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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As we approach the first anniversary of the inception of COG-UK, Sharon Peacock reflects on the last 12 months — and considers our next steps for the future.

Dear Consortium Members,

As we approach the first anniversary of the inception of the COVID-19 Genomics UK (COG-UK) consortium, it is timely to reflect on the last 12 months — as well as consider our next steps.

It has been an honour to work with so many talented people to provide SARS-CoV-2 sequencing expertise to support the pandemic response, and to make a difference to the people of the United Kingdom. Although we study virus genomes from individuals, we bring value at the level of populations. For example, understanding how the virus evolves and transmits is important in planning future vaccines, and in public health interventions. However, I would like to recognise that each of the SARS-CoV-2 genomes that we have sequenced originated from a person who had COVID-19, some of whom have died. The number of genomes we have sequenced serves as a daily reminder of the toll that this infection has taken on people in the UK and beyond. Thus while the success of our genome sequencing efforts in the UK is often lauded, for me it is bittersweet. The driving force behind our work is the ongoing provision of sequence data that leads ultimately to a reduction in illness and death.

Recently, the emergence of SARS-CoV-2 variants has made our contribution more apparent to a wider range of people. But I would also like to acknowledge that our work has been built on a decade or more of technological innovation, funding investment, research, and the efforts of our scientific community — who all understood the benefits of using pathogen genome sequencing for public health good.

This is also a moment to thank a great many people for their contribution towards the achievements of COG-UK. The consortium is made up of hundreds of people, who fulfil a very wide range of roles that are vital to acquiring and sequencing samples, and in data analysis. Many people have worked excessive hours for many months. This has an impact on their lives and well-being, but also on that of their family. As one of numerous possible examples, many people were called to work over Christmas to generate data relating to the newly emerging B.1.1.7 variant. My grateful thanks go to you, and to your family.

I would like to take this opportunity to acknowledge the incredible and mutually supportive interactions that we have had with health care providers, the wider health infrastructure, other stakeholders, and the government. A big ‘thank you’ to colleagues in the 100 or more NHS testing labs and the Lighthouse labs with whom we work closely. Laboratories across the consortium have been incredible over the last 12 months, reshaping the way that they work, reassigning staff to work on SARS-CoV-2 and in the case of the Wellcome Sanger Institute entirely redesigning labs and purchasing new equipment to bring a degree of automation and scale previously unimagined for pathogen genomics. Equally vital contributions have been witnessed in the development of the logistic and computational pipelines and tools needed to meet the ever-growing volume of genome data coming off the sequencers. All of these efforts have impacted on the outputs of our non-COVID-19 work, which remains vital, but which needed to be balanced with the demands of the pandemic responses.

Many consortium members are employed elsewhere but support COG-UK on a voluntary basis. What this means in practice is that their work for COG-UK is often supported financially by universities or research funders. Furthermore, none of the funds awarded by the government in April 2020 to COG-UK went to support university infrastructure. In other words, the cost of keeping the lights on in research labs and maintaining a safe working environment has been met by universities themselves. This contribution needs to be highlighted, since without this, our many achievements would not have been possible. Almost all of our funding has gone on the cost of sequencing, data storage and analysis, which has meant excellent value for the money received from the public purse, but which must be viewed in the correct context of the support received from our academic institutional partners.

I also want to reflect on our impact. We have generated a large amount of sequence data, which forms the basis for our understanding of the frequency, distribution and transmission of variants of concern. This information is important in the UK, but also globally. All of the genomes that we generate are shared openly with international colleagues. But data have also been used to understand transmission and outbreaks in universities, hospitals, care homes and other environments. We have also described the pattern of SARS-CoV-2 importations during the first and second waves. This information has been reviewed and used by numerous government departments. Consortium members have also developed, refined and shared sequencing methods and tools that analyse the data. Again, all are openly available. This represents a substantial contribution towards the global sequencing effort.

So, what does the next 12 months hold for the consortium? We were largely established as a research consortium, albeit one that has gone on to provide essential data to public health agencies and governments. One of our greatest assets is the sequence data generated, and in the next few months we aim to enhance the quality and depth of these data by linking sequence information to numerous other data sets that have been produced in parallel to ours. This includes human genome data, immunological data, and detailed clinical information. We will also use the remaining research funding budget to support consortium members to mine these datasets and publish their findings. Such work could support pilot studies that generate data for future grant applications. We will also seek to further support global interaction by consortium members, who currently collaborate with around 30 different international institutions.

Integral to our inception was a wish to provide the foundations of a national, public health-led sequencing network. This is an important legacy, and one that is becoming a reality as public health agencies and governments come together to create plans to take on the sequencing role that we provide. This will be achieved through a carefully planned handover, which will progress over the next six months. We stand ready to support colleagues who will benefit from the transfer of knowledge and know-how, as well as passing on our carefully developed network that brings together a mechanism for samples to flow to one of our sequencing sites. This will also be a time of readjustment and future planning for researchers, whose skills will remain as vital as ever as we develop a sequencing network that continues to innovate and encompass other infectious disease challenges in 2021 and beyond.

 

With grateful thanks to you all, and best wishes

Professor Sharon Peacock

Executive Director and Chair, COG-UK