Jon Deeks

More False Positives Than True Positives in the First Two Weeks of School Testing

A member of SAGE warned back in February that the return of unvaccinated children to the classroom would create a “significant risk of a resurgence” of Covid infections. This was not the case – only 0.06% of rapid Covid tests of students produced positive results in the week that schools reopened. But how many of these results were actually positive? Professor Jon Deeks, a biostatistician from the University of Birmingham, said in March: “We would expect far more false positives than true positives amongst those testing positive in schools.” New data from the Department of Health and Social Care has now confirmed that more false positive results were produced than true positives in the first two weeks of school testing.

Department of Health and Social Care

This data, as Professor Deeks points out, is a damning indictment of the use of rapid Covid testing in schools and has resulted in many children having to isolate at home unnecessarily – with their classmates often being sent home too. (At one stage, more than 200,000 schoolchildren were having to self-isolate, forcing them to miss out on much-needed catch-up work in classes.)

[The] proportion[s] false were 62% and 55% in these two weeks.

Of 2,304 positive tests, 1,353 were likely false, with one positive per 6,900 tests done.

The use of PCR tests to confirm or (in more cases) deny lateral flow test results is itself a strange choice, as Lockdown Sceptics’ Will Jones points out, and could mean that the true impact of rapid testing in schools is even worse than this data suggests.

It is interesting that they assume confirmation from a PCR test defines true and false positives, even though PCR tests are more sensitive than LFTs so are no less likely to give a positive from fragments or contamination. What if in some cases the PCR tests are just confirming the false positive of the lateral flow tests?

The British Medical Journal has been warning against the use of PCR tests for “case finding, mass screening, and disease surveillance” since last September (if not before):

PCR is not a test of infectiousness. Rather, the test detects trace amounts of viral genome sequence, which may be either live transmissible virus or irrelevant RNA fragments from previous infection. When people with symptoms or who have been recently exposed receive a positive PCR result they will probably be infectious. But a positive result in someone without symptoms or known recent exposure may be from live or dead virus, and so does not determine whether the person is infectious and able to transmit the virus to others.

Clearly, testing requirements for schools must now change. But the problem is not limited to the classroom. Professor Deeks says that false positive data should now be released for all forms of lateral flow testing.

Mass Covid Testing a “Waste of Time and Money”, MPs Told

Biostatistics Professor Jon Deeks has criticised the Government’s mass Covid testing plan as a waste of “time and money”, highlighting that in some areas only one positive case has been found after 10,000 tests. Professor Deeks, a Senior Researcher at the Institute of Applied Health Research at Birmingham University, told the All Party Parliamentary Group (APPG) on Coronavirus that there is “no evidence” to show mass testing works. He is quoted in the Telegraph:

“For this mass test, the Innova test, we have the Liverpool study and the University of Birmingham study, that’s a total of 78 cases where we know how well it detects (positive cases).

“That is absolutely outrageous that we are now testing the whole population based effectively on data from 78 people, which actually showed it doesn’t work very well…

“In the South West at the moment, I think we are down to 0.09% prevalence and that probably means we would be using 10,000 tests to find one case in the next few weeks.

“I don’t think that’s a good use of people’s time or money or public health capital to do that. There are far better things we could be doing.”

The APPG is chaired by Liberal Democrat MP Layla Moran, who said: “[Mass testing] seems to be the panacea at the moment… [but] how reliable is it?”

Earlier this month, the Government promised twice-weekly Covid tests for everyone in England. Sky News had the story.

The Government says the offer is currently for England only and the devolved administrations in Scotland, Wales and Northern Ireland will make their own decisions.

A major marketing campaign encouraging people to take up the offer of twice-weekly lateral flow tests will also start in England this Friday…

The programme is effectively the long-delayed “Operation Moonshot” of 10 million Covid tests a day, costing an estimated £100 billion, promised by Health Secretary Matt Hancock last summer.

When he told the Commons it would start as early as December, MPs laughed, prompting Mr Hancock to brand them “nay-sayers” and telling them to “get with the programme”.

Now the Government says that alongside vaccination, regular Covid testing will be an essential part of easing lockdown restrictions and help quickly suppress the spread of variants.

The Telegraph report is worth reading in full.

Climate of “Fear” Prevents Experts From Questioning the Handling of Covid

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We’re reproducing an article by Lucy Johnston for the Express on the “climate of fear” that is preventing experts from speaking out against the Government’s handling of Covid because it is hard to read on the newspaper’s website. And it’s a must-read.

A climate of fear is preventing experts from questioning the handling of the pandemic, with reputations smeared, jobs lost and even families threatened.

Much abuse has come from within academic or professional circles, with one professor saying debate was becoming impossible because “we are not talking to each other properly. We are being thrown into confrontational positions”. Many leading experts have withdrawn from the debate after having reputations smeared, jobs lost and even families threatened for raising questions about pandemic policy. This month alone has seen one leading medic, working to protect vulnerable children, forced to abandon a project to safeguard youngsters after their name was sullied when they questioned the Government approach.

Another expert has been sidelined from a vital role on a Government advisory group, while senior NHS staff have been threatened with disciplinary measures for questioning the Government approach online or in the media.

Senior academics say they have feared losing vital funding, warned not to speak out with the threat of disciplinary action or deemed “outliers” for their views on lockdown.

At least two scientists have been subjected to public abuse by scientific colleagues who disagreed with their academic view.

One critic posted a grotesque image superimposed on a professor after he disagreed with his view. Other posts by scientists have branded colleagues “charlatans” and “snake oil merchants”.

A prominent professor accused a fellow academic of “deliberately subverting public health” on a Twitter post after disagreeing with her views on managing the pandemic.

In another case a Government scientific advisor called a university boss to try to stop one of its professors from criticising Government policy.

Retired Supreme Court Lord Sumption told a podcast this week that he was a reluctant figurehead for questioning lockdown – but felt obliged because of the way critics had been treated.

He said scientists and politicians had been”subjected to an extraordinarily unpleasant campaign of personal abuse”. He added:

I know a lot of people that would prefer not to put their head above the parapet. From the very moment I started to make these points I began to get emails from politicians who agreed with what I had to say but that they themselves didn’t dare to speak out. That I think is a very serious state of affairs.

He added that he knew of one scientist whose family had also been targeted: “People ought to be entitled to voice their differences of opinion.”

Testing Regime in Schools Ignores Problem of False Positives

Biostatistics Professor Jon Deeks has written a critical piece on the shortfalls of the current mass testing regime for children in schools. Of particular concern is the occurrence of false positives. UnHerd has the story.

The fitness for purpose [of the testing regime] is a combination of the sensitivity of the test (what percentage of infected cases it correctly identifies) and the specificity (what percentage of uninfected people it correctly says are negative). But it also depends on how, where and when a test is used.

Different studies of the UK Innova lateral flow test (the test being used in schools) have reported variously that its sensitivity is 78%, 58%, 40% and even 3%. The higher 78% and 58% figures come from using the test among people with symptoms, the lower 40% and 3% figures come from using it for mass testing among people without symptoms, as is being done in schools. (And none of these studies have assessed how well the test detects infection in children). So although the test can pick up people who have the infection, it will miss quite a few – so there is a risk that disinhibition after a negative test could actually exacerbate case numbers if children incorrectly think they are safe and the rules no longer apply.

But the more concerning aspect are the false positives, related to the specificity. The original Government studies found only around 3 in 1,000 people were getting false positives, and this dropped to 1 in 1,000 in the Liverpool study. Doesn’t sound like a lot, right?

But consider the problem from the perspective of a pupil who has just got a positive test result. The reasonable question for them (and their parents) to ask is “what are the chances that this is a false positive?” Given that a positive test result means the pupil, their family and their school bubble will have to isolate for 10 days, a high false positive probability is a real problem.

Jon, who is a Senior Researcher in the Institute of Applied Health Research at Birmingham University, goes on to outline three scenarios regarding the prevalence of the disease and the accuracy of the tests.

Where 1 in 100 pupils have the infection (Scenario A), by testing a million we would find 5,000 cases but get 990 false positives. This ratio of true to false positives is quite favourable – 5 out of every 6 with positive results actually would have COVID-19 infection – so the probability that the pupil genuinely has the infection is over 80%.

However, the picture becomes less favourable as the infection becomes rarer: if only 1 in 1,000 pupils were infected (Scenario B) we would detect 500 cases but get 999 false positives. The ratio of true to false positives is now unfavourable – one true result for every two false results.

If only 1 in 10,000 had the infection there would be one true result for every 20 false results (Scenario C). Why would anybody consent to a test where the chances that a positive result is wrong are so much higher than it is right? This isn’t the fault of the test – it’s the application in a low prevalence setting. Using any test – even one with an incredibly high specificity – will lead to more false than true positive results when the disease becomes rare.

Worth reading in full.

Stop Press: The Government’s refusal to let pupils use follow-up tests to confirm positive Covid results is “ruining” their return to school, parents say.

Stop Press 2: Professor Deeks made the same point in an interview for Radio 5 Live.