Virus discovery and epidemic tracing from high throughput metagenomic sequencing

Project Information

VIROGENESIS

Grant agreement ID: 634650

DOI 10.3030/634650

Project closed

EC signature date 27 March 2015

Start date 1 June 2015

End date 31 May 2018

Funded under

• SOCIETAL CHALLENGES - Health, demographic change and well-being

Total cost € 2 995 969,98

EU contribution € 2 995 968,74

Coordinated by

KATHOLIEKE UNIVERSITEIT LEUVEN
Belgium

Deliverables

Other (12)

GUI Epidemiological analysis tools for pilot study
Epidemiological tracing tool
GUI entire platform for pilot study

GUI entire platform for pilot study

Virome comparison tool
Report on use of HPM for NGS data analysis
Pan-viral typing tool
NGS assembly tool
Classification tool
Phylogenetic analysis method for reticulation
GUI NGS assembly tool for pilot study
GUI Virome comparison tools for pilot study
GUI Pan-viral typing tool for pilot study

Documents, reports (4)

Colloquium
Plan for the dissemination and exploitation of results
Report pilot studies
Training module NGS data analysis

Publications

Peer reviewed articles (7)

Phylogenetic analysis as a forensic tool in HIV transmission investigations

Author(s): Ana B. Abecasis, Marta Pingarilho, Anne-Mieke Vandamme
Published in: AIDS, 2018, Page(s) 1, ISSN 0269-9370
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1097/QAD.0000000000001728

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes

Author(s): Filip Bielejec, Guy Baele, Bram Vrancken, Marc A. Suchard, Andrew Rambaut, Philippe Lemey
Published in: Molecular Biology and Evolution, Issue 33/8, 2016, Page(s) 2167-2169, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msw082

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Author(s): Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno R. Faria, Daniel J. Park, Jason T. Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah L. Caddy, Matthew Cotten, Jonathan D’Ambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour, Michael J. Elmore, Lawrence S. Fakoli, Ousmane Faye, Merle L. Gilbert, Sahr M. Gevao, Stephen Gire, Adri
Published in: Nature, Issue 544/7650, 2017, Page(s) 309-315, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature22040

The multi-faceted dynamics of HIV-1 transmission in Northern Alberta: A combined analysis of virus genetic and public health data

Author(s): 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
Published in: Infection, Genetics and Evolution, Issue 52, 2017, Page(s) 100-105, ISSN 1567-1348
Publisher: Elsevier BV
DOI: 10.1016/j.meegid.2017.04.005

Challenges in the analysis of viral metagenomes

Author(s): Rebecca Rose, Bede Constantinides, Avraam Tapinos, David L Robertson, Mattia Prosperi
Published in: Virus Evolution, Issue 2/2, 2016, Page(s) vew022, ISSN 2057-1577
Publisher: Oxford Journals
DOI: 10.1093/ve/vew022

Visual programming for next-generation sequencing data analytics

Author(s): Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia Prosperi
Published in: BioData Mining, Issue 9/1, 2016, ISSN 1756-0381
Publisher: BioMed Central
DOI: 10.1186/s13040-016-0095-3

Genome Sequences of a Novel Vietnamese Bat Bunyavirus

Author(s): Bas B. Oude Munnink, My V. T. Phan, Lia van der Hoek, Paul Kellam, Matthew Cotten
Published in: Genome Announcements, Issue 4/6, 2016, Page(s) e01366-16, ISSN 2169-8287
Publisher: Genome Announcements
DOI: 10.1128/genomeA.01366-16