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Reviews 1: "Viral Sequencing Reveals US Healthcare Personnel Rarely Become Infected with SARS-CoV-2 Through Patient Contact"

Published onApr 13, 2022
Reviews 1: "Viral Sequencing Reveals US Healthcare Personnel Rarely Become Infected with SARS-CoV-2 Through Patient Contact"
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key-enterThis Pub is a Review of
Viral sequencing reveals US healthcare personnel rarely become infected with SARS-CoV-2 through patient contact

SummaryBackgroundHealthcare personnel (HCP) are at increased risk of infection with the severe acute respiratory coronavirus 2019 virus (SARS-CoV-2). Between 12 March 2020 and 10 January 2021, >1,170 HCP tested positive for SARS-CoV-2 at a major academic medical institution in the Upper Midwest of the United States. We aimed to understand the sources of infections in HCP and to evaluate the efficacy of infection control procedures used at this institution to protect HCP from healthcare-associated transmission.MethodsIn this retrospective case series, we used viral genomics to investigate the likely source of SARS-CoV-2 infection in 96 HCP where epidemiological data alone could not be used to rule out healthcare-associated transmission. We obtained limited epidemiological data through informal interviews and review of the electronic health record. We combined viral sequence data and available epidemiological information to infer the most likely source of HCP infection.FindingsWe investigated 32 SARS-CoV-2 infection clusters involving 96 HCP, 140 possible patient contacts, and 1 household contact (total n = 237). Of these, 182 sequences met quality standards and were used for downstream analysis. We found the majority of HCP infections could not be linked to a patient or co-worker and therefore likely occurred in the outside community (58/96; 60.4%). We found a smaller percentage could be traced to a coworker (10/96; 10.4%) or were part of a patient-employee cluster (12/96; 12.5%). Strikingly, the smallest proportion of HCP infections could be clearly traced to a patient source (4/96; 4.2%).InterpretationInfection control procedures, consistently followed, offer significant protection to HCP caring for COVID-19 patients in a representative American academic medical institution. Rapid SARS-CoV-2 genome sequencing in healthcare settings can be used retrospectively to reconstruct the likely source of HCP infection when epidemiological data are not available or are inconclusive. Understanding the source of SARS-CoV-2 infection can then be used prospectively to adjust and improve infection control practices and guidelines.FundingThis project was funded in part through a COVID-19 Response grant from the Wisconsin Partnership Program at the University of Wisconsin School of Medicine and Public Health to T.C.F. and D.H.O. Author N.S. is supported by the National Institute of Allergy and Infectious Diseases Institute (NIAID) Grant 1DP2AI144244-01.Research in contextEvidence before this studyOn 16 January 2021 we searched for “SARS-CoV-2” AND “healthcare workers” AND “viral sequencing” in Google Scholar. This search returned 57 results, and included a number of preprint articles. We found two studies that used viral sequencing to investigate healthcare-associated outbreaks in the Netherlands 1 and the United Kingdom 2. To our knowledge, no study has used viral sequencing to specifically investigate the source of SARS-CoV-2 infections in healthcare workers in the United States. Although we and others have written about the potential utility of sequencing as an infection control asset 3–6, few have demonstrated the practical application of such efforts.Added value of this studyOur study suggests infection control measures in place at the institution evaluated in this case series are largely protecting healthcare personnel (HCP) from healthcare-associated SARS-CoV-2 infections. Even so, the majority of healthcare-associated infections we did identify appeared to be linked to HCP-to-HCP spread so additional messaging and guidelines to reduce HCP-to-HCP spread in and out of the workplace may be warranted. In addition, we demonstrated how rapid viral sequencing can be combined with, even limited, epidemiological information to reconstruct healthcare-associated SARS-CoV-2 outbreaks.Implications of all the available evidenceHealthcare-associated SARS-CoV-2 infections negatively affect HCP, patients, and communities. Infections among HCP add further strain to the healthcare system and put patients and other HCP at risk. We found the majority of HCP infections appeared to be acquired through community exposure so measures to reduce community spread are critical. This further emphasizes the importance of mask-wearing, physical distancing, robust testing programs, and the rapid distribution of vaccines.

RR:C19 Evidence Scale rating by reviewer:

  • Potentially informative. The main claims made are not strongly justified by the methods and data, but may yield some insight. The results and conclusions of the study may resemble those from the hypothetical ideal study, but there is substantial room for doubt. Decision-makers should consider this evidence only with a thorough understanding of its weaknesses, alongside other evidence and theory. Decision-makers should not consider this actionable, unless the weaknesses are clearly understood and there is other theory and evidence to further support it.



In this study the authors investigated SARS-CoV-2 acquisition of healthcare personnel (HCP) from SARS-CoV-2 infected patients. The investigation of nosocomial SARS-CoV-2 transmission is important to determine which infection prevention and control measures are indicated for the protection of staff and patients.

The authors analysed SARS-CoV-2 strains obtained from 8.2% (96/1,172) of infected HCP between March 2020 to January 2021, 140 patient contacts and 1 household contact by whole genome sequencing. 96 infected HCP were selected from 32 nosocomial clusters. 60.4% of HCP were infected with SARS-CoV-2 strains with a minimum of 2 single nucleotide polymorphisms difference to strains obtained from patients and HCP colleagues indicating likely acquisition outside of the hospital. 10.4% of HCP SARS-CoV-2 sequences were linked to other HCP and 12.5% of HCP sequences were linked to a patient/HCP cluster. Only 4.2% (4/96) could be clearly linked to a SARS-CoV-2 infected patient. 12.5% of HCP infections could not be classified. The authors deduce from their study that local infection prevention and control guidelines were successful in preventing significant transmission from Covid-19 patients to HCP.

This is an important study which would benefit from providing additional epidemiological information. 96 HCP viral strains were selected from 32 outbreak scenarios? How were these clusters defined, SARS-CoV-2 infected HCP and patients on the same ward? Were only symptomatic HCP tested for SARS-CoV-2 or were all HCP tested in a cluster/outbreak scenario or serially? All inpatients were tested for SARS-CoV-2 on admission but no information is provided if patients were subsequently tested again. Were inpatients only tested when they developed symptoms typically associated with SARS-CoV-2 or were asymptomatic patients tested in cluster/outbreak scenarios as well? Could asymptomatically infected patients have been a source of SARS-CoV-2 transmission to HCP in cases where no obvious link was identified by whole genome sequencing?

The data presented in the manuscript is encouraging from an IPC perspective but additional epidemiological information is required for full interpretation. In this author’s experience SARSCoV-2 transmission from patients to HCWs most frequently occurs when patients are not known to be Covid-19 positive with or without HCP not adhering to optimal PPE usage all the time. Whereas transmission from suspected or confirmed patients to HCP is rare, transmission occurs more frequently if SARS-CoV-2 infection has not been suspected yet so the title of the manuscript is not precise enough.

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