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

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dc.contributor.authorSantos, João Dourado
dc.contributor.authorSobral, Daniel
dc.contributor.authorPinheiro, Miguel
dc.contributor.authorIsidro, Joana
dc.contributor.authorBogaardt, Carlijn
dc.contributor.authorPinto, Miguel
dc.contributor.authorEusébio, Rodrigo
dc.contributor.authorSantos, André
dc.contributor.authorMamede, Rafael
dc.contributor.authorHorton, Daniel L.
dc.contributor.authorGomes, João Paulo
dc.contributor.authorBigarré, Laurent
dc.contributor.authorFernández-Pinero, Jovita
dc.contributor.authorPais, Ricardo J.
dc.contributor.authorMarcacci, Maurilia
dc.contributor.authorMoreno, Ana
dc.contributor.authorLilja, Tobias
dc.contributor.authorØines, Øivind
dc.contributor.authorRzeżutka, Artur
dc.contributor.authorMathijs, Elisabeth
dc.contributor.authorVan Borm, Steven
dc.contributor.authorRasmussen, Morten
dc.contributor.authorSpiess, Katja
dc.contributor.authorBorges, Vítor
dc.date.accessioned2024-05-24T14:18:34Z
dc.date.available2024-05-24T14:18:34Z
dc.date.issued2024
dc.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.pt_PT
dc.description.abstractBackground: 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).pt_PT
dc.description.sponsorshipThis 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).pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationGenome Med . 2024 Apr 25;16(1):61pt_PT
dc.identifier.doi10.1186/s13073-024-01334-3pt_PT
dc.identifier.eissn1756-994X
dc.identifier.urihttp://hdl.handle.net/10451/64874
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherSpringer Naturept_PT
dc.relation22153-01/SAICT/2016pt_PT
dc.relation773830pt_PT
dc.relation2021/PHF/23776pt_PT
dc.relationEU4H-2022-DGA-MS-IBA-1pt_PT
dc.relation101102733pt_PT
dc.relation2020.08493.BDpt_PT
dc.relation.publisherversionhttps://genomemedicine.biomedcentral.com/pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.titleINSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillancept_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.issue1pt_PT
oaire.citation.titleGenome Medicinept_PT
oaire.citation.volume16pt_PT
person.familyNameFresca Mamede
person.givenNameRafael
person.identifier8uAfOnIAAAAJ&hl
person.identifier.ciencia-id8010-DA91-FC9D
person.identifier.orcid0000-0002-8691-0771
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isAuthorOfPublication0104fdc4-a779-4414-8cec-dd110143f805
relation.isAuthorOfPublication.latestForDiscovery0104fdc4-a779-4414-8cec-dd110143f805

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