Whole-genome sequencing to investigate transmission of SARS-CoV-2 in the acute healthcare setting: a systematic review

D. Hare, K. M. Dembicka, C. Brennan, C. Campbell, U. Sutton-Fitzpatrick, P. J. Stapleton, C. F. De Gascun, C. P. Dunne

Research output: Contribution to journalReview articlepeer-review

Abstract

Background: Whole-genome sequencing (WGS) has been used widely to elucidate transmission of SARS-CoV-2 in acute healthcare settings, and to guide infection, prevention, and control (IPC) responses. Aim: To systematically appraise available literature, published between January 1st, 2020 and June 30th, 2022, describing the implementation of WGS in acute healthcare settings to characterize nosocomial SARS-CoV-2 transmission. Methods: Searches of the PubMed, Embase, Ovid MEDLINE, EBSCO MEDLINE, and Cochrane Library databases identified studies in English reporting the use of WGS to investigate SARS-CoV-2 transmission in acute healthcare environments. Publications involved data collected up to December 31st, 2021, and findings were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Findings: In all, 3088 non-duplicate records were retrieved; 97 met inclusion criteria, involving 62 outbreak analyses and 35 genomic surveillance studies. No publications from low-income countries were identified. In 87/97 (90%), WGS supported hypotheses for nosocomial transmission, while in 46 out of 97 (47%) suspected transmission events were excluded. An IPC intervention was attributed to the use of WGS in 18 out of 97 (18%); however, only three (3%) studies reported turnaround times ≤7 days facilitating near real-time IPC action, and none reported an impact on the incidence of nosocomial COVID-19 attributable to WGS. Conclusion: WGS can elucidate transmission of SARS-CoV-2 in acute healthcare settings to enhance epidemiological investigations. However, evidence was not identified to support sequencing as an intervention to reduce the incidence of SARS-CoV-2 in hospital or to alter the trajectory of active outbreaks.

Original languageEnglish
Pages (from-to)139-155
Number of pages17
JournalJournal of Hospital Infection
Volume140
DOIs
Publication statusPublished - Oct 2023

Keywords

  • COVID-19
  • Healthcare-associated infection
  • Infection prevention and control
  • Nosocomial transmission
  • SARS-CoV-2
  • Whole-genome sequencing

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