D- JRP16-ET2.2-TELEVIR-WP2 - Open-sourced Bioinformatics platform that allows the user-friendly handling of high-throughput sequencing data (second and third generation) for detection and monitoring of viral emerging threats
Creators: name: Dourado Santos, João
name: Sobral, Daniel
name: Pinheiro, Miguel
name: Isidro, Joana
name: Pinto, Miguel
name: Pais, Ricardo
name: Eusébio, Rodrigo
name: Bogaardt, Carlijn
name: Cordoni, Guido
name: M. Padra, Joaquin
name: Gomes, João Paulo
name: L. Horton, Daniel
name: Borges, Vítor
Publisher: name: Zenodo
Year: 2022
Subjects: Metagenomic virus detection
Routine genomic surveillance
Bioinformatics platform
OneHealth
Viral threats

description: ___________________________ <strong>D- JRP16-ET2.2-TELEVIR-WP2 - Open-sourced Bioinformatics platform that allows the user-friendly handling of high-throughput sequencing data (second and third generation) for detection and monitoring of viral emerging threats</strong> <strong>WP Leader: </strong>Vítor Borges (INSA) <strong>WP2 main participants: </strong>INSA (João Santos, Daniel Sobral, Miguel Pinheiro, Joana Isidro, Miguel Pinto, Ricardo J. Pais, Rodrigo Eusébio, João Paulo Gomes, Vítor Borges), UoS (Carlijn Bogaardt, Guido Cordoni, Joaquin Prada, Daniel L. Horton) <strong>WP2 contributors: All partners provided data for platform testing</strong>, namely Laurent Bigarré (ANSES), Artur Rzezutka (PIWET), Jovita Fernández-Pinero (INIA), Ana Moreno (IZSLER), Maurilia Marcacci (IZSAM), Elisabeth Mathijs (Sciensano), Tobias Lilja (SVA), Øivind Øines (NVI), Anna Fomsgaard (SSI), Morten Rasmussen (SSI), Anders Fomsgaard (SSI) and Katja Spiess (SSI) ___________________________ On behalf of the One Health European Joint Programme (OHEJP) TELEVIR (https://onehealthejp.eu/jrp-tele-vir/) project, and also as a response to COVID-19 pandemic and, later on, on multi-country Monkeypox (MPXV) outbreak, <strong>the existing INSaFLU </strong>(https://insaflu.insa.pt/)<strong> platform has been improved and adapted to better accommodate the routine genome-based analyses of the novel coronavirus (SARS-CoV-2), influenza, MPXV and other viruses</strong>. In parallel, targeting one of main TELEVIR goals of developing a point-of-incidence (poi) toolbox for identification and characterisation of emerging virus threats for humans and/or domestic and wildlife animals, a brand <strong>new module (TELEVIR) for metagenomics (second- and third-generation sequencing) virus identification was developed. </strong>The achieved INSaFLU-TELEVIR versatility and functionality is expected to supply public health laboratories and researchers with <strong>user-oriented “start-to-end” bioinformatics framework</strong> <strong>that can potentiate a strengthened and timely metagenomics virus detection and routine genomics surveillance. </strong> This <strong>deliverable</strong> describes the main outcomes of TELEVIR Workpackage 2 (WP2), detailing the main activities behind the: <strong>1. </strong><strong>Upgrade the existing “surveillance-oriented” bioinformatics component</strong> <strong><em>2. </em></strong><strong>Development and implementation of a novel metagenomics virus identification module </strong> INSaFLU-TELEVIR is a free web-based, and locally installable, platform available at https://insaflu.insa.pt.