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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.

Field of science

  • /medical and health sciences/health sciences/public and environmental health/epidemics prevention/modeling of disease spread
  • /medical and health sciences/health sciences/infectious disease/RNA virus/coronavirus

Call for proposal

H2020-PHC-2014-two-stage
See other projects for this call

Funding Scheme

RIA - Research and Innovation action

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)

ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM
Netherlands
EU contribution
€ 586 010
Address
Dr Molewaterplein 40
3015 GD Rotterdam
Activity type
Higher or Secondary Education Establishments
THE UNIVERSITY OF MANCHESTER
United Kingdom
EU contribution
€ 231 050
Address
Oxford Road
M13 9PL Manchester
Activity type
Higher or Secondary Education Establishments
CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France
EU contribution
€ 362 500
Address
Rue Michel Ange 3
75794 Paris
Activity type
Research Organisations
UNIVERSITY OF KWAZULU-NATAL
South Africa
EU contribution
€ 150 000
Address
University Road, Chiltern Hills
3630 Westville
Activity type
Higher or Secondary Education Establishments
RIJKSINSTITUUT VOOR VOLKSGEZONDHEID EN MILIEU
Netherlands
EU contribution
€ 282 753,75
Address
Antonie Van Leeuwenhoeklaan 9
3721 MA Bilthoven
Activity type
Research Organisations
EMWEB
Belgium
EU contribution
€ 405 500
Address
Duigemhofstraat 101
3020 Herent
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
UNIVERSITY OF FLORIDA
United States
EU contribution
€ 233 897,50
Address
Grinter Hall 223
32611 5500 Gainesville
Activity type
Higher or Secondary Education Establishments