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VIROGENESIS

Virus discovery and epidemic tracing from high throughput metagenomic sequencing

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

VIROGENESIS project word cloud

Explore the words cloud of the VIROGENESIS project. It provides you a very rough idea of what is the project "VIROGENESIS" about.

pipelines public subjects full epidemiological virology coronavirus clear laboratories resistance developers generation length virogenesis respiratory ngs clinical tools syndrome fragments pathogenic embl run made global analysed size virus incorporated medium more software overcome sequencing academic variety origin mers daily pressing offers middle algorithms diagnostics speed piloted obstacles phylodynamics free market ncbi cov source flexibility difficult data modular sequence east millions initiated enterprises bioinformatics small platform industry health underpinned machineries sme viruses proper transmission datasets brings discoveries viral models drug identifier routine microbial repertoire lack basis handle private phylogeography gmi

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 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.	BE (LEUVEN)	coordinator	744˙257.00
2	ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAM Organization address address: DR MOLEWATERPLEIN 40 city: ROTTERDAM postcode: 3015 GD website: www.erasmusmc.nl contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	NL (ROTTERDAM)	participant	586˙010.00
3	EMWEB EMWEB Organization address address: DUIGEMHOFSTRAAT 101 city: HERENT postcode: 3020 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	BE (HERENT)	participant	405˙500.00
4	CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS Organization address address: RUE MICHEL ANGE 3 city: PARIS postcode: 75794 website: www.cnrs.fr contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	FR (PARIS)	participant	362˙500.00
5	RIJKSINSTITUUT VOOR VOLKSGEZONDHEID EN MILIEU RIJKSINSTITUUT VOOR VOLKSGEZONDHEID EN MILIEU Organization address address: Antonie Van Leeuwenhoeklaan 9 city: BILTHOVEN postcode: 3721 MA website: www.rivm.nl contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	NL (BILTHOVEN)	participant	282˙753.00
6	UNIVERSITY OF FLORIDA UNIVERSITY OF FLORIDA Organization address address: GRINTER HALL 223 city: GAINESVILLE postcode: 32611 5500 website: http://www.ufl.edu contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	US (GAINESVILLE)	participant	233˙897.00
7	THE UNIVERSITY OF MANCHESTER THE UNIVERSITY OF MANCHESTER Organization address address: OXFORD ROAD city: MANCHESTER postcode: M13 9PL website: www.manchester.ac.uk contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (MANCHESTER)	participant	231˙050.00
8	UNIVERSITY OF KWAZULU-NATAL UNIVERSITY OF KWAZULU-NATAL Organization address address: University Road, Chiltern Hills city: WESTVILLE postcode: 3630 website: www.ukzn.ac.za contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	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

List of publications.
year	authors and title	journal	last update
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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