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Resources and collaboration key to the Earlham Institute meeting the COVID-19 challenge

© Earlham Institute

During the summer of 2020, the pandemic was still in its early stages. Governments across the globe were relying on nationwide COVID-19 testing to track the spread and severity of the disease. Students were also set to return to universities, causing concerns over how this might affect case rates. To combat this, institutions across Norwich Research Park, including the Earlham Institute (EI), the University of East Anglia (UEA), the Norfolk and Norwich University Hospitals NHS Foundation Trust (NNUH), Quadram Institute, John Innes Centre, and The Sainsbury Laboratory, collaborated on a pilot study called the Norwich Testing Initiative (NTI) (ref 1, ref 2). The lessons learnt from the pilot were actively applied to a regional testing programme, increasing testing capacity and alleviating the pressure on the local NHS hospitals. EI used BBSRC-funded, nationally significant capabilities and infrastructure to enable and streamline their rapid response to the pandemic.

Key impacts

  • The Earlham Institute (EI) collaborated with several institutes across Norwich Research Park on a pilot study, the Norwich Testing Initiative (NTI).
  • Rapid pivoting of research capabilities has been enabled by sustained UKRI-BBSRC investment into Norwich Research Park, including national capabilities (NCs) and infrastructure. EI’s national capabilities in genomics and single-cell analysis, the Biofoundry, research e-infrastructure, and training has enabled the NTI, the regional testing programme and ongoing COVID-19 research.
  • The NTI showed testing programmes that used centralised lab testing could be effective and informed a later regional testing programme for NHS/key workers. The results were shared around the world to use and to inform testing programmes for other Institutions.
  • EI loaned equipment to the Norfolk and Norwich University Hospital (NNUH) and produced a new automated test for the regional programme, increasing testing capacity seven-fold. The increase alleviated pressure on the local hospitals and benefited local NHS workers.
  • A call for volunteers across the Norwich Research Park generated over 200 volunteers in 48 hours, 35 of which supported NNUH’s pathology labs undertaking COVID-19 testing.
  • A dedicated testing lab at EI was built with a processing capacity of 35,000 tests per week.
  • EI invested in changes that made the ELIXIR_GALAXY platform more accessible for COVID-19 research, which researchers can now use for computational COVID-19 research and pan-genome analysis.

Figuring out the how – a test within itself

“We predicted that the student environment would be a particular problem in terms of the pandemic come the autumn, so we did a pilot over the summer testing university and Norwich Research Park staff,” highlights Dr Neil Hall, Director of the Earlham Institute.

The pilot aimed to test whether an asymptomatic testing programme could be implemented and effective for universities and similar institutions. “Before the vaccines, testing and distancing were the only defences people had against COVID-19,” Neil explains, “my feeling was that we should be exploring asymptomatic testing to prevent spread in response to increasing numbers.”

The NTI was ambitious, carrying out more than 3,000 tests on around 800 Norwich Research Park staff and students, with each participant completing four swabs (ref 1, ref 2).

The UK underwent a reagent shortage during the pandemic, and this began to limit testing rates. “The team at the Norwich Research Park designed an alternative test that didn't rely on the reagents that were in short supply,” says Sarah Cossey, the Director of Operations at EI.

EI and the Quadram Institute, both BBSRC strategically-funded Institutes, loaned equipment to the local hospital, NNUH, to increase NHS testing capacity. EI used their BBSRC-funded ‘national capabilities’ - unique and internationally important expertise, facilities or infrastructure that enable world-leading research. The University of East Anglia designed a manual test whilst EI automated it, with technical experts from teams in EI’s 1st and 2nd national capabilities - Genomics and the Biofoundry - programming the loaned equipment (ref 3). The new automated test and equipment increased the hospital’s testing capacity by seven times.

About Norwich Research Park

Norwich Research Park is a unique cluster of world-class institutions, all located within a 1 km radius. It is home to a major university teaching hospital, the Norfolk and Norwich University Hospitals NHS Foundation Trust, a leading university, the University of East Anglia, and several internationally significant research institutions: the Sainsbury Laboratory and three Institutes strategically funded by BBSRC - the Earlham Institute, Quadram Institute and John Innes Centre.

Norwich Research Park fosters a culture of collaboration not only between members of the research and innovation community on campus but also with the local area.

“If you’re trying to set up a new test in a hospital, which is already dealing with the pandemic, you're asking someone to service their engine whilst they're driving a car,” Neil illustrates, “the hospital was able to work with experts next door, who were able to focus and dedicate the time to set it up.”

“The Norwich Testing Initiative used a qPCR (ref 4) lab-based test, which is extremely accurate – it’s the gold standard of NHS testing. If you go to one of the drive-in centres because you're symptomatic, that's the test you get,” clarifies Sarah.

The Earlham Institute’s existing infrastructure smoothed and accelerated the process of setting up a centralised lab for the qPCR tests. Staff from EI’s 3rd and 4th capabilities - e-infrastructure (high-performance computing) and advanced training respectively - helped with the logistics and setting up data communication systems. With the UEA, the NTI project management team also produced an app to let individuals know their results, which also utilised EI’s e-infrastructure capability.

In numbers:

35,000 Test processing capacity of the dedicated testing lab at the Earlham Institute
7x Increased capacity for regional NHS testing
200 Volunteers across the Norwich Research Park to help with testing
3,046 Samples processed during the initial pilot Norwich Testing Initiative (ref 1, ref 2).

“The operational teams have done an amazing job in supporting EI’s science during the pandemic,” says Sarah, “without them, our research wouldn’t have continued as effectively, nor would we have been able to deliver essential COVID-19 testing to support the research park, local hospital and region. They should be immensely proud of what they have achieved in the last year.”

Through the support of the NTI project and its partners, the local hospital (NNUH) never ran out of lab capacity or staff and could offer testing to the hospital and region when needed.

Furthermore, the pilot was very successful, with a low rate of false positives and a higher than expected uptake (85%) of tests. It also proved that a programme that used a lab-centralised testing method could be effective, with the turnaround time for results being as low as 5 hours and the majority of tests completed within 24 hours (ref 2).

It was vital that they were able to inform people quickly, Neil points out, “with Fresher’s week, that’s a mass spreader event just waiting to happen. Students could also feel comfortable going home for Christmas to see their grandparents. All of those things were critical, and it did utilise a lot of the national capability funding.”

Local testing, local lab work

With valuable lessons learnt from the NTI and their capabilities and expertise, EI was in a unique position to help the local hospitals. The Department of Health and Social Care (DHSC) contracted EI and NNUH to provide loop-mediated isothermal amplification (LAMP) testing. Together with other partners across the park, they built a local programme.

Sarah highlights one of the key lessons, “With the turnaround time and the cost, we knew qPCR wasn't long-term sustainable or massively scalable for asymptomatic testing, which is one of the reasons why we supported moving over to LAMP.”

Direct LAMP tests, which also uses a centralised lab, do not require users to swab, making them easier to use and reducing human error. They also bring several other benefits over non-centralised test types, Neil explains, “The test result is recorded by the lab so you can accurately record prevalence rates. Also, you have a sample that you could go back to if you wanted to look at whether this is a Variant of Concern (VOC).”

“We were one of the first labs nationally to get it up and running,” Sarah adds, “we were able to take it forward, set it up really well and offer it out. It was only possible because we've been through the NTI and we have the skills that we have in the national capabilities.”

EI also used their available lab space to set up a dedicated facility that was operational in under eight weeks. The lab added a processing capacity of up to 35,000 samples a week (ref 5).

A rush of volunteers

EI also ran a Norwich Research Park volunteer drive, with over 200 volunteers from every Institute across the park offering their services (ref 3). Two volunteers from EI volunteered full time for the NHS testing facilities, with a further 35 from across the park working in the NNUH pathology labs during the next 6 months to process COVID-19 tests.

“That was one of the most amazing experiences when everyone was still getting used to the lockdown shock,” says Sarah, “to see 200 people come forward so quickly within 48 hours - I was overwhelmed with how many people had stepped forward. The NHS was given these very good microbiologists that could process qPCR samples with no problems. That made a big difference to the region, I'm sure.”

“Everybody realised there was an emergency,” said James Lipscombe, a Senior Research Assistant at EI who worked on the automated protocols for the qPCR testing. “There was a real sense of teamwork and togetherness, everybody pulling in the same direction. I really enjoyed working in that atmosphere. We worked with a great bunch of people over at UEA, and we got a lot done.”

Infrastructure to the rescue

The Earlham Institute’s third national capability is in e-infrastructure. EI is the coordinating office for ELIXIR-UK, part of a trans-European data infrastructure for life sciences. It houses datasets and provides resources and tools for analysis, allowing researchers to collaborate and agree on best practices. EI also hosts a Galaxy Node - a biomedical data analysis platform that is coordinated with other resources in the ELIXIR (ref 6) infrastructure.

The Galaxy team at EI organised a hackathon to develop tools for analysing COVID-19 data (ref 5). Neil explains how researchers could use the platform, “You can analyse variant sequences to see where particular strains may have come from. You can model 3D structures of proteins to look at the vaccine targets (ref 7).”

“It’s a really good example of where science comes to the rescue with tests, vaccines and epidemiology,” he continues, “it shows why you need these sorts of infrastructures. It’s the same reason you need a fire brigade or an army. You have to keep paying for them when everything's fine because when it isn’t, you need them. With computational infrastructure, it might not be as obvious, but with hundreds of thousands of strains being sequenced around the world every week, you need computational infrastructure to be able to share and analyse them. All the people who are tracking different variants or looking at escape mutants must have the tools, processes, and storage available to be able to do that. That’s the point of e-infrastructure, such as ELIXIR and Galaxy.”

EI and their fellow collaborators will continue to contribute to the regional testing programme. With the new relationships forged during the pandemic, Neil and Sarah are excited to see where the collaborations will go next.

Final say…

“A lot of the capabilities we have in the NCs are generic; they can be applied to most problems. Being able to automate and do thousands of assays instead of 10s of assays, or being able to analyse large data sets, are capabilities that could be deployed for lots of different purposes. For BBSRC-funded institutes, food and agriculture is a big focus of a lot of what we do, but there is no reason why that can't be deployed, in these times, for biomedical applications.” - Dr Neil Hall

“We've now got clinicians working with researchers and university staff in a very different way than we did just a year ago. The collaboration has really grown, and it's been really lovely to see.” - Sarah Cossey


References

  1. T Berger Gillam, J Cole, K Gharbi, E Angiolini, T Barker, P Bickerton, T Brabbs, J Chin, E Coen, S Cossey, R Davey, R Davidson, A Durrant, D Edwards, N Hall, S Henderson, M Hitchcock, N Irish, J Lipscombe, G Jones, G Parr, S Rushworth, N Shearer, R Smith, N Steel, Norwich COVID-19 testing initiative pilot: evaluating the feasibility of asymptomatic testing on a university campus, Journal of Public Health, Volume 43, Issue 1, March 2021, Pages 82–88, https://doi.org/10.1093/pubmed/fdaa194
  2. Norwich Testing Initiative: COVID-19 testing resources for universities | Earlham Institute
  3. Covid-19 one year on: responding to a global pandemic | Earlham Institute
  4. Bustin, S.A. & Nolan, T., 2020. RT-qPCR Testing of SARS-CoV-2: A Primer. International Journal of Molecular Sciences, 21(8), p.3004. Available at: http://dx.doi.org/10.3390/ijms21083004
  5. How Earlham Institute is tackling the global challenges of the COVID-19 pandemic | Earlham Institute
  6. Galaxy Community | ELIXIR-EUROPE
  7. Exploring and monitoring COVID-19 variants with Galaxy | ELIXIR-EUROPE

Images

All images © Earlham Institute.