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dc.contributor.authorvan Rijn, Anneloes L.en_US
dc.contributor.authorvan Boheemen, Sanderen_US
dc.contributor.authorSidorov, Igoren_US
dc.contributor.authorCarbo, Ellen C.en_US
dc.contributor.authorPappas, Nikosen_US
dc.contributor.authorMei, Hailiangen_US
dc.contributor.authorFeltkamp, Marieten_US
dc.contributor.authorAanerud, Marianneen_US
dc.contributor.authorBakke, Per S.en_US
dc.contributor.authorClaas, Eric C.J.en_US
dc.contributor.authorEagan, Tomas Mikalen_US
dc.contributor.authorHiemstra, Pieter S.en_US
dc.contributor.authorKroes, Aloys C.M.en_US
dc.contributor.authorde Vries, Jutte J.C.en_US
dc.Publishedvan Rijn, van Boheemen, Sidorov, Carbo, Pappas, Mei, Feltkamp, Aanerud M, Bakke PS, Claas EC, Eagan TML, Hiemstra PS, Kroes, de Vries. The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. PLOS ONE. 2019;14(10):e0223952eng
dc.description.abstractIntroduction: Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), and respiratory bacterial and viral infections are an important trigger. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis of the complete virome, but has not yet been applied in COPD exacerbations. Objectives: To study the respiratory virome in nasopharyngeal samples during COPD exacerbations using mNGS. Study design: 88 nasopharyngeal swabs from 63 patients from the Bergen COPD Exacerbation Study (2006–2010) were analysed by mNGS and in-house qPCR for respiratory viruses. Both DNA and RNA were sequenced simultaneously using an Illumina library preparation protocol with in-house adaptations. Results: By mNGS, 24/88 samples tested positive. Sensitivity and specificity, as compared with PCR, were 96% and 98% for diagnostic targets (23/24 and 1093/1120, respectively). Additional viral pathogens detected by mNGS were herpes simplex virus type 1 and coronavirus OC43. A positive correlation was found between Cq value and mNGS viral normalized species reads (log value) (p = 0.002). Patients with viral pathogens had lower percentages of bacteriophages (p<0.001). No correlation was found between viral reads and clinical markers. Conclusions: The mNGS protocol used was highly sensitive and specific for semi-quantitative detection of respiratory viruses. Excellent negative predictive value implicates the power of mNGS to exclude any pathogenic respiratory viral infectious cause in one test, with consequences for clinical decision making. Reduced abundance of bacteriophages in COPD patients with viral pathogens implicates skewing of the virome during infection, with potential consequences for the bacterial populations, during infection.en_US
dc.publisherPublic Library of Science (PLOS)eng
dc.rightsAttribution CC BYeng
dc.titleThe respiratory virome and exacerbations in patients with chronic obstructive pulmonary diseaseen_US
dc.typePeer reviewed
dc.typeJournal article
dc.rights.holderCopyright 2019 The Author(s)
dc.source.journalPLoS ONE

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