About: Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections

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About: Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections Goto Sponge NotDistinct Permalink

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

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections
Creator	Goodfellow, Ian Parmar, Surendra Hosmillo, Myra Baker, Stephen Dougan, Gordon »more»
source	MedRxiv
abstract	Background The burden and impact of healthcare-associated COVID-19 infections is unknown. We aimed to examine the utility of rapid sequencing of SARS-CoV-2 combined with detailed epidemiological analysis to investigate healthcare-associated COVID-19 infections and to inform infection control measures. Methods We set up rapid viral sequencing of SARS-CoV-2 from PCR-positive diagnostic samples using nanopore sequencing, enabling sample-to-sequence in less than 24 hours. We established a rapid review and reporting system with integration of genomic and epidemiological data to investigate suspected cases of healthcare-associated COVID-19. Results Between 13 March and 24 April 2020 we collected clinical data and samples from 5191 COVID-19 patients in the East of England. We sequenced 1000 samples, producing 747 complete viral genomes. We conducted combined epidemiological and genomic analysis of 299 patients at our hospital and identified 26 genomic clusters involving 114 patients. 66 cases (57.9%) had a strong epidemiological link and 15 cases (13.2%) had a plausible epidemiological link. These results were fed back clinical, infection control and hospital management teams, resulting in infection control interventions and informing patient safety reporting. Conclusions We established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and demonstrated the benefit of combined genomic and epidemiological analysis for the investigation of healthcare-associated COVID-19 infections. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection control interventions to reduce further healthcare-associated infections.
has issue date	2020-05-14(xsd:dateTime)
bibo:doi	10.1101/2020.05.08.20095687
has license	medrxiv
sha1sum (hex)	4d36064ba1c0826232da3009195d60bc87a17130
schema:url	https://doi.org/10.1101/2020.05.08.20095687
resource representing a document's title	Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections
resource representing a document's body	covid:4d36064ba1c0826232da3009195d60bc87a17130#body_text
is schema:about of	named entity 'impact' named entity 'utility' named entity 'infections' named entity 'SARS-CoV-2' named entity 'healthcare-associated' »more»

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