Repository logo
 
Publication

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

2020-03Journal article Restricted access
Simple item page
dc.contributor.authorDeng, X.
dc.contributor.authorAchari, A.
dc.contributor.authorFederman, S.
dc.contributor.authorYu, G.
dc.contributor.authorSomasekar, S.
dc.contributor.authorBártolo, I.
dc.contributor.authorYagi, S.
dc.contributor.authorMbala-Kingebeni, P.
dc.contributor.authorKapetshi, J.
dc.contributor.authorAhuka-Mundeke, S.
dc.contributor.authorMuyembe-Tamfum, J. J.
dc.contributor.authorAhmed, A. A.
dc.contributor.authorGanesh, V.
dc.contributor.authorTamhankar, M.
dc.contributor.authorPatterson, J. L.
dc.contributor.authorNdembi, N.
dc.contributor.authorMbanya, D.
dc.contributor.authorKaptue, L.
dc.contributor.authorMcArthur, C.
dc.contributor.authorMuñoz-Medina, J. E.
dc.contributor.authorGonzalez-Bonilla, C. R.
dc.contributor.authorLópez, S.
dc.contributor.authorArias, C. F.
dc.contributor.authorArevalo, S.
dc.contributor.authorMiller, S.
dc.contributor.authorStone, M.
dc.contributor.authorBusch, M.
dc.contributor.authorHsieh, K.
dc.contributor.authorMessenger, S.
dc.contributor.authorWadford, D. A.
dc.contributor.authorRodgers, M.
dc.contributor.authorCloherty, G.
dc.contributor.authorFaria, N. R.
dc.contributor.authorThézé, J.
dc.contributor.authorPybus, O. G.
dc.contributor.authorNeto, Z.
dc.contributor.authorMorais, J.
dc.contributor.authorTaveira, N.
dc.contributor.authorHackett, J. Jr
dc.contributor.authorChiu, C. Y.
dc.date.accessioned2020-10-22T09:58:40Z
dc.date.available2020-10-22T09:58:40Z
dc.date.issued2020-03
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.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationDeng, X., Achari, A., Federman, S. et al. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat Microbiol 5, 443–454 (2020). https://doi.org/10.1038/s41564-019-0637-9pt_PT
dc.identifier.doi10.1038/s41564-019-0637-9pt_PT
dc.identifier.issn2058-5276
dc.identifier.urihttp://hdl.handle.net/10400.26/33745
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherSpringer Naturept_PT
dc.relation.publisherversionhttps://doi.org/10.1038/s41564-019-0637-9pt_PT
dc.subjectInfectious diseasespt_PT
dc.subjectMetagenomicspt_PT
dc.subjectInfectious-disease diagnosticspt_PT
dc.subjectMicrobial geneticspt_PT
dc.subjectVirologypt_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.startPage443pt_PT
oaire.citation.titleNature Microbiologypt_PT
oaire.citation.volume5(3)pt_PT
rcaap.embargofctPolítica de copyright do editorpt_PT
rcaap.rightsrestrictedAccesspt_PT
rcaap.typearticlept_PT

Files

Original bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
Artigo_NTaveira_2020_01.pdf
Size:
1.85 MB
Format:
Adobe Portable Document Format
Download

Collections

EM - Artigos Científicos