Among the resistance genotyping tests performed in two hospitals in Paris, France during the last 6 years, either for an indication of virological failure or for an indication of initial diagnosis of HIV infection, we identified cases of virus exhibiting protease gene insertions, and retrospectively collected therapeutic, immunological

and virological data. The proportion of patients infected with HIV-1 non-B subtypes in the two hospitals was 39.9% (including Gefitinib 2.9% CRF01_AE, 22.6% CRF02_AG and 1.2% G). GRT was performed on samples available before and/or after the initial detection of a protease insertion. GRT was performed using the consensus technique developed by the Agence Nationale de Recherche sur le SIDA (ANRS) Resistance Study Group, as previously described [14]. The mutations reported in this study are given in the 2008 International AIDS Society (IAS-USA) list [15]. In order to assess the archiving of the insert-containing virus in the cellular reservoir, GRT was performed on HIV DNA obtained from peripheral blood mononuclear cell (PBMC) specimens when HIV-1 RNA plasma viral load was undetectable, at two different time-points in patient 1 and at one time-point Selleck Cabozantinib in patient 4. Phenotypic resistance

to PIs was determined using the HIV-Phenoscript® PI assay (Eurofins, Kalamazoo, MI) as previously described [16,17]. The gag-protease fragment includes cleavage sites p24/p2, p2/p7, p7/p1 and p1/p6. Furthermore, to assess the replicative capacity of different primary viruses, the region spanning the gag cleavage sites as well as the protease and part of the RT were amplified [18]. The results of the assay are expressed as the sensitivity fold change (FC) 50% inhibitory concentration (IC50) values and as the percentage of replicative capacity

compared with the control wild-type virus (NL4-3). All available PIs, except darunavir (DRV), were tested: amprenavir (APV), atazanavir (ATV), indinavir (IDV), lopinavir (LPV), nelfinavir (NFV), saquinavir (SQV) Pyruvate dehydrogenase lipoamide kinase isozyme 1 and tipranavir (TPV). Eleven patients were found to harbour plasma virus with a protease insertion, giving a frequency of 0.24% (11 of 4500 patients). Two patients were ARV-naïve, one was PI-naïve and eight were PI-experienced (Table 1). The inserts were composed of one or two amino acids which mapped between codons 33 and 39 for 10 patients and at codon 19 for one patient (Table 1). The nucleic acid composition of the inserts mainly consisted of duplications of neighbouring sequences (Table 2). At the time of detection, the insertion-containing virus had a median of 9 mutations associated with PI resistance (range 3–13). Six patients (55%) were infected with a HIV-1 non-B subtype (three with CRF02_AG, one with CRF01_AE, one with subtype A and one with subtype G) and most of the mutations were subtype-specific polymorphisms, as confirmed by the Stanford database (http://hivdb.stanford.edu/cgi-bin/MutPrevBySubtypeRx.cgi) (Table 1).