Genotypic prediction of HIV-1 tropism has been considered a practical surrogate for phenotypic tests and recently an European Consensus has set up recommendations for its use in clinical practice. Twenty-five antiretroviral-experienced patients, all heavily treated cases with a median of 16 years of antiretroviral therapy, had viral tropism determined by the Trofile assay and predicted by HIV-1 sequencing of partial env, followed by interpretation using web-based tools. Trofile determined 17/24 (71%) as X4 tropic or dual/mixed viruses, with one nonreportable result. The use of European consensus recommendations for single sequences (geno2pheno false-positive rates 20% cutoff) would lead to 4/24 (16.7%) misclassifications, whereas a composite algorithm misclassified 1/24 (4%). The use of the geno2pheno clinical option using CD4 T cell counts at collection was useful in resolving some discrepancies. Applying the European recommendations followed by additional web-based tools for cases around the recommended cutoff would resolve most misclassifications.

Raltegravir is an integrase inhibitor (INI) licensed for clinical use and other INI are in advanced stage of development. Different resistance mutations in HIV integrase from patients using these antiretroviral drugs have been described and G148H/R/K, N155H and less frequently Y143C/H/R are considered major resistant mutations to raltegravir. Both Stanford Database and Geno2Pheno list F121Y as conferring intermediate resistance "in vitro" both to raltegravir and elvitegravir. We report for the first time the "in vivo" selection F121Y and evolution to Y143R in a 31years old male clade B HIV-1 infected patient failing a raltegravir-containing salvage regimen. Plasma samples nine months prior to raltegravir (RAL-Naïve) and at weeks 32, 40 and 88 after RAL-containing regimen were analyzed. Antiretroviral susceptibility was evaluated at Stanford and Geno2Pheno from sequences obtained with RT-PCR. After a Viral load at week 12 below 50 copies/mL, viremia raised at week 20 to 4.5log10. The emergence of F121Y was observed at week 32 and 40, alongside with L74I, T97A, Q137H and V151I. At week 88 F121Y was no longer detected, L74I and T97A were maintained and Y143R emerged. F121Y might be an alternative pathway to Y143R. Changing of RAL-containing regimen upon the identification of F121Y might avoid the evolution of raltegravir resistance.

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Background: Resistance is a major cause of virologic failure in HIV-1-infected patients; genotypic analyses optimize salvage therapy but technical constraints limit testing in plasma viral load (pVL) below 1000 copies/ml. Nevertheless a great amount of patients are failing therapy with a persistent low viral load, it is possible to obtain genotypic information at lower viremias although slight modifications are required during genotype standard procedures. Objective: To assess genotypic resistance in HIV-1-infected patients with persistent low level viremia and virologic response after switching to genotype-guided salvage therapy. To evaluate viral selection of mutation when previous genotypic information were available. Study design: Cohort prospective study in which eligible patients were at least 18 years old, provided informed consent, were on HAART for at least 12 months with two consecutive pVL between 200–999 copies/ml after achieving and maintaining viral suppression (two pVL <50 copies/ml). Modifications in genotype standard procedures included a larger volume of starting plasma, concentrating the sample by centrifugation and higher viral RNA input. Resistance was defined as the detection of any NRTI, NNRTI or PR major resistance mutations. Virologic response was assessed 12 weeks after salvage therapy. Results: Eighteen patients, 50% male, median age 52, median CD4 405 cells/mm3, median pVL 596 copies/ml, median of number of previous regimens 5, 17 (94%) with successful genotype. Resistance mutations were detected in 14 patients (77%). All patients had NRTI mutations, four patients had NNRTI mutations and ten patients had PR mutations, most common mutations were M41L, D67N, M184V, K103N, M46I, I47V, I54V and L90M. Of these fourteen patients, nine started a genotype-guided salvage regimen and presented a pVL < 50 copies/ml after 12 weeks of follow up. For two patients there was previous genotypic information highlighting the selection and accumulation of resistance mutation during persistent low level viremia. Conclusion: In this group of heavily pretreated patients with persistent low viremia, a high frequency of genotypic resistance was observed; obtaining genotypic information may prevent further accumulation of resistance mutation and preserve future therapeutic options