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Jon Deeks FMedSci 💙

17 Jun, 11 tweets, 4 min read

@educationgovuk

What do we known about ORIENT GENE used in the Daily Contact Testing Trial by the @educationgovuk and @DHSCgovuk?

There have been claims that this test is as good as others and has been reviewed by @MHRAgovuk for use in assisted testing. This is not right

1/10

The process does not make sense.

The MHRA never review products for assisted testing as they are professional use tests, which go through the self-certification process to get a CE-IVD mark.
MHRA doesn't go near this process.

2/n

In fact ORIENT GENE is not even on the MHRA register of products which is a requirement. You can check here - both for the product and manufacturer (sorry for the messy link).

3/n

aic.mhra.gov.uk/era/pdr.nsf/na…

There are two sets of data on ORIENT GENE we can find in the world's literature. Both are in the Porton Down report here
thelancet.com/journals/eclin…

4/n

The Phase 3a study was an analytical valdiity type study testing viral transport media (not swabs) from biobanked samples from the Oxford hospital (presume from patients but detail not given). This is not an assessment of using test according to manufacturers instructions.

5/n

The Phase 3b study used swabs from people with symptoms at test-and-trace centres. The 95 samples were tested by scientists at Porton Down. This sample size is pretty small to assess comparability.

6/n

There are no data from using the test
(a) by non-scientific experts
(b) in people without symptoms
(c) in children
All of which we would expect to lead to lower sensitivity

7/n

The MHRA Target Product Profile for using tests to rule infection states data from 150 cases from the real world setting need to be assessed with a sensitivity of 97%. These data do not get close to this.

8/10

It is not clear to me how the Daily Contact Tracing Trial will estiamte the accuracy of Orient Gene. There was no component in the protocol to do this, and there is no scheduled double testing with Orient Gene and PCR at the same time

9/10

The summary information sheets from the trial do not provide any summary of the data supporting Orient Gene and this seems a pretty weak basis for using a test in 1000s of children. This is why I have concerns with this test being used in this trial.

10/10

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Jon Deeks FMedSci 💙

@deeksj

17 Jun

@MHRAgovuk

IMPORTANT: MHRA New standards for LFT self tests for SARS-CoV-2 in people without symptoms.

@MHRAgovuk just published new Target Product Profile.

This is a guidance document based upon the best available evidence and independent expert opinion.

1/12

gov.uk/government/pub…

Important to note that the MHRA see these tests as for detecting “Current Infection”. That is detecting active infection, but is bigger than checking whether people are infectious. It also includes people who are pre-infectious.

2/12

They give guidance on reference standards to detect this. There are challenges here in establishing scientifically valid clinical reference standards. RT-PCR is regarded as acceptable which is what most are using.

3/12

Read 13 tweets

Jon Deeks FMedSci 💙

@deeksj

29 Apr

The 1st 2 weeks of school testing did find MORE FALSE POSITIVES than TRUE POSITIVES - data are finally public.

Proportion false were 62% and 55% in these 2 weeks. Of 2304 positive tests, 1353 were likely false, with 1 positive per 6900 tests done.

@RoyalStatSoc

Remember that the law made kids, teachers, families and bubbles had to isolate for 10 days even when the PCR came back negative, despite the @RoyalStatSoc spending days trying to explain the issues to @DHSCgovuk.

Never ever say tests don't do harm.

To be clear as some still can't see the problem. 2 weeks testing in every school only found 954 true cases. To find each one used 6884 tests (cost £144,564) and 1.4 false negatives were put into unnecessary isolation with bubble and family- 500 person days if a bubble affected 36

Read 5 tweets

Jon Deeks FMedSci 💙

@deeksj

28 Apr

Well here is some real data from 27 health care workers who picked up symptomatic Covid-19 infections whilst being tested twice weekly using RT-PCR. The paper develops models to look at impact of testing frequency, but also hypotheses on LFT performance
bmcmedicine.biomedcentral.com/articles/10.11…

There is excellent presentation of the original data in the paper, as well as results from the models. Kudos to the authors.

Plots of Ct values from PCR are provided, which show that RT-PCR with Ct<37 had a peak sensitivity for detecting infection of 77% 4 days after infection.

No LFTs were used in the study, but the paper considered test results with Ct<28 and Ct<25 as illustrations of how LFTs might perform. At Ct<28 the red spots are +ve LFT results, the black are -ve LFT results, peak sensitivity is 64% at 4.3 days post infection.

Read 5 tweets

Jon Deeks FMedSci 💙

@deeksj

17 Apr

@theJeremyVine

For the sake of clear Public Health messages, listening to this interview on @theJeremyVine I'm tweeting some responses to the claims made by Peto

https://twitter.com/deeksj/status/1383168237911871490

#1 "the lateral flow test has the remarkable ability of only picking up people who are likely to be infectious, or other words a danger to others."

It doesn't just pick out ONLY infectious people
It doesn't pick out ALL infectious people
Linkage to infectiousness is unclear.

It can only gives +ve results when viral loads are high (a limitation not an ability). Studies show viable virus in many people with low viral loads.

Read 19 tweets

Jon Deeks FMedSci 💙

@deeksj

15 Apr

@JoshHalliday

Senior staff at Department of Health have concerns that Mass Testing needs to stop ...

Great article from @JoshHalliday

Rapid Covid testing in England may be scaled back over false positives theguardian.com/world/2021/apr…

From leaked emails ....

Ben Dyson, an executive director of strategy at the health department and one of Matt Hancock’s advisers, stressed the “fairly urgent need for decisions” on “the point at which we stop offering asymptomatic testing”.

“As of today, someone who gets a positive LFD result in (say) London has at best a 25% chance of it being a true positive, but if it is a self-reported test potentially as low as 10% (on an optimistic assumption about specificity) or as low as 2% (on a more pessimistic assumption

Read 6 tweets

Jon Deeks FMedSci 💙

@deeksj

9 Apr

@dhscgov

Take note - @dhscgov rapid tests are being sent out (certainly in schools) with two different (and conflicting) information sheets, one in the box and one given out separately.

(the crumpled one with the picture is in the box, the glossy one is handed out separately).

1/10

The clue to which one is most up to date is on the back page (the one in the box is the out of date version).

2/10

The important difference in on page 2, which has far more info in the box (1st) version than the version given out about who should use the test and what they should do.

3/10

Read 11 tweets

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