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Testing

UK “Rapid Turnaround” Covid-19 Tests

Here’s another extract from Boris Johnson’s Covid-19 “lockdown 2” briefing on October 31st:

I am optimistic that this will feel very different and better by the spring

It is not just that we have ever better medicine and therapies, and the realistic hope of a vaccine in the first quarter of next year

We now have the immediate prospect of using many millions of cheap, reliable and above all rapid turnaround tests

Tests that you can use yourself to tell whether or not you are infectious and get the result within ten to 15 minutes

And we know from trial across the country in schools and hospitals that we can use these tests not just to locate infectious people but to drive down the disease

And so over the next few days and weeks, we plan a steady but massive expansion in the deployment of these quick turnaround tests

Applying them in an ever-growing number of situations

From helping women to have their partners with them in labour wards when they’re giving birth to testing whole towns and even whole cities

The army has been brought in to work on the logistics and the programme will begin in a matter of days

Working with local communities, local government, public health directors and organisations of all kinds to help people discover whether or not they are infectious, and then immediately to get them to self-isolate and to stop the spread

The precise nature of all these “cheap, reliable and above all rapid turnaround tests” is rather vague though. Presumably Boris has his “Operation Moonshot” in mind?

Shortly after the initial Moonshot revelations in September the BMJ had this to say:

The documents talk about “buying large scale capabilities” from partners such as the drug company GSK to “build a large scale testing organisation.” However, under “potential partners for increasing laboratory capacity” the documents list only the company AstraZeneca. Under logistics and warehousing, the documents list potential partners as Boots, Sainsbury’s, DHL, Kuehne+Nagel, G4S, and Serco. Under workforce are listed universities, the Society of Microbiologists, and the British Society of Immunology.

Alongside mainly commercial partnerships, the documents also state that a number of new tests and technologies would need to be used, including some that do not yet exist.

“Delivering testing at the scale and level of ambition set by the prime minister is likely to mean developing, validating, procuring, and operationalising testing technology that currently does not exist,” the plans state. Lower sensitivity testing for “screening/enabling purposes” could also be used, with polymerase chain reaction (PCR) testing then used to “confirm positive results or in situations where accuracy is needed for highest risk individuals.”

Testing technology listed in the documents includes qrt-PCR, Endpoint PCR, LAMP, LamPORE, lateral flow antigen test, and whole genome sequencing. Two of these tests—lateral flow antigen tests and LAMP—are listed as having a “lower sensitivity” of between 80% and 100%.

I cannot help but wonder how development of those “tests that do not yet exist” is coming along? According to the Financial Times today:

As England prepares to enter its second national lockdown on Thursday, the government’s Operation Moonshot plan to deliver a mass population testing programme is back under the spotlight. According to documents reviewed by the Financial Times, the Department of Health has awarded contracts worth at least £1bn to companies providing rapid testing. Many of the technologies relating to these contracts will feed into the Liverpool trial, in which everyone living or working in the city will be eligible for a test from Friday. The strategy will hinge on new lateral flow tests, which give results in 20 minutes and can be performed on a throat or a saliva sample, as well as conventional swab tests and loop-mediated isothermal amplification (LAMP) technology.

The pilot is expected to last about two weeks, with tests being deployed by the army, and could allow teachers, pupils and hospital staff to be tested weekly. But scientists have raised concerns over the accuracy of some of the lateral flow tests being used, which are prone to missing cases of active infection. Meanwhile, delays in assessing technologies produced in the UK have led to frustration over government contracts being awarded to overseas companies.

The government has signed at least 10 contracts with companies based in the UK, US and China, totalling more than £1bn, for rapid testing technology and logistics, according to publicly available contracts on the EU public procurement site, Ted, and information shared with the non-profit legal firm the Good Law Project.

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News

England’s Covid-19 Lockdown Redux

My apologies for the rather more than brief hiatus in this series of articles. One reason is that on June 18th The Guardian reported that:

The government has been forced to abandon a centralised coronavirus contact-tracing app after spending three months and millions of pounds on technology that experts had repeatedly warned would not work.

In an embarrassing U-turn, Matt Hancock said the NHS would switch to an alternative designed by the US tech companies Apple and Google, which is months away from being ready.

Another reason is that I am currently sat at my keyboard on Burrator Ward at Derriford Hospital in Plymouth, where I am recovering from a non trivial triple coronary artery bypass operation, and have just washed my hands in accordance with the instructions in the unisex toilets:

There are other reasons too, but for now let’s continue with the latest news from the Downing Street propaganda machine:

Amongst a variety of other words uttered during yesterday evening’s press conference Boris Johnson had this to say:

Even in the South West, where incidence was so low, and still is so low, it is now clear that current projections mean they will run out of hospital capacity in a matter of weeks unless we act.

And let me explain why the overrunning of the NHS would be a medical and moral disaster beyond the raw loss of life

Because the huge exponential growth in the number of patients – by no means all of them elderly, by the way – would mean that doctors and nurses would be forced to choose which patients to treat

Who would get oxygen and who wouldn’t

Who would live and who would die,

And doctors and nurses would be forced to choose between saving covid patients and non-covid patients

And the sheer weight of covid demand would mean depriving tens of thousands, if not hundreds of thousands, if not millions, of non-covid patients of the care they need

It is crucial to grasp this that the general threat to public health comes not from focusing too much on covid, but from not focusing enough, from failing to get it under control.

I am told that it is quite normal to experience a wide range of emotions when recovering from a major operation.

This morning I awoke in a howling rage. My blood pressure is currently 134/82.

[Edit – November 6th]

A video update from Ann James, Chief Executive of University Hospitals Plymouth NHS Trust:

Our [Covid-19] numbers are beginning to rise, and they’re rising quite quickly. So at a really important time, a critical time, we set out what our next steps are to make sure that we can keep everyone safe and supported during what I know is another really difficult time for everyone.

We have already needed to make some changes to the hospital. We’ve had to change the use of some of our wards as we increasingly care for a growing number of Covid patients, and we’re looking to change some of our other services.

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News

When was the first UK coronavirus case?

Over recent days the mainstream media have been vying with each other to reveal the identity of the United Kingdom’s Covid-19 “patient zero”.

According to The Guardian on June 1st:

In the UK, the first confirmed cases of coronavirus came on 31 January when two Chinese nationals staying in a hotel in York tested positive. But as the crisis has rolled on, and the virus’s range of distinctive symptoms become more widely known, many – some in letters to the Guardian – have asked themselves if they or their loved ones could have had it earlier.

The article reports that:

A day before the first confirmed fatality from coronavirus outside mainland China was reported on 2 February this year, the death of the influential guitarist and musician Andy Gill was announced. The 64-year-old, who fronted the post-punk band Gang of Four, died of pneumonia after two weeks in St Thomas’ hospital in London.

The trajectory of Gill’s illness, which took medics looking after him in January by surprise, is now familiar – sudden deterioration, low oxygen levels and organ failure. He had fallen sick after his band returned from a trip to China in late November.

Then on June 8th The Sunday Times published an article by their chief foreign correspondent, Christina Lamb describing her own Covid-19 like symptoms in early January and reporting that:

“Thousands of people have emailed me with classic Covid symptoms from late December and January,” said Professor Tim Spector, a leading epidemiologist at King’s College London, who runs the Covid-19 Symptom Study app to which 3.8 million people have signed up.

“Either there was another virus behaving in a similar way which has since disappeared or these were early cases.”

If so, why was it not reflected in a spike in hospital admissions or deaths? “That’s the medical mystery,” said Spector.

There were, he said, possible explanations. “People who got it were young and healthy and didn’t transfer it to the elderly, obese and so on. Many of those early cases were skiers coming back from holidays. Or the virus was in some way different and didn’t have that final stage which attacks the immune system.

Christina points out that:

Officially, the first case involving a Briton was Steve Walsh, 53, a businessman from Hove… On February 6 he was diagnosed and transferred to Guy’s Hospital in London.

Before suggesting that:

It now seems likely that Walsh was not the UK’s “patient zero”. A month earlier, Susannah Ford… had fallen ill after flying back from a skiing holiday in Austria. [She] became ill on January 6, two days after her return from a new year trip.

Ford had spent a week in the resort of Obergurgl, near the Italian border, with her husband and two teenage daughters, flying back into Gatwick on January 4. She was the only one in the family who fell ill and assumed it was something she had picked up on an earlier trip to Trinidad.

Last week Ford paid for a test that shows whether the patient’s blood contains the antibodies that form when a person successfully fights off the disease. It came back positive, confirming that she had had Covid-19, although not when.“I’m convinced it’s when I was ill in January,” she said. “I can’t prove it was then but I haven’t been ill since or come into contact with people with it.”

Is there any advance on early January? Not as far as I am aware in the UK, but there have been several reports that European athletes who attended the Military World Games in Wuhan, China in October 2019 fell ill with symptoms resembling those of Covid-19.

According to an article in The Times on May 8th:

A French athlete who fell ill after competing in Wuhan in October says she has been told by doctors that Covid-19 was the likely cause of her ailment.The claim by Élodie Clouvel, an Olympic silver-winning pentathlete, has bolstered speculation that the coronavirus may have been present in the Chinese city several weeks before it was declared and then carried around the world by those who had taken part in an international competition there.

However according to the Global Times on February 24th:

A Wuhan hospital clarified the clinical diagnoses of five foreign athletes at the 7th CISM Military World Games held in Wuhan, Central China’s Hubei Province in October 2019, saying that they contracted malaria and were not infected by the novel coronavirus.

And what of the science? According to a paper published in “Infection, Genetics and Evolution” in early May:

We observe an estimated time to the Most Recent Common Ancestor, which corresponds to the start of the COVID-19 epidemic, of 6 October 2019–11 December 2019 (95% CIs). These dates for the start of the epidemic are in broad agreement with previous estimates performed on smaller subsets of the COVID-19 genomic data using various computational methods.

It seems that it’s not beyond the bounds of possibility that several athletes brought the SARS-CoV-2 virus to Europe from Wuhan in late October 2019.

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News

UK “Covid-19 Hypoxia” Trial Announced

According to an article by Emily Morgan on the ITV News web site:

A month ago Robert Peston and I highlighted the worrying condition known as ‘happy hypoxia’ which has been affecting thousands of coronavirus patients.

It has become apparent over the course of the pandemic that some patients appear absolutely fine and apparently not in distress but have oxygen levels so low they would normally be unconsciousness or even dead.

We highlighted it because medics raised the alarm that many people were getting to hospital too late and should be brought in much sooner.

We’d noticed the mention of what we called ‘Covid-19 hypoxia’ in the medical literature rather more than a month ago, which was one of the reasons why in the middle of April we applied to Innovate UK, the UK’s innovation agency, for R&D funding to develop a “Covid-19 eHealth Data Acquisition Unit:

Today we are delighted to be able to announce that our application has been successful! We’ll be making a formal announcement in the near future, but getting back to Emily’s article for now:

NHS England told me exclusively they were looking at changing guidelines for 111 call handlers and they were looking at giving patients devices that could monitor their oxygen levels at home.

For the families of those who have died it was a small victory.

Today the NHS has made good its pledge to look at it.

A pilot is now underway in 11 hospital trusts where some Covid-19 patients and at risk patients are being given oximeters.

A “pulse oximeter” is one of the sensors we will be connecting to the “domestic” version of our Covid-19 data acquisition unit, which will use “Artificial Intelligence”, or perhaps more accurately “Machine Learning”, to infer the state of a person’s health from the information it receives from its assorted inputs.

Emily continues:

These are really simple devices which clip on your finger and give you a quick and easy reading of oxygen levels in your blood.

The results are pinged via an App back to doctors who can keep an eye on them.

It’s so simple and so clever that Dr Andy Barlow from Watford General Hospital says it will absolutely save lives.

Here’s a picture of one such “life saving” device:

A picture of our very own Covid-19 eHealth data acquisition unit will be available in due course!

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News

UK Excess Deaths Due to Covid-19 Hypoxia?

The UK’s Office For National Statistics has just released a report which “Examines death registrations not involving coronavirus (COVID-19), to understand the apparent increase in deaths”. It nonetheless suggests that a significant number of the UK’s recent “excess deaths” that make no mention of Covid-19 on the death certificate might well have been caused by the SARS-CoV-2 virus. In section 5 concerning “Deaths due to dementia and Alzheimer disease” the ONS point out that:

The sudden rise in deaths due to dementia and Alzheimer disease is so sharp that it is implausible that the full increase observed could have happened by chance. The absence of large rises in deaths due to this cause that mention conditions that could exhibit similar symptoms to COVID-19 suggests that if COVID-19 is involved in the increase in deaths due to dementia and Alzheimer disease, the usual symptoms of COVID-19 were not apparent. This could fit with recent clinical observations, where atypical hypoxia has been observed in some COVID-19 patients. In someone with advanced dementia and Alzheimer disease, the symptoms of COVID-19 might be difficult to distinguish from their underlying illness, especially with the possibility of communication difficulties.

The terms “Covid-19 Hypoxia” and “silent hypoxia” have been used in the medical literature for quite some time, amongst other things to suggest that “overuse of intubation” for Covid-19 patients should be addressed.

We await further news on the attribution of UK deaths to the many effects of the SARS-Cov-2 virus with interest.

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News

Covid-19 in the UK in June 2020

Today is a Tuesday, which means that The Office for National Statistics have just released their latest weekly “death certificate” data, which brings us up to May 22nd. The “main points” are:

  • A total of 43,837 deaths involving COVID-19 were registered in England and Wales between 28 December 2019 and 22 May 2020 (year to date).
  • In England, including deaths that occurred up to 22 May but were registered up to 30 May, of those we have processed so far, the number involving COVID-19 was 42,210; the comparative number of death notifications reported by the Department of Health and Social Care (DHSC) on GOV.UK was 32,666 and NHS England numbers, which are deaths in hospitals only, showed 25,875 deaths.
  • In Wales, including deaths that occurred up to 22 May but were registered up to 30 May, of those we have processed so far, the number involving COVID-19 was 2,122; the comparative number of death notifications reported by the DHSC on GOV.UK was 1,260 and Public Health Wales (PHW) numbers, which come from the same source as the DHSC figures but are continuously updated, showed 1,275 deaths.
  • In England, the number of deaths involving COVID-19 in care homes that were registered by 22 May was 12,142, while in Wales the number of deaths was 591.
  • The Care Quality Commission (CQC) provides numbers of deaths involving COVID-19 in care homes in England that were notified between 10 April and 29 May, which showed 11,186 deaths, of which 531 occurred in the week up to 29 May.
  • The Care Inspectorate Wales (CIW) provides the number of deaths involving COVID-19 in care homes in Wales that occurred between 17 March and 29 May, which showed 462 deaths, of which 35 occurred in the week up to 29 May.

Here’s the “graphic” representation of those numbers:

Here is an alternative view on weekly “death occurrences in England and Wales” over recent years from EuroMOMO:

Publishing the number of death occurrences is outside EuroMOMO’s terms of reference, but their “Z-scores” provide a graphic illustration of how badly England in particular has been doing over the course of the 2020 Covid-19 epidemic.

[Edit – June 9th]

The latest weekly data from the ONS has been released:

  • The number of deaths registered in England and Wales in the week ending 29 May 2020 (Week 22) was 9,824; this was 2,464 fewer than in Week 21 but 20.2% (1,653 deaths) higher than the five-year average.
  • Of the deaths registered in Week 22, 1,822 mentioned “novel coronavirus (COVID-19)”, the lowest number of deaths involving COVID-19 in the last eight weeks; this accounts for 18.5% of all deaths and is 767 deaths fewer than in Week 21.
  • People aged 90 years and over continued to have the highest number of COVID-19 deaths in Week 22.
  • In Week 22, the proportion of deaths occurring in care homes decreased to 25.5% while deaths involving COVID-19 as a percentage of all deaths in care homes decreased to 28.2%.
  • In Week 22, the number of deaths in care homes was 819 higher than the five-year average, while in hospitals the number of deaths was 30 fewer than the five-year average; the total number of excess deaths involving COVID-19 continued to decrease.

Here’s a graphic representation of the overall “excess death” numbers:

By way of explanation:

The number of deaths was around or below the five-year average up to Week 12. The number of deaths increased between Weeks 13 and 16 before decreasing between Weeks 17 and 22, with the exception of Week 20 where the deaths increased.

The number of death registrations in Week 20 was impacted by the early May Bank Holiday, which took place on Friday 8 May 2020 (in Week 19). The number of deaths registered on the early May Bank Holiday fell to 88 deaths compared with 2,950 deaths registered on the previous Friday (Friday 1 May 2020). Trends seen in Week 19 and Week 20 should therefore be interpreted with caution, as deaths not registered on the early May Bank Holiday were likely registered in the following week (Week 20). Week 22 also included the late May Bank Holiday but as this was on a Monday, we have seen less of an effect on death registrations.

The number of death registrations involving the coronavirus (COVID-19) decreased from 2,589 in Week 21 to 1,822 in Week 22. Of all deaths registered in Week 22, 18.5% mentioned COVID-19; this is down from 21.1% in Week 21.

Similar patterns can be seen for England and Wales separately, with the number of deaths in England decreasing from 11,586 in Week 21 to 9,228 in Week 22, which was 1,621 deaths higher than the Week 22 average. Of the Week 22 deaths, 18.6% (1,715 deaths) involved COVID-19 in England.

In Wales, the number of deaths decreased from 692 deaths in Week 21 to 587 deaths in Week 22, 41 deaths higher than the Week 22 average. Of these Week 22 deaths, 17.9% (105 deaths) involved COVID-19 in Wales.

[Edit – June 10th]

Today’s Downing Street Briefing was somewhat unusual. Boris Johnson was master of ceremonies, and what’s more he was accompanied by some scientists! Boris began by referring to “the progress we as a country have made against our 5 tests for adjusting lockdown”

Instead of listening to what was said, let’s take a look at some of the data that was referred to shall we?


The overall aim is evidently to “reduce the rate of infection to manageable levels” whilst “not risk[ing] a second peak of infections that overwhelms the NHS”. Boris hopes that the latest lockdown “adjustments” will be “underpinned by NHS Test and Trace”, so let’s also see how that’s coming along shall we? As luck would have it the Independent Sage committee also reported this yesterday:


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News

UK Covid-19 Messaging – Episode 3

For previous episodes in our UK “Covid-19 messaging” series please click here.

Today’s Covid-19 headlines come to you via the Twitter feed of Allie Hodgkins-Brown. Compare and contrast the following front page “messages” from the Great British mainstream media:

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News

UK Covid-19 Messaging – Episode 2

For the start of our UK “Covid-19 messaging” series please click here.

This is the message Boris Johnson apparently wanted to impart to the citizens of England on May 22nd 2020:

Then came the news that BoJo’s “senior aide” Dominic Cummings had risked spreading the virus by driving from London to Durham. By the morning of May 24th the front pages of the “conservative” mainstream media looked like this, with thanks once again to Neil Henderson‘s Twitter feed:

On the evening of May 24th Boris retweeted a message from 10 Downing Street, then somewhat unusually stood behind the lectern at the Covid-19 daily briefing and refused to throw his top aide to the dogs. Try starting to watch the video at around 4:30:

The following morning I found myself agreeing with a Daily Mail headline for probably the first time in living memory:

Alternative points of view were less critical of Mr. Cummings’ actions:

I wonder how the Times’ promised “cabinet backlash” will pan out? I also cannot help but wonder how many Great British citizens will ignore the messages imparted in any future Tweets by Boris Johnson.

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News

Why are so many English workers dying from Covid-19?

This surprising news from John Burn-Murdoch of the Financial Times greeted me on my Twitter feed this morning:

The article by Janine Aron and John Muellbauer that John linked to points out that:

Excess mortality is a count of deaths from all causes relative to what would normally have been expected. In a pandemic, deaths rise sharply, but causes are often inaccurately recorded. The death count attributed to Covid-19 may thus be significantly undercounted. Excess mortality data overcome two problems in reporting Covid-19-related deaths: miscounting from misdiagnosis or under-reporting of Covid-19-related deaths is avoided. Excess mortality data include ‘collateral damage’ from other health conditions, left untreated if the health system is overwhelmed by Covid-19 cases.

To obtain cross-European comparisons requires data collation from individual national agencies – unless the Z-scores compiled by EuroMOMO for 24 states are used. EuroMOMO’s timely measures of weekly excess mortality in Europe allow comparisons of the mortality patterns between different time periods and countries, and by age groups.

Analysing excess mortality using EuroMOMO Z-scores rather than just deaths attributed to Covid-19 Aron and Muellbauer discovered that:

Most disturbing is the comparative story for the 15-64 age group, where England’s relative record in excess mortality in the Covid-19 era is strikingly higher than in the European countries. The 15-64 age group includes the mass of the working age population. At its peak in week 15, it is 2.8 times worse than the weekly peak in next worst country, Spain, around 4 times worse than France and Belgium, and more than 5 times worse than in Italy. Within the UK, excess deaths for this age group are also strikingly worse for England than for the other nations. Puzzling too, is that Z-scores in the 65-74 age group for England, see Table 2, are similar to the 15-64 age group. By contrast, in the five European countries, excess deaths in the 65-74 age group are about twice as high as for the 15-64 age group, though still below the 65+ age group.

England is the only country in Europe, for which Z-scores for the 15-64 group had not decreased below about 2 by week 18, ending 3 May.

What is the reason for this strange English anomaly? Watch this space!

Categories
Testing

The UK Government’s Covid-19 recovery strategy

Fresh from some very mixed messaging in the United Kingdom’s mainstream media, yesterday the UK Government announced the release of their “Covid-19 recovery strategy”:

This document describes the progress the UK has made to date in tackling the coronavirus (COVID-19) outbreak, and sets out the plans for moving to the next phase of its response to the virus.

The strategy sets out a cautious roadmap to easing existing measures in a safe and measured way, subject to successfully controlling the virus and being able to monitor and react to its spread. The roadmap will be kept constantly under review as the epidemic, and the world’s understanding of it, develops.

The section of the roadmap of most interest to us is 5.6, “Testing and tracing”. There we learn that:

Mass testing and contact tracing are not, in themselves, solutions, but may allow us to relax some social restrictions faster by targeting more precisely the suppression of transmission. The UK now has capacity to carry out over 100,000 tests per day, and the Government has committed to increase capacity to 200,000 tests per day by the end of May.

The Government has appointed Baroness Harding to lead the COVID-19 Test and Trace Taskforce. This programme will ensure that, when someone develops COVID-19-like symptoms, they can rapidly have a test to find out if they have the virus – and people who they’ve had recent close contact with can be alerted and provided with advice. This will:
● identify who is infected more precisely, to reduce the number of people who are self isolating with symptoms but who are not actually infected, and to ensure those who are infected continue to take stringent self-isolation measures; and
● ensure those who have been in recent close contact with an infected person receive rapid advice and, if necessary, self-isolate, quickly breaking the transmission chain.

This cycle of testing and tracing will need to operate quickly for maximum effect, because relative to other diseases (for example SARS) a proportion of COVID-19 sufferers almost certainly become infectious to others before symptoms are displayed; and almost all sufferers are maximally infectious to others as soon as their symptoms begin even if these are initially mild.

For such a system to work, several systems need to be built and successfully integrated. These include:
● widespread swab testing with rapid turn-around time, digitally-enabled to order the test and securely receive the result certification;
● local authority public health services to bring a valuable local dimension to testing, contact tracing and support to people who need to self-isolate;
● automated, app-based contact-tracing through the new NHS COVID-19 app to (anonymously) alert users when they have been in close contact with someone identified as having been infected; and
● online and phone-based contact tracing, staffed by health professionals and call handlers and working closely with local government, both to get additional information from people reporting symptoms about their recent contacts and places they have visited, and to give appropriate advice to those contacts, working alongside the app and the testing system.

All of this begs several questions, from our perspective at least:

  • Why the sole emphasis on “widespread swab testing”? Why not so called “saliva tests” for example?
  • How is the “new NHS COVID-19 app” going to work? Not least because the most vulnerable people in our communities are unlikely to be the proud possessors of a recently released smartphone.
  • How will the “valuable local dimension to testing, contact tracing and support” be integrated with the eventual NHS Covid-19 app?

Watch this space to discover if we ever get answers to these and other questions!