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

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 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.

Healthcare associated coronavirus disease 2019 among health care workers in Normandy, France: a multi-center study

“…The risk among HCWs has been the subject of several studies [ [23] , [24] , [25] , [26] , [27] , [28] , [29] ]. In February 2020, the Chinese Center for Disease Control and Prevention published a major report on more than 72,000 cases of COVID-19 [ 23 ].…”

“…Adapted and correctly applied prevention measures reduce the nosocomial risk for HCWs, as shown by a study of the seroprevalence in medical staff several weeks after taking care of COVID-19 patients [ 27 ]. However, proven nosocomial infections occurred during loosening of barrier measures between HCWs, [ 28 ] lead outbreaks that can reached high attack rates [ 29 ]. In March 2020, Belingheri et al.…”

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“…Most countries struggled with insufficient testing capacity in the first months of the pandemic, which hampered early detection of emerging outbreaks and implementation of infection control measures. Increasing experience now suggests that every suspected healthcare associated infection should trigger a bundle of immediate infection control measures, including extensive screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), quarantining of all patients on the affected ward, physical distancing between personnel, and use of reinforced PPE during all contact with patients on the affected ward, in order to prevent larger outbreaks 101112…”

“…Working in intensive care units is not associated with an increased risk of infection, possibly owing to the protection afforded by high level PPE or to the decrease in infectivity that occurs in the later stages of the illness, even among critically ill patients 1315. The greatest risk to healthcare workers may be their own colleagues or patients in the early stages of unsuspected infections when viral loads are high 12…”

SARS-CoV-2 infection in asymptomatic healthcare workers at a clinic in Chile

“…Previous studies have shown high nosocomial transmission rates of SARS-CoV-2 between HCWs and/or patients [ 15 ]. However, our sequencing results suggest that infection of HCWs occurred in their respective communities, outside of the clinic and was not nosocomial.…”