Local control of COVID-19 community and hospital outbreaks

As a new pandemic took hold across the UK, hospital admissions of patients with COVID-19 surged, including at the Cambridge University Hospital. It was very important to understand where and how these infections were spreading. The recently established COVID-19 Genomics Consortium UK 1 swung into action; a world-leading distributed network of hospitals, public health agencies, and academic partners, with a mission to provide rapid, high-throughput whole-genome sequencing of SARSCoV-2 samples.

The local Public Health England clinical microbiology laboratory and the University of Cambridge Department of Pathology worked together to sequence pathogen genomes from healthcare-associated COVID-19 infections within 24 hours of receiving samples from patients. They analysed combined genomic and epidemiological data, revealing a level of detail not detectable from the epidemiological data alone. In six weeks, they found over thirty different clusters of related cases from 1,000 viral genomes — including small outbreaks that would otherwise have been hidden amid the bigger picture of infections. This made it possible to identify distinct outbreaks linked to specific locations in hospital and community settings, information that was immediately fed back to doctors, managers, and infection control experts, allowing them to act quickly to prevent further infections from the sources identified3. For example, results revealed a cluster of COVID-19 patients in different parts of the hospital with near-identical sub-types of the SARS-CoV-2 virus, strongly suggestive of a shared origin for these cases. It was found that these patients all had kidney disease and had visited the hospital outpatient dialysis clinic on the same day, most travelling in the same patient transport vehicle. Closing the dialysis clinic was not an option, so instead both clinic and vehicle were intensively cleaned, and new personal protective equipment and social distancing measures swiftly put in place. There were no further cases amongst the dialysis patients.

"We’re able to combine genomic data with patients’ medical records to provide real time information to help the hospital review its infection control on a weekly basis. It’s also highlighted possible transmission networks less well documented, such as care homes, outpatient units and ambulance services. - Professor Ian Goodfellow, University of Cambridge4

Examination of the viral genome sequences helped to reveal outbreaks and sources that would otherwise have been lost to view. The genomic data also supported wider efforts, feeding into a central database and enabling a national genomic epidemiology overview of the spread of SARS-CoV-2 across the UK — for example, determining that there had been over 1,300 separate early introductions of the virus to the country, mostly from other countries in Europe such as Spain and Italy, rather than from China where the pandemic began.

1. COVID-19 Genomics UK Consortium. 2020. Available at: https://www.cogconsortium.uk [Accessed: 01 February 2021]

2. The Washington Post. Scientists have a powerful new tool for controlling the coronavirus: Its own genetic code. 2020; Available at: https://www.washingtonpost.com/ graphics/2020/health/coronavirus-genetic-code [Accessed: 01 February 2021]

3. Meredith, L. W., Hamilton, W. L., Warne, B., et al. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. Lancet Infect Dis. 20(11):1263- 1272 (2020). 37

4. University of Cambridge. Rapid genome sequencing and screening help hospital manage COVID-19 outbreaks. 2020. Available at: https://www.cam.ac.uk/research/news/ rapid-genome-sequencing-and-screening-help-hospitalmanage-covid-19-outbreaks [Accessed: 01 February 2021]