INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance

Bibliographic Details
Main Author: Santos, João Dourado
Publication Date: 2024
Other Authors: Sobral, Daniel, Pinheiro, Miguel, Isidro, Joana, Bogaardt, Carlijn, Pinto, Miguel, Eusébio, Rodrigo, Santos, André, Mamede, Rafael, Horton, Daniel L., Gomes, João Paulo, Bigarré, Laurent, Fernández-Pinero, Jovita, Pais, Ricardo J., Marcacci, Maurilia, Moreno, Ana, Lilja, Tobias, Øines, Øivind, Rzeżutka, Artur, Mathijs, Elisabeth, Van Borm, Steven, Rasmussen, Morten, Spiess, Katja, Borges, Vítor
Format: Article
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10451/64874
Summary: © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
id RCAP_54a1d1880cca0ef4690ab9eeea70dee9
oai_identifier_str oai:repositorio.ulisboa.pt:10451/64874
network_acronym_str RCAP
network_name_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository_id_str https://opendoar.ac.uk/repository/7160
spelling INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.Background: Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification. Results: The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis. Conclusions: The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).This study was partially supported by the TELEVIR project, the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme. The improvement of the computational capacity of the online tool and its integration in INSA genomic surveillance workflows was also co-funded by the European Union through the Health Emergency Preparedness and Response (HERA) grant “Grant/2021/PHF/23776″ and the project “Sustainable use and integration of enhanced infrastructure into routine genome-based surveillance and outbreak investigation activities in Portugal” (https://www.insa.min-saude.pt/category/projectos/geneo/) on behalf of EU4H programme (EU4H-2022-DGA-MS-IBA-1). The development of the findONTime tool and a few platform updates performed in 2023 were also co-financed through the DURABLE project. The DURABLE project has been co-funded by the European Union, under the EU4Health Programme (EU4H), Project no. 101102733. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. IZSLER participation was partially funded by the Italian national Research program no. B93C22001210001: CCM-SURVEID—Studio pilota per la sorveglianza di potenziali minacce da malattie infettive emergenti (EIDs) di origine virale mediante una piattaforma diagnostica basata sul sequenziamento metagenomico di nuova generazione (mNGS). CISA-INIA-CSIC participation was partially funded by MCIN/AEI/10.13039/501100011033 and by the EU “NextGenerationEU”/PRTR” through the Spanish project no. PLEC2021-007968: Development of New Technologies to Track Emerging Infectious Threats in Wildlife and the Environment (NEXTHREAT). Rafael Mamede was supported by the Fundação para a Ciência e Tecnologia (FCT) (grant 2020.08493.BD).Springer NatureRepositório da Universidade de LisboaSantos, João DouradoSobral, DanielPinheiro, MiguelIsidro, JoanaBogaardt, CarlijnPinto, MiguelEusébio, RodrigoSantos, AndréMamede, RafaelHorton, Daniel L.Gomes, João PauloBigarré, LaurentFernández-Pinero, JovitaPais, Ricardo J.Marcacci, MauriliaMoreno, AnaLilja, TobiasØines, ØivindRzeżutka, ArturMathijs, ElisabethVan Borm, StevenRasmussen, MortenSpiess, KatjaBorges, Vítor2024-05-24T14:18:34Z20242024-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/64874engGenome Med . 2024 Apr 25;16(1):6110.1186/s13073-024-01334-31756-994Xinfo:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2025-03-17T15:15:55Zoai:repositorio.ulisboa.pt:10451/64874Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-29T03:38:39.454214Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
title INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
spellingShingle INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
Santos, João Dourado
title_short INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
title_full INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
title_fullStr INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
title_full_unstemmed INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
title_sort INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
author Santos, João Dourado
author_facet Santos, João Dourado
Sobral, Daniel
Pinheiro, Miguel
Isidro, Joana
Bogaardt, Carlijn
Pinto, Miguel
Eusébio, Rodrigo
Santos, André
Mamede, Rafael
Horton, Daniel L.
Gomes, João Paulo
Bigarré, Laurent
Fernández-Pinero, Jovita
Pais, Ricardo J.
Marcacci, Maurilia
Moreno, Ana
Lilja, Tobias
Øines, Øivind
Rzeżutka, Artur
Mathijs, Elisabeth
Van Borm, Steven
Rasmussen, Morten
Spiess, Katja
Borges, Vítor
author_role author
author2 Sobral, Daniel
Pinheiro, Miguel
Isidro, Joana
Bogaardt, Carlijn
Pinto, Miguel
Eusébio, Rodrigo
Santos, André
Mamede, Rafael
Horton, Daniel L.
Gomes, João Paulo
Bigarré, Laurent
Fernández-Pinero, Jovita
Pais, Ricardo J.
Marcacci, Maurilia
Moreno, Ana
Lilja, Tobias
Øines, Øivind
Rzeżutka, Artur
Mathijs, Elisabeth
Van Borm, Steven
Rasmussen, Morten
Spiess, Katja
Borges, Vítor
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Santos, João Dourado
Sobral, Daniel
Pinheiro, Miguel
Isidro, Joana
Bogaardt, Carlijn
Pinto, Miguel
Eusébio, Rodrigo
Santos, André
Mamede, Rafael
Horton, Daniel L.
Gomes, João Paulo
Bigarré, Laurent
Fernández-Pinero, Jovita
Pais, Ricardo J.
Marcacci, Maurilia
Moreno, Ana
Lilja, Tobias
Øines, Øivind
Rzeżutka, Artur
Mathijs, Elisabeth
Van Borm, Steven
Rasmussen, Morten
Spiess, Katja
Borges, Vítor
description © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
publishDate 2024
dc.date.none.fl_str_mv 2024-05-24T14:18:34Z
2024
2024-01-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/64874
url http://hdl.handle.net/10451/64874
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Genome Med . 2024 Apr 25;16(1):61
10.1186/s13073-024-01334-3
1756-994X
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
_version_ 1833601774433337344