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A team from the University of Manchester has applied new techniques to detect and track the transmission of COVID-19 in hospitals.

The proof-of-concept system combines the movement and interaction of staff and patients with genomic sequencing of the virus and helps identify ways in which patient pathways, staff movement and risk can best be improved.

They identified hospital hotspots where patients and staff were likely to have had contact and shared similar or identical variants of the SARS-CoV-2 virus that causes COVID-19.

The data collected between March and June 2020 is the result of a unique collaboration between Manchester scientists, clinical staff and hospital executives, the results of which were published in eLife magazine.

The work being done in five hospitals in northwest England could have an important impact on infection control. The team applied genome sequencing to throat and nasal swabs obtained from 173 healthcare workers and patients.

Viruses, like all organisms, accumulate small genetic changes over time that are usually completely neutral and do not add any additional benefit to the virus.

The Manchester team took advantage of the virus’s natural genetic alterations to understand how closely related samples were from various workers and patients affected by the virus.

When one affected individual’s COVID-19 genome is almost identical to that of another, it indicates that they share a common, nearby source of infection.

By combining this information with data on patient and staff movement, it can be determined where and when clusters of infections occur.

While COVID-19 variants are identified using genome sequencing in a process that can take at least a week, the team is confident that the process can now be completed within 48 hours. The approach is therefore able to scale quickly.

Dr. Jamie Ellingford of the University of Manchester said, “The methods used in this study to fully characterize the appearance of the virus in each sample go beyond routine testing strategies.

“And that can help identify areas in hospitals where outbreaks occur and help alert infection control teams.”

One possible limitation of the approach is that at any given time, two people may happen to share a similar variant, rather than because of related infections.

To overcome this, the team sequenced the virus in people collected in the emergency room and over 30 hospital locations.

Using data from this larger group, collected at a similar point in time, they were able to identify groups of people who shared viruses that were more genetically similar than randomly expected.

Dr. Ellingford said, “Understanding the effectiveness of infection control methods is extremely important if we are to reduce and prevent SARS-CoV-2 transmission in the hospital.

“While vaccines can reduce the risk for people in the hospital, the risk of infection remains and infection control is urgently needed to ensure the safety of patients and staff.

“However, we believe that viral genome sequencing is an important tool in infection control that provides a realistic way of tracking and identifying the causes of hospital-acquired transmissions.

“It is able to alert us to people who have been in contact during a certain period of time and who share genetically similar virus samples.

“And that can lead to targeted interventions and ultimately prevent avoidable harm to vulnerable people who acquire COVID-19 in the hospital.”

Graeme Black is Professor of Genetics and Ophthalmology at the University of Manchester.

He said, “Once hospitals identify clusters, there are a number of steps they can take to keep them safe.

“With this information, hospital managers can, for example, evaluate existing infection control methods and easily check which are working most effectively. The use of PPE could also be adapted to the location of a cluster.

“However, we also suggest that these data support the widespread adoption of screening strategies for healthcare workers who may be presymptomatic or asymptomatic triggers of SARS-CoV-2 that are important contributors to the SARS outbreak -CoV-2 afford.

“We also believe that developing methods to more accurately track movement in the hospital could be useful in expanding the characterization of person-to-person contacts and understanding the accuracy of the assumptions enforced in this study.”

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More information:
Jamie M. Ellingford et al. Genomic and Health Dynamics of Nosocomial SARS-CoV-2 Transmission, eLife (2021). DOI: 10.7554 / eLife.65453

Journal information:
eLife Provided by the University of Manchester

Quote: The monitoring system tracks COVID infection hotspots in hospitals (2021, March 30th) as of March 30th, 2021 from html

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