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VIROGENESIS

Virus discovery and epidemic tracing from high throughput metagenomic sequencing

Total Cost €

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EC-Contrib. €

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Partnership

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Project "VIROGENESIS" data sheet

The following table provides information about the project.

Coordinator
KATHOLIEKE UNIVERSITEIT LEUVEN 

Organization address
address: OUDE MARKT 13
city: LEUVEN
postcode: 3000
website: www.kuleuven.be

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Belgium [BE]
 Project website http://www.virogenesis.eu
 Total cost 2˙995˙969 €
 EC max contribution 2˙995˙968 € (100%)
 Programme 1. H2020-EU.3.1.6. (Health care provision and integrated care)
 Code Call H2020-PHC-2014-two-stage
 Funding Scheme RIA
 Starting year 2015
 Duration (year-month-day) from 2015-06-01   to  2018-05-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    KATHOLIEKE UNIVERSITEIT LEUVEN BE (LEUVEN) coordinator 744˙257.00
2    ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM NL (ROTTERDAM) participant 586˙010.00
3    EMWEB BE (HERENT) participant 405˙500.00
4    CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS FR (PARIS) participant 362˙500.00
5    RIJKSINSTITUUT VOOR VOLKSGEZONDHEID EN MILIEU NL (BILTHOVEN) participant 282˙753.00
6    UNIVERSITY OF FLORIDA US (GAINESVILLE) participant 233˙897.00
7    THE UNIVERSITY OF MANCHESTER UK (MANCHESTER) participant 231˙050.00
8    UNIVERSITY OF KWAZULU-NATAL ZA (WESTVILLE) participant 150˙000.00

Map

 Project 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.

 Deliverables

List of deliverables.
Pan-viral typing tool Other 2019-10-03 18:20:54
Phylogenetic analysis method for reticulation Other 2019-10-03 18:20:54
GUI Pan-viral typing tool for pilot study Other 2019-10-03 18:20:54
GUI Epidemiological analysis tools for pilot study Other 2019-10-03 18:20:54
Report pilot studies Documents, reports 2019-10-03 18:20:54
Classification tool Other 2019-10-03 18:20:54
Virome comparison tool Other 2019-10-03 18:20:54
NGS assembly tool Other 2019-10-03 18:20:54
GUI entire platform for pilot study Other 2019-10-03 18:20:54
Report on use of HPM for NGS data analysis Other 2019-10-03 18:20:54
Colloquium Documents, reports 2019-10-03 18:20:54
Training module NGS data analysis Documents, reports 2019-10-03 18:20:54
GUI NGS assembly tool for pilot study Other 2019-10-03 18:20:54
GUI Virome comparison tools for pilot study Other 2019-10-03 18:20:54
Epidemiological tracing tool Other 2019-10-03 18:20:54
Plan for the dissemination and exploitation of results Documents, reports 2019-10-03 18:20:54

Take a look to the deliverables list in detail:  detailed list of VIROGENESIS deliverables.

 Publications

year authors and title journal last update
List of publications.
2017 B. Vrancken, D. Adachi, M. Benedet, A. Singh, R. Read, S. Shafran, G.D. Taylor, K. Simmonds, C. Sikora, P. Lemey, C.L. Charlton, J.W. Tang
The multi-faceted dynamics of HIV-1 transmission in Northern Alberta: A combined analysis of virus genetic and public health data
published pages: 100-105, ISSN: 1567-1348, DOI: 10.1016/j.meegid.2017.04.005
Infection, Genetics and Evolution 52 2019-10-03
2016 Filip Bielejec, Guy Baele, Bram Vrancken, Marc A. Suchard, Andrew Rambaut, Philippe Lemey
SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes
published pages: 2167-2169, ISSN: 0737-4038, DOI: 10.1093/molbev/msw082
Molecular Biology and Evolution 33/8 2019-10-03
2016 Bas B. Oude Munnink, My V. T. Phan, Lia van der Hoek, Paul Kellam, Matthew Cotten
Genome Sequences of a Novel Vietnamese Bat Bunyavirus
published pages: e01366-16, ISSN: 2169-8287, DOI: 10.1128/genomeA.01366-16
Genome Announcements 4/6 2019-10-03
2016 Rebecca Rose, Bede Constantinides, Avraam Tapinos, David L Robertson, Mattia Prosperi
Challenges in the analysis of viral metagenomes
published pages: vew022, ISSN: 2057-1577, DOI: 10.1093/ve/vew022
Virus Evolution 2/2 2019-10-03
2016 Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia Prosperi
Visual programming for next-generation sequencing data analytics
published pages: , ISSN: 1756-0381, DOI: 10.1186/s13040-016-0095-3
BioData Mining 9/1 2019-10-03
2018 Ana B. Abecasis, Marta Pingarilho, Anne-Mieke Vandamme
Phylogenetic analysis as a forensic tool in HIV transmission investigations
published pages: 1, ISSN: 0269-9370, DOI: 10.1097/QAD.0000000000001728
AIDS 2019-10-03

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