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

2024-04-25Research article Open access
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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.authorTELEVIR Consortium
dc.contributor.authorBorges, Vítor
dc.date.accessioned2025-03-21T16:34:30Z
dc.date.available2025-03-21T16:34:30Z
dc.date.issued2024-04-25
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).eng
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. 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).
dc.identifier.citationGenome Med. 2024 Apr 25;16(1):61. doi: 10.1186/s13073-024-01334-3
dc.identifier.issn1756-994X
dc.identifier.pmid38659008
dc.identifier.urihttp://hdl.handle.net/10400.18/10454
dc.language.isoeng
dc.peerreviewedyes
dc.publisherBioMed Central
dc.relationPromoting One Health in Europe through joint actions on foodborne zoonoses, antimicrobial resistance and emerging microbiological hazards.
dc.relationPUBLIC HEALTH EMERGENCY PREPAREDNESS AND RESPONSE
dc.relationInter-laboratory reproducibility and expansion of the gene-by-gene typing approach in an era of whole genome sequencing
dc.relation2020.08493.BD
dc.relation.hasversionhttps://genomemedicine.biomedcentral.com/articles/10.1186/s13073-024-01334-3
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.titleINSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance
dc.typeresearch article
dspace.entity.typePublication
oaire.awardTitlePromoting One Health in Europe through joint actions on foodborne zoonoses, antimicrobial resistance and emerging microbiological hazards.
oaire.awardTitlePUBLIC HEALTH EMERGENCY PREPAREDNESS AND RESPONSE
oaire.awardTitleInter-laboratory reproducibility and expansion of the gene-by-gene typing approach in an era of whole genome sequencing
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/773830/EU
oaire.awardURIhttp://hdl.handle.net/10400.18/10440
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//2020.08493.BD/PT
oaire.citation.issue1
oaire.citation.startPage61
oaire.citation.titleGenome Medicine
oaire.citation.volume16
oaire.fundingStreamH2020
oaire.fundingStreamCOORDINATING OFFICE FOR TERRORISM PREPAREDNESS AND EMERGENCY RESPONSE
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameEuropean Commission
project.funder.nameFundação para a Ciência e a Tecnologia
relation.isProjectOfPublication94d118fb-33ce-49fa-b1ed-d5bddf63581d
relation.isProjectOfPublication1506d1ea-8d7e-4336-ba0a-aa86e88c5732
relation.isProjectOfPublicationacc6c86f-0d49-4c95-9cb2-ae39a8a70c64
relation.isProjectOfPublication.latestForDiscovery94d118fb-33ce-49fa-b1ed-d5bddf63581d

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