Working in our outbreak lab during the COVID-19 pandemic

Posted on: 1 July 2020 by Dr Shona Moore in July posts

Dr Shona Moore working in the lab
Dr Shona Moore working in the lab.

Shona, Postdoctoral Research Associate in Clinical infection, Microbiology and Immunology, has led the expansion of the University's outbreak lab which processes thousands of COVID-19 positive samples each week. Read her blog to find out what it's been like scaling up operations and the challenges the team have overcome during the COVID-19 pandemic.

"I’ll never forget the day that the first COVID-19 patient sample arrived in the outbreak lab. It was one of those moments I’ll always remember, just like where you were when a major news story breaks.

Back then, sample processing was juggled around the busy schedule in one of our high containment Biosafety Level-3 (BSL-3) laboratories where other research was still ongoing, and around my own research. A novel coronavirus had emerged in China in December and was establishing itself in the UK.

Fast forward a whirlwind four months and Outbreak Lab Liverpool is now a slick operation with a large and absolutely incredible, hardworking team of volunteers processing samples. We now have a technical support dream team, a team forever running between buildings collecting and moving samples. Our support team from the University's GCLP Facility have taught us a huge amount about Good Clinical Laboratory Practice in a very short space of time.

Some of the team preparing a shipment of samples

Some of the team preparing a shipment of samples.

ISARIC (International Severe Acute Respiratory and Emerging Infections Consortium) established itself in 2012. The consortium exists to allow for the rapid collection of clinical data and biological samples in response to an outbreak of any severe or potentially severe acute infection of public health interest. ISARIC4C (the clinical characterisation protocol) allowed a rapid UK research response to COVID-19 and mobilised from as early as January 2020.

We are a major biorepository for ISARIC4C samples, receiving samples from hospital sites across the UK. We feed samples into the nationwide consortium of researchers, whose aim is to characterise SARS-Cov-2 and answer clinical questions about COVID-19.

We have established ourselves in collaboration with our Scottish counterparts, led by Dr Sarah McDonald at the University of Glasgow, who receive samples from NHS Scotland sites. The team in Liverpool currently process 4000 samples a week, shipping them in from hospital sites. We check the condition of samples, isolating cells or aliquoting where required. They are then carefully logged on a lab information management system (LIMS) and stored in an ever-expanding network of freezers.

Most of these samples are acute clinical samples, so this requires a highly skilled and thorough workforce, working within BSL-3. At the same time, the team pick samples of interest for researchers, often based on clinical characteristics of patients, or sample time point post-symptom-onset. We ship the samples out to both consortium members and external collaborators. This involves careful tracking of samples within the LIMS software.

Biotherm boxes stacked awaiting collection

Biotherm boxes stacked awaiting collection.

The volunteer team from a range of research backgrounds have stepped into a very different role to their normal one. The work that we do facilitates a large volume of research across the UK, as the data output by the consortium is fed by SAGE into government decision making. It’s a very demanding job; there is pressure to keep up with the colossal scale of recruitment and sampling, and we aim to ship samples out to researchers as efficiently as possible.

Volunteers have stepped out of their usual roles and seamlessly into this new and rapidly evolving role in order to facilitate SARS-CoV-2 research. Their resolve and spirit are humbling and reminiscent of wartime efforts. The UK research output is already providing answers to questions which we couldn’t answer back in February, on pancake day, the day that first sample changed everything."