Journal Article

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

Hall, Grant, Yakovleva, Anna, Jahun, Aminu S, Khokhar, Fahad A, Roddick, Iain, Moore, Elinor, Brown, Nicholas, Sridhar, Sushmita, Török, M Estée, Houldcroft, Charlotte J, Curran, Martin D, Caller, Laura G, Caddy, Sarah L, Reacher, Mark, Gouliouris, Theodore, Meredith, Luke W, Dougan, Gordon, Parmar, Surendra, Forrest, Sally, Goodfellow, Ian, Warne, Ben, Hamilton, William L, Peacock, Sharon J, Popay, Ashley, Feltwell, Theresa, Hosmillo, Myra, Weekes, Michael P, Baker, Stephen

2020

Overview

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 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. We 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. COVID-19 Genomics UK (supported by UK Research and Innovation, the National Institute of Health Research, the Wellcome Sanger Institute), the Wellcome Trust, the Academy of Medical Sciences and the Health Foundation, and the National Institute for Health Research Cambridge Biomedical Research Centre.

• Publisher: Elsevier Ltd,Elsevier B.V,Elsevier Limited,The Authors. Published by Elsevier Ltd
• Subject: Adolescent / Adult / Aged / Aged, 80 and over / Analysis / Betacoronavirus - genetics / Child / Child, Preschool / Coronavirus Infections - epidemiology / Coronavirus Infections - prevention & control / Coronavirus Infections - virology / Coronaviruses / COVID-19 / Cross Infection - epidemiology / Cross Infection - prevention & control / Cross Infection - virology / Diagnostic systems / DNA sequencing / England - epidemiology / Epidemiology / Female / Genetic research / Genome, Viral - genetics / Genomes / Genomic analysis / Genomics / Health aspects / Health care / Health policy / Hospitals, University / Humans / Infant / Infant, Newborn / Infection Control - methods / Infectious diseases / Investigations / Male / Medical research / Medicine, Experimental / Middle Aged / Nosocomial infections / Nucleotide sequencing / Pandemics - prevention & control / Patient Safety / Patients / Phylogeny / Pneumonia, Viral - epidemiology / Pneumonia, Viral - prevention & control / Pneumonia, Viral - virology / Polymerase Chain Reaction - methods / Polymorphism, Single Nucleotide / Porosity / Prospective Studies / Public health / Respiratory diseases / SARS-CoV-2 / Severe acute respiratory syndrome / Severe acute respiratory syndrome coronavirus 2 / Surveillance / Target recognition / Viral diseases / Whole Genome Sequencing - methods / Young Adult