Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19.
Open accessAbstract
COVID-19 is a complex disease phenotype where the underlying microbiome could influence morbidity and mortality. Amplicon and metagenomic MinION based sequencing was used to rapidly (within 8 hours) identify SARS-CoV-2 and assess the microbiome in nasopharyngeal swabs obtained from patients with COVID-19 by the ISARIC 4C consortium.
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The nasopharyngeal bacterial population of COVID-19 patients varied with the length of viral infection.
“Metagenomic sequencing has found that the nasopharyngeal bacterial population of COVID-19 patients varied with the length of viral infection.”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Moore et al., 2020
Fusobacterium periodonticum significantly decreased 3 days after infection in COVID-19 patients.
“For example, Fusobacterium periodonticum significantly decreased 3 days after infection (Moore et al., 2020).”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Moore et al., 2020
In patients infected by SARS-CoV-2, Fusobacterium periodonticum significantly decreased in the nasopharynx, while in the gut, the proportion of probiotics (like Bifidobacterium, Lactobacillus, and Eubacterium) was significantly reduced, and the proportion of conditioned pathogenic bacteria was significantly increased, such as Corynebacterium and Ruthenibacterium, which could lead to microbial tran
“What’s more, the imbalance of microbiota was also found in patients infected by SARS-CoV-2, Fusobacterium periodonticum significantly decreased in the nasopharynx (Moore et al., 2020),while in the gut, the proportion of probiotics (like Bifidobacterium, Lactobacillus, and Eubacterium) was significantly reduced, and the proportion of conditioned pathogenic bacteria was significantly increased, such”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Moore et al., 2020
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- Authors
- Moore, S. C., Penrice-Randal, R., Alruwaili, M., Dong, X., Pullan, S. T., Carter, D. P., Bewley, K., Zhao, Q., Sun, Y., Hartley, C., Zhou, E.-M., Solomon, T., Beadsworth, M. B. J., Cruise, J., Bogaert, D., Crook, D. W., Matthews, D. A., Davidson, A. D., Mahmood, Z., Aljabr, W., Druce, J., Vipond, R. T., Ng, L. F. P., Renia, L., Openshaw, P. J. M., Baillie, J. K., Carroll, M. W., Semple, M. G., Turtle, L., & Hiscox, J. A.
- Affiliations
- University of Liverpool (GB)
- Public Health England (GB)
- Northwest A&F University (CN)
- Liverpool University Hospitals NHS Foundation Trust (GB)
- University of Oxford (GB)
- University of Bristol (GB)
- Peter Doherty Institute (AU)
- Agency for Science, Technology and Research (SG)
- Imperial College London (GB)
- Roslin Institute (GB)
- Corresponding author
- Turtle, Lance
- Hiscox, Julian A.
- ORCID
- Moore, Shona C.
- Penrice-Randal, Rebekah
- Alruwaili, Muhannad
- Dong, Xiaofeng
- Pullan, Steven T.
- Carter, Daniel P.
- Bewley, Kevin
- Zhao, Qin
- Sun, Yani
- Hartley, Catherine
- Solomon, Tom
- Cruise, James
- Crook, Derrick W.
- Matthews, David A.
- Davidson, Andrew D.
- Mahmood, Zana
- Aljabr, Waleed
- Druce, Julian
- Vipond, Richard T.
- Ng, Lisa F. P.
- Openshaw, Peter J. M.
- Baillie, J. Kenneth
- Carroll, Miles W.
- Semple, Malcolm G.
- Turtle, Lance
- Hiscox, Julian A.
- Venue
- Viruses
- Publisher
- openRxiv
- Published
- 2020-03-08
- Volume
- 12
- Issue
- 10
- Pages
- 1164-1164
- ISSN
- 1999-4915 (ISSN-L)
- PMC
- PMC7602519
- OpenAlex
- W3092684668
- Cited by
- 121
- References
- 33
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 9 · 2023: 15 · 2022: 27 · 2021: 36 · 2020: 27
- FWCI
- 3.44
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Viruses (publishedVersion, cc-by)
- medRxiv (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- Spiral (Imperial College London) (submittedVersion, cc-by)
- Funders
- Wellcome Trust (205228/Z/16/Z)
- National Institute for Health Research Health Protection Research Unit
- National Institute for Health and Care Research (IS-HPU-1112−10117, CO-CIN-01, CL-2013-07-005, NF-SI-0514-10177, NF-SI-0513-10150)
- University of Liverpool
- Public Health England (205228/Z/16/Z)
- King Fahad Medical City (019-003)
- Hamilton Health Sciences Foundation
- U.S. Food and Drug Administration (HHSF223201510104C)
- Medical Research Council (MR/R502121/1, 1991596, MC_PC_19025, COVID-19)
- Biotechnology and Biological Sciences Research Council (BB/M02542X/1)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Keywords
- SARS-CoV-2, COVID-19 pandemic, viral genome sequencing, Oxford Nanopore MinION, interferon antagonism, viral recombination, nasopharyngeal swab, false negative detection, molecular epidemiology
- MeSH terms
- Betacoronavirus, COVID-19, SARS-CoV-2, COVID-19 Vaccines, COVID-19 Testing, DNA, Viral, Humans, Pneumonia, Viral, RNA, Viral, Genome, Viral, Sequence Analysis, Molecular Epidemiology, DNA, Complementary, Coronavirus Infections, Clinical Laboratory Techniques, Pandemics, High-Throughput Nucleotide Sequencing, Multiplex Polymerase Chain Reaction, Real-Time Polymerase Chain Reaction
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