̽��ֱ�� of Cambridge - Sharon Peacock

̽��ֱ�� academics ranked among best in the world

hcf38 — Thu, 21 Dec 2023 10:57:57 +0000

̽��ֱ��Research.com Best Female Scientists in the World 2023 rankings are based on an analysis of more than 166,000 profiles of scientists across the globe. Position in the ranking is according to a scientist’s total ‘H-index’ - rate of the publications made within a given area of research as well as awards and recognitions. Only the top 1000 scholars with the highest H-index are featured in the ranking.

Kay-Tee Khaw, an Emeritus Professor in Gerontology and a Gonville & Caius Fellow, is placed fifth worldwide and tops the list for Europe. Professor Khaw, who was named a CBE in 2003 for Services to Medicine, published a study on how modest differences in lifestyle are associated with better life expectancy which informed the UK Government’s ‘Small changes, big difference’ campaign in 2006.

Also high in the rankings is Barbara Sahakian, Professor of Clinical Neuropsychology in the Department of Psychiatry and a Fellow of Clare Hall, who is placed sixth in the UK. Professor Sahakian’s recent research includes a study showing the benefits to mental health and cognitive performance of reading for pleasure at an early age, and seven healthy lifestyle factors that reduce the risk of depression.

Joining Professor Khaw and Professor Sahakian in the top 10 in the UK is Carol Brayne, Professor of Public Health Medicine in the Department of Psychiatry and Fellow of Darwin. Awarded a CBE in 2017 for Services to Public Health Medicine, Professor Brayne has pioneered the study of dementia in populations.

Nine other ̽��ֱ�� of Cambridge scientists also make the rankings:

Professor Gillian Murphy (Department of Oncology), an international leader in the field of metalloproteinases, who has defined their roles in arthritis and cancer.

Professor Claudia Langenberg (MRC Epidemiology Unit), a public health specialist combining her expertise with research focused on molecular epidemiology.

Professor Nita Forouhi (MRC Epidemiology Unit), a physician scientist, MRC Investigator and Programme Leader in Nutritional Epidemiology, whose research on the link between diet, nutrition and chronic diseases like type 2 diabetes has informed health policy.

Professor Alison Dunning (Centre for Cancer Genetic Epidemiology, Department of Oncology), a genetic epidemiologist working on the risk of breast and other hormonal cancers.

Professor Karalyn Patterson (MRC Cognition and Brain Sciences Unit, Cambridge Centre for Frontotemporal Dementia and Related Disorders), a Fellow of Darwin College, who specialises in what we can learn about the organisation and neural representation of language and memory from the study of neurological patients suffering from the onset of brain disease or damage in adulthood.

Professor Dame Clare Grey (Department of Chemistry), a materials chemist whose work has paved the way for less expensive, longer-lasting batteries and helped improve storage systems for renewable energy, she is Chief Scientist and co-founder of Nyobolt, a company that is developing ultrafast-charging batteries for electric vehicles.

Professor Sharon Peacock (Department of Medicine), who has built her scientific expertise around pathogen genomics, antimicrobial resistance, and a range of tropical diseases, was the founding director of the COVID-19 Genomics UK Consortium which informed the COVID-19 pandemic response.

Professor Maria Grazia Spillantini (Department of Clinical Neurosciences and Fellow of Clare Hall) has been researching the cause of dementia for many years and was the first to identify the specific protein deposit found in Parkinson’s disease.

Professor Dame Theresa Marteau (Department of Public Health and Primary Care and Honorary Fellow of Christ’s College), a behavioural scientist, focuses on the development and evaluation of interventions to change behaviour (principally food, tobacco and alcohol consumption) to improve population health and reduce health inequalities, with a particular focus on targeting non-conscious processes.

Speaking on publication of this year’s rankings, Imed Bouchrika, Co-Founder of Research.com and Chief Data Scientist, said: “ ̽��ֱ��purpose of this online ranking of the world's leading female scientists is to recognize the efforts of every female scientist who has made the courageous decision to pursue opportunities despite barriers.

“Their unwavering determination in the face of difficulties serves as a source of motivation for all young women and girls who pursue careers in science.”

Twelve academics from the ̽��ֱ�� of Cambridge have been ranked among the top female scientists in the world - with one claiming the top spot for Europe.

Gonville & Caius College

Professor Kay-Tee Khaw who has been named as the top female scientist in Europe by Research.com

̽��ֱ��text in this work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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COVID-19 showed the importance of genomic surveillance – we need it to help fight antimicrobial resistance

cjb250 — Tue, 14 Nov 2023 23:30:16 +0000

AMR already causes substantial sickness and death worldwide, responsible for approximately 1.27 million deaths in 2019. Some estimates suggest that by 2050, it could kill as many as 10 million people each year.

Professor Sharon Peacock at the ̽��ֱ�� of Cambridge – the driving force behind the UK’s pioneering COVID-19 Genomics UK Consortium – said: “Over the past century, antibiotics have transformed our ability to treat infection and illness and reduce mortality. But bacteria are becoming increasingly resistant, and with a limited pipeline of new antibiotics, we risk effectively returning to the pre-antibiotic era where we can no longer treat infections.

“When the world was hit by the COVID-19 pandemic, we showed how powerful a tool genomic surveillance could be in helping us fight back. This work grew out of its increasing application to real-world problems such as detecting outbreaks in hospitals and in the community – including food borne outbreaks. We now need to take what we learned from the pandemic including its bold and largescale use and reapply it to the complex problem of AMR.”

̽��ֱ��genome, which is ‘written’ in DNA or RNA, consists of a string of nucleotides. Each time a copy of the genome is made, errors can arise – for example, one of the A, C, G and T nucleotides of DNA might get swapped. These changes allow scientists to create lineages – family trees – showing how the genome has evolved and spread. In the case of SARS-CoV-2, they allowed scientists to identify sources of infection, spot so-called ‘variants of concern’ and see whether public health measures such as lockdown, travel restrictions and vaccination were working.

̽��ֱ��potential to improve surveillance of AMR pathogens may be even higher than for SARS-CoV-2 as the genome data can detect and track outbreaks, provide a prediction for effective antibiotic treatment, reveal the mechanism for resistance including mutations and the acquisition of new DNA, and help understand the movement of resistance mechanisms between bacteria.

Although surveillance of AMR bacteria is already used in some settings, the growing evidence of its potential has largely not translated into routine use. Writing today in ̽��ֱ��Lancet Microbe, a working group has set out how genomic surveillance could be applied to the problem of AMR more widely, including the barriers that need to be overcome, presenting a series of recommendations including building capacity, training of existing and new workforces, standardising the way that surveillance is done to detect AMR, and agreeing equitable data sharing and governance.

̽��ֱ��group, which is funded by Wellcome, was initiated by Professor Peacock in conjunction with Wellcome SEDRIC (Surveillance and Epidemiology of Drug Resistance Infection Consortium) and delivered by a team of nearly 100 experts co-led by Professor Kate Baker and Dr Elita Jauneikaite. Five papers will be published in the same edition of the journal, highlighting the breadth of review and analysis undertaken by the team.

̽��ֱ��series covers multiple areas for the application of genomic AMR surveillance including in hospital settings to help identify outbreaks and inform infection prevention and control and informing clinical decision-making at a patient level. They also highlight applications at a public health level to detect emerging threats and to design and assess suitable interventions like vaccination. It even has the potential to track AMR pathogens moving between humans, animals, and the environment. ̽��ֱ��team also considered future innovations in genomic surveillance of AMR, looking at how the next phase of genomic technologies and analysis methods might further transform the surveillance landscape.

A number of barriers will first need to be overcome, however. These include a lack of resources and political will, and the need for more training, particularly around bioinformatics (the analysis of genome data). There are also practical barriers, including in many countries a weak epidemiological surveillance and microbiology infrastructure, poor supply chains and pricing structures, and issues around effective cooperation and data sharing.

Professor Kate Baker, ̽��ֱ�� of Cambridge, said: “We are on the cusp of realising the full potential for genomics in tackling AMR, but there is still a lot of work that needs to be done. We need the scientific, public health and political communities to work together to make this happen. AMR is an urgent problem. It is not something that will happen in years to come – it is happening now.”

Dr Elita Jauneikaite, Imperial College London, said: “We are going to be locked in an ongoing arms race with bacterial pathogens indefinitely. Genomic surveillance offers real promise to help us fight back, providing invaluable information to limit the spread and impact of AMR.”

Professor Peacock added: “It was clear from the pandemic that sequencing was a vital tool that was needed in every country worldwide. AMR is a global problem and once again we need to make sure countries worldwide are in a position both to contribute to, and benefit from genomic surveillance data.”

Janet Midega, AMR Research Lead at Wellcome and SEDRIC Board member, said: “Genomic research and surveillance are pivotal to detect pathogens and understand the transmission and trends of drug resistance in both high- and low-income settings. In order to respond effectively to this data, we need to ensure that the tools being developed are accessible and can be utilised by public health agencies around the world.”

Reference
Baker, K, et al. Overview: Harnessing genomics for antimicrobial resistance surveillance. ̽��ֱ��Lancet Microbe; 14 Nov 2023; DOI: 10.1016/S2666-5247(23)00281-1

During the COVID-19 pandemic, genomic surveillance proved vital in helping understand the evolution and spread of the SARS-CoV-2 virus. Now, an international group of researchers is calling for its potential to be harnessed to tackle antimicrobial resistance (AMR), a major global challenge that could ultimately result in many more deaths than the coronavirus pandemic.

We are on the cusp of realising the full potential for genomics in tackling AMR, but there is still a lot of work that needs to be done

Kate Baker

NIH Image Gallery

Scanning electron micrograph of methicillin-resistant Staphylococcus aureus bacteria (yellow) and a dead human white blood cell (red)

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Minority ethnic doctors less likely to get specialty NHS training posts while some specialties show gender bias

cjb250 — Wed, 19 Apr 2023 23:01:16 +0000

Their analysis, published today in BMJ Open, also found that while female applicants are more successful overall, particular specialities tend to appeal to different genders.

Researchers from the ̽��ֱ�� of Cambridge and Cambridge ̽��ֱ�� Hospitals NHS Foundation Trust examined data from applicants to Specialty Training Posts through Health Education England for the recruitment cycle 2021-22 to look at potential disparities in the success of applicants according to gender, ethnicity and disability.

During this period, there were just under 12,500 successful applicants to Health Education England for training posts – a success rate of one in three (32.7%). Overall, females were more successful than males (37.0% versus 29.1%).

̽��ֱ��researchers found clear evidence that certain specialities were more attractive to females or to males. Of note, surgical specialities and radiology had the highest proportion of male applicants (65.3% and 64.3% respectively), while obstetrics and gynaecology and public health had the highest proportion of female applicants (72.4% and 67.2% respectively).

Senior author Professor Sharon Peacock, from the Department of Medicine at the ̽��ֱ�� of Cambridge, said: “ ̽��ֱ��success by female applicants in many specialties is a positive step towards gender balance, and perhaps reflects existing efforts to address disparities. But the skew in applications and subsequent recruitment by gender, particularly amongst surgical specialities, is concerning.”

Gender disparities are known to have knock-on effects. For example, a lack of female representation contributes towards a male dominated culture, which can then result in fewer female role models to inspire and encourage aspiring female doctors.

̽��ֱ��researchers say there are several reasons for these disparities. In surgical specialities, for example, a male-dominated workplace culture, bullying and harassment, few female role models, and career inflexibility, have been suggested as factors that deter females from applying. Female surgeons have reported quality of life and fewer unsocial hours as explanations of why women prefer other clinical specialities, in addition to the fear that working less-than-full-time or taking career breaks is perceived negatively.

Approximately half (50.2%) of the applicants were non-UK graduates. ̽��ֱ��overall success rate of UK graduates was 44.5%, compared with 22.8% for non-UK graduates.

When it came to minority ethnic groups, after adjusting for country of graduation, applicants from eleven out of fifteen groups (73.3%) were significantly less likely to be successful compared to White British. Those who fared worst were those of Mixed White and Black African ethnicity, who were only half as likely (52%) to be successful as White British applicants.

Dr Dinesh Aggarwal, the study’s first author, also from the Department of Medicine, said: “ ̽��ֱ��data suggests there’s a need to review recruitment policies and processes from a diversity and inclusion perspective. But the issues extend beyond recruitment – doctors from minority ethnic groups can struggle to progress within the NHS and report disproportionately high levels of discrimination from colleagues.

“More than four in ten of the medical and dental workforce in NHS trusts and clinical commissioning groups in England are from a minority ethnic group, and ensuring that they are able to work within an inclusive environment, that allows them to thrive and progress, should be a priority.”

Although only a very small proportion of successful applicants (1.4%) declared a disability, they were more likely to be successful (38.6% compared with 32.8% of non-disabled applicants). However, there were no disabled applicants to 22.4% of the specialities, and for a further 36.2% of specialities, no disabled applicants were accepted.

Dr Dinesh Aggarwal added: “It’s encouraging to see a high proportion of acceptances among individuals disclosing a disability. ̽��ֱ��NHS needs to ensure that application and recruitment processes are accessible and open to adjustments for all disabilities, eliminate any fear of discrimination, and provide assurance that all NHS workplaces will accommodate reasonable adjustments to ensure that disabled doctors can carry out their work. This will not only help to encourage more disabled applicants, but also allow disabled clinicians to feel more comfortable disclosing this information.”

Professor Peacock added: “ ̽��ֱ��NHS is the largest employer in the UK and it’s vital that it nurtures diverse talent to benefit patient care. People from diverse backgrounds bring different lived experiences and perspectives, which in turn strengthens the pool of knowledge and skills within the NHS. A lack of workforce diversity can be detrimental to patient care, and research shows that inherent biases can influence how clinicians treat patients.”

Dr Aggarwal is a PhD student at Churchill College. Professor Peacock is a Fellow at St John’s College.

Reference
Aggarwal, D et al. Applications to medical and surgical specialist training in the UK National Health Service, 2021-22: a cross-sectional observational study to characterise the diversity of successful applicants. BMJ Open; 20 April 2023; DOI: 10.1136/bmjopen-2022-069846

Most minority ethnic groups are less successful than their White British counterparts when applying to specialty training programmes in the NHS, Cambridge researchers have shown.

̽��ֱ��NHS is the largest employer in the UK and it’s vital that it nurtures diverse talent to benefit patient care

Sharon Peacock

DarkoStojanovic

Doctor's white coat with stethoscope and pens

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Cambridge scientists to take part in Royal Institution Christmas Lectures

cjb250 — Thu, 04 Nov 2021 14:34:12 +0000

Professors Julia Gog, Ravi Gupta and Sharon Peacock, each of whom have played a key role in the UK’s response to the on-going COVID-19 pandemic, will lead the on-screen exploration into their area of scientific expertise, with two Guest Lecturers appearing in each episode.

Together, they will offer insights to the Christmas Lectures’ young audience into the world of viruses – how they arise and proliferate, and how we humans respond – from testing and modelling to vaccine development and infection control. They will reveal why discoveries and advances made during the on-going pandemic will have an impact far beyond COVID-19 and are set to change the future of medicine.

̽��ֱ��Guest Lecturers will support the 2021 Christmas Lecturer Jonathan Van-Tam to demonstrate that tackling pandemics is a collaborative and interdisciplinary scientific effort.

Professor Julia Gog OBE, is Professor of Mathematical Biology at the Department of Applied Mathematics and Theoretical Physics at the ̽��ֱ�� of Cambridge and the David N. Moore Fellow and Director of Studies in Mathematics at Queens' College, Cambridge. During the pandemic she has contributed to scientific advice to the UK government through SAGE and SPI-M, the group which provides input based on infectious disease modelling and epidemiology.

Professor Ravi Gupta, is Professor of Clinical Microbiology at the Cambridge Institute for Therapeutic Immunology and Infectious Disease. Using his expertise in RNA virus genetics and biology, Ravi’s work during the pandemic has included reporting the first genotypic-phenotypic evidence for immune escape of SARS-CoV-2 within an individual, defining the process by which new variants are likely to arise, and defining the immune escape and transmissibility advantage of the Delta variant as the driver behind its global expansion.

Professor Sharon Peacock CBE, is Professor of Public Health and Microbiology in the Department of Medicine at the ̽��ֱ�� of Cambridge. During the pandemic Sharon has Chaired the COVID-19 Genomics UK (COG-UK) Consortium, delivering large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government, and helping to inform UK public health interventions and policies.

Also taking part as Guest Lecturers are:

Professor Katie Ewer, a cellular immunologist and Associate Professor at the Jenner Institute at the ̽��ֱ�� of Oxford.
Professor Teresa Lambe OBE, an Associate Professor based in the Oxford Vaccine Group at the ̽��ֱ�� of Oxford.
Professor Catherine Noakes OBE, Professor of Environmental Engineering for Buildings at the ̽��ֱ�� of Leeds.

Lucinda Hunt, Director of the Royal Institution, said: “We are delighted that Jonathan will be joined by such an exciting and expert group of scientists during this year’s series of three Christmas Lectures.

“They will work together to take us on a journey through the world of viruses – how they arise, how they proliferate, and how science and society responds – just as they are doing in tackling the current pandemic. What a strong and positive message that will be for our young audience, about the power of collaborative science.”

Patrick Holland, BBC Director, Factual, Arts and Classical Music Television, said: “Scientists across the world have responded to the Covid crisis with expertise and ingenuity that is humbling for us all. It is no exaggeration to say that the path of history has been changed because of the work of vaccine scientists and epidemiologists.

“Jonathan and his team will give us another exciting and thought-provoking series of Lectures, covering so much more than COVID-19. This will be a celebration of science and of the scientists whose advances are shaping our world.”

In the 2021 Christmas Lectures, ‘Going viral: How Covid changed science forever’, epidemiologist and one of England’s two Deputy Chief Medical Officers, Jonathan Van-Tam, will take a deep dive into many and varied viruses, including COVID-19, and reveal why discoveries and advances made during the on-going pandemic – from early detection techniques to new vaccines – mean biological science will never be the same again.

̽��ֱ��2021 Christmas Lectures will be broadcast on BBC Four and iPlayer between Christmas and New Year.

̽��ֱ��2021 Christmas Lectures are co-produced by the Ri and Windfall Films for BBC Four and iPlayer. They were commissioned by Patrick Holland, Director, Factual, Arts and Classical Music Television and Jack Bootle, Head of Commissioning, Science and Natural History. ̽��ֱ��Commissioning Editor for the BBC is Tom Coveney. The Series Producer is Henry Fraser and the Executive Producer is David Dugan.

Adapted from a press release by the Royal Institution

Three Cambridge researchers are among six leading UK scientists who will share the presenting duties with Professor Jonathan Van-Tam during this year’s Christmas Lectures from the Royal Institution.

Royal Institution

Audience at Royal Institution Christmas Lecture

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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Film: the race to sequence COVID-19

fpjl2 — Mon, 04 Oct 2021 12:50:01 +0000

Hear from some of the scientists behind the UK’s nationwide sequencing effort to track SARS-CoV-2. Sir Patrick Vallance (the government’s Chief Scientific Adviser) also describes how the expertise that came together during the pandemic is now recognised across the world – and why it’s crucially important to continue to sequence to be ready for future pandemics.

This pioneering work is being carried out by the COVID-19 Genomics UK (COG-UK) consortium, which comprises numerous academic institutions, four public health agencies and the Wellcome Sanger Institute, and is administered by the ̽��ֱ�� of Cambridge.

“Incredibly impressive, incredibly high quality and incredibly focused on the mission to make sure that as many people benefited from the science as possible,” Sir Patrick Vallance.

̽��ֱ��variant hunters are helping us to understand how and why the COVID-19 virus is spreading, allowing us to fight back against the COVID-19 pandemic.

̽��ֱ��Variant Hunters

Yes

Hunting for COVID-19 variants

cjb250 — Mon, 22 Mar 2021 11:06:50 +0000

Professor Sharon Peacock explains the story behind the UK's world-leading SARS-CoV-2 genomics capability.

Q&A with Sharon Peacock, coronavirus variant hunter

cjb250 — Mon, 22 Feb 2021 13:35:28 +0000

̽��ֱ��Conversation spoke to Professor Peacock about that day and what happened after.

Q: When did you first get the idea to set up Cog-UK? And how was it formed?

In late February 2020, it dawned on me that we were going to need genome sequencing capabilities across the UK for the novel coronavirus. It was predictable that the virus was going to develop mutations that could become problematic.

On March 4, I emailed five colleagues, asking if they’d be interested in helping me set up a UK sequencing consortium. A week later we met at the Wellcome building on Euston Road in London with the aim of thrashing out a plan. We looked to draw in people who might be able to help us put together a blueprint and a network for sequencing in the UK.

There were about 20 people in the meeting. They were clinical virologists, experts in human genomes and pathogen genomes, epidemiologists and immunologists. During that day, we worked through what we thought an end-to-end sequencing pipeline would be, and we debated whether the sequencing would be centralised or distributed or both, and who would do what. By the end of the day, we had the blueprint.

̽��ֱ��notes from the meeting were written up into a formal proposal for Sir Patrick Vallance, the UK government’s chief scientific adviser.

It’s unusual because if you have four public health agencies and lots of researchers from different institutions and the NHS, it would take a year or more to do something like that normally. But we just sat down and did it, and that’s how Cog-UK was born.

Q: How did you get funding?

̽��ֱ��application was on Sir Patrick Vallance’s desk by March 15. He and Professor Chris Whitty, the chief medical officer for England, had what they called a “COVID-19 fighting fund”. They reviewed our proposal and strongly supported it.

I also contacted Sir Mike Stratton, director of the Wellcome Sanger Institute in Cambridge. I asked Mike if they could support us as they have the technology to do large-scale sequencing. He said yes, and since then, Sanger has contributed a great deal.

So at the outset, we got about £14.5 million from the government, plus in-kind funding from Sanger, which together came to a total of around £20 million.

We started on April 1, but we’d already done quite a lot of sequencing by then. About 260 coronavirus sequences were already in the bag.

Q: So the sequencing began even before Cog-UK was launched?

Because a lot of people had sequencing instruments and expertise, they had already started work. There are sequencing instruments in labs across the country. We hadn’t catalogued where or what at that stage. And, in fact, we weren’t particularly prescriptive about what types of sequencing instruments we asked the labs to use. People used what they thought worked well for them.

Q: How did other scientists react?

They were hugely supportive. Some people were worried that the virus would not accumulate enough mutations to make it worth our while. It would mean that we would end up sequencing the same virus over and over again because it only mutates once or twice a month. It could all have been a waste of time.

What we hadn’t bargained for was the 100 million cases – but perhaps even as high as a billion, if you include undiagnosed cases. And each time the virus infects a person it has an opportunity to make a mistake in its genome.

We considered the risk of lack of genetic variation, but went ahead. What we did was rather bold at the time.

Q: How does it work in practice, from the time someone is swabbed to the time the sequence is uploaded onto the shared Gisaid database that holds all of the world’s sequences of SARS-CoV-2?

Laboratory testing for COVID-19 using the so-called PCR test in the UK is roughly divided into two testing pathways. If you are hospitalised with COVID-19, your sample will get tested in a local laboratory. We call that pillar one.

Cog-UK collects samples from about 90 different laboratories at the moment, which is quite a logistical challenge. These are sent to regional sequencing hubs that focus mostly on sequencing from their region. These are really important samples because they are from the sickest people with COVID-19.

Pillar two testing is done in the Lighthouse labs, which were set up to analyse community testing samples. These are sequenced at the Wellcome Sanger Institute.

We also provide sequencing to major government projects, like the Office for National Statistics study. We also support the React study, [a major programme of home testing for COVID-19 to track the progress of the infection across England] and vaccine trials.

We can’t sequence all of the positive samples at the moment. When we first started, we were aiming for a minimum of 10%. At the moment it’s under 10%, but we hope to get to around 20%, and we’ll build from there.

Q: And as a total of the viruses sequenced in the world, what proportion is Cog-UK sequencing, and how does it compare with other countries?

We have sequenced about 45% to 48% of all SARS-CoV-2 genomes in the Gisaid database.

Q: Given the importance of tracking mutations, are other countries starting to increase their sequencing efforts?

Yes. ̽��ֱ��country where I think we will see a big shift is the US because of all the changes they’re making in their response to the pandemic. I would anticipate quite a few other countries beginning to come up, too. I know that Germany is looking to increase its sequencing capacity. But there are some really big gaps in the map.

Q: Worrying coronavirus variants have been widely reported on in the last few months. ̽��ֱ��so-called “UK variant”, B117, was raised as a concern in November, but the sample was from September. Is that right?

Yes, September 20. There were very few cases of B117 initially, and it’s one of hundreds of different variants. So there was no reason to be concerned about it initially. We are learning all the time about which mutations might be important, particularly when they crop up all around the world. So the first time the UK variant was in the database, you probably wouldn’t give it a second thought. It’s only once you start to learn about what the mutations really mean, or when an event occurs, that you start to zoom in on specific variants. And with B117, Public Health England noticed that there was a surge in cases in Kent, which was odd because there was a lockdown and there weren’t any surges elsewhere. That was a striking observation.

So that could be due to human behaviour, such as a super-spreader event. It was at that point, towards the beginning of December, that it became clear that there was not only a surge in cases, but those cases were caused by B117. It had a really striking genome in that it had 23 mutations, which were far more than we were used to seeing. That’s when researchers began to find evidence that it was more transmissible. And it took a bit longer to do the essential science so that we could be certain that this variant was indeed associated with increased transmission.

Q: Why are we suddenly seeing all of these mutations that give the coronavirus an advantage now?

It’s not the first time that we have observed mutations that have given the virus an advantage. At the end of March 2020, we noticed something for the first time in the UK: a mutation in the spike protein called D614G. This wasn’t in the original virus that was first detected in China. But the virus with this mutation rapidly expanded and replaced the other viral lineages circulating at the time.

We talked about this at Sage, the government’s scientific advisory group for emergencies, quite early on. And we calculated that it caused an increase in the R0, which represents the average number of people infected by one infectious individual. So we knew then that this type of event could happen – it was a practice run for more serious variants to come.

̽��ֱ��D614G mutation gave the virus a modest increase in transmissibility. But it swept across the world. It’s now present in almost all SARS-CoV-2 viruses.

̽��ֱ��next variant to worry people emerged in Denmark and was related to SARS-CoV-2 being transmitted between mink and people – referred to as the “cluster 5 variant”. People were concerned that evolution had been accelerated by passage through mink and had been transmitted back to humans. But only 12 people in Denmark were ever found to have that variant. So that fizzled.

A third worrying variant emerged in Spain in the summer. It seemed to be spreading very quickly around Europe. One possible reason for this was a particular mutation in the spike protein. But over time it became clear that it was being transmitted because people were moving around on their summer holidays. There was no evidence that it was more transmissible.

We also reported to Sage another mutation in the spike protein last October, called N439K. And that change in the spike protein appears to affect the body’s immune response, at least based on laboratory experiments.

So the idea that variants have only just arisen is not the case. We’ve been talking about variants since the early days of the pandemic, which might surprise some people.

Q: Is the original virus from Wuhan still around?

Lineages can expand and then go extinct, so we don’t expect the same lineage to necessarily be around forever. This was shown by work in Wales and in Scotland, where they looked at the lineages in the first wave and then in the second wave.

In the first wave, these were largely imported from Europe. In the summer as cases fell, most of those original lineages disappeared. Then, in the second wave, numerous new lineages were introduced from overseas, which kicked off the second wave. So it’s quite a dynamic process. As particular lineages have a fitness advantage, then that is probably what is circulating at any particular time.

Q: Is there a base type that you compare changes against? And is it the original virus or the current dominant variant?

We compare changes against the original virus sequenced in Wuhan in January 2020 – it’s the reference genome. But it’s quite confusing because different groups use different names and different naming conventions. I hope that the World Health Organization will help us to reach a common international nomenclature.

It worries me that people name variants after where they were first identified. Evolution is not a function of geography, it’s a function of nature. I very much hope that we move away from calling coronaviruses, the UK variant or the South African variant or the Brazilian variant. I tend to try and say the variant first detected in South Africa, or whatever. Because it could be quite stigmatising in the longer term.

Q: Is a certain amount of evolutionary selective pressure created when we start to vaccinate lots of people? Or is the greater number of people in which the virus has the opportunity to mutate the greater problem of the two?

At the moment, I think it’s the number of cases that is important because the variant detected in the UK emerged when vaccines weren’t yet being rolled out, but when cases were high. And the same is true in South Africa and Brazil.

Some people have contacted me to say: “Do you think it was the vaccine trials that led variants to emerge?” But if you compare the relatively small number of people who’ve been in vaccine trials versus the very large number of people who are infected – 100 million people infected. I think the biggest driver of mutation emerging is the number of opportunities the virus has had to mutate.

And people say, “Well, isn’t the vaccine going to drive the emergence of new variants?” It may be one of the pressures, but if you’re in a population where, say, 50% have been infected and have so-called “natural immunity”, then it doesn’t matter how you get the immunity to the virus, the virus will try to find a crack in that armour. But in that instance, it’s a naturally acquired infection rather than immunisation. So this problem has been around long before vaccination.

Q: And of the variants of concern that we know of, which one is the most worrying?

Right now, it’s the variant first detected in South Africa. It has already been reported in 31 countries and identified in 750 sequences so far. Although this is probably a gross underestimate because quite a few countries that surround South Africa do not have sequencing capacity at the moment. This variant appears to be more transmissible in South Africa and reduces the effectiveness of our immune response, be that from natural infection or vaccination.

P1 is also on the watch list. This variant first identified in Brazil has mutations associated with being more transmissible and with a reduced immune response. If you look at the global spread of P1 though, unlike some of the other variants, I don’t really see it taking hold at the moment. It’s been linked to just nine countries so far.

I’m also looking at what else might be emerging in the coming weeks and months. What I’m particularly concerned about is that now that B117 causes almost all COVID-19 cases in the UK – what new mutations will arise in this? This new variant is likely to start to develop constellations of different mutations in its descendants. And what I’m watching for is something like E484K, the “escape mutation”, being increasingly found in B117. So far, this has arisen independently several times and includes a cluster of cases in Bristol and south-west England, but the number of cases is low.

Q: How important is what Cog-UK does to the vaccine effort?

Sequencing is absolutely integral to vaccine development. We are going to need to have sequence data.

We’re going to need to keep sequencing for the foreseeable future so that we can adapt our vaccines to keep them effective. It’s going to be a long-term job to run the two in parallel. Vaccine manufacturers are already working to tweak their vaccines for the South Africa variant, for example, to make sure it’s going to be effective against that variant.

There are going to be new variants arising in the future and we’re going to have to adapt our response to these as we go along. Sequencing and vaccine development are key partners. I suspect that this is going to be ongoing throughout my life and beyond. Of concern is that we don’t have global coverage, so we are not sighted globally in terms of new variants.

Q: So it’s going to be like the flu vaccine every year, depending on how long immunity lasts?

Yes, quite similar, but it might be a bit less predictable than a single vaccine booster each year. SARS-CoV-2 could ratchet up its characteristics over time, and the diversity of mutation combinations in different variants could change over time. So it could be more complex than flu.

We’ve also known that immunity wanes over time. So we’re going to have to be thinking about long-term strategies with this virus.

Sharon Peacock, Director, COVID-19 genomics UK Consortium (COG-UK) and Professor of Public Health & Microbiology, ̽��ֱ�� of Cambridge

This article is republished from ̽��ֱ��Conversation under a Creative Commons license. Read the original article.

̽��ֱ��UK is a world leader in sequencing SARS-CoV-2, the virus that causes COVID-19. Of all the coronavirus genomes that have been sequenced in the world, nearly half have been sequenced by COVID-19 Genomics UK Consortium (Cog-UK). ̽��ֱ��consortium began life on 4 March 2020 when Sharon Peacock, a professor of public health and microbiology at the ̽��ֱ�� of Cambridge, emailed a handful of scientists and asked for their help.

Professor Sharon Peacock

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Cambridge-led SARS-CoV-2 genomic surveillance consortium receives £12.2 million

Anonymous — Mon, 16 Nov 2020 08:00:17 +0000

̽��ֱ��additional investment will enable COG-UK to grow and strengthen current genomic surveillance efforts spearheaded by the Wellcome Sanger Institute and the ̽��ֱ�� of Cambridge, together with the four UK Public Health Agencies and other COG-UK partners, with the aim of increasing sequencing capacity across the national network and reducing turnaround time from patient sample to genome sequence.

̽��ֱ��viral genome sequencing data will be integrated within the four UK Public Health Agencies & NHS Test and Trace to help understand outbreaks and strengthen infection control measures. Integrating real-time viral genomic data into outbreaks investigations identifies patterns linking individual cases and can reveal otherwise unidentifiable opportunities for intervention. Viral genome sequencing also enables monitoring of the evolution of the virus for mutations that may impact on the efficacy of vaccines.

̽��ֱ��COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents a major threat to health. ̽��ֱ��COG-UK Consortium was created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres, Public Health Agencies and the UK government.

Led by Professor Sharon Peacock of the ̽��ֱ�� of Cambridge & Director Of Science at Public Health England, COG-UK is an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and 12 academic institutions from across the UK providing world leading expertise in SARS-CoV-2 genomics and supporting sequencing and analysis capacity nationwide.

Since its launch in March 2020, COG-UK has generated and made publicly available more than 100,000 SARS-CoV-2 genomes, making up over 45 per cent of the global total. This unprecedented effort has not been achieved previously for any pathogen, anywhere in the world.

COG-UK researchers have built a central database and developed cutting-edge analytical methodology and data pipelines for SARS-CoV-2 genomics. COG-UK has led the development of analytical software to define viral lineages and shares methods globally.

Collectively, these data and tools have provided important scientific insights into the spread and evolution of the virus, at local, regional, national and international scales.

However, the steadily rising numbers of cases in the UK requires a prompt increase in the national SARS-CoV-2 genome sequencing capacity, to ensure that the benefits of using genome sequence data can be realised in a rapid and robust manner.

Professor Sharon Peacock, who is the Director of COG-UK, Professor of Public Health and Microbiology at the ̽��ֱ�� of Cambridge and a Director Of Science (Pathogen Genomics) at Public Health England, said: “To fully understand the spread and evolution of the SARS-CoV-2 virus, we must sequence and analyse the viral genomes. ̽��ֱ��pattern of accumulation of mutations in the genomes enables us to determine the relatedness of virus samples and define viral lineages in order to understand whether local outbreaks are caused by transmission of single or multiple viral lineages. Analysis of viral genome sequences also allow us to monitor the evolution of SARS-CoV-2 and assess whether specific mutations influence transmission, disease severity, or the impact of interventions such as vaccines.”

̽��ֱ��four UK Public Health Agencies and COG-UK are working to link SARS-CoV-2 genome data with epidemiological, clinical and contact tracing records nationally.

This will help establish a comprehensive national dataset linking viral sequencing with host genomics, immunology, clinical outcomes and risk factors.

Adapted from a press release from COG-UK

̽��ֱ��COVID-19 Genomics UK (COG-UK) Consortium has been backed by the Department for Health and Social Care Testing Innovation Fund to expand whole genome sequencing of positive SARS-CoV-2 virus samples to map how COVID-19 spreads and evolves. ̽��ֱ��£12.2M funding will facilitate the genome sequencing capacity needed to meet the increasing numbers of COVID-19 cases expected in the UK this winter.

To fully understand the spread and evolution of the SARS-CoV-2 virus, we must sequence and analyse the viral genomes

Sharon Peacock

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Transmission electron micrograph of SARS-CoV-2 virus particles, isolated from a patient

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