Blog

8 May 2020

Commentary: COG-UK Report 5, 7th May 2020

Commentary

Commentary: COG-UK Report 5, 7th May 2020

The 5th report from COG-UK includes analysis of a total of 10,483 SARS-CoV-2 genomes, sequenced before 7th May 2020.

The report also includes analysis of viral genomes sequenced from five care homes in London. The samples were taken from staff and residents between 13th and 15th of April 2020. Of the 210 samples assessed, 91 were positive for SARS-CoV-2. 55 of these samples were of high enough quality for analysis. These data were used for phylogenetic studies within each care home, and for comparison with 277 non-care home viral genomes originating in London.

Analysis of the data suggests that in one care home, there were at least four separate introductions of the virus. A similar pattern of multiple introductions of the virus was observed in two other care homes, although less data were available for these sites. There was also some evidence that following an introduction of the virus, in some cases, there was transmission within a care home.

No common pattern or direction was seen for transmission, either between staff and residents or between symptomatic and asymptomatic people.

Further analysis identified a putative cluster of viral sequences, containing samples from multiple care homes. The presence of similar sequences across different care homes could suggest either transmission of SARS-CoV-2 between care homes, or separate introductions of the same viral lineage to different care homes from the community or other healthcare settings. Since the completion of this report, additional sequence data have been analysed. This analysis indicated that the sequences from care homes are part of a widespread viral lineage and consequently it is not possible to determine which of these scenarios is the case.

The findings highlight the importance of ongoing, larger studies, with additional metadata. Such studies will be vital to study transmission in care settings and inform control strategies.

The researchers anticipate that as the number of genomes sequenced increases, they will be able to provide a high resolution view of viral lineage diversity in the UK. This will make it possible to distinguish dominant local lineages and track viral spread from one part of the UK to another.

In such a fast-moving situation, the consortium members note it is important to consider the limitations of phylogenetic analysis, and the importance of caveats when interpreting data.

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Blog / Events / Women in COG

7 Dec 2022

“I want to be able to push the boundaries all the time”: In conversation with Dr Sam Barrell, CBE

For the last edition of Women in COG, our Associate Director, Dr Katerina Galai, spoke to Dr Sam Barrell about her career as an accomplished healthcare leader, including her leadership role at Europe’s largest single-site biomedical research organisation, the Francis Crick Institute, during the COVID-19 pandemic. Before joining the Crick, Sam led the formation of the South Devon and Torbay Clinical Commissioning Group, after which she took up the role of Chief Executive of the Taunton and Somerset NHS Foundation Trust.

For the last edition of Women in COG, our Associate Director, Dr Katerina Galai, spoke to Dr Sam Barrell about her career as an accomplished healthcare leader, including her leadership role at Europe’s largest single-site biomedical research organisation, the Francis Crick Institute, during the COVID-19 pandemic. Before joining the Crick, Sam led the formation of the South Devon and Torbay Clinical Commissioning Group, after which she took up the role of Chief Executive of the Taunton and Somerset NHS Foundation Trust.

Sam “only ever planned one thing…and that was to be a doctor.” But her career to date has spanned a range of different experiences and skills, from medicine to healthcare management, to non-executive leadership roles. None of the roles that Sam has had have been straightforward – but this is by design. “For me, it’s just about being open-minded, enjoying challenges and being able to overcome them.” Above all, though, Sam prioritises one factor when considering a position: “they have to be purpose-led.”

In her role as Deputy Chief Executive at the Crick – a leading purpose-led institution – Sam is faced with challenges, and opportunities to push boundaries, on a regular basis. There has arguably been no better example of this than during the COVID-19 pandemic. In March 2020 University College London Hospitals NHS Foundation Trust (UCLH), which is located close to the Crick, had a major problem: they were not able to access PCR tests for their patients and staff. So they approached the Francis Crick Institute and asked for support. The Crick, however, was not a diagnostic testing lab, so had to work closely with partners from UCLH and Health Services Laboratories (HSL) to set up a PCR testing pipeline within four weeks. This collaboration managed to deliver over 600,000 PCR tests to about 150 care homes and 10 hospitals in North London. “There were huge numbers of people involved in that project at UCLH, and HSL, as well as Crick scientists – it was a really big endeavour”, Sam says.

After opening the testing pipeline in April 2020, Sam recalls that the senior leadership team at the Crick had a “lightbulb moment.” There was a realisation that the Crick’s own scientists could be tested to see if they were SARS-CoV-2 positive. “We really needed them in their labs – it wasn’t really going to work for them to be at home.” And so, by May 2020 a project was established with exactly this goal in mind. However, this was before any other organisations had really started systematically testing their staff. “There was no blueprint for this at the time, we didn’t have a recipe to follow.” To try to keep staff as safe as possible, Sam and her team set up a test, track and trace system internally with a 24-hour, 7-day-a-week on-call team, which included HR professionals, clinician scientists, and many others. This undertaking was critical in keeping the Crick productive during the pandemic. “We had maybe a thousand people in most days during the pandemic, doing critical research for government, including lots of labs doing COVID-19 research.”

Despite all her accolades and experience in leadership positions – at the Crick and beyond – Sam thinks her greatest professional achievement is probably her resilience. “Running an NHS hospital can be quite tough from time to time, and then when I first started at the Crick that was a big challenge too.” Early in her career, Sam faced difficulties too. “Being a doctor, dealing with some really harrowing patient stories, and supporting patients in really difficult circumstances, can be quite tough.”

“It can be quite hard to keep yourself resilient and optimistic, to remain a positive leader, have fun and still keep your energy.” The key, Sam notes, is that she has never stopped her introspection over the years. “I reflect and think – all of the time – about how to keep myself resilient.”

To watch the full recording of the event, please click here.

Dr Sam Barrell 

Dr Sam Barrell is the Deputy Chief Executive Officer of the Crick and is responsible for leading the operational management and running of the institute. She joined the Crick in September 2017 from a career in the NHS as a noted healthcare leader. Sam was Chief Executive of the Taunton and Somerset NHS Foundation Trust. Before that, she was the Accountable Officer and led the formation of the South Devon and Torbay Clinical Commissioning Group. Sam was awarded the CBE in 2014 for services to healthcare.


COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.