Evidence map›Paper›PMID 32679081›Full record

ArticleThe Lancet. Infectious diseases2020

Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study.

Luke W Meredith, William L Hamilton, Ben Warne, Charlotte J Houldcroft, Myra Hosmillo, Aminu S Jahun, Martin D Curran, Surendra Parmar, Laura G Caller, Sarah L Caddy and 18 more

Erratum issuedOpen access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Lancet. Infectious diseases, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 259 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
259citing papers in PubMed, 1 pooled it
9.8field-weighted citation impact, top 2% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

259 citing papers in PubMed, 1 synthesis or guideline pooled it, 430 citations in OpenAlex.

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  6. Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027
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199 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

28 authors at 4 institutions in 1 country.

Luke W MeredithDepartment of Pathology, University of Cambridge, Cambridge, UK.
William L HamiltonDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK.
Ben WarneDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK.
Charlotte J HouldcroftDepartment of Medicine, University of Cambridge, Cambridge, UK.
Myra HosmilloDepartment of Pathology, University of Cambridge, Cambridge, UK.
Aminu S JahunDepartment of Pathology, University of Cambridge, Cambridge, UK.
Martin D CurranPublic Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK.
Surendra ParmarPublic Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK.
Laura G CallerDepartment of Pathology, University of Cambridge, Cambridge, UK; Francis Crick Institute, London, UK.
Sarah L CaddyDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK.
Fahad A KhokharDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK.
Anna YakovlevaDepartment of Pathology, University of Cambridge, Cambridge, UK.
Grant HallDepartment of Pathology, University of Cambridge, Cambridge, UK.
Theresa FeltwellDepartment of Medicine, University of Cambridge, Cambridge, UK.
Sally ForrestDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK.
Sushmita SridharDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK; Wellcome Sanger Institute, Hinxton, UK.
Michael P WeekesDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK.
Stephen BakerDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK.
Nicholas BrownPublic Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK.
Elinor MooreCambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK.
Ashley PopayField Epidemiology, Field Service, National Infection Service, Public Health England, Cambridge, UK.
Iain RoddickField Epidemiology, Field Service, National Infection Service, Public Health England, Cambridge, UK.
Mark ReacherField Epidemiology, Field Service, National Infection Service, Public Health England, Cambridge, UK.
Theodore GouliourisCambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK; Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, UK.
Sharon J PeacockDepartment of Medicine, University of Cambridge, Cambridge, UK; National Infection Service, Public Health England, London, UK.
Gordon DouganDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge, UK.
M Estée TörökDepartment of Medicine, University of Cambridge, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK. Electronic address: et317@cam.ac.uk.
Ian GoodfellowDepartment of Pathology, University of Cambridge, Cambridge, UK. Electronic address: ig299@cam.ac.uk.
University of Cambridge · GBPublic Health England · GBNational Health Service · GBThe Francis Crick Institute · GB

Funding

Medical Research Council MC_PC_19027Medical Research Council MR/N029399/1Wellcome Trust 204870/Z/16/ZWellcome Trust 207498/Z/17/Z
6 · The paper itself

Abstract

backgroundThe burden and influence of health-care associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unknown. We aimed to examine the use of rapid SARS-CoV-2 sequencing combined with detailed epidemiological analysis to investigate health-care associated SARS-CoV-2 infections and inform infection control measures.

methodsIn this prospective surveillance study, we set up rapid SARS-CoV-2 nanopore sequencing from PCR-positive diagnostic samples collected from our hospital (Cambridge, UK) and a random selection from hospitals in the East of England, enabling sample-to-sequence in less than 24 h. We established a weekly review and reporting system with integration of genomic and epidemiological data to investigate suspected health-care associated COVID-19 cases.

findingsBetween March 13 and April 24, 2020, we collected clinical data and samples from 5613 patients with COVID-19 from across the East of England. We sequenced 1000 samples producing 747 high-quality genomes. We combined epidemiological and genomic analysis of the 299 patients from our hospital and identified 35 clusters of identical viruses involving 159 patients. 92 (58%) of 159 patients had strong epidemiological links and 32 (20%) patients had plausible epidemiological links. These results were fed back to clinical, infection control, and hospital management teams, leading to infection-control interventions and informing patient safety reporting.

interpretationWe established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and showed the benefit of combined genomic and epidemiological analysis for the investigation of health-care associated COVID-19. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection-control interventions to further reduce health-care associated infections. Our findings have important implications for national public health policy as they enable rapid tracking and investigation of infections in hospital and community settings.

fundingCOVID-19 Genomics UK funded by the Department of Health and Social Care, UK Research and Innovation, and the Wellcome Sanger Institute.

Indexed as

AdolescentAdultAgedAged, 80 and overBetacoronavirusChildChild, PreschoolCoronavirus InfectionsCOVID-19Cross InfectionEnglandFemaleGenome, ViralHospitals, UniversityHumansInfant

Identifiers

PMID32679081
PMCPMC7806511
OpenAlexW3043177992

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.