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

doi:10.1016/j.jhin.2023.08.002

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

J Hosp Infect. 2023 Oct:140:139-155. doi: 10.1016/j.jhin.2023.08.002. Epub 2023 Aug 9.

Authors

D Hare¹, K M Dembicka², C Brennan³, C Campbell³, U Sutton-Fitzpatrick³, P J Stapleton⁴, C F De Gascun³, C P Dunne⁵

Affiliations

¹ UCD National Virus Reference Laboratory, University College Dublin, Ireland; School of Medicine, University of Limerick, Limerick, Ireland. Electronic address: daniel.hare@ucd.ie.
² School of Medicine, University of Limerick, Limerick, Ireland.
³ UCD National Virus Reference Laboratory, University College Dublin, Ireland.
⁴ University Hospital Limerick, Limerick, Ireland.
⁵ School of Medicine, University of Limerick, Limerick, Ireland; Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.

PMID: 37562592
DOI: 10.1016/j.jhin.2023.08.002

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 1^st, 2020 and June 30^th, 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 31^st, 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.

Keywords: COVID-19; Healthcare-associated infection; Infection prevention and control; Nosocomial transmission; SARS-CoV-2; Whole-genome sequencing.

Publication types

Systematic Review
Review

MeSH terms

COVID-19* / epidemiology
COVID-19* / prevention & control
Cross Infection* / epidemiology
Cross Infection* / prevention & control
Delivery of Health Care
Disease Outbreaks / prevention & control
Humans
SARS-CoV-2 / genetics