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

Lancet Infect Dis. 2020 Nov;20(11):1263-1272. doi: 10.1016/S1473-3099(20)30562-4. Epub 2020 Jul 14.

Abstract

Background: 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.

Methods: 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.

Findings: 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.

Interpretation: 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.

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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Betacoronavirus / genetics*
  • COVID-19
  • Child
  • Child, Preschool
  • Coronavirus Infections / epidemiology*
  • Coronavirus Infections / prevention & control*
  • Coronavirus Infections / virology
  • Cross Infection / epidemiology*
  • Cross Infection / prevention & control*
  • Cross Infection / virology
  • England / epidemiology
  • Female
  • Genome, Viral / genetics
  • Hospitals, University
  • Humans
  • Infant
  • Infant, Newborn
  • Infection Control / methods*
  • Male
  • Middle Aged
  • Pandemics / prevention & control*
  • Patient Safety
  • Phylogeny
  • Pneumonia, Viral / epidemiology*
  • Pneumonia, Viral / prevention & control*
  • Pneumonia, Viral / virology
  • Polymerase Chain Reaction / methods
  • Polymorphism, Single Nucleotide
  • Prospective Studies
  • SARS-CoV-2
  • Whole Genome Sequencing / methods
  • Young Adult