Viral sequencing reveals US healthcare personnel rarely become infected with SARS-CoV-2 through patient contact

Abstract

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.

Assessment of SARS-CoV-2 Infection among Healthcare Workers of a German COVID-19 Treatment Center

“…Five of these employees were involved in an outbreak at the very beginning of the pandemic in March 2020. The low rate of patient-to-HCW transmission is in line with a recent, sequencing-based investigation demonstrating that only 4.2% of COVID-19 infections in HCWs in a US academic medical institution could be traced to a patient contact [41]. The small proportion of infections that were attributed to patient-to-HCW transmission in our study suggests that the hygiene measures applied at SLK Clinics during the first wave of the COVID-19 pandemic were effective.…”

“…Although physical distancing is an important component in limiting the spread of COVID-19, Keller et al identified restricted space in break rooms or work areas, the need to communicate confidential patient information or the wish to maintain relationships at work as barriers to adhering to these rules [45]. That HCW-to-HCW transmission or especially contacts outside the hospital might be a more relevant source of infection in HCWs has also been appreciated by others [36,41,46,47].…”

COVID-19 in Health Care Personnel

“…Our study and others suggest that SARS-CoV-2 transmission to HCP within the hospital environment is relatively rare if strict infection control practices are followed. 12,[21][22][23][24] Neither patients nor HCP contacts were associated with higher odds of testing positive for SARS-CoV-2. However, HCP who had contact with a COVID-19epositive family or community member experienced a greater than four-fold increased odds of a positive test.…”

Universal Use of N95 Respirators in Healthcare Settings When Community Coronavirus Disease 2019 Rates Are High

“…This corresponds to measures of viral dynamics: viral loads are highest just before symptom onset and rapidly decline thereafter [ 4 , 5 ]. This helps explain why asymptomatic and presymptomatic people account for the majority of SARS-CoV-2 transmissions and why secondary transmissions rarely occur after 5 days following symptom onset [ 3 , 6 ]. By the time most patients develop symptoms and progress to the point of requiring medical attention, their viral loads have typically fallen and they tend to be less contagious [ 7 , 8 ].…”

“…By contrast, infected healthcare workers pose a substantial risk to uninfected patients on non-COVID wards. There are now a plethora of reports documenting COVID-19 transmissions in healthcare settings, almost all in non-COVID wards [ 6 , 9 , 11 , 12 , 18 ]. Many have been traced to staff members who introduced SARS-CoV-2 into the facility or who served as vectors to carry the virus from patient to patient [ 9 , 19 , 20 ].…”