The Nottingham University Hospitals (NUH) Microbiology Laboratory service were fast to react to the need for increased testing for SARS-COV-2, taking around 500 samples a day, achieving a 24-hour turnaround and becoming one of the UK’s first UKAS-accredited labs for this testing. We asked Dr Gemma Clark about how the service managed to rise to the colossal challenge at speed, working across the hospital with multiple departments and pulling together to respond to a rapidly changing environment.

Who are you, what is your role within the service and how long have you been at the service?

I am Gemma Clark, a consultant clinical scientist who specialises in virology within the NUH Microbiology Laboratory service. I am also the research and development lead for the service. I joined the team in Nottingham back in 2012 as a trainee clinical scientist, and progressed through Higher Specialist Science Training (HSST) to become a consultant clinical scientist.

The focus of my role shifted considerably during the early weeks of the pandemic as I became focused on implementing a SARS-CoV-2 polymerase chain reaction (PCR) service for our trust, from completing the initial verification and validation work, to overseeing ongoing developments to the service.

How did you discover and get into virology?

I have been interested in viruses from a young age, from watching films about outbreaks to learning about viruses during my time at university. Following my undergraduate degree in microbiology and subsequent PhD, I wanted to do a job where I could use the research and technical skills I’d developed to improve the diagnosis of viral infections.

There has been a significant increase in interest in careers in virology since the COVID-19 pandemic began, and I see this as a positive as we need more virologists in this rapidly evolving specialist field!

Do you do anything as a centre to encourage experience or recruitment into this field?

I am passionate about promoting careers in healthcare science and have taken part in initiatives such as STEM, the Big Bang Science Fair and local careers events, to get the message out there about careers in healthcare science. There has been a significant increase in interest in careers in virology since the COVID-19 pandemic began, and I see this as a positive as we need more virologists in this rapidly evolving specialist field!

What’s the setup of the virology team within the lab – how many people are in the team and what are their job roles? How has this changed since the start of the pandemic?

Our virology service in Nottingham is an integral part of the microbiology laboratory, which consists of more than 100 team members. We have an excellent team consisting of medical laboratory assistants, associate practitioners, biomedical scientists, clinical scientists, and medical virologists and microbiologists They all support each other to offer essential diagnostic virology testing for NUH and the Nottinghamshire area. For example, we offer antenatal infectious disease screening services for the local area, pre- and post-transplant virological screening within the trust, and have great working relationships with our specialist infectious diseases, GU medicine and hepatitis services.

During the COVID-19 pandemic, we reviewed what routine services we offered following guidance from the Royal College of Pathologists. We amended these services to ensure we could continue to deliver essential virology diagnostic results within clinically meaningful timelines, while still rising to the challenge of providing SARS-CoV-2 PCR results within 24 hours of receiving the sample. The virology team excelled during this challenge and we were able to rapidly implement a local PCR test for SARS-CoV-2 and introduce an extended hour’s service utilising volunteers from microbiology and other specialisms within pathology. We’ve managed to maintain a COVID-19 testing service for patients and staff within the trust and have supported other hospitals within the region when needed.

Could you tell us how you test for SARS-CoV-2? For example, what techniques and equipment are used and how long does it take?

In our laboratory we offer molecular testing for SARS-CoV-2. This means the test is able to detect the SARS-CoV-2 virus itself, suggesting a current infection. This test requires a sample to be taken from a patient with symptoms suggestive of COVID-19 infection (fever, shortness of breath, loss of sense of smell or taste). The most commonly taken sample is a swab of the nose and throat, which is then transported to the laboratory for testing.

We have been able to report results back to the requesting clinicians within 24 hours of the swab being received in the laboratory, which is an incredible achievement when you consider that we had to implement a brand new test in the lab, using new equipment and saw a rapid increase in demand for testing.

Once the swab arrives with us in the laboratory, we register the sample on our computer system so we are able to track the process of that sample throughout the lab until a final result is generated. The first step in processing is to extract all nucleic acid present in the sample, which may include SARS-CoV-2 viral RNA if the patient has COVID-19. We then apply a specialist technique, PCR, to that sample, which is able to detect nucleic acids that are specific to the SARS-CoV-2 virus, indicating a current infection. We have been able to report results back to the requesting clinicians within 24 hours of the swab being received in the laboratory, which is an incredible achievement when you consider that we had to implement a brand new test in the lab using new equipment and saw a rapid increase in demand for testing.

Our colleagues in immunology have now also set up a SARS-CoV-2 antibody testing service, which is used to detect evidence of a previous COVID-19 infection. Although we routinely use serological testing in virology to help us understand the timings of a viral infection, this test is still very new and there isn’t a good understanding yet of how the results can be used to either diagnose a past infection or tell us whether someone who has antibodies is protected from further infection.

How do you work with medical microbiologists and other infectious disease colleagues to help stop the spread of infection?

Our medical microbiology and virology team reviews all positive SARS-CoV-2 PCR results to ensure that appropriate follow up action is taken. For example, if the result is from a patient who is currently hospitalised, we liaise with the infection prevention and control team and the clinical team to ensure that appropriate measures are in place to prevent further spread (e.g. isolation of the patient and appropriate PPE use). We also actively engage with community infection control teams and the local PHE health protection team to support them in their role of stopping the spread of infection in community institutions.

We worked with the amazing sexual health team at NUH to set up an excellent rapid testing programme for staff members and their household contacts, with a result being available within 24 hours. This means that we can take rapid action to prevent COVID-19 being spread by staff members within our institution.

On a wider scale, we are also actively researching COVID-19 and the impact it has on our patients and environment. We submit positive samples to the COG-UK initiative for rapid genome sequencing, which is undertaken by our colleagues at the University of Nottingham. The data that this initiative provides is helping us to better understand the transmission dynamics of the virus, and can help to identify transmission clusters.

Describe an average day for the service or team at the moment? How does this differ to pre-pandemic times?

In response to the COVID-19 pandemic, and the need to provide timely results, our laboratory team implemented a voluntary rota which extended the working hours of the service from 9am–5pm to 6am–10pm, 7 days a week. On average, the laboratory processes around 500 samples per day for SARS-CoV-2, but this does fluctuate at times of increased demand and as the national guidance around testing changes. We have had to be much more reactive to changes in policy since the start of the pandemic, and planning the future of the service has been incredibly challenging due to changing requirements and the shortage of critical reagents for testing.

On average, the laboratory processes around 500 samples per day for SARS-CoV-2, but this does fluctuate at times of increased demand and as the national guidance around testing changes.

As we have team members who lead various aspects of the COVID-19 service, from strategic development to operational delivery and infection prevention, there are multiple weekly meetings that the team attend and we then feedback to each other during weekly departmental meetings. We have changed the way in which we hold meetings due to social distancing requirements, so have become proficient in the use of Microsoft Teams to keep in touch. It’s not quite the same as a face-to-face meeting, but it’s nice to see a friendly face on the other end of the computer.

What are the biggest challenges you face as a service during the pandemic and how have you taken steps to overcome these?

The largest challenge for the service has been the need to rapidly respond to the changing environment. Pre-pandemic, we would have taken the time to carefully plan the implementation of a new diagnostic test, but we have found ourselves working to unprecedented timescales with a need to provide a rapid testing service for our patients and staff members. The whole team pulled together to do this by working lots of additional hours and supporting each other through difficult times.

All of these factors helped us to become one of the first laboratories within the UK to obtain UKAS accreditation as a SARS-CoV-2 testing service, which demonstrates the high-quality service we are able to deliver and is a testament to the sheer determination of our laboratory team.

During the early weeks, the shortage of reagents for testing made it a challenging and worrying time, but we responded by working closely with our suppliers to try and maintain a stable supply chain that meant we could provide testing for those that needed it. We were also able to support other hospitals within the region at times when they weren’t able to provide SARS-CoV-2 testing. This required incredibly careful planning from our operational management team and support from our trust to invest in the equipment and staff that we needed to run the service.

We also had support from our colleagues at the University of Nottingham, who helped us to research alternative and faster methods for testing. All of these factors helped us to become one of the first laboratories within the UK to obtain UKAS accreditation as a SARS-CoV-2 testing service, which demonstrates the high-quality service we are able to deliver and is a testament to the sheer determination of our laboratory team.

Is there anything that you think is particularly unique to your virology service/lab?

We have a team here in Nottingham that embraces the need to change and adapt, which is why I think we have responded so well to the challenges posed by the pandemic. We have very well-established quality processes in place to ensure that this is done with the utmost regard to preserving quality. We are also lucky to have a dedicated R&D group within the microbiology service, who literally dropped everything to rally round and support the implementation of the SARS-CoV-2 PCR testing service. This meant that we were able to start testing locally much quicker than some other services.

And what do you think makes the team work well together?

The team here in Nottingham is very open, and we regularly invite feedback from team members and also service users as ideas for improvement are always welcome. We have several forums where members of the laboratory and medical teams come together to discuss the delivery of the test and come up with solutions to any problems and ways to continually improve. We have a multidisciplinary team meeting each week where we can discuss complicated cases and take advice from colleagues, which may be based on previous experiences or the evidence base surrounding the case.

The next big revolution in virology will be the movement away from batch testing to random access, which will enable us to provide test results for a wide range of viruses in very short time frames.

We also have brilliant working relationships with other specialties within the trust, which means we are able to discuss specialist scenarios and ensure that we are able to provide the best service that is needed to impact on patient care and management. Personally, I feel these links our team has built with the wider trust and community mean that we can provide a truly reactive and fit-for-purpose service.

How have improvements in technology helped virology? How do you make sure you are always up to date with the latest technology as much as your budget will allow?

Technology has had a substantial impact on the world of diagnostic virology in the past decade, largely with the implementation of molecular testing methods, which mean that we are now able to detect a wider range of viruses than ever before, in faster timeframes than ever before. It is due to the implementation of these technologies that we have been able to respond to the challenge to provide rapid SARS-CoV-2 testing and it is these technological breakthroughs that we will rely upon as we move into an unprecedented winter when viruses such as SARS-CoV-2 and influenza will be circulating at the same time.

The next big revolution in virology will be the movement away from batch testing to random access, which will enable us to provide test results for a wide range of viruses in very short timeframes.

What’s been the most interesting or innovative thing that you have worked on at Nottingham University Hospital?

We are a keen research centre here in Nottingham, continually horizon scanning for the next big development in diagnostic technology. We have built fantastic collaborative links with colleagues in the University of Nottingham and through our joint research endeavours we are improving our understanding of local epidemiology and are developing new and improved diagnostic techniques. A particularly exciting initiative that we are currently working on is to bring next generation sequencing to the service to improve our ability to diagnose infections that have previously proved technically challenging, while providing a greater understanding of these pathogens and helping to inform better antimicrobial treatment and infection control practices.