Whole-Genome Sequencing Confirms SARS-CoV-2 Transmission between Healthcare Workers and Patients

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 analyse transmission routes of SARS-CoV-2 in hospital-acquired (HA) COVID-19. Methods: An epidemiological investigation was undertaken for all HA cases of COVID-19 from March to April 2020. Fifty patient and healthcare worker (HCW) samples in which SARS-CoV-2 RNA was detected were analysed by WvGS and their phylogenetic relationship established. Findings: WvGS identified six clusters of nosocomial SARS-CoV-2 transmission and revealed transmission events previously undetected by epidemiological analysis. WvGS also provided evidence for SARS-CoV-2 transmission between HCWs and patients and among HCW themselves. The majority of HA COVID-19 cases occurred in patients highly dependent on nursing care, suggesting that the likely route of transmission was by close contact or droplet, rather than aerosol, transmission. Mortality among HA COVID-19 infections in this elderly dependent population was recorded as 33%. Interpretation: This study provides for the first time clear evidence that when SARS-CoV-2 is circulating in the community, transmission occurs from symptomatic and asymptomatic HCWs to patients. Interventions including comprehensive screening of HCWs for COVID-19 associated 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 optimal control measures in an emergency pandemic situation caused by a virus with undefined transmission modus. Funding Statement: This study was funded by University College Dublin. Declaration of Interests:KS and LF report advisory board or ad-hoc consultancy fees from Menarini, Pfizer, Novartis, MSD, Astellas, Astra-Zeneca and Gilead. The remaining authors have no interest to declare. Ethics Approval Statement: Approval was granted by the institution’s ethics committee.