About: Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19

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About: Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19 Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19
Creator	Zhang, Fen Chan, Francis Liu, Qin Ng, Siew Chan, Paul Tso, Eugene Chen, Zigui Lui, Chung-Yan Shi Boon, Siaw Yeoh, Yun Zuo, Tao
Source	Medline; PMC
abstract	OBJECTIVE: Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was detected in faeces of patients with COVID-19, the activity and infectivity of the virus in the GI tract during disease course is largely unknown. We investigated temporal transcriptional activity of SARS-CoV-2 and its association with longitudinal faecal microbiome alterations in patients with COVID-19. DESIGN: We performed RNA shotgun metagenomics sequencing on serial faecal viral extractions from 15 hospitalised patients with COVID-19. Sequencing coverage of the SARS-CoV-2 genome was quantified. We assessed faecal microbiome composition and microbiome functionality in association with signatures of faecal SARS-CoV-2 infectivity. RESULTS: Seven (46.7%) of 15 patients with COVID-19 had stool positivity for SARS-CoV-2 by viral RNA metagenomic sequencing. Even in the absence of GI manifestations, all seven patients showed strikingly higher coverage (p=0.0261) and density (p=0.0094) of the 3’ vs 5’ end of SARS-CoV-2 genome in their faecal viral metagenome profile. Faecal viral metagenome of three patients continued to display active viral infection signature (higher 3’ vs 5’ end coverage) up to 6 days after clearance of SARS-CoV-2 from respiratory samples. Faecal samples with signature of high SARS-CoV-2 infectivity had higher abundances of bacterial species Collinsella aerofaciens, Collinsella tanakaei, Streptococcus infantis, Morganella morganii, and higher functional capacity for nucleotide de novo biosynthesis, amino acid biosynthesis and glycolysis, whereas faecal samples with signature of low-to-none SARS-CoV-2 infectivity had higher abundances of short-chain fatty acid producing bacteria, Parabacteroides merdae, Bacteroides stercoris, Alistipes onderdonkii and Lachnospiraceae bacterium 1_1_57FAA. CONCLUSION: This pilot study provides evidence for active and prolonged ‘quiescent’ GI infection even in the absence of GI manifestations and after recovery from respiratory infection of SARS-CoV-2. Gut microbiota of patients with active SARS-CoV-2 GI infection was characterised by enrichment of opportunistic pathogens, loss of salutary bacteria and increased functional capacity for nucleotide and amino acid biosynthesis and carbohydrate metabolism.
has issue date	2020-07-19(xsd:dateTime)
bibo:doi	10.1136/gutjnl-2020-322294
bibo:pmid	32690600
has license	cc-by-nc
sha1sum (hex)	a947b34459ff14daeedfc3e3ab29a02824282508
schema:url	https://doi.org/10.1136/gutjnl-2020-322294
resource representing a document's title	Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19
has PubMed Central identifier	PMC7385744
has PubMed identifier	32690600
schema:publication	Gut
resource representing a document's body	covid:a947b34459ff14daeedfc3e3ab29a02824282508#body_text
is schema:about of	named entity 'faecal' named entity 'COVID' named entity 'gut microbiota' named entity 'SARS-CoV-2' named entity 'metagenomics' named entity 'viral RNA' named entity 'infection' named entity 'faeces' named entity '5' end' named entity '8-OHdG' named entity 'clinical practice' named entity 'Library Preparation' named entity 'intestine' named entity 'metagenomics' named entity 'viruses' named entity 'Bacteroides' named entity 'research results' named entity 'hypoxia' named entity 'indole' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity '5' end' named entity 'FDR' named entity 'faecal samples' named entity 'infection' named entity 'infectivity' named entity 'SARS-CoV-2' named entity 'Enterococcus avium' named entity 'metagenome' named entity 'SARS-CoV-2' named entity 'COVID' named entity 'faeces' named entity 'host cells' named entity 'electronic medical records' named entity 'infectivity' named entity 'COVID' named entity 'quality score' named entity 'DNA extraction' named entity 'cytokine' named entity 'infectivity' named entity 'transcriptional activity' named entity 'genome' named entity 'genome' named entity 'viral infection' named entity 'infection' named entity 'meta-analysis' named entity 'host immunity' named entity 'faecal pellet' named entity 'COVID-19' named entity 'COVID' named entity '4 April 2020' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity 'genome' named entity 'infectivity' named entity 'genome' named entity 'Nextera' named entity 'glycolysis' named entity 'biosynthesis' named entity 'SARS-CoV-2' named entity 'infectivity' named entity 'metagenome' named entity 'viral RNA' named entity 'transcriptomics' named entity 'infection' named entity 'viral RNA' named entity 'microbial' named entity 'A. onderdonkii' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2'

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