual activity against partially resistant viruses (14). Thus, it might be more realistic to consider drugs as having greater or lesser activity against viruses that are more or less susceptible to the particular drugs.

4/15/01