Whole-genome Sequencing to Track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission in Nosocomial Outbreaks

Mary Lucey; Guerrino Macori; Niamh Mullane; Una Sutton-Fitzpatrick; Gabriel Gonzalez; Suzie Coughlan; Aisling Purcell; Lynda Fenelon; Séamus Fanning; Kirsten Schaffer

doi:10.1093/cid/ciaa1433

Whole-genome Sequencing to Track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission in Nosocomial Outbreaks

Clin Infect Dis. 2021 Jun 1;72(11):e727-e735. doi: 10.1093/cid/ciaa1433.

Affiliations

¹ Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland.
² School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin, Ireland.
³ National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland.
⁴ Department of Occupational Health, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland.

Abstract

Background: During the first wave of the coronavirus disease 2019 (COVID-19) pandemic, outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions posed a significant problem. Due to limited evidence, guidance on appropriate infection prevention and control (IPC) measures such as the wearing of face masks varied. Here, we applied whole virus genome sequencing (WvGS) to analyze transmission routes of SARS-CoV-2 in hospital-acquired (HA) COVID-19.

Methods: An investigation was undertaken for all HA cases of COVID-19 from March to April 2020. Fifty SARS-CoV-2 samples were analysed by WvGS and their phylogenetic relationship established.

Results: WvGS identified transmission events previously undetected by epidemiological analysis and provided evidence for SARS-CoV-2 transmission between healthcare workers (HCW) and patients and among HCW themselves. The majority of HA COVID-19 cases occurred in patients highly dependent on nursing care, suggesting the likely route of transmission was by close contact or droplet, rather than aerosol, transmission. Mortality among HA COVID-19 infections was recorded as 33%.

Conclusions: This study provides evidence that SARS-CoV-2 transmission occurs from symptomatic and asymptomatic HCWs to patients. Interventions including comprehensive screening of HCWs for COVID-19 symptoms, PCR testing of asymptomatic HCWs upon identification of HA cases and implementation of universal use of surgical masks for all clinical care is indicated to prevent viral transmission. Our study highlights the importance of close collaboration between guidance bodies and frontline IPC experts for developing control measures in an emergency pandemic situation caused by a virus with undefined transmission modus.

Keywords: infection prevention and control; nosocomial outbreaks; severe acute respiratory syndrome coronavirus 2; whole virus genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19*
Cross Infection* / epidemiology
Disease Outbreaks
Health Personnel
Hospitals
Humans
Phylogeny
SARS-CoV-2