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Jon Deeks 💙 Profile picture
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22 Mar, 4 tweets, 2 min read
More disappointing data on sensitivity of LFT for mass testing - this time from Wales.

This report includes data from mass testing Nov-Dec
cwmtafmorgannwg.wales/whole-area-tes…

I think it is with Innova but report does not actually say.

(Note: sens/spec calculations in the report are wrong)
Data from Merthyr Tydfil

You can't compute sens and spec directly from this (but the authors did) as only 2.1% of LFT -ves were included compared to 42% of LFT +ves

Correcting for sampling fraction
sensitivity is 17.5%
specificty is 99.7%
Data from the lower Cynon Valley

Again their is a sampling issue with
4.1% of LFT-ves being verified compared with 59.1% of LFT +ves.

Sensitivity 25.6%
Specificity 99.6%
Now this is in a period when case numbers were rising, thus many of the missed cases would have been pre-symptomatic and infectious.

There are serious issues here.

This is no way to get out of a pandemic.

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More from @deeksj

Jon Deeks 💙 Profile picture
22 Mar
Sorry - but there is a dreadful mistake made in computing the sensitivity and specificty of LFT in this report. If you look at Figure 32 (day 1 for example) the estimates of sens and spec are based on a subsample of the study with 364 LFT+ve and 686 LFT -ve. 34.7% are LFT+VE
However, in the whole sample 33,315 LFD tests were completed across 12 centres. Of these, 763 were positive, representing a positivity rate of 2.3%.

Thus the sample used in the test accuracy study is biased to include many more LFT+ves (34.7% compared to 2.3%).
This means overcounting of true positives and false positives, undercounting of true negatives and false negatives - but a large order of magnitude.

Sensitivity and specificity estimates are badly affected
Read 8 tweets
Jon Deeks 💙 Profile picture
18 Mar
Data on TESTING in SCHOOLS

Results just published to 10th March (;ast Wednesday)
2.8 million tests in secondary school kids, 1324 positives- 0.048% or 1 in 2086. Lowest rate ever observed

Government figures would have predicted around 10,000.
Will post more analysis shortly
Using the Government figures from @ab4scambs conservativehome.com/platform/2021/…

Sens=50.1% Spec 99.7% Prevalence of 0.5%
of 2,762,775 tests we would expect 6921 true positives and 825 false positives - nearly 6 times more test positives than have been reported.
To get down to the 1324 positives actually observed, either the prevalence has to be 0.036% (1 fourteenth of the expected rate) - 36 per 100,000
Read 5 tweets
Jon Deeks 💙 Profile picture
16 Mar
Great that @ab4scambs shows some MPs understand the laws of probability (beginning to doubt that there was one) but this justification why we don't need to PCR kids who have positive LFT sadly starts with a fatal flaw

1/8
conservativehome.com/platform/2021/…
This is the second time I have tweeted this as one decimal place went for a wander in my first set of tweets. Nothing else changes. Thanks to @d_spiegel for spotting it.

2/8
It presumes that the prevalence to use for Covid infection in these calculations is that in the general population - 0.5% or 1 in 200. And then shows that 30% of those who are LFT+ and then PCR - will still have Covid infection. Can you spot the error?

3/8
Read 9 tweets
Jon Deeks 💙 Profile picture
14 Mar
Can we give @DHSCgovuk and @educationgovuk a lesson in probablilty? This is A level stuff - if there are Year 12 and 13s in isolation please try it (you can do it with Venn diagrams or a Tree diagram) and send your full workings to @GavinWilliamson @MattHancock @SMHopkins
(a) In 1,000,000 children of which 0.1% have Covid-19, if a test gives +ve results with probability 0.5 in those with Covid-19 and -ve results with probability 0.999 in those without, how many +ve results would you get, and how many of these would actually have Covid-19?
For Further Maths geeks:
(b) If those +ve on the first test and tested with a second test which gave -ve results in those without disease with probability 0.990, how many will not have Covid-19 infection AND have a +ve result on the 1st test AND have a +ve result on the 2nd test?
Read 4 tweets
Jon Deeks 💙 Profile picture
11 Mar
Thursday – Test-and-Trace data time

So are Lateral Flow Tests are becoming more useful?

Eh – No

Last week 2,764,845 tests done (new record high) and 4,353 were positive. That’s 0.16% (new record low).

So probably lots are false positives. Lots of money spent– little found
In secondary school 663,332 were tested, only 328 positive. Testing has move than doubled on previous week, numbers detected have not.

We are now down to 0.05% being positive – that is only 1 in every 2000 tested – another record low.
Given what we know about the infection rates from ONS and REACT – these data raise serious concerns that the LFTs are not doing the job that we expect. Many more cases should have been detected.
Read 4 tweets
Jon Deeks 💙 Profile picture
10 Mar
@UnHerd asked me to write about school testing – and why PCR matters so much.

From @DHSCgov data I estimate 70%-95% of school positive cases could be false. Hope I’m wrong, but unless PCR confirmation is done we will never know.

unherd.com/thepost/why-th…
1/8
The mistake being made is to think that all that matters is that false positives are rare. However, if true positives are even rarer then we are in trouble. Test positivity data from Test-and-Trace (1 in 1500 positive) raises serious concerns that is the case.

2/8
If 1 in 100 pupils had Covid-19, we would be fine. Five out of every six test positives would be true positives. But it looks like we are somewhere between 1 in 1,000 and 1 in 10,000 (we don’t know).

3/8
Read 10 tweets

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