Genetic epidemiology of SARS-CoV-2 in hospitals and care facilities

These findings further emphasize the importance of mask-wearing, physical distancing, robust testing programs, and the rapid distribution of vaccines in healthcare settings.

– Dr. David O’Connor

At a Glance

SARS-CoV-2, the virus that causes COVID-19, genetically changes across populations at a predictable rate of one mutation approximately every 15 days. Understanding the transmission of COVID-19 in healthcare facilities, which are at the core of the pandemic in Wisconsin, is crucial to help resolve the directionality and source of infection.

In order to understand if healthcare workers are becoming infected through patient contact, the research team used information such as viral lineage and consensus sequence provided by Oxford Nanopore Technology. The researchers had an initial goal of sequencing ten transmission clusters per month from UW Hospitals and Clinics. They far surpassed this goal and have investigated 55 transmission clusters involving over 400 individuals. After identifying likely and unlikely sources of infection in healthcare workers (HCW) and comparing patient sequences to local outbreaks, they found little evidence for widespread transmission, suggesting that HCWs are most likely to become infected with SARS-CoV-2 in the community.

The Challenge

Although severely ill patients who tested positive for COVID-19 require hospitalization and intensive care, people continue to require hospitalization for other conditions like cancer, heart disease and stroke. Should these vulnerable patients become infected with SARS-CoV-2, they are even more susceptible to a severe infection. In turn, not only are the healthcare personnel that treat SARS-CoV-2-infected patients at risk of becoming infected, they also risk spreading the virus to coworkers, patients and people outside of the hospital setting.

Project Goals

The overarching goal of this project was to characterize likely origins and path of spread for SARS-CoV-2 infections. The researchers generated SARS-CoV-2 sequences from UW Health outbreaks that are considered to be the most important according to infection control. They compared the outbreak to the broader community in order to see how the infected healthcare worker fit into the local pandemic. This comparison of hospital outbreaks to SARS-CoV-2 sequences in the broader community was expected to lead to more specific inferences about the directionality and source of infection, while understanding how these infected healthcare workers fit into the larger community outbreak.

Results

The researchers’ sequencing efforts resulted in outbreak reports for 55HCW-associated clusters involving over 400 individuals, 12 of which (involving 77 individuals) took place during this grant. The results from these reports suggest the majority of HCW infections are acquired through community exposure, indicating that measures to reduce community spread are critical. These results show that infection control measures in University of Wisconsin Hospital and Clinics are predominantly protecting HCWs from healthcare associated SARS-CoV-2 infections. However, a majority of healthcare-associated infections that were identified appeared to be linked to HCW-to-HCW spread. Additional messaging and guidelines to reduce HCW-to-HCW spread in and out of the workplace may be needed.

Looking to the Future

Although HCWs were one of the first groups to receive vaccines against SARS-CoV-2, the Pfizer and Moderna vaccines are not fully protective until two weeks after the second dose and there exists a window of time where HCWs are still susceptible to infection. In addition, protective antibodies from vaccination are not universally achieved. The research team is seeking to sequence viruses from HCWs who become infected post-vaccination in order to understand whether the vaccine-induced immunity is as effective against the variants. In addition, a manuscript describing the team’s findings has been revised and is under consideration at the Clinical Infectious Diseases journal by Oxford University Press.

Lasting Impact

The successful completion of this project will hopefully improve the safety of healthcare workers, patients, and others who spend time in hospitals. It will also provide insight into the nature of SARS-CoV-2 transmission in healthcare facilities and allow ongoing assessment of infection control practices. UW Hospitals and Clinics implemented a number of changes to their infection control guidelines based on these sequencing results.