Jon Deeks Profile picture
19 Dec, 6 tweets, 2 min read
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.
In these circumstances, a test with 50% sensitivity will halve the chances of disease, a test with 35% sensitivity will reduce it by one-third, a test with 70% sensitivity will reduce it by just over two-thirds.
Does that help?
Postscript - at the moment a negative lateral flow result will never be low enough to be "safe" - I've said it in the BMJ, the Royal College of Pathologists have said it, WHO said it in September, the manufacturers of Innova say it, the CMO says it and now SAGE too have said it.

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More from @deeksj

21 Dec
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

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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 16 tweets
13 Dec
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
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

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