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Virus discovery and epidemic tracing from high throughput metagenomic sequencing

Virus discovery and epidemic tracing from high throughput metagenomic sequencing

Objective

NGS analysis pipelines are rapidly becoming part of the routine repertoire of research, clinical and public health laboratories in the public sector and private industry. Middle East Respiratory Syndrome-coronavirus (MERS-CoV) is only one example of the many recent virus discoveries made through analysis of next-generation sequencing (NGS) data. Yet, only a small part of the several millions of short-length sequence fragments generated by NGS machineries, many of which are expected to be of viral origin, can be analysed with current methods in bioinformatics. Even for well-known (pathogenic) viruses, proper epidemiological analyses are becoming more and more difficult due to the lack of bioinformatics tools that can handle the large and growing size of datasets. The VIROGENESIS consortium will overcome the most pressing bioinformatics obstacles to making full use of NGS by developing a software platform for end-users with tools underpinned by novel algorithms, models and bioinformatics methods. The speed and flexibility of the tools will make it possible to run analyses on a daily basis for a variety of subjects, including diagnostics, phylogeography, phylodynamics and transmission of drug resistance. The tools will be piloted and incorporated in the many available bioinformatics pipelines and software programmes used in the field. We will make our tools available in a modular, free and open source software platform that offers opportunities to SME’s to further exploit this market. The VIROGENESIS consortium brings together leading European academic and private small and medium enterprises (SME) bioinformatics developers and virology end-users who initiated this project in response to a clear interest from EMBL, NCBI and the Global Microbial Identifier (GMI) platform.
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Coordinator

KATHOLIEKE UNIVERSITEIT LEUVEN

Address

Oude Markt 13
3000 Leuven

Belgium

Activity type

Higher or Secondary Education Establishments

EU Contribution

€ 744 257,49

Participants (7)

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ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM

Netherlands

EU Contribution

€ 586 010

THE UNIVERSITY OF MANCHESTER

United Kingdom

EU Contribution

€ 231 050

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS

France

EU Contribution

€ 362 500

UNIVERSITY OF KWAZULU-NATAL

South Africa

EU Contribution

€ 150 000

RIJKSINSTITUUT VOOR VOLKSGEZONDHEID EN MILIEU

Netherlands

EU Contribution

€ 282 753,75

EMWEB

Belgium

EU Contribution

€ 405 500

University of Florida

United States

EU Contribution

€ 233 897,50

Project information

Grant agreement ID: 634650

Status

Closed project

  • Start date

    1 June 2015

  • End date

    31 May 2018

Funded under:

H2020-EU.3.1.6.

  • Overall budget:

    € 2 995 969,98

  • EU contribution

    € 2 995 968,74

Coordinated by:

KATHOLIEKE UNIVERSITEIT LEUVEN

Belgium