Appendix 1: List of interview transcripts

Dr Khalil Abudahab, Senior Software Engineer for data visualisation and integration, Centre for Genomic Pathogen Surveillance (CGPS) 7th July 2022

Dr Khalil Abudahab talks about how and his colleagues at the Centre for Pathogen Genomics adapted different software tools they already had developed for bacterial genomes to help the data sets collected by COG-UK for the SARS-CoV-2 virus. A key objective of the work was to make it easier for COG-UK members to upload data and also visualise the virus as it evolved. One of the key challenges they faced was preventing the graph component of their programme Microreact from crashing as more and more data began to come in. This required finding a way to draw more responsive phylogenetic trees as more data got uploaded. Until now Microreact had been written to have between 1,000 and 2,000 isolates in a tree. But now it faced having to upload potentially 200,000 data points in a fraction of a second. In order to solve the problem they turned to a technology mainly used for drawing lots of graphics in the gaming industry and an opensource library designed by Uber to use lots of data points to map out trips made by its taxis. Based on this they managed to build the world's first web GL viewer for genetic data on the web. Released as an open source tool, this allows anyone to draw phylogenetic trees. All the programming Abudahab did while at the same time sharing childcare. This meant he found himself coding well into the late night. But he really enjoyed the fun of the maths and logic behind the work and saw it as a light relief at a time when his daily routine was otherwise extremely repetitive.

Dr Dinesh Aggarwal, Wellcome Clinical PhD Fellow, University of Cambridge15th February 2022

Dr Dinesh Aggarwal starts by talking about his experience working as an infectious disease registrar when the first COVID-19 cases were admitted to the Hospital for Tropical Diseases in London and then the Royal Free Hospital. Feeling as though the early infections were like a sudden call to arms, the number of cases went very quickly from something that seemed relatively contained to being more widespread. At times he felt overwhelmed by the number of patients who were unable to breathe. This was not helped by the fact that the virus was still very new and the best treatments had not yet been found. In August 2020 he joined the COG-UK effort. Having little training in genomics or bioinformatics, Aggarwal underwent an intense couple of months trying to learn as much as possible before starting to investigate situations where the virus was being imported, such as through travel. He also looked at transmission within care homes and among students at Cambridge University, seeking to understand what public health measure could help mitigate transmission. Even though still a junior researcher, he was quickly roped into presenting to the SAGE Committee. While daunting, he found the experience invaluable. He also treasures the other opportunities COG-UK gave him for networking with pioneering scientists in the field.

Dr Louise Aigrain, Former head of Research Operations, Wellcome Sanger Institute and now part of the MRC Epidemiology Unit at Addenbrooke’s Hospital 26th January 2022

Dr Louise Aigrain speaks about her role in the development of new pipelines to roll out the sequencing of the SARS-CoV-2 virus as part of the COG-UK effort undertaken at the Wellcome Sanger Institute. Her previous experience in developing DNA pipelines for the UK Biobank Sequencing Project was very helpful in preparing her for the task. Juggling the demands of working from home with very young children Aigrain took on jobs that could be done remotely. Seeing the project as the chance of a life-time, Aigrain continued working despite experiencing extreme exhaustion for six months from long-COVID. Working with a team of 20 scientists, Aigrain was responsible for piecing together pipelines taken from other projects to create an end-to-end process for sequencing the COVID-19 samples. Each part of this process needed to be validated and optimised. Among the challenges she and her team was not only coping with the high volume of samples but also preventing contamination which required the development of little tricks, such as creating a device to hold plates tightly on the bench-side to make it easier to remove the seal. She also describes the development of a dashboard to track the samples as they went through the process which could also flag up where contamination occurred or where negative or positive controls had not worked. Reflecting back on the operation, Aigrain thinks that what helped was the sense that everyone was pulling in the same direction. Within the Sanger this was the first time that people from lots of different projects dropped everything to work together on the same project.

Dr Nabil-Fareed Alikhan, Bioinformatics Scientific Programmer at the Quadram Institute3rd February 2022

Dr Nabil-Fareed Alikhan switched from working on food-borne pathogens to get involved in the COG-UK effort at the Quadram Institute. Much of his work involved checking spreadsheets to make sure data had been correctly entered from patient records for the sequenced samples. In addition he was responsible for checking that there had not been any contamination of the samples or any sample mix-ups. One of the challenges he faced was having to deal with slightly different spreadsheets because Quadram was handling sample comping from four or five different hospitals across Norfolk and Suffolk. At times the workload was such that it was easy to get number blind. Another challenge he faced was that the way information got collected was constantly getting updated which required going back to update old data. He remembers in particular the stress of getting all the data cleaned up in time for uploading on Metadata Fridays. Over time the work shifted from helping to investigate outbreaks in places like poultry factories to trying to determine where the virus might be transmitted between wards within a hospital. Alikhan recalls feeling like the place became a battle station following the discovery of the Alpha and guilt of having everyone's Christmas plans being cancelled because of it. What proved useful with the new variant, however, was the serendipitous finding that it had a unique gene signature which meant it could be quickly identified with certain PCR diagnostic tests without waiting for genome sequencing.

Dr Cristina Ariani, Lead Genomic Surveillance Operations, Wellcome Sanger Institute18th March 2022

Dr Ariani begins her interview outlining how she and colleagues initially enrolled hospitals to send COVID-19 samples to the Sanger Institute for sequencing. She then discusses the challenges of processing samples from the Lighthouse labs and the logistics surrounding that. One of the first issues they had to deal with was programming the robots to help cherry-pick the thousands of samples arriving each day. Working from home, Ariani helped develop and document the standard operating procedures. She also talks about the incremental improvements made along the way to help speed up the turnaround time from the time samples were were received to when their sequencing data was uploaded. Ariani then goes on to talk about the role she played on a daily basis to convey the results to public health authorities for them to determine what measure to take to deal with outbreaks. Her interview also highlights how the sample moved through the system at the Sanger Institute, which she describes being like a factory production line. For her COG-UK was a game-changer in terms of genomic surveillance.

Dr Matthew Bashton, Computational Biologist, Northumbria University25th January 2022

Dr Matthew Bashton was just settling into a new job at Northumbria University when he got alerted to the COG-UK effort by one of the reps from Oxford Nanopore who was phoning him on a different matter. Within a month of the call he and his colleagues had become fully part of the COG-UK operation. Bashton immediately welcomed the challenge as it took his mind off the fact that he could not do another project he had just started focused on thinking about bacteria and fungi in the built environment. Having access to lots of people on Slack through COG-UK also meant that he never felt alone even though he was working remotely from home. In charge of data analysis, Bashton faced the challenge of collecting metadata and feeding that back to local hospitals to understand outbreaks and the transmission point between different wards. One pivotal moment he remembers was how the genomic sequencing helped establish how the SARS-CoV-2 virus mutated in an immunosuppressed cancer patient. What Bashton treasures about COG-UK is the strong collaboration between everyone which helped galvanise improvements all a long the way. He also really liked was the lack of paperwork and everyone had equal access to the scientific leaders and tools. For him COG-UK represents a world-first not just in terms of the scale of sequencing it undertood, but also the shared infrastructure it built which helped open up more direct discussions with the local infection teams and testing labs.

James Blackstone, Clinical Project Manager, University College London21st February 2022

James Blackstone recounts how the HOCI study was set up and run to evaluate the effectiveness of rapid genomic sequencing for reducing the transmission of the SARS-CoV-2 virus within hospitals. Set up with COG-UK funding, one of the first hurdles the study was getting NHS site teams to come on board when they were already overloaded. Another was getting data sharing sorted out and asking COG sequencing labs to generate high quality sequences at speed for the study while conducting work to fulfil the national requirements for national surveillance. Unlike clinical trials set up to evaluate drugs, the HOCI study had no precedents to draw on so was a huge learning curve. The study revealed a great heterogeneity of approach and training among infection control teams in hospitals. It also showed the difficulty of slowing down transmission within the hospital when a disease is already spreading widely in the community.

Dr Declan Bradley, COG-UK Principal Investigator at the Public Health Agency, Northern Ireland 15th February 2022

Dr Declan Bradley talks about how his work around medical informatics and healthcare records helped facilitate the partnership between the Public Health Agency in Northern and COG-UK. One of the key challenges at the beginning was Northern Ireland did not have any guidelines about when patient data could be shared. During the interview Bradley discusses the workflow used for sequencing samples in Northern Ireland and how ad hoc requests to investigate specific samples could disrupt this process. He goes on to talk about the dashboard he helped to develop for routine hospital environment infection surveillance that routinely takes outputs from CLIMB and rapid genotyping tests to inform infection control teams in hospitals. Bradley sees the legacy of COG-UK being that it has helped normalise the use of pathogen genomics overall.

Judith Breuer, Professor of Virology, University College London24th November 2022

Professor Judith Breuer first developed an interest in pathogen genome sequencing as a result of her doctoral research into HIV in the late 1990s and deepened her expertise in the field through work on the Varicella Zoster virus. As part of this work, she developed a targeted enrichment method which made it much easier to sequence large viral genomes. Thereafter, Breuer sequenced a number of pathogens and became involved in the application of genome sequencing to investigate disease outbreaks in hospitals. Prior to COVID-19 she had begun exploring the possibility of using a mixed model of centralised and localised sequencing to monitor and control norovirus outbreaks across the UK. Invited by Peacock to the first COG-UK meeting, Breuer played a pivotal role in the discussions and provided an important framework for upscaling the nation’s sequencing capacity for COVID-19. She also provides an overview of the background behind the Hospital-Onset COVID-19 Infections (HOCI study) and the challenges she and her colleagues had in running it.

Mrs Tanya Brooklyn, Genomics Surveillance Implementation Manager, Wellcome Sanger Institute17th February 2022

Tanya Brooklyn talks about her role as project manager in helping the Sanger Institute to establish its programme for sequencing the genome of the SARS-CoV-2 virus as part of COG-UK. From the start the key challenge was the high volume of samples the Institute received and had to process which was unprecedented. Getting the samples sent in the right form and finding enough storage were major issues for the team. This was solved by placing five large refrigerators, known as reefers, in the staff car park which had the ability to store up to 9 million samples. Another issue was the complex logistics of transporting the samples so there was no spillage and the management of waste. On top of this everything had to be sorted out at speed and demanded very long working hours from everyone involved. The skills that Brooklyn brought to the table was getting people to think through ways to shorten the process by asking why work was done in certain ways. Working collaboratively the team managed to radically reduce the turnaround times of sequencing by undertaking a constant assessment of what they were doing. Seeing the effort as a huge learning exercise, Brooklyn believes the immediacy and scale of the response means the Sanger will be able to do it again. She also reflects on how genomic surveillance has become a household term as a result of the work.

Dr Sarah Buchan, Lecturer in immunology, Bournemouth University1st February 2022

Dr Sarah Buchan remembers the swift transfer of equipment from Bournemouth University to Poole Hospital that she and her colleagues did to get PCR testing underway for diagnostic purposes at the start of the pandemic. Initially perched in a cytology laboratory testing sperm samples, they landed up running the PCR testing in a portacabin with minimal. On top of this supply shortages were a constant problem as was limited access to NHS databases which meant patient data had to be scribbled on pieces of paper and typed up afterwards. Despite these difficulties they managed to get RNA extracted from about 1000 patient samples. These were sent to the team at Portsmouth University to sequence for the COG-UK effort. All of this she and her colleague did while juggling homeschooling of their children and getting new lectures written. For Buchanan the work was far from her own interests, but she got involved because she felt there was a need to understand the virus and would eventually provide data that would be useful for research.

Dr Alessandro Carabelli, Research Associate, University of Cambridge Department of Medicine, leader of COG-UK’s Mutational Analysis working group 28th February 2022

Dr Alessandro Carabelli joined COG-UK just as the pandemic was about to reach the second wave. He was given responsibility for overseeing the working group looking at SARS-CoV-2 mutations. One of the biggest challenges the group had was keeping up with the volume of papers and preprints coming out on a daily basis and in the area. They also needed to find a way to manage the uncertainties and ensuring they put out a clear message so that they did not contribute to any confusion generated in the media. A core component of the group's work involved building a dashboard to pull together data from all the literature and sequencing in one place. This led to the development of Mutation Explorer which provides structural information on the mutations of the SARS-CoV-2 virus correlated with how this impacts the efficacy of treatments and vaccines. Carabelli flags up the strong sense of collaboration among the scientists who came from different backgrounds institutions that went into making the dashboard. What also sticks out for him was the ability of Sharon Peacock to reiterate the importance of collaboration and seeing the big picture whenever the pressure mounted.

Sir Professor Mark Caulfield, Vice Principal for Health, Queen Mary University’s Faculty of Medicine and Dentistry, COG-UK contributor, former Chief Scientist at Genomics England 1st March 2022

Sir Professor Mark Caulfield outlines how sequencing the human genome became embedded right from the start in the work undertaken by COG-UK alongside the sequencing of the SARS-CoV-2 viral genome. Invited to attend the first COG-UK meeting, Caulfield was incredibly impressed with the camaraderie of everyone present and then how quickly they managed to mobilise the infrastructure for pathogen sequencing in both academic and NHS environments. Alongside this he helped found a subsection on the COG-UK's Steering Committee to work on understanding the human genetics of severe COVID-19. He discusses the strategy adopted for doing this work which provided powerful insights into the interaction between the viral and host genome. By linking the viral sequences with human sequences taken from patients critically ill with COVID and a control group, this flagged particular risk regions in the genetic code important in the aetiology of severe disease. Caulfield goes on to talk about how the work has been informed by the 100,000 Genomes Project and what it means for the future in terms of Genomics Medicine. He also praises the leadership skills of Sharon Peacock, whose foresight and ability to manage everything with gentle persuasion was critical to getting COG-UK off the ground and making sure everyone was treated with fairness and equity.

Dr Michael Chapman, Director of Health Informatics, Health Data Research UK Cambridge22nd March 2022

Dr Michael Chapman talks about the challenges of networks of laboratories, each with their own information systems and protocols, combining together to link genomic sequences with patients' medical records. The key issue was finding a way to make sure all patients' data was kept confidential while not slowing down the immediate work COG-UK needed to do to track the spread of COVID-19. Fortunately both he and people in PHE already had very good expertise in the collection of health data so knew how to get the right ethical and legal permissions in place. But it took many hours to get sorted. Another obstacle Chapman recalls was the enormous demand for staff skilled in informatics across the board which made recruitment difficult. To some extent this shortage was plugged by academic volunteers. He also speaks about the challenge posed by the huge number of samples and data flowing in.

Dr Tim Cutts, Formerly Head of Scientific Computing, Wellcome Sanger Institute 25th January 2022

Dr Tim Cutts talks about how he pivoted from IT support for the sequencing of the UK Biobank genome project to helping Sanger staff get set up at home to work remotely. Following this he became involved in expanding the cloud infrastructure capacity for Sanger to be able to contribute to the COG-UK effort. Having already built in patient confidentiality into the UK Biobank system, Cutts points out that this gave them a head start when it came to designing the architecture for the COG-UK work. What also helped was getting the Amazon Web Services on board to help speed up the computing process for sequencing and analysing the SARS-CoV-2 genome data. This has meant that whenever there is new data it gets incorporated into the genetic tree within an hour. What Cutts liked most about the work he did as part of COG-UK was the sense that everyone was working on the same project and pulling together in the same direction for the public good.

Dr Ana Da Silva Filipe, Research fellow, NGS Facility Manager, Centre for Virus Research, University of Glasgow21st December 2021

Dr Da Silva Filipe talks about the work she did at the Glasgow University Centre for Virus Research (CVR) to support the sequencing of SARS-CoV-2 virus genomes for COG-UK. Prior to joining COG-UK, she and her team had already sequenced the first COVID-19 cases Scotland using the ARTIC methodology. Da Silva Filipe highlights that CVR quickly formed a collaboration with Andrew Rambaut and his team at the University of Edinburgh which provided an important foundation for the work they did with COG-UK. She outlines how the two hubs worked out which parts of Scotland they would each cover and the challenges they faced educating different laboratories in the supply of samples for sequencing. Over time she notes that the volume of sequencing increased as a result of improvements made to the protocol which also reduced the number of staff needed to perform the work. She also discusses the importance of COG-UK in providing a network of people to talk to for problem-shooting.

Professor Thushan de Silva, Principal Investigator of COG-UK, Senior Clinical Lecturer at the University of Sheffield25th January 2022

Professor Thushan de Silva was asked to join the COG-UK effort out of the blue after he and and his colleagues reported on Twitter that they had sequenced two samples from some of the first UK patients with COVID-19. Having just returned from spending some time working on infectious diseases in Gambia, de Silva was still in the midst of establishing his team when he became involved in the Consortium. According to de Silva one of the strengths the Sheffield COG-UK team was how well they worked together across the NHS and the University. This meant they could quickly go seamlessly from patient to sequence. Initially their sequencing was supported from other research funding. It later got supported by COG-UK, without which de Silva thinks they would not have continued sequencing. Results from the sequencing were rapidly fed back to the infection control teams and clinical teams in the hospital to help put in measure to reduce transmissions between wards. Working very long hours both in the clinic and analysing sequence data, de Silva recalls one of the major challenges was just keeping on top of the seer volume of samples coming through and making sure they produced high quality data at speed. He also put in a lot of time to understand new variants that appeared to be causing ward clusters. Like many involved in COG-UK, one of the watershed moments for de Silva was the discovery of the Alpha variant which shifted the debate as to the importance of mutations in the virus.

Professor Darren Smith, Personal Chair in Bacteriophage Biology, Northumbria University15th December 2022

Professor Darren Smith outlines how he and his team's work for COG-UK was assisted by the availability of new laboratory equipped with a number of sequencers that had just opened for a project designed to look at the use of biological processes to aid the sustainability of the built environment. Opened just prior to the pandemic with a large grant from Research England, this laboratory allowed his group to support COG-UK work across the large North-East of England region. As well as carrying out sequencing for surveillance purposes, the group also targeted samples linked to important sites like care homes and prisons and also sequenced some wastewater samples. Overall the team went from sequencing about 100 samples per week to thousands per week. Smith also talks about how the civet tool developed by the team in Edinburgh was a game changer for talking to clinicians about the data for infection control purposes.

Dr Nicholas Ellaby, Bioinformatician, Public Health England (now UK Health Security Agency)25th January 2022

Dr Nicholas Ellaby recounts how the sequence data posted on CLIMB by COG-UK was used by at Public Health England to conduct outbreak investigations associated with COVID-19. In particular he talks about how this helped inform outbreaks observed in hospitals, schools, prisons and nursing care homes. He also highlights how closely he and others within Public Health England worked with academics like Andrew Rambaut, Eric Volz and Nick Loman to analyse the data. For him the work undertaken by COG-UK helped accelerate the development of a national genomic surveillance system within Public Health England. Ellaby also describes the methods used to identify variants of concern and the reporting mechanism used for this. A lot of this work is done under the umbrella of the Horizon Scanning group in Public Health England which monitors different streams to establish if there are signals of concern.

Sir Jeremy Farrar, Director of the Wellcome Trust13th January 2022

Sir Jeremy Farrar credits the foundation and success of COG-UK to the vision and ability of Sharon Peacock. When Farrar opened what turned out to be the inaugural meeting of COG-UK his impression was a room full of people with enormous expertise in pathogen genomics and great enthusiasm and energy to see the project succeed. At the time no one knew how important COG-UK would be for turning what was at the time effectively an academic research exercise into becoming a mainstream tool for public health. He points out that up until that moment most of the focus had been on pathogen genomics in lower-middle income countries for diseases like malaria and HIV. Another issue was that the research community and public health communities had been relatively siloed. For Farrar genomic sequencing has played a key role in the appreciation of the shifting nature of the SARS-CoV-2 virus and its massive diversity at the global level. What encouraged Farrar about COVID-19 was that it forced people to come to work together for the common good. Based on the model COG-UK established he hopes that going forward people do not return back to just working in silos. He also makes the point that global health in highly dependent on making sure all countries have equal access to the tools for genomic surveillance.

Amy Gaskin, Bioinformatician and Genomic Epidemiologist at Pathogen Genomics Unit (PenGU), Public Health Wales4th April 2022

Amy Gaskin recalls the work that she did for the COG-UK effort as part of PenGU at Public Health Wales. She points out that Wales was well-equipped to contribute to the COG-UK initiative because it already had a strong infrastructure for genome sequencing which began to be put in place from 2014. Just how well prepared Wales was can be seen from the fact that by June 2021 Wales had a higher sequencing coverage than England. Being a bioinformatician, the bulk of Gaskin's work during COVID has involved collating genomic sequencing data with patient metadata from different centres for analysis which the Welsh government used to inform their public health policies such as when they closed the border to cause a firebreak. For Gaskin, COG-UK has provided an invaluable opportunity for networking and also a model of collaboration. Gaskin highlights some of the challenges she faced switching off from her COVID-19 work and the difficulties of answering questions from friends about the SARS-CoV-2 when so little was still unknown scientifically about it. At the end of the discussion Gaskin reflects on how she came to study bioinformatics and where she sees its importance for the future. She also highlights the need to make genomic sequencing accessible worldwide to help in the detection of how the virus is evolving and transmitting around the world.

Dr Sharon Glaysher, Specialist Biomedical Scientist who manages Portsmouth Hospitals University NHS Trust's Research Laboratory25th May 2022

Dr Sharon Glaysher discusses how she and her team at Portsmouth NHS Hospitals Trust that normally supports clinical trials and in-house research became part of the COG-UK hub in the southern region sequencing COVID-19 samples for the COG-UK effort. This they did alongside continuing to support other clinical research. Among the challenges they faced was training different sites to send samples in the right format. Having only limited staff and doing everything by hand meant the work was intense. She recalls having to work alone throughout the Christmas period following the discovery of Alpha in December 2020. What got her through was listing to music and audiobooks. While only a small group, the team in Portsmouth never felt they were alone because of the links they had to other COG-UK members through Slack and regular Teams updates. Reflecting back she thinks the work undertaken for COG-UK helped clinicians, nurses and others on the ground understand the benefits of genome science and how it could improve care.

Dr Sonia Goncalves, Head of Service Delivery, Genomic Surveillance in the Genomic Surveillance Unit, Wellcome Sanger Institute16th March 2022

Dr Sonia Goncalves quickly became involved in early meetings at Sanger to determine how it could contribute to sequencing COVID-19 samples for the COG-UK initiative. A lot of the effort at the beginning was about coordinating all the communications between the many different external labs involved and setting up processes for how to receive samples. One of the biggest challenges at the time was Sanger was getting a lot of samples in different formats which made it difficult to standardise. She immediately allocated her team to liaise with different sites to know how they operated and help them understand the best way to send in the samples. Looking back, she reflects that what was novel for Sanger at that moment in time was the coming together of people from many different internal teams to all focus on one project. Also she believes that why the work was so successful at Sanger is because everybody had a clear sense of purpose and knew how their work fitted into the whole process from beginning to end. She also talks about how the sequencing process changed over time both in terms of being able to prioritise certain samples as new variants appeared and reducing turnaround time. All of this helped Sanger set up a completely new laboratory dedicated to COVID work which now works directly with the UKHSA.

Dr William Hamilton, academic clinician working in infectious disease and microbiology at Cambridge University Hospitals NHS Foundation Trust17th February 2022

Dr William Hamilton recounts the first few months of the pandemic working as an infectious disease physician on the COVID wards where he encountered the challenge of working fast enough to get through the high volume of patients. Working on the ward he was able to see in real-time the beneficial impact of the introduction of treatments like dexamethasone. He also remembers the relief he felt once he was able to get the COVID-19 vaccine and the hope it generated among himself and his colleagues. Having a position both at the Sanger Institute and at Addenbrooke's Hospital meant Hamilton was uniquely positioned for accessing clinical data needed for patient samples sequenced for the COG-UK effort. He rapidly became involved in writing a computer code to link the sequenced samples with patient data which he did in combination with his clinical work. Following this he worked with colleagues to use the sequencing data to investigate local outbreaks. This resulted in them publishing one of the largest genomic study of care home outbreaks in the world. He also helped do a lot of prospective hospital outbreak investigation which prompted a lot of doctors on the ground contacting them for more information. For Hamilton this is a true testament to the unity genomic sequencing provided for surveillance which he believes needs to be advanced further into a dashboard so that it does not rest on the shoulders of individual people working with their laptops. Towards the end he also flags up the complex ethical challenges involved in preserving patient confidentiality which he and the COG-UK team had to deal with when sharing data.

Dr Ian Harrison, SARS CoV-2 genomics analysis cell, Public Health England (UKHSA) 3rd March 2022

Dr Ian Harrison remembers how he became roped into the effort undertaken by the Genomics Cell at Public Health England in April to pull together the COG-UK network of academic laboratories to kick start the sequencing process. Floating around to help where things needed to get sorted, he initially became involved in establishing the COG-Consortium agreement. For him one of the unique features of COG-UK was the way in which the academic community was linked into the public health response so that they could feed in to it. This was pivotal to to detecting Alpha and other variants of concern early on. One of the biggest challenges in this process was working out how to share data without breaking patient confidentiality. He also talks about the difficulties of joining up what the test and tract system was doing with what COG-UK was doing. Part of the problem was the process was very new to the vast majority of people and everyone was having to learn very quickly. Another major obstacle they had was the fact patients do not have a unique personal NHS identifier across the country because it has been set up based on localities. This makes it difficult to join up databases across the entire country.

Dr Ewan Harrison (Deputy Director COG-UK and UKRI Innovation Fellow, Wellcome Sanger Institute, Senior Research Associate, Department of Medicine, University of Cambridge) and Dr Andrew Jermy (External Communications Advisor COG-UK) 22nd January 2022

Dr Ewan Harrison and Dr Andy Jermy look back at the very early days of helping to set up the COG-UK structure and the challenge of getting agreements with different partners. Acting initially as an advisor, Jermy soon found himself playing a pivotal role informing the Scientific Advisory Group for Emergencies through his reports of COG-UK findings which was fed into government policy. As he points out, initially the genomic sequencing was not quick enough to establish what was happening in the community or help with particular outbreaks, but its value became much more obvious once variants of concern began appearing towards the end of 2020. The key thing was making sure not to over-claim what the genetics could say. Meanwhile, Harrison was at the front end of bringing on board a large network of sequencing sites which involved a lot of challenges concerning data sharing and also allocating appropriate funding to each of them. Many sites that joined the effort later were not named on the funding application so joined at their risk. Harrison also remembers a lot of wrangling about who was to take responsibility for the risks around potential patient data breaches, but, as he says, was absolutely critical to making sure data could get into the system so that public health agencies and academics could start analysing it. The hardest challenge from his perspective was linking a sample to a patient. He goes on to discuss how Sanger managed to increase the capacity for sequencing samples and reduce the turnaround time for processing them with help of robotics. Towards the end of the interview Harrison and Jermy reflect on how they managed to juggle the heavy workload while balancing the needs of their family and home life. They also talk about the importance of genome sequencing within the context of the variants both for diagnostics and having the right primers to perform sequencing.

Dr Verity Hill, Member of COG-UK, former PhD student at University of Edinburgh, now a postdoctoral researcher at Yale School of Public Health16th February 2022

Verity Hill discusses the role she played in the development of analytical tools for helping the COG-UK effort to visualise the evolution and spread of the SARS-CoV-2 virus. This she did by building on the model she developed as part of her PhD project for understanding the dynamics of the Ebola virus in Sierra Leone. She discusses the background behind the development of the Pangolin tool, which helps name different lineages of the SARS-CoV-2 virus. As part of COG-UK she also helped to create Civet which enables people to pull out specific genomic sequence data from CLIMB and GISAID to understand what is happening with the virus within a local context such as in a hospital or NHS Trust. She also talks about developing Grinch, a software tool that makes it possible to see how new variants of concern change day to day. One of the key challenges she faced was cleaning the geographical metadata for mapping the spread of the virus.

Dr Emma Hodcroft, Molecular epidemiologist, Institute for Social and Preventive Medicine, University of Bern, co-developer of Nextstrain 12th May 2022

Dr Emma Hodcroft remembers the very early days of the pandemic when she and her colleagues began collecting SARS-CoV-2 genome sequences from around the world to upload online into Nexstrain's central open source database as a way of tracking how the virus was evolving. With just a few hundred sequences to start with this task was relatively easy at first, but became increasingly harder as more and more data flooded in. Aware of the need to upload the sequences as fast as possible she remembers copying and pasting them out of browsers while travelling on buses, trains and when sitting in airports. What immediately struck her in this process was how how uneven genomic sequencing was around the world and how hard it was to convince governments of the need to invest in sequencing. For this reason she was absolutely amazed by the national sequencing initiative mounted by COG-UK. She was not only impressed by the remarkable speed with which COG-UK got off the ground but also the number of sequences it generated. According to her, COG-UK really shifted attitudes around the world about what is possible with genomic sequencing and set a gold standard for going forward.

Professor Matthew Holden, Director of Impact, St Andrews University, Whole Genome Sequencing Advisor, Public Health Scotland23rd February 2022

The first part of Professor Matthew Holden's interview provides an overview of how COVID-19 testing was set up in different areas of Scotland. He then talks through how he became involved in assisting Public Health Scotland to engage with the work undertaken by COG-UK. To do this he worked closely with teams at the Centre for Virus Research at the University of Glasgow and the University of Edinburgh. A key element of his role was facilitating links between the different groups involved so that Public Health Scotland had access to the data generated. For him COG-UK did an exceptional job in demonstrating the utility of the genome data collected which proved highly beneficial when it came to passing on the information to the Scottish government to implement public health measures. On the back of this, he and his colleagues were able to secure government funding to establish an NHS sequencing service in Scotland.

Stephanie Hutchings (Trainee Clinical Scientist in Infection Sciences), Hannah Pymont (Qualified Clinical Scientist, Trainee Consultant Clinical Scientist in Microbiology), Public Health Laboratory, Bristol 23rd February 2022

Stephanie Hutchings and Hannah Pymont talk about how they got roped into helping to sort and pick out COVID-19 samples to send off to the Sanger Institute and other COG-UK sites when their Scientific Training Programme at the Public Health Laboratory got interrupted at the start of the pandemic. With the laboratory initially testing everything within the Southwest region, the work involved a lot of co-ordination with many different people and shifting to working a 24 hour rota. Keeping track of samples and on top of the huge volume of emails proved particularly challenging. At the beginning they also needed to inactivate the samples and do a lot of manual preparation for PCR testing which involved a lot of pipetting. While they tried their best to automate as much as possible, surges in testing made the process unpredictable. They also highlight the difficulties they encountered arranging for the delivery of dry ice and couriers to transport samples between different sites. Another issue they flag up is the amount of waste generated by the process of testing because nothing could be recycled due to the risk of infecting people. Pitching in wherever they could help, Hutchings and Pymont feel they gained invaluable insights into genomic sequencing which their training programme did not cover. They also appreciate the leadership skills they picked up through the COG-UK work and value accorded to women scientists.

Dr Leigh Jackson (Lecturer in Genomic Medicine, University of Exeter and Scientific Lead, COG-Train) and Peter Thomas-McEwen (COG-Train Programme Manager, University of Cambridge)11th February 2022

Dr Leigh Jackson and Peter Thomas-McEwan got involved in COG from different backgrounds. Jackson came armed with the experience he had of dealing with Ebola in Sierra Leone, while Thomas-McEwan had done a lot of work around influenza to inform vaccine strain selection each year. To start with Jackson was brought in just when the Alpha wave was breaking to help scale up the network's capacity for sequencing and speed up turnaround time and improve quality. What struck him immediately was how different all four nations were when it came to data agreements and material transfer. Alongside attempting to help identify and resolve bottlenecks around the country, Jackson was soon called upon to also provide scientific advice to policymakers. By contrast Thomas-McKewan was hired in September 2021 as progamme manager for COG-Train to help deliver the training programme to expand genomic sequencing capacity and analysis across the world. Together Thomas-McEwan and Jackson point out that COG-Train was founded on Sharon Peacock's emphasis on inclusivity and equality with the objective of being a global learning endeavour aimed at people sharing how they have tackled genomic sequencing in different settings around the world. In delivering the training programme worldwide, they are highly aware not only of the potential cultural and language barriers but also the wide disparity in the type of scientific infrastructures, internet capacity and networks that exist in different countries. At the heart of the project is the recognition that there is no point in just two or three countries being good at genomic surveillance because of the global nature of the pandemic and other infectious diseases.

Dr Phil James (Associate Director, Clinical Applications), Dr David Stoddart (Senior Director of Sample Technology, Applications) and Sarah Foxton (Communications), Oxford Nanopore Technologies Ltd17th March 2022

Dr Phil James and Dr David Stoddart recall how the public release of the first genome of the SARS-CoV-2 virus and RNA from another common coronavirus. 229E, enabled them to design an early protocol to help others begin sequencing COVID samples. This involved them testing different lengths of amplicons and working out how much material was needed for the preparation step. As they point out, they were not the only ones, working out what to do. So too was Joshua Quick and Nick Loman, with whom they already had a close collaboration. Both teams converged on the same sort of method but from slightly different tracks. They go on to talk about the steps taken to streamline the preparation time in the protocol so that people could sequence platefuls of samples as case numbers increased. One way they did this was to tweak the barcoding method using a different wash buffer. Towards the end of the interview Sarah Foxton reflects on how Oxford Nanopore supported the different laboratories around the world during the pandemic to get up and running with sequencing to help with surveillance. A key theme running through the interview is the strong collaboration between industry and academics and unprecedented scale of open sharing of data.

Dr Ian Johnston, Head Of Sequencing Operations & R&D, Wellcome Sanger Institute22nd March 2022

Dr Ian Johnston discusses how quickly the team at the Sanger settled on adapting its pre-existing single cell RNA sequencing pipeline for processing vast numbers of COVID-19 samples as part of COG-UK. What was good about the pipeline was it had a high throughput and good automation. Extremely mindful of the supply shortages, the team immediately looked into ways to reduce the number of steps in the sequencing process including the primer method. This not only reduced the pressure on consumables like plastic pipettes tips, which were in short supply globally, but also made things much simpler, freed up laboratory equipment and paved the way to significantly scaling up. Johnston indicates that a game changer for Sanger was when the Lighthouse Labs got set up because this provided access to RNA extracts being thrown out after completing the testing process. Fortuitously, Johnston had a direct line to his former colleague Tony Cox who headed up the Lighthouse operation. The advantage of the RNA extracts was they are much safer than primary samples because they do not require live virus. They also came in 96 plates which slotted perfectly into the Sanger's pre-existing processes. This made it possible for the Sanger to scale up very quickly. Getting the Lighthouse labs on board required the Sanger to put in place large container freezers to store the samples and a lot of co-ordination to ensure it got the right information and metadata as well as making sure the samples were packaged and shipped correctly. Initially the Sanger also had to put in place measures to cherry-pick positive samples because the Lighthouse was supplying plates with mixed positive and negative samples. Johnston also speaks about the iterative changes made to the process over time which both cut down the turnaround time and increased capacity. What Johnston particularly valued in working with COG-UK was the collaborative spirit of everyone involved.

Dr Beatrix Kele (Clinical Scientist), Dr Maria Teresa Cutino-Moguel (Virology Clinical Lead), Barts Health NHS Trust4th February 2022

Dr Beatrix Kele and Dr Maria Teresa Cutino-Moguel recall their experiences of earlier epidemics in their home countries and how COVID-19 was handled there. They then shift to talking about how the team in the testing lab got enrolled in the COG-UK effort to sequences SARS-CoV-2 samples from hospitalised patients for Northeast London. From the start the team decided to do the sequencing themselves in-house. This was in part because they did not have the resources or staff to send away the samples. But they also saw it as a huge opportunity to expand the sequencing capacity within their laboratory for the future. Funding for the sequencing came out of their own budget and also a grant from Barts Charity. One of the biggest challenges they faced was the lab was seriously understaffed. Another issue they faced was constantly troubleshooting because of shortages in reagents and consumables. To get the data analysis underway they also had to call on the goodwill of Beatrix's husband and his expertise in coding and programming. They are also extremely grateful to the support they got from COG-UK which provided them with the key knowledge they were missing as well as the primers and ready-to use protocol. By comparison with other places like the Sanger, Barts sequenced far fewer samples. But, as they point out, the samples they did were important because they came from hospitalised patients and from a deprived and diverse ethnic population. Going forward they are grateful for the work they did with COG-UK because it forced them to gain new expertise in sequencing technology and become good at troubleshooting.

Dr Anna Kinsey, Head of Epidemic Preparedness, Medical Research Council, UKRI7th February 2022

Dr Anna Kinsey kicks off the interview by talking about the types of high-level research priorities the UKRI and MRC set out in its rapid response call at the start of the pandemic. She provides an overview of the MRC's track record in funding genomic sequencing prior to the pandemic in Africa and previous support of CLIMB, the cloud computing infrastructure which proved a pivotal foundation for COG-UK. As observer on the Consortium's monthly meetings of Steering Committee from September 2020, Kinsey saw a lot of the work that went into establishing the mechanisms of working and different agreements. She saw first hand the challenges public health agencies, academics and NHS organisations, each with their own priorities and concerns, had working together to deliver under significant pressure. What struck her was the overwhelmingly positive atmosphere throughout as well as the goodwill and recognition of everyone's effort. Towards the end she turns her attention to thinking through the legacy of COG-UK and working how that can be carried forward for pathogen genome sequencing in the future internationally.

Petra Korelevic, Research Fellow, Wellcome Sanger Institute22nd August 2022

Petra Korelevic volunteered very quickly to help with Sanger’s sequencing of COVID-19 samples as part of COG-UK. Not able to continue her own research because of lockdown, she leapt at the chance to contribute because otherwise she would have gone stir crazy. Starting in June 2020, she joined the team responsible for the management and disposal of samples once they had been sequenced. A great deal of her work involved physical labour shifting and stacking boxes that arrived at Sanger from different testing sites around the country. Many of the boxes had to be loaded into very cold freezers. To cope with the chilly conditions they had to wear very thick jackets and gloves as well as special boots. As Korelevic points out this was not always comfortable because of the very hot summer. Because the work was very physical, volunteers were deliberately given very short shifts. She goes on to talk of the difficulties of not having a car and needing to rely on taxis when called in to help transfer samples when one of the freezers malfunctioned. Looking back, she believes the experience was invaluable for getting her accustomed to the regulations around masks and social distancing when she went back to her normal routine.

Professor Dominic Kwiatkowski, Head of Parasites and Microbes Programme at the Wellcome Sanger Institute in Cambridge and Professor of Genomics at University of Oxford10th January 2022

Professor Dominic Kwiatkowski begins by talking about the strategy that the Wellcome Sanger Institute outlined prior to COVID-19 for developing systematic longitudinal genomic surveillance for public health. In his case, this was informed by the work he had done over the previous decades for malaria. They had just put forward this vision in the application to renew their five-yearly cycle of funding from the Wellcome Trust which they were awarded just before the pandemic. Kwiatkowski then switches to discussing the first meeting held to set up COG-UK and the thinking that went into why the Institute decided to become the central sequencing hub to help cover areas in the country that did not have the capacity to do sequencing. Unable to easily contribute to the fast turnaround of samples required for outbreak investigations, the Institute decided to focus its efforts on sequencing samples for national surveillance. Its effort in this area was greatly helped by the setting up of the Lighthouse Labs for community testing. Importantly this gave the Institute access to a large source of samples which could be easily slotted into its sequencing operation. But it did pose challenges in terms of storage and putting in place a system to cherry-pick the positive samples. Once sorted, the Institute set to work on improving its sequencing process to speed up the turnaround time which was achieved by continually looking at where iterative changes could be made to different parts of the pipeline.

Dr Cordelia Langford, Director of Scientific Operations, Wellcome Sanger Institute2nd February 2022

Dr Cordelia Langford talks through the very early brainstorming sessions held at the Sanger Institute about how they could contribute to combating the pandemic and discussion they had with Sir Patrick Vallance to bring him up to speed on what genomic sequencing could offer. This happened before the first meeting to set up COG-UK by which time the Sanger had already prepared some feasibility models for sequencing large numbers of samples based on its existing infrastructure. Reflecting on the first meeting, she recalls a huge sense of humility and modesty among the participants and desire to come up with a collective plan to address COVID-19. Everyone was acutely aware of the grave situation. Following the meeting, Langford established a number of guiding principles to help Sanger build out of its sequencing operation. The first was to make sure the health of the staff was always protected. Another was to design and scale up the pipeline with equipment in way that it did not adversely affect what were already overburdened supply chains. An enormous amount of effort also went into looking at the molecular biology process to see how it could be streamlined to speed it up. According to Langford the game-changing moment for Sanger was when they started to receive vast quantities of samples from the Lighthouse Labs. This was essentially waste product from the testing it was doing among people in the community. To cope with the volume the Sanger had to build a frozen storage compound in the car park. Made up of five large freezers the size of lorries, this provided capacity to potentially store six million samples. Another key turning point was the identification of the Alpha variant in December 2020 which raised public awareness of the importance of genomic surveillance.

Rich Livett, Senior Scientific Manager of Laboratory Information Management systems (LIMS) for core informatics, Wellcome Sanger Institute.21st February 2022

Rich Livett speaks about how he helped build the software for the Sanger pipeline to support its sequencing for the COG-UK effort. What impressed him was how well he and his team were able to develop the software remotely without having to watch the scientists directly on-site. Instead they relied on the scientists providing diagrams and videoing themselves to show the work process. Very quickly he and his team became involved in developing the software to programme the robots to cherry pick the positive SARS-CoV-2 samples that arrived on the plates from the Lighthouse Labs. They also wrote a piece of software to automatically prioritise certain samples over others to make sure that a good cross section of samples was sequenced from across the UK. Being able to pick samples smartly across the UK was important in terms of not having to increase capacity. He highlights the pressure of having to build software quickly without the luxury of time to test it first in a safe environment. One of the reasons he believes they were successful was because the core Laboratory Management Systems team already had a good working relationship for a number of years. He also says he was able to cut some of the bureaucracy in the first few days because Tony Cox, who headed up the Lighthouse Labs, was his former boss. This made it easy for him to communicate directly with him. At the end he discusses Sanger's plans to establish a Genomics Surveillance Unit which is an important legacy from the work done with COG-UK.

Professor Matt Loose, Professor of Developmental and Computational Biology, University of Nottingham 8th December 2022

Professor Matt Loose discusses the strict measures he and his team put in place in the laboratory to prevent contamination to carry out sequencing for the COG-UK effort. Initially the team began by sequencing samples from the hospitals in Nottingham, but this soon expanded to also taking in samples from Leicester and from community test sites. At the height of its sequencing it was taking in samples from five different hospital networks. This raised several challenges in terms of logistics and also capturing the metadata. On the ground, Loose highlights how his team was able to feed the sequencing data to the local hospital infection control team to help them identify what was happening with particular outbreaks. In many ways this work helped strengthen the ties between Loose's team and the hospital which is now being carried forward into other projects.

Dr Catherine Ludden, Director of Operations, COG-UK and Beth Blane, Logistics Manager for COG-UK, Research Assistant in the Department of Medicine, University of Cambridge5th January 2022

Dr Catherine Ludden and Beth Blane talk through the important role they had at the beginning in building up the logistics behind COG-UK. A lot of this involved working closely with different laboratories to determine what capacity they had for sequencing samples and finding a way to bring them on board. Both Ludden and Blane came from a background of working on antimicrobial resistance but had different expertise for undertaking this task. In Ludden's case she was able to draw on the work she had done in Sweden to persuade scientists to voluntarily collaborate in the building of a European surveillance system for monitoring antibiotics resistance. By contrast, Blane had a deep knowledge of NHS laboratories and microbial laboratories within the UK which was important for an understanding of how to approach them to contribute samples to the COG-UK effort. Initially samples were distributed to different laboratories based on requests from public health agencies looking to investigate outbreaks, but over time the process became more organised. In terms of the day-to-day organisation, Blane and Ludden found Slack and Zoom incredibly useful for communicating and coordinating the distribution of samples across the country. Early on Ludden became passionate about developing a map of the different laboratories on-boarded and coverage reports which was important for tailoring capacity and improving the process. She also points out that capacity was not a black and white issue and dependent on a number of variables including whether the samples were supplied in individual tubes or as RNA extracts on microwell plates.

Professor Patrick Maxwell, Physician and the Regius Professor of Physic at the University of Cambridge23rd February 2022

Professor Patrick Maxwell discusses the complex facilitator role that University of Cambridge played in the establishment of COG-UK. While the University was central to the time-consuming process of rolling out contracts and legal work behind COG-UK, from the start it was careful to promote the project as a broad collaboration with many partners. A lot of success of COG-UK Maxwell attribute to skillful leadership of Sharon Peacock and her effective and diplomatic management of the different stakeholders which helped to reduce any potential friction. One of the major challenges from the start was handling the uncertainty of starting work before grant contracts had been signed which posed a significant risk for the researchers involved. Maxwell also highlights that there were considerable difficulties negotiating the data transfer agreements in relation to public health data. Reflecting on the achievements that were made, Maxwell points in particular to the genomic information that was collected through the mass asymptomatic testing of students. Conducted in real time this provided invaluable data to enable students to isolate when they were infected and also showed no cross-infection between students and the wider city community. Towards the end of the interview, Maxwell reflects on the complex politics that surrounded the transition to centralised genomic surveillance away from the hub and spoke model of COG-UK. Overall he believes that the legacy of COG-UK going forward is that it shows that you can form an effective network with many centres and that the genomic information yields invaluable information which cannot be obtained through any other route.

Georgie McManus, Former Communications Coordinator, COG-UK1st November 2021

Georgie McManus starts the interview recounting the difficulties she faced flying back to the UK from Australia. When she applied to join COG-UK she had little idea what her role would involve. Her first task was to help build out the website for the Consortium so that the public could better understand the purpose of COG-UK and the partners involved. Initially little interest was shown in what COG-UK was doing. As McManus points out this all changed following the discovery of the Alpha variant in late December 2020, which resulted in an avalanche of media requests. Similarly the number of Twitter followers increased from about 2,000 to 10,000 in the space of a week.

Lizzie Meadows, Project manager, Quadram Institute Bioscience15th March 2022

Lizzie Meadows was just switching jobs when she first heard about the outbreak of the new virus in Wuhan and soon after was hired by the Norwich Research Park Biorepository to oversee the installation of its new laboratory information management system. Hearing about her friends living abroad who had already gone into lockdown, she immediately set about thinking about how the new system could be rolled out if it they had to start working remotely. Due to go live with the system on 23 March 2020, the day the UK went into lockdown, a few days before Meadows found herself thrown off course when a number of key staff came down with COVID. With not many hours to go, she sat down to learn how to operate MSTeams and then trained other members of the project team half an hour before the management system went live. The same morning she received news about Quadram's partnership with COG-UK and within two days was helping to determine what needed to be done. It quickly became clear that the biorepository was ideally placed to act as an intermediary to handle the metadata needed for samples sequenced by the Quadram team. Unlike the biorepository, which already has governance structures in place to handle patient samples and their data, Quadram could only work with anonymised data. This saw Meadows taking on the role of relationship manager to make sure the process flowed smoothly. In the end the work not only helped strengthen the ties between the two institutions but also raised the profile of the Biorepository within Norfolk & Norwich University Hospital.

Dr Julia Miskelly, Manager of the Genomics Core Technology Unit, Queen's University Belfast28th February 2022

Dr Julia Miskelly starts off by discussing the major challenges she and her team faced at the start of the pandemic as a result of the shutting down of the border by Brexit which made it very difficult to access reagents which impacted their ability to deliver on sequencing. In order to overcome the problem they turned to miniaturising the whole assay. Subsequently adopted by other teams in COG-UK, their miniaturisation method made it possible to dramatically cut down the amount of reagents needed. Alongside this they also had to make 69 gallons of lysis buffer to send to hospitals and testing sites in Northern Ireland which they needed to deactivate the SARS-CoV-2 virus in samples put through PCR tests. Miskelly points out that Northern Ireland took some time to fully get on the COG-UK map because of the major shortage of staff and consumables which continued to be a problem until the summer of 2020. Despite the slow start, Miskelly believes the collaboration with COG-UK was invaluable for Northern Ireland because it helped increase the equipment available for doing genomic sequencing and also expanded the team at Queen's University Belfast for doing such work. For Miskelly the experience has really shown what Northern Ireland is capable of doing in the way of genomics and playing an equal part with the rest of the UK.

Dr Peter Muir, Clinical scientist at Public Health England (now UKHSA), Public Health England, Public Health Laboratory Bristol 10th February 2022

Dr Peter Muir discusses how the Public Health Laboratory Bristol collaborated with the Sanger Institute in processing COVID-19 samples from the SouthWest region for sequencing as part of the COG-UK effort. After talking about the ethical and logistic challenges involved in the work, Muir highlights how participation in the COG-UK effort helped the laboratory establish the infrastructure for carrying out genome sequencing locally on a routine basis. He also discusses how results from COG-UK have helped inform public health measures around COVID-19 on the ground. Another benefit he has seen with COG-UK has been the value its has accorded to women scientists.

Dr Richard Myers, Head of the Bioinformatics Unit at Public Health England (now UKHSA), Principal Investigator COG-UK15th December 2021

Dr Richard Myers begins his interview by going back to February 2020 when Public Health England first began to receive and sequence positive SARS-CoV-2 samples in February 2020 and was beginning to gear up for what seemed to be a significant pandemic. He recalls soon after being contacted by Sharon Peacock to discuss the idea of setting up a consortium to ramp up genomic sequencing for national surveillance. As he points out PHE already had undertaken pathogen genomic sequencing for pathogens such as TB and food borne pathogens for a number of years. What was new about COG-UK was the scale, ambition and speed with which it was set up. It was also novel in that it would be as inclusive as possible and include the academic community, NHS Trusts and public health authorities from all four devolved nations. At the heart of the idea was a sense that the UK should take a lead in sequencing to provide genomic level information about the virus as the pandemic unfolded. Not everyone, as he reflects, were initially convinced of the value of the exercise because at first it was unclear what the genomic data would reveal, but over time the need for such information began to be recognised following the detection of Alpha and other new variants. Indeed, the government increasingly began to rely on the insights from sequencing to take action. He also highlights the pivotal role academics played not only in helping set up COG-UK but also continue to play in the analysis of data and determining new variants.

Dr Rachel Nelson, Head of CGaP, Cellular Generation & Phenotyping Core Facility, Wellcome Sanger Institute 21st February 2022

Dr Rachel Nelson remembers having just a matter of weeks to prepare her to team to process any type of sample that came into Sanger for the COG-UK effort. Highly concerned about the safety of her staff, her first priority was to find a means to inactivate the SARS-CoV-2 virus so it did not pose a risk. This process changed over time and became less important once Sanger switched over to sequencing RNA extracts from the Lighthouse labs instead of patient samples received from hospitals. Having already established a very agile and adaptive team to process different types of cells at speed for various projects within Sanger, Nelson immediately found herself having to manage a completely new team with volunteers drawn from across the institution. What helped was the standard operating procedures handbook and training process she had developed over the previous four years, which made it very easy and quick to train staff. Because of the intense pressure and importance of the work, Nelson remembers volunteering to process the first sample to break the ice. Although the work was intense and involved very long hours, Nelson was sad when her team's involvement came to an end once the Lighthouse Labs came fully on board. But, as she says, the experience was invaluable for building her confidence in the operational side of things.

Dr Áine O’Toole, Postdoctoral research associate, University of Edinburgh3rd February 2022

Dr Áine O’Toole recounts how she switched from developing tools for outbreak surveillance of different viruses for her doctorate to applying it to the SARS-CoV-2 virus. She began this work by helping to sequence the first samples taken from patients hospitalised with COVID-19 at the Royal Infirmary in Edinburgh. Following this she began working with COG-UK and her colleagues at Edinburgh University to develop software tools to map the evolution and spread of the virus. This involved integrating sequencing data collected by COG-UK with data from all around the world. An important part of the effort was developing a uniform nomenclature system for the different lineages as they emerged which was done in tandem with discussions with WHO. Known as the Pango-lineage system, this made it easier for scientists and health professionals to communicate with each other. O'Toole also helped to develop a software tool called Civet which made it possible to automatically prepare reports in real-time on sequenced samples for use in outbreak investigations.

Dr Andrew Page, Head of Informatics, Quadram Institute, Principal Investigator, COG-UK 10th December 2021

Dr Andrew Page recalls how the Quadram Institute got involved with COG-UK in the sequencing of COVID-19 samples from patients admitted to the Norwich and Norfolk University Hospital and from five other hospitals in the Norfolk and Suffolk region. He highlights that the Quadram was able to draw on its previous sequencing of food-borne pathogens for the COG-UK effort. As part of this work they demonstrated how COVID-19 outbreaks spread between different care homes within the area as well as between poultry factories and also from a pub into a particular village. He also talks about how clinicians on the ground gained awareness of the importance genome sequencing as a result of the reports he and his colleagues generated using the data collected for COG-UK.

Professor Julian Parkhill, Department of Veterinary Medicine, University of Cambridge2nd February 2022

Professor Julian Parkhill looks back at how he first got contacted by Sharon Peacock to discuss the idea of launching a sequencing effort for COVID-19 based on their previous work together on real-time transmission and detection of bacterial pathogens in hospitals. He points out that an important impetus for the COVID-19 work was also laid by the previous rapid reaction sequencing for viral outbreaks for Ebola. From the very first meeting the question was how to stitch together a national sequencing pipeline based on the current capabilities within the UK. It quickly became apparent that the best approach would be to take a hub and spoke model using the expertise already available in academic centres and linking that with public health agencies. Parkhill also highlights the UK was very well prepared for undertaking such a venture because of it strong historical development of sequencing and investment in the area. Early on Parkhill became involved in helping to draw up a sampling framework for COG-UK to make sure that it could be used to inform local outbreaks as well as provide data for national surveillance.

Dr Naomi Parks, Senior Staff Scientist in DNA pipelines R&D, Wellcome Trust Sanger Institute16th September 2022

Dr Naomi Park talks through how she helped to streamline the sequencing process at Sanger based on her expertise of multiplex PCR. This proved much more difficult than she originally anticipated. One of the major challenges was reducing the number of steps involved in PCR without diminishing the quality of the output. It was only after a lot of trial and error and discussions with other COG-UK members that she finally hit upon an idea to put tailed primers in the second PCR. She remembers her huge sense of relief when she saw it work. The Sanger quickly integrated the approach into its sequencing process and it was also adopted by other COG-UK sites. First introduced in November 2020, the new tailed process was used to process the majority of COVID-19 samples in the UK. By reducing the number of steps, the new method had a much smaller footprint in terms of kit and staff. In her interview Parks provides an insight into the ways into how meetings and the workflow was organised within COG-UK. As she points out, COG-UK provided an important space for sharing ideas and giving everyone a chance to say how things were going at their end. She also highlights the important role of the ARTIC protocol for COG-UK work. One of the reasons it was adopted was because it was easy to integrate and copy by everyone. It could also be quickly redesigned to meet the challenge of the new variants.

Sharon Peacock, Professor of Public Health and Microbiology in the Department of Medicine, Cambridge University and Executive Director of the COVID-19 Genomics UK (COG-UK) Consortium 5th January 2022

Professor Sharon Peacock revisits the circumstances that led her to help found COG-UK at the start of the COVID-19 pandemic in March 2019 based on her previous work around antimicrobial resistance. Among the issues she discusses are the challenges she and her team of colleagues faced in setting up the Consortium and where they have had their major achievements. Her interview reveals the complexities of data linkage and the power of collaboration between academics and public health agencies in setting up a national pathogen surveillance network for dealing with infectious diseases. She also discusses the importance of COG-UK in uncovering the new variants associated with SARS-CoV-2 which has had an important role in the development of public health measures, vaccines and therapeutics.

Dr Joshua Quick, UKRI Future Leaders Fellow, University of Birmingham 26th January 2022

Dr Joshua Quick discusses how the protocols he and his colleagues developed for the ARTIC Network to help combat the Ebola Virus and the Zika virus was a crucial starting point for getting COG-UK up and running. He highlights some of the streamlining he and others did to the protocols which helped reduce the workload and speed up the sequencing process. One of the advantages with the protocol, he points out, was that different laboratories around the country could adapt it to suit their own sequencing platforms. Quick also talks about the enormous workload he experienced at the start of the pandemic sending out primer kits to enable laboratories to start sequencing SARS-CoV-2 and the importance of Zoom meetings to trouble-shoot issues different people around the country were experiencing. What also sticks out for him is the enormous amount of goodwill that helped propel COG-UK forward and the speed with which it got up and running compared to initiatives in other countries like Canada and the USA. For him one of the strengths of COG-UK was that it had a decentralised structure and showed how to rapidly assemble a wide group of experts to respond to a crisis.

Piers Ricketts, Chief Executive, Eastern Academic Health Science28th January 2022

Piers Ricketts initially became aware of COG-UK while heading up a team to look at diagnostic testing innovation which included exploring genomic sequencing. Knowing that COG-UK only had funds to support its work up to September 2020, in August Ricketts began building out the business case for a new round of funding. Working with the COG-UK team, by October 2020 he had helped secure £12 million from the Department of Health. Some of the funding was to help reimburse the costs of academics who had voluntarily contributed their time to COG-UK over the previous six months and fund future sequencing. The funding marked a turning point for COG-UK because it shifted the dynamics from what was originally an academic collaboration of the willing to being a more formal part of the Public Health infrastructure. What was novel about COG-UK, Ricketts believes, was its ability to link up a team of national experts at short notice and get them to agree to work together with a standard set of terms of conditions while at the same time integrating their findings into the Public Health infrastructure.

Professor David L Robertson, Head of MRC-University of Glasgow Centre for Virus Research's Bioinformatics group, Member of COG-UK10th February 2022

Professor David L Robertson reflects on the how the establishment of the GISAID and CLIMB databases before COVID-19 provided an important resource for uploading data collected through COG-UK's sequencing work. He also talks about the pivotal role Virological and Twitter played in disseminating information about the first sequence of the SARS-CoV-2 virus and for discussing its likely animal origin. Early on he remembers a strong collaboration between the teams working in both Edinburgh and Glasgow to get the sequencing going and uploading of data. This was helped by a large number of volunteers who manually secured metadata from patient medical records to be matched with the sequenced samples. A lot of the early effort went into analysing the data to understanding the introductions of the virus into Scotland. Quite early into the process they spotted a mutation in the virus genome sequenced from a cluster of cases in Scotland. This alerted them to the high level of plasticity and malleability of the virus. It also soon became clear that people with long-term or chronic infections can potentially generate more divergent variants of the virus. Robertson goes on to discuss the different data analytical tools developed, including Civet and Mutation Explorer which give feedback about what is happening with the virus allowing for quick investigations into outbreaks. For Robertson, the COG-UK effort is historically important because it has allowed for a pandemic virus to be studied in real-time. What also proved very useful was the Pangolin nomenclature system developed for naming the different lineages. A lot of the work undertaken within COG-UK, he points out, rests on the coming together of invaluable expertise and knowledge built up by people responding to other virus outbreaks in the past.

Dr Sam Robson, Principal Research Fellow (Bioinformatics), Angela Beckett, Specialist Technician (Research), Faculty of Science & Health, School of Biological Sciences, Centre for Enzyme Innovation, University of Portsmouth 13th January 2022

Dr Sam Robson and Angela Beckett muse on how quickly they became a key sequencing hub for COG-UK in the Southeast and South region. As Robson points out it was all kicked off after he he sent request to get more information on what COG-UK was doing. Little did he realise just what he was getting into. Immediately asked to participate in COG-UK meetings with experts, for the first few months Robson was convinced that he had been invited there by mistake. Having only just hired her to help Robson with plastic research, Beckett also found herself thrown in at the deep end. While Robson found himself spending many hours at home confronting the challenges of uploading and analysing data, Beckett was wrestling with the time-consuming and laborious process of sequencing samples. Beckett's descriptions of pipetting and other preparation work are invaluable for giving a sense of the repetitive manual work and high degree of concentration required for sequencing samples. She describes the little tricks she developed to keep alert in the process which was crucial for preventing any errors and contamination. The difficulties of recruiting extra staff with bioinformatic skills, meant the responsibility of data processing weighed heavily on Robson. He was acutely aware that if anything happened to him there would be no one else to run the samples through. Reflecting on their work, Robson and Beckett feel that dogged determination and hard work allowed them to work through the challenges, which were innumerable. They also both believe COG-UK was invaluable to building up their confidence and gave them benefits for the careers in the future.

Dr James Shepherd, Specialty Registrar in Infectious Diseases and Medical Microbiology, Clinical research fellow MRC Centre for Virus Research, University of Glasgow14th February 2022

Dr James Shepherd recounts how he paused his doctoral research on the Rhabdovirus in Uganda and interrupted his paternity leave to help with the COG-UK effort undertaken at the Centre for Virus Research at the University of Glasgow. By virtue of the fact that he works as physician within the NHS and also in research, Shepherd was able to play a pivotal role in both collecting patient samples for sequencing and linking that with the patient metadata. He describes the laborious process of hunting for and extracting samples and trawling through electronic patient records together with colleagues and medical student volunteers. Initially the metadata had to be collected by hand because a lot of the information that was of interested was not recorded on the database. Part of this work was used to understand the introduction of the SARS-CoV-2 virus into Scotland. He reflects on how much genome sequencing has advanced our understanding of viral evolution and how the technique can be used for future emerging infectious diseases.

Lesley Shirley, Head of Automation, Wellcome Sanger Institute3rd August 2022

Lesley Shirley remembers the positive atmosphere when she attended the first stand-up meeting called within Sanger to get sequencing moving as part of the COG-UK effort. At that point everyone was focused on finding a way to get the DNA pipeline up and running to make it operational as quickly as possible with a view to improving the process once it was in place. She highlights the importance of Zoom for getting everything set up at a time when most people were working at home. Where it proved particularly helpful was connecting scientists working with their instruments in the lab with those who were working remotely to develop software to automate the flow of samples all to way from receipt to the final uploading of the data. She also talks about the challenge of training staff who were regularly changing and in the wake of shifting requirements in the process. What she values about the experience is how it helped break silos between groups within the Sanger and how they learnt to advance robotics and automation to support future projects. For her one of the pivotal moments was when she watched the traceline appearing on the bioanalyser in real-time following the sequencing of the first samples. This was important for knowing the pipeline worked and could be scaled up. Another key point was when she saw the cherry-picking integrated go live for the first time, which marked the culmination of six months of work. It was also the final piece of the puzzle Sanger needed to significantly scale up its volume of sequencing.

Dr John Sillitoe, Head of Surveillance Operations, Wellcome Sanger Institute8th April 2022

An engineer by background, Dr John Sillitoe explains how he got involved in helping to stand up large-scale sequencing at the Sanger Institute for COG-UK. To do this he drew on the expertise he had built up through managing the malaria grant at the Sanger Institute which entailed building a pipeline for large scale global sequencing and surveillance. His interview provides an overview of the different processes that needed to be set up within Sanger to start sequencing the large volume of COVID-19 samples that flowed in each day from the Lighthouse Labs. He highlights some of the challenges that were involved in handling the large quantities of 96 microwell plates coming in and how to get the data in a usable format so that it could help inform policy decisions. Sillitoe captures some of the pressures he and his team were under to deliver the project, which at times he says felt like running a marathon at the pace of a sprint.

Andrew Stronach, Head of External Relations and Engagement, Quadram Institute28th February 2022

Andrew Stronach talks about how he and his communications team connecting everyone within the Institute who were working both internally and remotely during the pandemic. He highlights how members of the Quadram Institute stepped up to take an active part in the media and helped promote the work they were doing as part of COG-UK. One of the key issues they faced was providing outbreak information whilst maintaining confidentiality. He also talks about the speed with which the Quadram Institute and COG-UK were able to scale up sequencing which was helped by bringing together networks of scientists from around the country. At the end he considers the legacy of COG-UK and COVID-19 for handling future pandemics. As he points out this is dependent on leveraging the genomic training and capacity of scientists worldwide and expanding beyond the developed world.

Dr David Studholme, Associate Professor in Bioinformatics, University of Exeter27th January 2022

Dr David Studholme highlights that he and his colleagues had already begun thinking about undertaking genome sequencing of SARS-COV-2 samples on a local level to track the evolution and spread of the virus before they heard of COG-UK's national effort. For him the work was inspired by his involvement in a previous crowd sourced funded genomic sequencing project for an outbreak of E. coli in Germany. Overall, Studholme's major contribution to the COG-UK effort was to aid the computational analysis of the data once the sequencing of the samples had been done and feeding that to clinicians at the local hospital to help them understand transmission paths for infection control. Encouragingly the data indicated the infection control measures put in place were effective. It was also useful for detecting major variants before they began to take off. In the case of Exeter and the Southwest these tended to appear some time behind London and the rest of the country.

Shahiba Sultana, Biomedical scientist, Barts Health NHS Trust Diagnostic Laboratory, MSc student in Global health3rd February 2022

Shahiba Sultana recalls the heavy workload that she and her colleagues faced at St Bartholomew's Hospital sequencing COVID-19 samples both for helping clinicians treat admitted patients with the disease and to contribute to the COG-UK effort. The first laboratory to diagnose a positive COVID-19 sample in London, Sultana recalls how her sequencing load rapidly ramped up as the number of cases increased and the hard, repetitive manual labour involved. Her story gives a glimpse into the personal sacrifices of the many hidden scientists behind the COG-UK pioneering work to track SARS-CoV-2 and its emerging variants. In Sultana's case, she had to do this alongside continuing the laboratory's routine work to diagnose other blood-borne pathogens including HIV and hepatitis B and C. With every minute of her day counting in the throughput of samples, Sultana talks about how little time this left her for having lunch and toilet breaks. Often working late into the evening and overtime during the weekends, what kept her going was the support of her family and her work colleagues with whom she formed strong friendship bonds. Despite the challenges, Sultana is proud of what she and her team achieved and points out the high value clinicians now place on having sequencing within the hospital to maintain infection control.

Ben Temperton, Associate Professor of Microbiology, University of Exeter; Dr Steve Michell, Senior Lecturer in Molecular Microbiology, University of Exeter and COG-UK Principal Investigator 4th February 2022

Professor Ben Temperton and Dr Steve Michell discuss how they had never having worked together found themselves collaborating in the COG-UK effort to sequence COVID-19 samples from different places in the Southwest region. They remember that the number of samples coming through was very intense in the first wave, particularly during Christmas 2020, but then took a long time to pick up after the summer when the second wave hit. To do the sequencing they leveraged deep knowledge people at Exeter University had of Nanopore sequencing and strong links between the university, Royal Devon and Exeter NHS Trust and the clinical diagnostic laboratory. One of the key challenges they faced was finding a way to move away from laboriously going through spreadsheets to link patient metadata with sequencing data. What Temperton and Michell really liked about COG-UK was the sense of everyone pulling together to iron out problems, and the network's flexibility to distribute samples between different sites according to their individual sequencing capacities. This meant that when one place became overwhelmed another could step in to help out. They also praise the willingness of the university to financially step in to when waiting for money to come in from COG-UK. In terms of COG-UK's legacy it helped get pathogen genomics on the map in the Southwest and proved its clinical utility for infection control. On a more personal level, COG-UK encouraged Temperton to kick-start a whole new area of research focused on isolating and characterising phages for the therapy which could provide a new weapon in the fight against antimicrobial resistance.

Professor Emma Thomson, Clinical Professor in Infectious Diseases, Centre for Virus Research, University of Glasgow11th January 2022

Professor Emma Thomson discusses how the seriousness of the unfolding COVID-19 pandemic began to really dawn on her when she attended the first meeting to set up COG-UK. She outlines how her earlier involvement with a consortium to help advance treatment for hepatitis C and investigating virus causes of fevers of unknown origin in Uganda helped prepare her for participation in the COG-UK effort. Thomson then goes on to describe the work she and her colleagues at the Centre for Virus Research in Glasgow on COVID-19 which covered both the functional biology of the virus as well understanding how its evolution affected treatment. During her interview she discusses the strategies she developed to cope with the fast-paced nature of the work with COG-UK which she did alongside helping out with vaccine trials. She also highlights the early conversations that took place about how the SARS-CoV-2 virus was mutating and subsequent discussions about how the rise of new variants would affect the efficacy of vaccines and treatments. For Thomson, one of the overriding reasons COG-UK worked so well was the productive working relationships which was catalysed both by the emergency situation imposed by the pandemic as well as the leadership style of Sharon Peacock.

Dr Estée Török, Consultant at Cambridge University Hospitals NHS Foundation Trust and Senior Visiting Fellow University of Cambridge.24th February 2022

Dr Estée Török kicks off by discussing the very strict infection control measures she saw taken in Singapore both in hospitals and at the airport by contrast with the UK at the start of the pandemic. She then goes on to discuss how she worked with colleagues in Cambridge to set up a system for collecting and sequencing samples to identify new COVID cases and report the data back to the hospital infectious control teams to help curb the spread of the disease. This work early on helped determine the cause of an outbreak in the dialysis unit at Addenbrooke's Hospital and care homes in the East of England. Proud of what they managed to achieve in record time, Török treasures the incredible team effort and willingness of everyone to roll up their sleeves to meet the urgent challenge posed by the pandemic. Like everyone else around her, she landed up working extremely long hours over a period of four or five months without a day off or time to spend with her children. For her, one of the most fantastic things about COG-UK, was that it found a way to bring clinical, academic and public health institutions together to set up genomic surveillance for a new disease on a national scale in real time.

Dr Alex Trotter, Bioscience researcher, Quadram Institute24th February 2022

Dr Alex Trotter recalls how he got involved in the collection and sequencing of patient samples for the COG-UK effort as part of Quadram Institute. He recalls the many hours of managing the logistics of collecting patient samples from the hospital and setting up the process to sequence them. Finding and keeping track of the samples and sorting through the metadata to go with them he recalls being a big headache. On more than one occasion he would turn up to the hospital to collect samples which he could not find anywhere. Once the samples were found these had to be deactivated to make them safe and RNA extracted to perform the sequencing, all of which took time. Having to work long hours inevitably meant he was forced to pause work on his doctoral thesis. Some pivotal moments he recalls was being involved in helping understand the outbreak of COVID-19 infection in local chicken factories and a hospital. He also remembers the challenge of trying to achieve rapid turnaround time as part of an exercise to determine capacity for providing genomic information in the case of emergency outbreaks. He also talks about the work he and colleagues at the Quadram have done to help sequence SARS-CoV-2 samples from other countries, including for Zimbabwe. Finally, he discusses how participation in the COG-UK effort helped drive more collaboration between the Quadram Institute and Norfolk and Norwich University Hospitals. Another important collaborator he mentions is the Norwich Research Park Biorepository which proved pivotal to providing metadata for the COG-UK effort.

Dr Anthony Underwood, Formerly Head of Translational and Operational Bioinformatics, Centre for Genome Pathogen Surveillance, Oxford27th January 2022

Dr Anthony Underwood starts by talking about the shock of seeing images on TV of COVID causing deaths in the young not normally associated with mortality. He then switches to speaking about how his team adapted the software tools for SARS-CoV-2 they originally developed for delivering genomic sequencing for antimicrobial resistance into the hands of lower to middle-income countries. A lot of their work was devoted to making it easier to clean data, upload metadata and visualise the evolution of the virus and how it was spreading. This was done in close collaboration with other COG-UK members. What Underwood particularly liked was the 'can-do attitude' of everyone involved in COG-UK. One of the pivotal moments that sticks out for him was seeing a photo of the Prime Minister of New Zealand looking at a dashboard on a computer showing in real-time the place, time and genetic relationship between the genomes that had been sequenced by COG-UK. The dashboard is powered by Microreact, a programme that he and his colleagues built. Despite the huge impact visualisation tools have had in allowing experts, policy makers and the public to understand the pandemic, one of the biggest challenges he sees going forward is finding a way to develop open source software while being able to financially sustain the work.

Joanne Watkins, Senior Biomedical Scientist, Deputy Head, Pathogen Genomics Unit, Public Health Wales15th February 2022

Joanne Watkins highlights the fact that Public Health Wales was ideally situated to help in the COG-UK effort because of the Pathogen Genomics Unit it put in place in 2017. Prior to COVID it was already performing sequencing for antibiotic resistant bacteria and had a strong flu surveillance service. As early as March 5th 2020 Public Health Wales had everything in place both to diagnose patients with COVID and also sequence their samples. Despite this head start, they quickly got swamped with the number of samples and demand to investigate outbreaks in hospitals, nursing homes and food preparation factories. Hiring new staff helped ease the situation, but training the new recruits took time to implement. One of the key challenges she cites was the varying conditions in which samples arrived. This was subsequently helped when a Lighthouse lab got set up in the vicinity with which they had good communication. Another issue Watkins flags up was the supply difficulties they experienced particularly for reagents and plastics. At one point a change in the seals on plastics had a knock-on effect in terms of contamination. What really helped the operation was having COG-UK on board to help with the validations of different methods and finding suppliers.

Dr Tim Wyatt, Consultant Microbiologist at the Health and Social Care (HSC) Public Health Agency of Northern Ireland 22nd March 2022

Dr Tim Wyatt recounts how he got involved with COG-UK in his capacity as a consultant microbiologist at the Public Health Agency of Northern Ireland. Engaged to liaise between the Agency and microbiologists out in Trusts, Wyatt points out that historically Northern Ireland has always been heavily reliant on Public Health England. In part this has been because of a lack of resources as well as prioritisation. This has meant that Northern Ireland is less advanced in terms of setting up a national genomics surveillance infrastructure for public health. For Wyatt, the establishment of COG-UK has provided a golden opportunity to build genomic sequencing for public health on a more permanent footing within Northern Ireland. Importantly it has shown how to join up the sequencing capacity within Queen's University in Belfast and the Department of Agriculture, Environment and Rural Affairs. What stands out for Wyatt was the generous support he got from COG-UK as well as the challenges he and his colleagues faced in drawing up the data sharing agreement for the initiative.

Peijun Zhang, Research technician, Manager of the University of Sheffield’s COG-UK technical team8th February 2022

Peijin Zhang was hired in September 2020 to help with COG-UK. Originally a research technician in the plant field, Zhang saw the job as an opportunity to do something a bit different as well as make a contribution to the nation. After spending two months learning techniques to prepare patient swab samples for sequencing, Zhang was asked to lead the sequencing team in Sheffield for the HOCI study. This involved a lot of administrative work, logging patient samples into the laboratory and communicating with hospitals and bioinformaticians. She was also involved in the laboratory process of RNA extraction, PCR and sequencing, which involved a lot of hands on labour. In addition she was responsible for organising the laboratory's rota for ensuring technicians were on hand 24 hours to undertake the rapid sequencing required in the HOCI study. Coinciding with the discovery of Alpha she remembers the work load being particularly intense at that time, which lasted eight weeks. This meant that for a while she had to compromise on having any real home life. Having become used to the fast pace of the work involved with COG, Zhang really missed it once the UKHSA took over the sequencing.

Made possible by the generous support of COVID-19 Genomics UK Consortium (COG-UK)

COG-UK was supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute. This exhibition acknowledges use of data generated through the COVID-19 Genomics Programme funded by the Department of Health and Social Care. The views expressed are those of the author and not necessarily those of the Department of Health and Social Care or UKHSA.

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