Celebrating Unsung Heroes: A Spotlight on Pathogen Genomics

Throughout the last couple of years, one of our key GPW partners have been working tirelessly to keep us all safe. The Pathogen Genomics Unit has been at the frontline in the fight against Coronavirus and continue working under immense pressure to help us stay ahead of new variants as they evolve. 

PenGU IP5 Team

Georgia Pugh, Jessica Powell and Tara Annette.

This team of three joined us in February 2021 to man the IP5 Public Health Wales Surge Laboratory which is located adjacent to the Welsh Light-House Laboratory. The remit for this team was to cherry pick the Pillar 2 samples form the extract plates received for the Light-House laboratory.

The team are from varying backgrounds none of which are from a Diagnostic Laboratory so they were inexperienced and having to learn in very highly pressured environment. They hit the ground running, their professionalism, work quality and accuracy has been exemplary.

Prior to the team starting the sequencing rate for Welsh Pillar 2 samples was between 0.3%-5%, after they started the coverage jumped to 20.5% and once they felt their feet it went up to 40%. As we are unable to differentiate between those that are Welsh samples and those that are samples from the rest of the UK at the point of cherry picking, they have been helping in the overall UK sequencing coverage of Pillar 2 samples.

With their help PenGU have sequenced 14% of Welsh Pillar 2 samples since the start of the COVID Pandemic.

PenGU Wet Lab Team

Bree Gatica-Wilcox, Sara Summerhayes, Alec Birchley, Lee Graham, Jason Coombs, Sarah Taylor, Harry Williams, Jessica Hey, Alexander Adams

At the height of the Pandemic 2020 this team were sequencing 6,000 COVID Positives per week, manually; as automation wasn’t quick enough to have acceptable turnaround times for Valiant tracking. Not only did they achieve this, they also delivered the routine services, HIV Resistance, Mycobacteria Characterisation and TB Resistance, Clostridium difficile Characterisation and Antibiotic Resistance Bacteria Characterisation meeting the required turn-around times.

As if that wasn’t enough they continued to learn new techniques (required for scaling up the COVID sequencing) and undergo a re-visit for ISO 15189 accreditation for HIV Resistance and Mycobacteria Characterisation and TB Resistance and extension to scope for Clostridium difficile Characterisation and retain the accreditation for the prior and gain accreditation for the later.
This team is truly remarkable and a credit to Public Health Wales and the Pathogen Genomics Unit. They are now sequencing 7,000 COVID Positive per month PenGU has required a little extra help but the team is still meeting the challenge including ISO accreditation for COVID Characterisation and Variant calling.

Standout Individual

Jason Coombs

A member of the PenGU Wet-lab team whose workload was already pressured; he managed and juggled reagents to ensure all sequencing services continued un-impeded during the COVID pandemic. He was reactive to changes of which there were many, he also put in many hours of overtime and weekend working to ensure the PenGU ship kept sailing.

PenGU Dry Lab Team

Matt Bull, Sara Rey, Nicole Pacchiarini, Amy Gaskin and Catryn Williams

The Bioinformaticians team kept pace with the wet lab team; processing all the work/data generated by sequencing for existing services and COVID.
On top of this they were developing on the hoof pipelines for COVID. They were in constant demand by the Welsh Government, Epidemiologists and CDSC attending many meetings to ensure all the relevant people were kept up to date with the data and what it meant. As we all know this is the first Epidemic where sequencing has really been used in earnest so this was an education for a lot of people.

The Bioinformaticians compiled reports for outbreaks and outbreak tracing a service that was in high demand and an invaluable service to the Epidemiologists. They were also instrumental in providing the data that was used by Welsh Government for the Fire Break document, which stopped travel into Wales to help reduce the COVID burden by increased introductions

Organogram of PenGU Team

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