Jon Deeks Profile picture
13 Dec, 5 tweets, 2 min read
The John #MaddoxPrize 2020 – Standing Up For Science

During the Pandemic many scientists (including me) who were living quiet lives have found ourselves thrown into the public arena, as we know we have important and useful skills and things to say which we hope will help.
Some of this is great (such as the pride your isolated elderly Dad has starting his day by hearing you on the radio), but standing up for science generates some vitriolic nasty responses when people don’t want to hear the results.
Tomorrow @senseaboutsci @nature announce the #MaddoxPrize 2020 prize for the individual who has gone the greatest distance in Standing Up for Science in the past year – I am looking forwarding to reinvigorating my motivation from their story.
You can find out more here tomorrow senseaboutscience.org/Maddox.

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More from @deeksj

13 Dec
I’ve been horrified that my tweets about Covid tests now automatically generate responses and retweets stating “PCR is a poor test” (regardless of whether I mention PCR at all).

1/13
To be a good scientist you need to keep an open mind and be open to challenging argument. But the decider are the proper scientific studies that provide evidence. None have convinced me that “PCR is a poor test”.

2/13
Stating “PCR is a poor test” challenges the evaluations where PCR is the reference standard, as well as case counts, and to some the existence of COVID entirely. If we believed it, the cases that lateral flow tests miss would be classified as being overdiagnosed by PCR.

3/13
Read 14 tweets
4 Dec
So the next new Covid-19 testing technology to look at is the OPTIGENE LAMP test - as covered here in the Guardian.

1/13

Experts question claimed accuracy of Covid-19 saliva tests theguardian.com/world/2020/dec…
The main body of the report is here, appendicies with data tables can be obtained by email

2/13

gov.uk/government/pub…
The study looked at using the test on RNA extracted from swabs and saliva, and directly on swabs and saliva. Key results are here:

3/13 Image
Read 13 tweets
3 Dec
Mass testing in Liverpool MISSED ~50% of infections and ~30% with high viral loads. Results are in this Government document, but no actual numbers or details are given.

Absolutely URGENT that @DHSCgovuk reports full data today and HALTS IMPLEMENTATION

gov.uk/government/pub…
This test is NOT FIT FOR PURPOSE for the Government's plans

It is totally unsafe to use these tests to decide somebody does not have COVID nor “infectious”.

If it were a drug surely this would warrant an immediate withdrawal from use.
Missing 30% with high viral loads is NOT SAFE. PHE studies said missed <5% - so this is more than 6 times as many.

You cannot risk people with high viral loads visiting their elderly relatives.
Read 5 tweets
24 Nov
@BBCr4today invited me to speak about lateral flow tests this morning (can listen at 0650). All government plans are now about using tests to "release" people - this depends on reliability of negative result. This is what the manufacturer says:

1/16
The PHE Porton Down - Oxford University report included this graph showing sensitivity would be 58% when the test is delivered by a trained test-and-trace centre staff member. This is in symptomatics - not asymptomatics.

2/16
The Government's 77% sensitivity combines the other two groups - tests done by Porton Down lab staff, and tests done by NIHR Research Nurses - i.e. the experts and completely ignores the 58% group. That seems completely wrong.

3/16
Read 16 tweets
11 Nov
INNOVA test – time for critical appraisal of the report

What does the report say about the test and should we believe it?

1/20

ox.ac.uk/sites/files/ox…
There are a lot of data and studies reported - difficult to get your head round. Grateful to CI for talking to me this afternoon. He has worked at incredible speed to meet deadlines and says full report is forthcoming – there is more data and description to be added.

2/20
Phase 2 – spiked samples in controlled laboratory conditions

Phase 3a – samples from hospitals tested in controlled laboratory conditions

These do not tell us how well tests work in real world – important to do to move forward to what happens next, but pass by them now.

3/20
Read 21 tweets
10 Nov
How well is the Innova test working in Liverpool?

This is a speculative calculation informed by data available from Liverpool. The source is the Liverpool mayor - reported 23,170 tests done, with 0.7% positive (so about 162) here.

liverpoolecho.co.uk/news/liverpool…
Presume specificity 99.6%

No sensitivity data for this test - @UKPHE has data but not public

I estimate sensitivity of 75% based on independent evaluations done for WHO of other similar LFIA tests (range from 50% to 90%) - but in symptomatic patients

finddx.org/covid-19/sarsc…
Using a prevalence of 400 per 100,000 you get the following 2x2 table:
Read 5 tweets

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