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Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

2020-03Journal article Open access
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dc.contributor.authorDeng, Xianding
dc.contributor.authorAchari, Asmeeta
dc.contributor.authorFederman, Scot
dc.contributor.authorYu, Guixia
dc.contributor.authorSomasekar, Sneha
dc.contributor.authorBártolo, Inês
dc.contributor.authorYagi, Shigeo
dc.contributor.authorMbala-Kingebeni, Placide
dc.contributor.authorKapetshi, Jimmy
dc.contributor.authorAhuka-Mundeke, Steve
dc.contributor.authorMuyembe-Tamfum, Jean-Jacques
dc.contributor.authorAhmed, Asim A.
dc.contributor.authorGanesh, Vijay
dc.contributor.authorTamhankar, Manasi
dc.contributor.authorPatterson, Jean L.
dc.contributor.authorNdembi, Nicaise
dc.contributor.authorMbanya, Dora
dc.contributor.authorKaptue, Lazare
dc.contributor.authorMcArthur, Carole
dc.contributor.authorMuñoz Medina, José Esteban
dc.contributor.authorGonzalez Bonilla, Cesar
dc.contributor.authorLopez, Susana
dc.contributor.authorArias, Carlos F.
dc.contributor.authorArevalo, Shaun
dc.contributor.authorMiller, Steve
dc.contributor.authorStone, Mars
dc.contributor.authorBusch, Michael
dc.contributor.authorHsieh, Kristina
dc.contributor.authorMessenger, Sharon
dc.contributor.authorWadford, Debra A.
dc.contributor.authorRodgers, Mary
dc.contributor.authorCloherty, Gavin
dc.contributor.authorFaria, Nuno Rodrigues
dc.contributor.authorThézé, Julien
dc.contributor.authorPybus, Oliver G.
dc.contributor.authorNeto, Zoraima
dc.contributor.authorMorais, Joana
dc.contributor.authorTaveira, Nuno
dc.contributor.authorHackett Jr., John R.
dc.contributor.authorChiu, Charles
dc.date.accessioned2023-08-23T10:58:49Z
dc.date.available2023-08-23T10:58:49Z
dc.date.issued2020-03
dc.date.updated2023-02-03T12:42:52Z
dc.description.abstractMetagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use.pt_PT
dc.description.sponsorshipWe [the authors] thank N. Loman and J. Quick at the University of Birmingham for providing ZIKV tiling multiplex PCR primers. The following viral RNA extracts were obtained through Biodefense and Emerging Infections Resources, the National Institute of Allergy and Infectious Diseases (NIAID) and the National Institutes of Health (NIH): CCHFV, IbAr10200, NR-37382; LASV, Josiah, NR-31821; Rift Valley Fever Virus, ZH501, NR-37379; MeV, Edmonston strain, NR-44104. This work was also funded in part by Abbott Laboratories (C.Y.C.), NIH grant no. R33-AI129455 (C.Y.C.) from the NIAID, NIH grant no. R01-HL105704 (C.Y.C.) from the National Heart, Lung, and Blood Institute, the California Initiative to Advance Precision Medicine (C.Y.C.), the Charles and Helen Schwab Foundation (C.Y.C.), the Steven and Alexandra Cohen Foundation (C.Y.C.), United States Department of Defense award W81XWH-17-1-0681 (C.Y.C.), the Wellcome Trust and Royal Society/Sir Henry Dale Fellowship grant no. 204311/Z/16/Z (N.R.F.), the Global Challenges Research Fund grant no. 005073 (N.R.F.), the Oxford John Fell Research Fund grant no. 005166 (N.R.F.) and Africa Oxford grant no. AfiOx-48 (N.R.F.).pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationDeng X, Achari A, Federman S, Yu G, Somasekar S, Bártolo I, et al. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat Microbiol [Internet]. março de 2020;5(3):443–54. Disponível em: https://www.nature.com/articles/s41564-019-0637-9pt_PT
dc.identifier.doi10.1038/s41564-019-0637-9pt_PT
dc.identifier.eid2-s2.0-85077844387
dc.identifier.slugcv-prod-1108446
dc.identifier.urihttp://hdl.handle.net/10451/58967
dc.identifier.urihttp://hdl.handle.net/10451/58969
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherSpringer Naturept_PT
dc.relation.publisherversionhttps://www.nature.com/articles/s41564-019-0637-9pt_PT
dc.titleMetagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillancept_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage454pt_PT
oaire.citation.issue3
oaire.citation.startPage443pt_PT
oaire.citation.titleNature Microbiologypt_PT
oaire.citation.volume5pt_PT
person.familyNameBártolo
person.familyNameMuñoz Medina
person.familyNameGonzalez Bonilla
person.familyNameLopez
person.familyNameArias
person.familyNameFaria
person.familyNameTaveira
person.familyNameChiu
person.givenNameInês
person.givenNameJosé Esteban
person.givenNameCesar
person.givenNameSusana
person.givenNameCarlos F.
person.givenNameNuno Rodrigues
person.givenNameNuno
person.givenNameCharles
person.identifier84744
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person.identifier.orcid0000-0003-3130-4501
person.identifier.orcid0000-0001-8839-2798
person.identifier.orcid0000-0003-0176-5585
person.identifier.orcid0000-0003-2915-2094
person.identifier.ridB-6186-2015
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person.identifier.scopus-author-id56565491200
person.identifier.scopus-author-id6602999984
person.identifier.scopus-author-id57192677066
person.identifier.scopus-author-id36764482900
person.identifier.scopus-author-id7402302280
rcaap.cv.cienciaid661E-F5CB-F85A | Inês Bártolo
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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