A genomic giant: Public Health Wales' genomic sequencing and sharing efforts put Wales in top three worldwide as part of COVID-19 response

As part of the Welsh Government’s response to the COVID-19 pandemic, the 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 team’s efforts have led to Wales becoming a global leader in COVID-19 genomics, having sequenced and shared more SARS-CoV-2 genomes than any other country in the world except the United States and England.

Their work is feeding into a £20M project  being led by the COVID-19 Genomics UK (COG-UK) consortium, an innovative partnership of organisations across the UK including Public Health Wales, Genomics Partnership Wales and Cardiff and Vale University Health Board.

“A genome is effectively the blueprint containing the instructions to build an organism,” Dr Thomas Connor, Bioinformatics Lead, Public Health Wales, explained. “In the case of COVID-19, genomics has enabled us to study the evolution of the whole virus: how it has changed over time, as well as examining changes in the individual parts that make up the virus.

“This data has enabled us to track the spread of the virus in time and space. A lot can be done with that data, both locally and globally as part of the pandemic response in Wales and the wider world.”

With the coming of the pandemic, necessity quickly become the mother of invention. There had been no previous plan to use genomics for COVID-19, however, within 24 hours of being given approval to switch sequencing on for COVID-19, the Pathogen Genomics (PenGU) team had sequenced their first Welsh SARS-CoV-2 genome.

“We started sequencing on the 6th of March,” Connor recalled. “By the end of the month we had already provided our first analysis that fed into an outbreak investigation.”

The team has been sequencing every available Welsh COVID-19 case identified in a Welsh NHS laboratory, as well as supporting outbreak analysis across Wales, looking for important virus changes, and tracking the spread and entry of the virus in Wales and the UK.

The bioinformatics team has also built an analysis and reporting system from scratch. This was done so these systems can be applied to other genomics activities, to further benefit patients. The data is being shared with NHS colleagues at a local level, while the team is working within Public Health Wales at a national level to support the pandemic response.

The PenGU team has ultimately built a world-class COVID-19 sequencing service. They have sequenced and shared more genomes than every country in the world except the United States and England, having completed roughly a year’s worth of samples in about three months.

The work being done by the team is very much a collaborative effort with partner agencies such as the All Wales Medical Genomics Service and Cardiff University also providing a great deal of support.

“We had a huge amount of support from Cardiff University, who gave us additional lab space,” Dr Sally Corden, Head of PenGU, Public Health Wales Microbiology, said. “All the teams worked really hard. They also had to often adapt to different ways of working, including working from home.”

“Our whole team is relatively new,” Connor added. ”It’s been remarkable to see how everything and everyone came together in such short span of time. Keep in mind we’re doing this in the midst of a pandemic; and have stood up a service in a matter of days that has ended up sequencing more than most countries in the world to date.”