{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T05:51:35Z","timestamp":1790833895571,"version":"4.1.0"},"reference-count":53,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2020,11,20]],"date-time":"2020-11-20T00:00:00Z","timestamp":1605830400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,12,22]],"date-time":"2020-12-22T00:00:00Z","timestamp":1608595200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2020,12,22]]},"abstract":"<jats:p>\n                    SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to coinfections or the presence of other organisms that may impact SARS-CoV-2 disease progression and prognosis. Here, using direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing of NP swab specimens from 50 patients under investigation for COVID-19, we detected SARS-CoV-2 sequences by applying the CosmosID bioinformatics platform. Further, we characterized coinfections and detected a decrease in the diversity of the microbiomes in these patients. Statistically significant shifts in the microbiome were identified among COVID-19-positive and -negative patients, in the latter of whom a higher abundance of\n                    <jats:italic>Propionibacteriaceae<\/jats:italic>\n                    and a reduction in the abundance of\n                    <jats:named-content content-type=\"genus-species\">Corynebacterium accolens<\/jats:named-content>\n                    were observed. Our study also corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages of disease rather than with severity of disease. This work illustrates the utility of mNGS for the detection and analysis of SARS-CoV-2 from NP swabs without viral target enrichment or amplification and for the analysis of the respiratory microbiome.\n                  <\/jats:p>","DOI":"10.1128\/mbio.01969-20","type":"journal-article","created":{"date-parts":[[2020,11,23]],"date-time":"2020-11-23T07:52:04Z","timestamp":1606117924000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":169,"title":["Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients"],"prefix":"10.1128","volume":"11","author":[{"given":"Heba H.","family":"Mostafa","sequence":"first","affiliation":[{"name":"Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John A.","family":"Fissel","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Fanelli","sequence":"additional","affiliation":[{"name":"CosmosID, Inc., Rockville, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yehudit","family":"Bergman","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria","family":"Gniazdowski","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manoj","family":"Dadlani","sequence":"additional","affiliation":[{"name":"CosmosID, Inc., Rockville, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen C.","family":"Carroll","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rita R.","family":"Colwell","sequence":"additional","affiliation":[{"name":"CosmosID, Inc., Rockville, Maryland, USA"},{"name":"University of Maryland College Park, Institute for Advanced Computer Studies, College Park, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6134-151X","authenticated-orcid":false,"given":"Patricia J.","family":"Simner","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2020.1725399"},{"key":"e_1_3_2_3_2","article-title":"Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19","author":"Moore SC","year":"2020","unstructured":"Moore SC, Penrice-Randal R, Alruwaili M, Dong X, Pullan ST, Carter D, Bewley K, Zhao Q, Sun Y, Hartley C, Zhou E, Solomon T, Beadsworth MBJ, Cruise J, Bogaert D, Crook DWT, Matthews DA, Davidson AD, Mahmood Z, Aljabr W, Druce J, Vipond RT, Ng L, Renia L, Openshaw P, Baillie JK, Carroll MW, Semple C, Turtle L, Hiscox JA. 2020. Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19. MedRxiv 2020.03.05.20032011.","journal-title":"MedRxiv"},{"key":"e_1_3_2_4_2","doi-asserted-by":"crossref","unstructured":"Manning JE Bohl JA Lay S Chea S Ly S Sengdoeurn Y Heng S Vuthy C Kalantar K Ahyong V Tan M Sheu J Tato CM DeRisi J Baril L Dussart P Duong V Karlsson EA. 2020. Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia. BioRxiv 2020.03.02.968818.","DOI":"10.1101\/2020.03.02.968818"},{"key":"e_1_3_2_5_2","article-title":"Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses","author":"Wang M","year":"2020","unstructured":"Wang M, Fu A, Hu B, Tong Y, Liu R, Gu J, Liu J, Jiang W, Shen G, Zhao W, Men D, Yu L, Deng Z, Li Y, Liu T. 2020. Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses. 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Clinical diagnosis of 8274 samples with 2019-novel coronavirus in Wuhan. MedRxiv 2020.02.12.20022327.","journal-title":"MedRxiv"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(20)30211-7"},{"key":"e_1_3_2_15_2","article-title":"Precautions are needed for COVID-19 patients with coinfection of common respiratory pathogens","author":"Xing Q","year":"2020","unstructured":"Xing Q, Li G, Xing Y, Chen T, Li W, Ni W, Deng K, Gao R, Chen C, Gao Y, Li Q, Yu G, Tong J, Li W, Hao G, Sun Y, Zhang A, Wu Q, Ma G, Cao J, Li Z, Pan S. 5 March 2020. Precautions are needed for COVID-19 patients with coinfection of common respiratory pathogens. 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Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections. MedRxiv 2020.02.11.20021493.","journal-title":"MedRxiv"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1080\/1040841X.2018.1549019"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01725-15"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01051-12"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.200708-1151OC"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00245-10"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/9781555817381"},{"key":"e_1_3_2_36_2","first-page":"2911","volume-title":"Mandell, Douglas, and Bennett\u2019s principles and practice of infectious diseases. Part III. Infectious diseases and their etiologic agents","author":"Murphy TF","year":"2010","unstructured":"Murphy TF. 2010. Section F. 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R package version 0.4.0. https:\/\/github.com\/pmartinezarbizu\/pairwiseAdonis."}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mBio.01969-20","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mBio.01969-20","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T22:10:53Z","timestamp":1646691053000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mBio.01969-20"}},"subtitle":[],"editor":[{"given":"Sixto M.","family":"Leal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]},{"given":"Peter","family":"Gilligan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,12,22]]},"references-count":53,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2020,12,22]]}},"alternative-id":["10.1128\/mBio.01969-20"],"URL":"https:\/\/doi.org\/10.1128\/mbio.01969-20","relation":{},"ISSN":["2161-2129","2150-7511"],"issn-type":[{"value":"2161-2129","type":"print"},{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,12,22]]},"assertion":[{"value":"2020-07-14","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-10-28","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-11-20","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01969-20"}}