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

The Lancet Infectious Diseases
Luke W MeredithIan Goodfellow

Abstract

The 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. In 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. Between 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 epi...Continue Reading

References

Jun 15, 2012·The New England Journal of Medicine·Claudio U KöserSharon J Peacock
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Feb 4, 2016·Nature·Joshua QuickMiles W Carroll
Jan 17, 2017·Nature Reviews. Microbiology·Charlotte J HouldcroftJudith Breuer
Nov 14, 2017·Nature Reviews. Genetics·Jennifer L Gardy, Nicholas J Loman
Feb 21, 2018·Emerging Infectious Diseases·Derek R MacFaddenWilliam P Hanage
Dec 14, 2018·Nature Microbiology·Nathan D GrubaughKristian G Andersen
Feb 8, 2020·JAMA : the Journal of the American Medical Association·Dawei WangZhiyong Peng
Apr 15, 2020·Nature Medicine·Kristian G AndersenRobert F Garry

❮ Previous
Next ❯

Citations

Jun 21, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Hannah M RickmanCatherine F Houlihan
Jul 11, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Scott R Curry, Cassandra D Salgado
Sep 15, 2020·Occupational Medicine·Raymond Agius
Oct 17, 2020·Nature Communications·Roberto RaschettiDaniele De Luca
Oct 30, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Helene A C M VoetenEwout Fanoy
Dec 7, 2020·Briefings in Bioinformatics·Matteo ChiaraGraziano Pesole
Jul 8, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·James Richard PriceAlison H Holmes
Dec 2, 2020·Environmental Microbiology Reports·Kalia Bistolas, Rebecca Vega Thurber
Dec 11, 2020·Nature Communications·Rowena A BullIra W Deveson
Oct 19, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Craig S Conover
Jul 18, 2020·The Lancet Infectious Diseases·Ole Behrmann, Martin Spiegel
Nov 18, 2020·Open Forum Infectious Diseases·Sofia BanuDivya Tej Sowpati
Jan 8, 2021·Antimicrobial Resistance and Infection Control·Mohamed AbbasStephan Harbarth
Jan 30, 2021·Microbiology Resource Announcements·Manuele BiazzoDavid Pinzauti
Feb 16, 2021·The Lancet Infectious Diseases·Seth C InzauleJohn N Nkengasong
Jan 26, 2021·Curēus·Stephen J BordesSamer Ebaid
Feb 16, 2021·Journal of Biomolecular Structure & Dynamics·Francesco OrtusoFederico Manuel Giorgi
Feb 6, 2021·Nature·Steven A KempRavindra K Gupta
Feb 20, 2021·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Michael J WilsonHamid Jalal
Mar 2, 2021·The Journal of Hospital Infection·A H LøvestadH V Aamot
Mar 3, 2021·ELife·William L HamiltonUNKNOWN COVID-19 Genomics Consortium UK
Mar 12, 2021·Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association·Ben StoreyKatherine Bull
Mar 18, 2021·ELife·Jamie M EllingfordGraeme Cm Black
Apr 6, 2021·Computational and Structural Biotechnology Journal·Laura CiuffredaCarlos Flores
Apr 5, 2021·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·Slawomir KubikZhenyu Xu
Apr 16, 2021·PLoS Neglected Tropical Diseases·Nathalia BallesterosJuan David Ramírez
Apr 29, 2021·Best Practice & Research. Clinical Obstetrics & Gynaecology·Jennifer Jardine, Edward Morris
Apr 26, 2021·The Journal of Infection·Kathy K LiUNKNOWN COVID-19 Genomics UK (COG-UK) consortium
May 6, 2021·Nature Reviews. Genetics·Tim R Mercer, Marc Salit
May 14, 2021·Clinical Microbiology Reviews·Seyed Hamid Safiabadi TaliSana Jahanshahi-Anbuhi
May 14, 2021·The Lancet Infectious Diseases·William L HamiltonUNKNOWN Cambridge COVID-19 group
May 5, 2021·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Ernest R ChanCurtis J Donskey
Jan 22, 2021·Journal of Clinical Microbiology·Kumeren N Govender
Jun 1, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Stephanie EvansJulie Robotham
Jun 4, 2021·Clinical Medicine : Journal of the Royal College of Physicians of London·Tim DaviesTri Wangrangsimakul
Jun 3, 2021·Nature Reviews. Microbiology·William T HarveyDavid L Robertson

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR

Software Mentioned

tidyverse
Cluster Track
Microreact
R package ggtree
GISAID
dists
Epic Systems
PANGOLIN
TREE
IQ

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

MedRxiv : the Preprint Server for Health Sciences
T. BedfordJ. Duchin
MedRxiv : the Preprint Server for Health Sciences
Trevor BedfordKeith R Jerome
Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America
Naomi C A WhylerRhonda L Stuart
© 2021 Meta ULC. All rights reserved