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DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing

2020Journal article Open access
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dc.contributor.authorMendes, Catarina Inês
dc.contributor.authorLizarazo, Erley
dc.contributor.authorMachado, Miguel P.
dc.contributor.authorSilva, Diogo N.
dc.contributor.authorTami, Adriana
dc.contributor.authorRamirez, Mário
dc.contributor.authorCouto, Natacha
dc.contributor.authorRossen, John W. A.
dc.contributor.authorCarrico, Joao Andre
dc.date.accessioned2021-10-15T13:31:43Z
dc.date.available2021-10-15T13:31:43Z
dc.date.issued2020
dc.description© 2020 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License.pt_PT
dc.description.abstractDengue virus (DENV) represents a public health threat and economic burden in affected countries. The availability of genomic data is key to understanding viral evolution and dynamics, supporting improved control strategies. Currently, the use of high-throughput sequencing (HTS) technologies, which can be applied both directly to patient samples (shotgun metagenomics) and to PCR-amplified viral sequences (amplicon sequencing), is potentially the most informative approach to monitor viral dissemination and genetic diversity by providing, in a single methodological step, identification and characterization of the whole viral genome at the nucleotide level. Despite many advantages, these technologies require bioinformatics expertise and appropriate infrastructure for the analysis and interpretation of the resulting data. In addition, the many software solutions available can hamper the reproducibility and comparison of results. Here we present DEN-IM, a one-stop, user-friendly, containerized and reproducible workflow for the analysis of DENV short-read sequencing data from both amplicon and shotgun metagenomics approaches. It is able to infer the DENV coding sequence (CDS), identify the serotype and genotype, and generate a phylogenetic tree. It can easily be run on any UNIX-like system, from local machines to high-performance computing clusters, performing a comprehensive analysis without the requirement for extensive bioinformatics expertise. Using DEN-IM, we successfully analysed two types of DENV datasets. The first comprised 25 shotgun metagenomic sequencing samples from patients with variable serotypes and genotypes, including an in vitro spiked sample containing the four known serotypes. The second consisted of 106 paired-end and 76 single-end amplicon sequences of DENV 3 genotype III and DENV 1 genotype I, respectively, where DEN-IM allowed detection of the intra-genotype diversity. The DEN-IM workflow, parameters and execution configuration files, and documentation are freely available at https://github.com/B-UMMI/DEN-IM).pt_PT
dc.description.sponsorshipC. I. M. was supported by the Fundação para a Ciência e Tecnologia (grant SFRH/BD/129483/2017). E. L. received a Abel Tasman Talent Program grant from the UMCG, University of Groningen, Groningen, The Netherlands. This work was partly supported by the ONEIDA project (LISBOA-01–0145-FEDER-016417) co-funded by FEEI–Fundos Europeus Estruturais e de Investimento from Programa Operacional Regional Lisboa 2020 and by national funds from FCT–Fundação para a Ciência e a Tecnologia and by UID/BIM/50005/2019, project funded by Fundação para a Ciência e a Tecnologia (FCT)/ Ministério da Ciência, Tecnologia e Ensino Superior (MCTES) through Fundos do Orçamento de Estado.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationMicrob Genom. 2020 Mar;6(3):e000328pt_PT
dc.identifier.doi10.1099/mgen.0.000328pt_PT
dc.identifier.eissn2057-5858
dc.identifier.urihttp://hdl.handle.net/10451/49903
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherMicrobiology Societypt_PT
dc.relationLISBOA-01–0145-FEDER-016417pt_PT
dc.relationTRACI: Towards Accreditation in Metagenomics for Clinical Microbiology
dc.relationInstituto de Medicina Molecular
dc.relation.publisherversionhttps://www.microbiologyresearch.org/content/journal/mgenpt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectContainerizationpt_PT
dc.subjectDengue viruspt_PT
dc.subjectMetagenomicspt_PT
dc.subjectReproducibilitypt_PT
dc.subjectScalabilitypt_PT
dc.subjectSurveillancept_PT
dc.subjectWorkflowpt_PT
dc.titleDEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencingpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleTRACI: Towards Accreditation in Metagenomics for Clinical Microbiology
oaire.awardTitleInstituto de Medicina Molecular
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/OE/SFRH%2FBD%2F129483%2F2017/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID%2FBIM%2F50005%2F2019/PT
oaire.citation.issue3pt_PT
oaire.citation.titleMicrobial Genomicspt_PT
oaire.citation.volume6pt_PT
oaire.fundingStreamOE
oaire.fundingStream6817 - DCRRNI ID
person.familyNameMendes
person.familyNameMachado
person.familyNameSilva
person.familyNameRamos de Almeida Ramirez
person.familyNameCarrico
person.givenNameInês
person.givenNameMiguel
person.givenNameDiogo
person.givenNameMário Nuno
person.givenNameJoao
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project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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