̽��ֱ�� of Cambridge - Public Health England

Public health experts urge government to put health at centre of levelling up agenda

cjb250 — Fri, 10 Dec 2021 00:01:22 +0000

Based on decades of research around tackling health inequalities at local and regional level, the guidance is aimed at central and local government as well as other agencies with a stake in improving health.

̽��ֱ��team has published its report on the Cambridge Research Methods Hub website. It sets out five principles and eight policy recommendations that are designed to be used together long-term across national, regional and local systems.

̽��ֱ��principles are:

Allocating resources proportionate to need;
Working in partnership with local communities;
Developing long-term, multisector and cross-government programmes;
Offering bespoke services to disadvantaged groups;
Ensuring initiatives are healthy-by-default and easy to use.

Each principle is supported by case studies, such as Healthy New Towns, the Big Local initiative, and New Deal for Communities.

Dr John Ford, lead author and Clinical Lecturer in Public Health at the Primary Care Unit, ̽��ֱ�� of Cambridge, said: “ ̽��ֱ��new guidance has been produced to show how to level up health. We already know that progress on closing the gap is possible. ̽��ֱ��previous cross-government health inequalities programme reduced the socio-economic gap in life expectancy by six months and improved overall life expectancy. This was achieved through sustained, multi-component, and cross-government action over more than 10 years.”

Policy recommendations include: health being a core part of levelling up; development of a cross-government health inequalities strategy; establishing a consensus around what levelling up health means; and a focus on the social and structural factors that determine health.

Importantly, the report recommends a move away from initiatives that require individuals to invest time and effort to benefit from, such as promoting gym membership, because they tend to increase inequalities. Rather, the researchers recommend initiatives that make healthy choices the default and require minimal effort from the individuals, such as fluoridation of water and opportunistic screening for health problems during vaccine appointments.

Furthermore, the report calls for an end to competitive bidding of local areas to allocate public funds. Instead, it recommends allocating funding based on population need.

Health inequalities in England mean that men and women in deprived areas live an average of ten and eight years less respectively than men and women in more affluent places. Area-level health inequalities like these are driven by the conditions in which we live. Education and employment opportunities, housing, opportunities for exercise and a good diet are just some of the factors that directly affect our health.

Left-behind neighbourhoods, which have not prospered as much as other areas, experience greater health inequalities and the health of disadvantaged areas in the Northern regions has been falling further behind. For example, a baby boy born today in Blackpool can expect an additional 17 years of poor health compared to a baby boy born in Richmond upon Thames.

̽��ֱ��pandemic has exacerbated inequalities, and deaths related to COVID-19 in the most deprived areas of the country are double those in the least deprived. ̽��ֱ��long-term repercussions of the pandemic for some people – food and housing insecurity, debt and poverty – are expected to disproportionally affect those living in areas of higher deprivation, causing further damage to wellbeing and health.

̽��ֱ��researchers say that work to address area-level health inequalities is critically important for the UK Government’s levelling up agenda.

̽��ֱ��team reviewed data from over 650 research studies and 19 published reports. ̽��ֱ��12 case studies were selected from 143 potentially relevant examples from across England showing what works.

Professor Clare Bambra, Professor of Public Health at the ̽��ֱ�� of Newcastle, said: “Levelling up needs to urgently focus on health inequalities by addressing the unequal conditions in which we live, work and age.

“For too long, a lack of investment in key services has meant that more deprived, ‘Left Behind Areas’ – particularly in the north – have suffered disproportionately. ̽��ֱ��COVID-19 pandemic has worsened these inequalities and it will cast a long shadow across our future heath and economic prosperity as a country unless we act now. That’s why levelling up health is so central to the government’s overall approach to levelling up the country.”

̽��ֱ��new guidance was commissioned by Public Health England.

Reference
John Ford, Vic McGowan, Fiona Davey, Jack Birch, Isla Kuhn, Anwesha Lahiri, Anna Gkiouleka, Ananya Arora, Sarah Sowden, Clare Bambra. Levelling Up Health: A practical, evidence-based framework. December 2021

Health needs to be at the heart of the Government’s levelling up agenda, say researchers at the Universities of Cambridge and Newcastle. ̽��ֱ��team have today published practical guidance on how to reduce health inequalities.

̽��ֱ��new guidance has been produced to show how to level up health. We already know that progress on closing the gap is possible

John Ford

Francis Heathcote

Blackpool

̽��ֱ��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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Fewer than one in 20 people living with HIV in England expected to be unaware of status by 2025

cjb250 — Fri, 24 Sep 2021 07:49:11 +0000

In 2014, UNAIDS set an ambitious target of 90-90-90 by 2020 – that is, 90% of all people living with HIV will know their HIV status; 90% of all people with diagnosed HIV infection will receive sustained antiretroviral therapy; and 90% of all people receiving antiretroviral therapy will have viral suppression.

According to the Cambridge and PHE team, in 2019 there were an estimated 105,200 people living with HIV in the UK, of whom 94% were aware of their HIV status. In addition, 98% of those living with diagnosed HIV were on treatment, and 97% of these were virally suppressed. In other words, England had already reached the UNAIDS goals.

In a publication today in ̽��ֱ��Lancet Public Health, the researchers extended their analysis of evidence from multiple surveillance, demographic, and survey datasets relevant to HIV in England from estimating HIV prevalence in a single year to estimating the trends over time in HIV prevalence. Trends in the number of people living with HIV, the proportion of people unaware of their HIV infection, and the corresponding prevalence of undiagnosed HIV are reported.

According to their analysis, the estimated number of people in England living with HIV aged 15-74 years who were unaware of their infection halved from 11,600 in 2013 to 5,900 in 2019, with a corresponding fall in prevalence from 0.29 to 0.14 per 1,000 people.

At the same time, the increase in the number of people living with diagnosed HIV resulted in the total number of people living with HIV rising from 83,500 to 92,800 over the same period. ̽��ֱ��percentage of people living with HIV whose infection was diagnosed therefore steadily increased from 86% in 2013 to 94% in 2019, reaching the UNAIDS target in 2016 – and even earlier, in 2013, for Black African heterosexuals.

Professor Daniela De Angelis from the MRC Biostatistics Unit, the study’s senior author, said: “Overall, we see a positive picture for the HIV epidemic in England, with a dramatic fall in the number of people living with undiagnosed HIV. We estimate we are already several years ahead of the UNAIDS 2020 goals and are on target to reach 95% diagnosed by 2025 and to eliminate HIV infections by 2030.

Dr Anne Presanis from the MRC Biostatistics Unit added: “Examined more closely, the situation is not as positive for everyone. We estimate that areas of England outside London have not seen as steep a decrease in undiagnosed HIV prevalence as in London, and there is evidence of missed opportunities to diagnose HIV infections among some population subgroups.”

In England, gay, bisexual, and other men who have sex with men, and Black African heterosexuals remain disproportionately affected by HIV, with considerably higher undiagnosed HIV prevalence per population in 2019 than heterosexuals in other ethnic groups. However, undiagnosed HIV prevalence rates within these communities have seen dramatic falls: for gay, bisexual, and other men who have sex with men, prevalence fell from 13.9 to 5.4 per 1,000, and for Black African heterosexuals prevalence fell from 3.3 to 1.7 per 1,000 population.

London saw more dramatic falls in the prevalence of undiagnosed HIV during the study period than other regions of England, down from 0.74 to 0.31 per 1,000, compared to a decrease from 0.20 to 0.11 per 1,000 outside London.

Although sexual health clinics provide free and confidential HIV testing to all clinic attendees, the researchers estimated that among heterosexuals in an ethnic group other than Black African, undiagnosed prevalence in clinic attendees in 2019 was more than 30 times greater than in those who had not attended in the past year. This implies that sexual health clinics are missing opportunities for testing attendees. This is in line with findings from Public Health England that among individuals outside those subgroups at greatest risk of HIV infection, the proportion declining a HIV test had increased to more than one in four (27%) in 2016.

̽��ֱ��researchers say their estimates have important implications for efforts to eliminate HIV transmission in England and the UK.

Dr Valerie Delpech, head of the HIV Team at Public Health England said: “This research is good news and shows that combination prevention, and in particular HIV testing and early treatment, is working in England. ̽��ֱ��increasing use of pre-exposure prophylaxis among persons at higher risk of HIV has further amplified our response to end HIV transmission. Nevertheless, further reducing the number of people who remain undiagnosed with HIV infection will become very challenging in the coming years. This is particularly the case for heterosexuals who may not consider themselves at risk of HIV.

“ ̽��ֱ��priority must be to ensure that all sexual health clinic attendees are offered and encouraged to accept a HIV test, regardless of ethnicity, rather than the 73% that currently do test. If we can increase the number of clinic attendees unaware of their HIV status who get tested and diagnosed, as well as improve partner notification, the prospect of eliminating HIV transmission becomes increasingly likely.”

̽��ֱ��research was funded by the Medical Research Council and Public Health England.

Reference
Presanis AM, et al. Trends in undiagnosed HIV prevalence in England and implications for eliminating HIV transmission by 2030: an evidence synthesis model. Lancet Public Health; 23 Sept 2021; DOI: 10.1016/S2468-2667(21)0042-0

England is on track to have diagnosed 95% of people living with HIV by 2025, putting it in a strong position to eliminate HIV transmission by 2030, say researchers at the MRC Biostatistics Unit, ̽��ֱ�� of Cambridge, and Public Health England (PHE).

Overall, we see a positive picture for the HIV epidemic in England, with a dramatic fall in the number of people living with undiagnosed HIV

Daniela De Angelis

Andy McCarthy

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Patients with SARS-CoV-2 Delta variant were more likely to be admitted to hospital compared to patients with Alpha variant

sc604 — Tue, 31 Aug 2021 09:29:45 +0000

In a new study published in ̽��ֱ��Lancet Infectious Diseases, researchers at Public Health England and the MRC Biostatistics Unit, ̽��ֱ�� of Cambridge, found that the estimated risk of hospital admission was two times higher for individuals diagnosed with the Delta variant of the SARS-CoV-2 virus, compared to those with the Alpha variant, after adjusting for differences in age, sex, ethnicity, deprivation, region of residence, date of positive test and vaccination status. When broadening the scope to look at the risk of either hospital admission or emergency care attendance, the risk was 1.45 times higher for Delta than Alpha.

This is the largest study to date to report on the risk of hospitalisation outcomes for cases with the Delta compared to the Alpha variant, using 43,338 Alpha and Delta cases confirmed through whole-genome sequencing who tested positive for COVID-19 between 29th March and 23rd May 2021. It is crucial to note that most of the Alpha and Delta cases in the study were unvaccinated or only partially vaccinated: 74% were unvaccinated, 24% were partially vaccinated, and only 2% were fully vaccinated. ̽��ֱ��results from this study therefore primarily tell us about the risk of hospital admission for those who are unvaccinated or partially vaccinated. Given the small number of hospitalised vaccinated cases, it has not been possible to estimate reliably if the hospitalisation risk differed between Delta and Alpha cases who had been fully vaccinated.

̽��ֱ��Delta variant is now the most common SARS-CoV-2 lineage in several higher-income and lower-income countries on all continents, currently accounting for more than 99% of new cases in England [2]. ̽��ֱ��evidence provided in this study therefore has implications for healthcare practice, planning and response in countries with ongoing or future Delta variant outbreaks, particularly in unvaccinated or partially vaccinated populations. As previous studies have shown Delta and Alpha spread more rapidly than previous variants [2–4], the combination of faster transmission and the current study’s finding of higher risk of severe disease requiring hospital admission in unvaccinated populations implies a more severe burden on healthcare of Delta outbreaks than of Alpha epidemics.

Previous studies have shown the available COVID-19 vaccines are highly effective against symptomatic infections with the Alpha variant [5], and are effective against symptomatic infections with the Delta variant, particularly after a full vaccination cycle with two doses [6,7]. For those who despite vaccination become infected, the vaccination protects against admission to hospital [8].

Dr Anne Presanis, Senior Statistician at the MRC Biostatistics Unit said:

"Our analysis highlights that in the absence of vaccination, any Delta outbreaks will impose a greater burden on healthcare than an Alpha epidemic. Getting fully vaccinated is crucial for reducing an individual’s risk of symptomatic infection with Delta in the first place, and, importantly, of reducing a Delta patient’s risk of severe illness and hospital admission.”

Dr Gavin Dabrera, Consultant Epidemiologist at Public Health England, said:

“This study confirms previous findings that people infected with Delta are significantly more likely to require hospitalisation than those with Alpha, although most cases included in the analysis were unvaccinated.

We already know that vaccination offers excellent protection against Delta and as this variant accounts for over 99% of COVID-19 cases in the UK, it is vital that those who have not received two doses of vaccine do so as soon as possible.

It is still important that if you have COVID-19 symptoms, stay home and get a PCR test as soon as possible.”

Reference:
Katherine A Twohig et al. 'Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study.' ̽��ֱ��Lancet Infectious Diseases (2021). DOI: 10.1016/S1473-3099(21)00475-8

Largest study to date analysing more than 40,000 COVID-19 cases finds a two-fold increased risk of hospitalisation from delta versus alpha variant infections.

Getting fully vaccinated is crucial for reducing an individual’s risk of symptomatic infection with Delta in the first place, and, importantly, of reducing a Delta patient’s risk of severe illness and hospital admission

Anne Presanis

Steven Cornfield via Unsplash

Patient receives Covid-19 vaccine

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England on track to achieve elimination of HIV transmission by 2030 as model shows sharp decrease in HIV incidence

Anonymous — Thu, 10 Jun 2021 08:20:10 +0000

To manage the HIV epidemic among men who have sex with men (MSM) in England, enhanced testing and earlier treatment strategies were scaled-up between 2011 and 2015 and supplemented from 2015 by pre-exposure prophylaxis (PrEP). ̽��ֱ��researchers examined the effect of these interventions on the number of new infections and investigated whether the United Nations (UN) targets for HIV control and elimination of HIV transmission by 2030 might be within reach among MSM in England.

A complexity in this assessment is that HIV infections are not observed. Routine surveillance collects data on new HIV diagnoses, but trends in new diagnoses alone can be misleading as they can represent infections that occurred many years previously and depend on the testing behaviour of infected individuals.

To estimate new HIV infections among adult MSM (age 15 years and above) over a 10-year period between 2009 and 2018, the researchers used a novel statistical model that used data on HIV and AIDS diagnoses routinely collected via the national HIV and AIDS Reporting System in England, and knowledge on the progression of HIV. Estimated trends in new infections were then extrapolated to understand the likelihood of achieving the UN elimination target defined as less than one newly acquired infection per 10,000 MSM per year, by 2030.

̽��ֱ��peak in the number of new HIV infections in MSM in England is estimated to have occurred between 2012 and 2013, followed by a steep decrease from 2,770 new infections in 2013 to 1,740 in 2015, and a further steadier decrease from 2016, down to 854. ̽��ֱ��decline was consistent across all age groups but was particularly marked in MSM aged 25–34 years, and slowest in those aged 45 years or older. Importantly, this decrease began before the widespread roll-out of PrEP in 2016, indicating the success of testing and treatment as infection prevention measures among MSM in England.

Through extrapolation, the researchers calculated a 40% likelihood of England reaching the UN elimination target by 2030 and identified relevant age-specific targeting of further prevention efforts (i.e., to MSM aged ≥45 years) to increase this likelihood.

Senior author, Professor Daniela De Angelis, Deputy Director of the MRC Biostatistics Unit, ̽��ֱ�� of Cambridge, said: “This is very good news and suggests that prevention measures adopted in England from 2011 have been effective. With the rollout of PrEP, England looks on course to meet the goal of zero transmissions by 2030. Our study also shows the value of regular estimation of HIV incidence to recognise and respond appropriately to changes in the current downward trend. ̽��ֱ��challenge now is to achieve these reductions in all groups at risk for HIV acquisition.”

Valerie Delpech, Head of National HIV Surveillance at Public Health England, said: “We have made good progress towards ending HIV transmission by 2030 in England. Frequent HIV testing and the use of PrEP amongst people most at risk of HIV, together with prompt treatment among those diagnosed, are key to ending HIV transmission by 2030.

“You can benefit from life-saving HIV treatments if you are diagnosed with HIV and it also means you cannot pass the virus on.

“HIV and STI tests are still available through sexual health clinics during the COVID pandemic. Many clinics offer online testing throughout the year – people can order tests on clinic websites, take them in the privacy of their own home, return by post and receive results via text, phone call or post.”

This research is funded by the UK Medical Research Council, UK National Institute of Health Research Health Protection Unit in Behavioural Science and Evaluation, and Public Health England.

Reference
Brizzi, F et al. Tracking elimination of HIV transmission in men who have sex with men in England: a modelling study. Lancet HIV, 10 June 2021; DOI: 10.1016/ S2352-3018(21)00044-8

̽��ֱ��annual number of new HIV infections among men who have sex with men in England is likely to have fallen dramatically, from 2,770 in 2013 to 854 in 2018, showing elimination of HIV transmission by 2030 to be within reach – suggests work by researchers from the MRC Biostatistics Unit at the ̽��ֱ�� of Cambridge and Public Health England, published in ̽��ֱ��Lancet HIV.

This is very good news and suggests that prevention measures adopted in England from 2011 have been effective

Daniela De Angelis

Jason

#FreedomTo Know my HIV Status

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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

Yes

DNA test can quickly identify pneumonia in patients with severe COVID-19, aiding faster treatment

sc604 — Fri, 15 Jan 2021 06:00:00 +0000

For patients with the most severe forms of COVID-19, mechanical ventilation is often the only way to keep them alive, as doctors use anti-inflammatory therapies to treat their inflamed lungs. However, these patients are susceptible to further infections from bacteria and fungi that they may acquire while in hospital – so called ‘ventilator-associated pneumonia’.

Now, a team of scientists and doctors at the ̽��ֱ�� of Cambridge and Cambridge ̽��ֱ�� Hospitals NHS Foundation Trust, led by Professor Gordon Dougan, Dr Vilas Navapurkar and Dr Andrew Conway Morris, have developed a simple DNA test to quickly identify these infections and target antibiotic treatment as needed.

̽��ֱ��test, developed at Addenbrooke’s hospital in collaboration with Public Health England, gives doctors the information they need to start treatment within hours rather than days, fine-tuning treatment as required and reducing the inappropriate use of antibiotics. This approach, based on higher throughput DNA testing, is being rolled out at Cambridge ̽��ֱ�� Hospitals and offers a route towards better treatments for infection more generally. ̽��ֱ��results are reported in the journal Critical Care.

Patients who need mechanical ventilation are at significant risk of developing secondary pneumonia while they are in intensive care. These infections are often caused by antibiotic-resistant bacteria, and are hard to diagnose and need targeted treatment.

“Early on in the pandemic we noticed that COVID-19 patients appeared to be particularly at risk of developing secondary pneumonia, and started using a rapid diagnostic test that we had developed for just such a situation,” said co-author Dr Andrew Conway Morris from Cambridge’s Department of Medicine and an intensive care consultant. “Using this test, we found that patients with COVID-19 were twice as likely to develop secondary pneumonia as other patients in the same intensive care unit.”

COVID-19 patients are thought to be at increased risk of infection for several reasons. Due to the amount of lung damage, these severe COVID-19 cases tend to spend more time on a ventilator than patients without COVID-19. In addition, many of these patients also have a poorly-regulated immune system, where the immune cells damage the organs, but also have impaired anti-microbial functions, increasing the risk of infection.

Normally, confirming a pneumonia diagnosis is challenging, as bacterial samples from patients need to be cultured and grown in a lab, which is time-consuming. ̽��ֱ��Cambridge test takes an alternative approach by detecting the DNA of different pathogens, which allows for faster and more accurate testing.

̽��ֱ��test uses multiple polymerase chain reaction (PCR) which detects the DNA of the bacteria and can be done in around four hours, meaning there is no need to wait for the bacteria to grow. “Often, patients have already started to receive antobiotics before the bacteria have had time to grow in the lab,” said Morris. “This means that results from cultures are often negative, whereas PCR doesn’t need viable bacteria to detect – making this a more accurate test.”

̽��ֱ��test – which was developed with Dr Martin Curran, a specialist in PCR diagnostics from Public Health England’s Cambridge laboratory – runs multiple PCR reactions in parallel, and can simultaneously pick up 52 different pathogens, which often infect the lungs of patients in intensive care. At the same time, it can also test for antibiotic resistance.

“We found that although patients with COVID-19 were more likely to develop secondary pneumonia, the bacteria that caused these infections were similar to those in ICU patients without COVID-19,” said lead author Mailis Maes, also from the Department of Medicine. “This means that standard antibiotic protocols can be applied to COVID-19 patients.”

This is one of the first times that this technology has been used in routine clinical practice and has now been approved by the hospital. ̽��ֱ��researchers anticipate that similar approaches would benefit patients if used more broadly.

This study was funded by the National Institute for Health Research Cambridge Biomedical Research Centre.

Reference:
Mailis Maes et al. ‘Ventilator-associated pneumonia in critically ill patients with COVID-19.’ Critical Care (2021). DOI: 10.1186/s13054-021-03460-5

Researchers have developed a DNA test to quickly identify secondary infections in COVID-19 patients, who have double the risk of developing pneumonia while on ventilation than non-COVID-19 patients.

Using this test, we found that patients with COVID-19 were twice as likely to develop secondary pneumonia as other patients in the same intensive care unit

Andrew Conway Morris

Official U.S. Navy Page

Lt. Cmdr. Michael Heimes checks on a patient connected to a ventilator at Baton Rouge General Mid City campus

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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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AstraZeneca/GSK/ ̽��ֱ�� of Cambridge collaborate to support UK national effort to boost COVID-19 testing

plc32 — Tue, 07 Apr 2020 10:46:52 +0000

A new testing laboratory will be set up by AstraZeneca, GSK and Cambridge at the ̽��ֱ��’s Anne McLaren Building. This facility will be used for high throughput screening for COVID-19 testing and to explore the use of alternative chemical reagents for test kits in order to help overcome current supply shortages.

Alongside this new testing facility, AstraZeneca and GSK are working together to provide process optimisation support to the UK national testing centres in Milton Keynes, Alderley Park and Glasgow for COVID-19, providing expertise in automation and robotics to help the national testing system to continue to expand capacity over the coming weeks.

While diagnostic testing is not part of either company’s core business, we are moving as fast as we can to help where possible - with a focus on providing our world class scientific and technical expertise - working both with the Government’s screening programme and alongside the wider life sciences sector and specialist diagnostic companies.

Further updates on progress will be issued on this work in due course.

We continue to pay tribute to those working on the frontlines of this pandemic, in the UK and globally. Defeating COVID-19 requires a collective effort from everyone working in healthcare and we are committed to playing our part.

As part of the UK Government’s announcement of a new five pillar plan to boost testing for COVID-19, AstraZeneca, GSK and the ̽��ֱ�� of Cambridge have formed a joint collaboration to take action to support this national effort.

Everyone in this ̽��ֱ�� and private industry partnership is working hard to help our health service fight COVID-19.

Vice-Chancellor Stephen J Toope

Yes