Background:  Previous studies have identified the clinically relevant susceptibility threshold for reduced susceptibility to ritonavir-boosted indinavir (IDV/RTV 800 mg/200 mg twice daily) using the PhenoSenseHIV phenotypic assay (10-fold). No robust genotypic correlates of reduced susceptibility have been defined.

Methods: Using a database of phenotype and genotype data (n~20,000), genotypic patterns associated with reductions in IDV susceptibility of 10-fold or greater were determined. Univariate (Fisher exact test), classification tree (CART), and receiver-operator analyses were performed to identify the optimum set of protease mutations and numbers of mutations to be considered.

Results:  Protease mutations that were associated with IDV fold change  >10-fold included recognized primary (M46ILV, G48MSV, V82AFST, I84AV, L90M) and secondary (L10IFRV, K20IMRT, L24I, V32I, L33F, M36IL, I47AV, I54ALMSTV, L63PSATQVC, A71ILVT, G73ACST, N88ST) mutations as well as other unrecognized mutations (E34Q, K43T, L89V). Rules incorporating these PRM were tested in >8000 non-redundant, protease-resistant samples to determine the incidence of discordance: false positive (genotype "resistant," IDV fold change <10) and false negative (genotype "sensitive," IDV fold change > 10) calls. False positives that contained mixtures of wild-type and resistance-associated mutations were classified separately and not included in the calculation of discordance rates. An algorithm which groups samples based on the number of primary mutations (1, 2, 3, or more) and requires varying numbers of secondary mutations (6, 4, or 3, respectively) achieved the best overall concordance (89%) and balance between false positive (7.5%) and negative (3.2%) calls.

Conclusions:  This approach has enabled to establishment of a set of genotype interpretation rules for accurate prediction of reduced susceptibility to IDV/RTV (800 mg/200 mg twice daily). These rules should be validated by application to additional clinical outcome data.

Keywords: Genotype Interpretation; Protease Inhibitor; Indinavir