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UK variant hunters lead global race to stay ahead of COVID

Associated Press

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UK variant hunters lead global race to stay ahead of COVID

On March 4, 2020, when there were just 84 confirmed cases of COVID-19 in the U.K., professor Sharon Peacock recognized that the country needed to expand its capacity to analyze the genetic makeup of the virus.

The Cambridge University microbiologist understood that genomic sequencing would be crucial in tracking the disease, controlling outbreaks and developing vaccines. So she began working with colleagues around the country to put together a plan. Within a month, the government had provided 20 million pounds ($28 million) to fund their work.

The initiative helped make Britain a world leader in rapidly analyzing the genetic material from large numbers of COVID-19 infections, generating more than 40% of the genomic sequences identified to date. These days, their top priority is finding new variants that are more dangerous or resistant to vaccines, information that is critical to helping researchers modify the vaccines or develop new ones to combat the ever-changing virus.

“They’ve shown the world how you do this,” said Dr. Eric Topol, chair of innovative medicine at Scripps Research in San Diego, California.

Genomic sequencing is essentially the process of mapping the unique genetic makeup of individual organisms — in this case the virus that causes COVID-19. While the technique is used by researchers to study everything from cancer to outbreaks of food poisoning and the flu virus, this is the first time authorities are using it to provide real-time surveillance of a global pandemic.

Peacock, 62, heads Britain’s sequencing effort as executive director and chair of the COVID-19 UK Genomics Consortium, known as COG-UK, the group she helped create a year ago.

During the first week of this month, COG-UK sequenced 13,171 viruses, up from 260 during its first 12 days of operation in March last year.

Behind that growth is a system that links the science of genomic sequencing with the resources of Britain’s national health care system.

Positive COVID-19 tests from hospitals and community testing programs around the country are sent to a network of 17 laboratories, where scientists extract the genetic material from each swab and analyze it to identify that virus’ unique genetic code. The sequences are then cross-referenced with public health data to better understand how, where and why COVID-19 is spreading.

When mutations in the virus correspond with an otherwise unexplained increase in cases, that’s a clue that a new variant of concern is circulating.

The importance of genomic sequencing became obvious late last year as the number of new infections began to spike in southeastern England. When cases continued to rise despite tough local restrictions, public health officials went to work to find out why.

Combing through data from genome sequencing, scientists identified a new variant that included a number of mutations that made it easier for the virus to hop from one person to another. Armed with this information, Prime Minister Boris Johnson imposed a national lockdown, scrapping a strategy of local restrictions that had failed to contain the new variant.

The scientific sleuthing is crucial, but it’s like looking for a needle in a haystack. Researchers must sift through the genetic sequences from thousands of harmless variants to find the rare dangerous ones, Peacock said.

“It’s vital so that we can understand what variants are circulating, both in the United Kingdom and around the world, and therefore the implications of that on vaccine development and the way that we may have to adapt vaccines,” she said.

The effort is a worldwide collaboration, with more than 120 countries submitting sequences to GISAID, a data-sharing hub originally created to track influenza viruses.

Iceland, Australia, New Zealand and Denmark actually sequence a higher percentage of their COVID-19 cases than Britain, and Denmark does the work faster. But COG-UK’S work, combined with Britain’s size and high number of cases, have made it the world leader in sequencing COVID-19. The U.K. has submitted 379,294 of the almost 898,000 sequences in the GISAID database.

That work is paying dividends even for advanced countries like Denmark, where scientists use tools developed in Britain to analyze their own data, said Mads Albertsen, a professor at Denmark’s Aalborg University who is part of the country’s genomic sequencing effort.

“What the U.K. has just done by far best is the whole setup,” Albertsen said. “They have many more researchers and a much more professional structure around how to use the data.”

The U.S. is also trying to learn from Britain as the Biden administration reverses the anti-science policies of his predecessor that slowed the country’s sequencing efforts, said Topol. Representatives from COG-UK took part in a recent call with American researchers and the Rockefeller Foundation aimed at building capacity in the United States.

“To Peacock and the crew’s credit, they didn’t just stop at sequence,” Topol said. “They organized labs to do this other work, which is actually very intensive lab assessment. And then there’s the epidemiologic assessment, too. So everything has to fire on every cylinder, you know. It’s like a car with 12 cylinders. They all have to fire to move.”

The U.K.’s sequencing success was built on the foundation of ground-breaking genetic science in Britain, stretching back to the work of James Watson, Francis Crick and Rosalind Franklin, who were credited with discovering the chemical structure of DNA. Other British scientists developed early sequencing techniques and later new technology that slashed the time and cost of sequencing.

That success attracted investment, such as the Wellcome Trust’s 1992 decision to create the Sanger Centre to help map the human genome, further expanding the pool of expertise in Britain. And Britain’s National Health Service provided a wealth of data for researchers to study.

Yet colleagues say Peacock personally deserves much of the credit for COG-UK’s success, though she prefers to highlight the work of others.

A ferociously good organizer, she glued the nation’s DNA detectives together through goodwill and chatrooms. Part of the trick was persuading eminent scientists to put aside their egos and academic rivalries to work together to help fight the pandemic, said Andrew Page, an expert in computer analysis of pathogen genomics who is working with COG-UK.

Peacock’s work on the project has earned her the moniker of variant-hunter-in-chief. But she prefers a simpler term.

“I consider myself, first and foremost, a scientist that’s doing their best to try and help both the population in the United Kingdom and elsewhere to control the pandemic,’’ she said. “Perhaps there’s a better phrase for that, but scientist will do it.”

LONDON (AP) — By DANICA KIRKA

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EU throws weight behind Pfizer-BioNTech and new technology

Associated Press

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EU throws weight behind Pfizer-BioNTech and new technology

In a stinging rebuke to pharma giant AstraZeneca Wednesday, the European Union announced plans to negotiate a massive contract extension for Pfizer-BioNTech’s COVID-19 vaccine insisting the 27-nation bloc had to go with companies that had shown their value in the pandemic.

“We need to focus on technologies that have proven their worth,” said EU Commission President Ursula von der Leyen. She also announced that America’s Pfizer and Germany’s BioNTech would provide the EU with an extra 50 million doses in the 2nd quarter of this year, making up for faltering deliveries of AstraZeneca.

In contrast to the oft-criticized Anglo-Swedish company, von der Leyen said Pfizer-BioNTech “has proven to be a reliable partner. It has delivered on its commitments, and it is responsive to our needs. This is to the immediate benefit of EU citizens.”

Exacerbating the problems for AstraZeneca, Denmark decided Wednesday not to resume use of its vaccine, after putting it on hold last month following reports of rare blood clots in some recipients. The bulk of the shots given in the Scandinavian country so far have been the Pfizer-BioNTech vaccine.

The Johnson & Johnson jab, which uses the same base technology as AstraZeneca, hit a snag this week when U.S. regulators recommended a “pause” in administering Johnson & Johnson shots. Deliveries in the EU have been suspended.

AstraZeneca was supposed to be the workhorse of the EU’s vaccine drive this year — a cheap and easy-to-transport shot to break the pandemic’s back. Yet, the EU said that out of 120 million doses promised for the 1st quarter, only 30 million were delivered, and, of the 180 million expected, now there are only 70 million set for delivery in the 2nd quarter.

Because of that shortfall, the EU has come under crushing pressure as, even though it it is a major producer and exporter of vaccines, it cannot get its vaccinations even close to the levels of the United Kingdom and the United States.

The Our World in Data site said 47.5% of people in the U.K. have received at least one dose of COVID-19 vaccine, compared to 36.6% in the U.S. and 16.4% in the EU.

Now, Pfizer-BioNTech could well become the key to beat the pandemic on the continent.

With 200 million doses already earmarked for the bloc this quarter from Pfizer-BioNTech. the 50 million additional deliveries will be especially welcomed by EU nations dealing with supply delays and concerns over rare blood clots potentially linked to the Oxford-AstraZeneca vaccine.

Von der Leyen said the EU will start negotiating to buy 1.8 billion doses of the Pfizer-BioNTech vaccine through 2023.

“It will entail that not only the production of the vaccines, but also all essential components, will be based in the EU,” von der Leyen said.

The European Commission currently has a portfolio of 2.3 billion doses from half a dozen companies and is negotiating more contracts.

Von der Leyen expressed full confidence in the technology used for the Pfizer-BioNTech vaccine, which is different from that behind the Oxford-AstraZeneca vaccine.

The active ingredient in the Pfizer-BioNTech shot is messenger RNA, or mRNA, which contains the instructions for human cells to construct a harmless piece of the coronavirus called the spike protein. The human immune system recognizes the spike protein as foreign, allowing it to mount a response against the virus upon infection.

Astra Zeneca’s is made with a cold virus that sneaks the spike protein gene into the body. It’s a very different form of manufacturing: Living cells in giant bioreactors grow that cold virus, which is extracted and purified.

Von der Leyen said Europe needs to have a technology that can boost immunity, tackle new variants and produce shots quickly and massively. “mRNA vaccines are a clear case in point,” she said.

The planned negotiations with Pfizer left in the middle what the EU would do about any new contracts with AstraZeneca. “Other contracts, with other companies, may follow,” said von der Leyen.


BRUSSELS (AP) — By RAF CASERT Associated Press
Jan M. Olsen contributed from Copenhagen.

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MedTech

UK NHS Cancer backlog treated by digital tools, says report

Karim Hussami

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digital app

A report from ORCHA (The Organisation for the Review of Care and Health Apps), an NHS partner and a leading authority on health app trends and usage, says that MedTech digital tools can be part of the solution to the backlog in cancer services.

The report adds that patients must be supported by healthcare staff in their choice of apps and be extremely wary of poor-quality tools which could damage their health.

“There are excellent apps or digital tools supporting cancer patients. These have been developed with clinicians, rigorously reviewed and frequently updated. Apps such as these can be embedded into cancer services to provide tremendous support to patients and ease the healthcare system at a time of tremendous backlog,” former NHS clinician and founding CEO of ORCHA, Liz Ashall-Payne, said.

“For example, BELONG, Beating Cancer Together gives users access to oncologists, radiologists and doctors to answer questions and notifies users of available clinical trials around the world. Vinehealth Cancer Companion helps patients monitor their symptoms and track their medication,” he noted.

Around 40,000 fewer people started cancer treatment in 2020 due to COVID-19, putting potential pressure on services for years to come.

“We believe there is massive potential for intelligent apps such as these both to help patients and provide excellent returns on investment to the NHS,” Liz added.

According to ORCHA research, 3,603 digital tools in forms of apps to support cancer can be found in app stores. Worryingly, 74 percent of these have not been updated in the last 18 months. This means the vast majority have not kept pace with medical, data or usability guidelines.

Amongst the apps updated within 18 months, ORCHA reviewed 190 of the most downloaded, testing them against more than 350 health standards and measures including elements of the NICE framework. This diligence revealed that only 24.7 percent of the apps reviewed meet minimum quality thresholds.

Liz Ashall-Payne, said: “These statistics are deeply concerning, given how easy it is for vulnerable patients and care providers to search app stores and stumble across apps which may give poor or outdated advice or blatantly misuse their private data.”

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Wearable tech start-up aims to tackle head injuries in sport

Karim Hussami

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Wearable tech start-up

An Edinburgh-based business recently launched a Kickstarter campaign to help move into production of a technology to safeguard athletes against head injuries.

Based at the Edinburgh Business School (EBS) Incubator within Heriot-Watt University, the technology has been developed by start-up company HIT. The concept is wearable tech which measures and tracks head impact force in sport and recreational activities and is set to aid research and support informed decisions on the risk of brain injury.

Founder Euan Bowen, an avid rugby player, was inspired to develop the technology a teammate was injured. With brain injuries rarely reported, Bowen spotted a gap in the market for sportspeople to track brain health.

Bowen explained: “I found little technology available to monitor head impact, despite the severity of the issue across different sports.

“As a member of a rugby club in Edinburgh, I began researching and developing a project, working closely with the team to develop an initial prototype.”

Featuring a unique impact sensor, wearable across multiple sporting and activity applications, the device universally clips onto any helmet or halo headband, detecting g-force and recording impact via a companion app.

Using a traffic light system, the app records data and acts as an early warning notification for the user regarding the level of impact force recorded – highlighting the caution required in continued exercise.

“High impact sports are focusing increasingly on concussion mitigation with the Field – ‘Football’s Influence on Lifelong Health and Dementia Risk’ – study recently finding that former professionals are three and a half times more likely to die of dementia than the general population,” Bowen noted.

Kallum Russell, manager of the EBS Incubator said: “HIT Impact is a much-needed technology to track and support the current efforts to increase sports safety at a time when governing bodies across high impact sports are increasingly focused on minimizing head trauma.”

The current parliamentary inquiry into concussion recently heard evidence about the long-term implications of repetitive head trauma on sports people with MPs asking how sports could be made safer.

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