Project: Development of the PYROSEQ kit for the detection of minor drug-resistant HIV variants and for their clinical treatment.

Context_x000D_Human Immunodeficiency virus (HIV) exists as a viral quasispecies, (a “swarm” of genetically diverse virus strains). A proper diagnosis and treatment of HIV-infected persons requires the sensitive and accurate detection of all drug-resistant HIV strains, indeed, infection with drug-resistant HIV can lead to antiretroviral treatment (ART) failure and is associated with increased mortality. Unfortunately, not all of the viral strains that make up the “swarm” are detected by the standard resistance assays. For example, the Sanger standard sequencing method, used in clinically approved HIV genotypic resistance assays is typically restricted to the detection of known mutations that have 20% prevalence in clinical samples. However, recent data suggest that resistant viruses that make up as little as 1% of the viral population are clinically important, as resistant variants can grow rapidly under the selection pressure exerted by drugs and lead to virologic failure._x000D_Ultra-deep sequencing (UDS) has shown to provide a more sensitive method than Sanger one for identifying low-abundance drug-resistant viral variants that have an impact on clinical virologic outcomes. UDS is a massively parallel sequencing technique providing a high level of information. _x000D_However, the currently available kits based on UDS are not conceived and adapted to the diagnostic for clinical use. Indeed, such clinical diagnostic tests need to be sensitive, robust, easily- and quickly handled and cheap compared to the returned medical service. Although UDS clearly hits the target regarding the two former criteria, the two latter ones are not met._x000D_There is thus a need to develop a diagnostic tool exerting better sensitivity than the Sanger method but at a lower cost and with a more user-friendly approach compared to UDS in order to meet clinical market needs. Ideally, this test will to be used routinely by clinicians to identify, for each patient, the low-abundance drug-resistant HIV variants and the best treatment against the identified HIV resistant strains._x000D_One option will be to design a test based on the pyrosequencing method (see Annex 1), like UDS, but with a lower level of sensitivity (up to 1-2% would be sufficient). In addition, the coupling of such test with clinical information would lead to an improved analysis of the data, in turn offering a proposed therapeutic scheme to the clinician._x000D__x000D_Project goal_x000D_The strategic objective of the project will be to develop a new innovative user-friendly tool composed of:_x000D_1) a prototype of a new kit for the detection of the low abundant drug-resistant HIV viral variants, which is less expensive, more user-friendly and more reliable than the available kits based on Sanger and UDS technology. _x000D_ 2) its dedicated new software for the interpretation of the genetic data available for clinical purposes, to allow clinicians to choose the best therapy adapted to each individual patient._x000D__x000D_Consortium_x000D_The PYROSEQ project is composed of two SMEs with strong and complementary skills in the diagnostic field: ABL (L), leader in the development of algorithm-based genotype interpretation systems, will be the project coordinator; Alphabio (FR), specialist in the design of assay in drug resistance, is the reference laboratory for the development of diagnostics and therapies in the doCO of virology. Thus, PYROSEQ integrates crucial competences in the knowledge of HIV drug resistance, diagnostics & clinical studies, management of complex integrated clinico-virological databases. _x000D__x000D_Technical innovations and market applications_x000D_ALPHABIO will apply and develop the concept of pyrosequencing (see Annex 1) as the core technology for the sequencing kit. _x000D_The management and analysis of the huge amount of pyrosequencing-related data will be achieved through the development of the ABL ViroScore technology. The new DeepViroScore platform will be customized for the clinical use: it will integrate genotype interpretation, sequence database and analysis tools with a clinical web platform for the support of clinicians for the treatment of HIV infected patients._x000D_The technological development envisaged in the project will be reached through the completion of three phases: 1) Assay development 2)Platform development 3) Clinical validation._x000D_To address unmet medical needs, the PYROSEQ assay will allow the sequencing of HIV low-abundance strains and the analysis of the resistance profile of HIV patients, for the choice of the best treatment._x000D_PYROSEQ will open a new way to the genotypic testing for drug resistance that could be also applied to the study and treatment of other viral infections, such as Hepatitis._x000D_The PYROSEQ assay kit will address the in vitro diagnostic market of the genotypic tests for HIV diagnostics and treatment. The clinicians will routinely dispose of a user-friendly tool for the detection and treatment of low-abundance drug resistance HIV strains._x000D_

Acronym PYROSEQ (Reference Number: 6101)
Duration 01/03/2011 - 28/02/2014
Project Topic PYROSEQ will develop an innovative user-friendly tool composed of a kit for the detection of the low-abundance drug-resistant HIV viral variants and of its new dedicated platform for the interpretation of the genetic data, to allow clinicians to choose the best therapy adapted to each AIDS patient.
Network Eurostars
Call Eurostars Cut-Off 5

Project partner

Number Name Role Country
2 Advanced Biological Laboratories SA Group Coordinator Luxembourg
2 Alphabio laboratoire Partner France