As part of the Welsh Government’s response to the COVID-19 pandemic, Public Health Wales Pathogen Genomics Unit (PenGU) has been working collaboratively with key partners to sequence and analyse every available SARS-CoV-2 sample from patients in Wales.
The £20M project is being led by the COVID-19 Genomics UK (COG-UK) consortium consisting of an innovative partnership of organisations across the UK including Public Health Wales, Genomics Partnership Wales and Cardiff and Vale University Health Board.
This data has provided scientists and clinicians with tools to unlock the epidemiology of COVID-19, monitor community spread, uncover the origin of new cases and detect clusters of infections.
Minister for Health, Vaughan Gething said, “Wales has built a world class genomics system which has contributed to our understanding of the virus including how it spreads in hospitals and communities, as well as tracking mutations within the virus. We are using genomics to help identify when there are new introductions of COVID-19 in to Wales.
“Sequence data is being used in real time to track outbreaks and to support outbreak response on a local level. Importantly genomic analysis forms part of our circuit breakers; points where an immediate lockdown will happen and early warning indicators to let the Welsh Government know when a spike in cases could be on the way.”
To date, Wales has sequenced over 6,000 SARS-CoV-2 genomes, representing more than a third of all COVID-19 cases in Wales. This places Wales 3rd in the world for COVID-19 genomes sequenced, behind only the USA and England.
Public Health Wales has been able to use SARS-CoV-2 genome sequenced data to undertake outbreak investigations, support surveillance activities and provide evidence-based advice to Welsh Government and the UK government.
Dr Quentin Sandifer, Executive Director of Public Health Services and Medical Director at Public Health Wales said, “Our world-leading use of genomic sequencing as part of the response to COVID-19 in Wales has provided strong endorsement of the investment in a Welsh pathogen genomics service led by Public Health Wales, working in close collaboration with Professor Thomas Connor from Cardiff University.”
While data has been generated and processed in real-time in response to need, a set of automated analyses have also been produced weekly to better support the COVID-19 response