Jon Deeks Profile picture
7 Jan, 7 tweets, 2 min read
I'm rather concerned by the inability of Test-and-Trace to explain the diagnostic accuracy of the lateral flow test. This was the statement about the performance of Innova in the School Handbook sent out by Test-and-Trace before Xmas. Image
"As accurate in identifying as PCR" is simply not true. Specificity tells you about false positives, not true positives. It tells you the proportion of those without COVID who correctly get negative results. It doesn't tell you how could the test is at identifying cases.
And interesting that the high figure for specificity is stated, but no numbers for sensitivity are given (which are much lower - 40% in Liverpool). We don't want selective reporting from our Health Department.
Now I'm pleased the document has been updated, but I am not that impressed that it is replaced with: Image
An improvement, but the phrase "very accurate" is ambiguous and likely to imply to many that this is a good test. And nothing here actually tells you how well the test works. Its the sort of marketing type explanation you see from manufacturers, but what we want from the DHSC
This does not provide a "fully informed basis" for schools to decide what to do, or how to discuss the test with their pupils. If this were a clinical trial this would fail the ethics committees approval for the patient information sheet.
My suggested replacement is rather more words but hopefully more informative. Image

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More from @deeksj

2 Jan
MHRA exceptional authorisation of Innova for asymptomatic individuals was issued on 22nd Dec.

This is a LIMITED approval, and the details of how and why it is LIMITED are important. It does not cover all current uses of INNOVA by Government

1/8

gov.uk/government/new…
Details here have been provided by the @MHRAgovuk by email. If any fact is incorrect here @DHSCgovuk @MHRAgovuk please let me know and I will change – it is a bit complicated and rather unusual.

2/8
First, approved test is called the “NHS Test and Trace COVID-19 Self-Test kit” - the LFT test in it is the INNOVA test.

Second, the test manufacturer is stated as “Department of Health and Social Care”, and not Innova.

This determines who has the duty of care and safety.

3/8
Read 9 tweets
21 Dec 20
What was the sensitivity and how many false positives were there from Mass Testing of University students?

Results from University of Birmingham and Universities in Scotland don’t make good reading.

SENSITIVITY 3% (not a typo)
42% of Innova positives were FALSE POSITIVES

1/15
Testing at @unibirmingham was done in our Great Hall – impressively now a testing centre. We retested a random sample of 710 Innova test negs using PCR. We haven’t heard of anybody else doing this. Preprint soon, but here are key results.

2/15

.
Our results were posted on Twitter by @alanmcn1 who organised the testing in real time, and were sent to @DHSCgovuk at the same time.

3/15
Read 19 tweets
19 Dec 20
This is a really good question. If a test has an NPV of 99% usually we would think that is great as it means if you have a negative result you have a 1% chance of having Covid. However, a 1% chance of having Covid is actually very high.
Case rates where I am at the moment are 200 per 100,000, so 0.2%. So a totally "random test" would give an NPV of 99.8%. How low should the rate be to "rule out"? Maybe 20 per 100,000? That would be an NPV of 99.98%. Clearly we are getting into decimal place madness with NPVs
Thats why I don't use them, and because they are going to vary between places and times. My preference is to talk about how much a negative result reduces the chances of Covid. Given the event is rare, the specificity is nearly 1, this is simple to get from the sensitivity.
Read 6 tweets
13 Dec 20
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.
Read 5 tweets
13 Dec 20
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 20
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

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