Important paper in @bmj_latest from global leaders in test evaluation. Hope will improve quality of studies.
1/n

Guidance for the design and reporting of studies evaluating the clinical performance of tests for present or past SARS-CoV-2 infection bmj.com/content/372/bm…
Thanks to @JennyDoust @KatyJLBell @leeflang_m
@jacdinnes @SallyJLord @SueMallett Janneke van de Wijgert, Sverre Sandberg, Khosrow Adeli,@pmmbossuyt Andrea Horvath for working on this with me. Its a team which covers all important aspects of test evaluation.

2/n
From reading @DHSCgovuk @PHE_uk study reports and many others from organisations around the world, we are aware that the level of understanding about clinical test evaluation studies is often less than ideal.

This paper lays out clear steps to help improve.

3/n
We keep on hearing "you can't expect perfect studies in a pandemic". But this isn't time to PAN*IC it is time to make sure we do things well so that the answers are both informative and likely to be true. It requires good planning and team input as is described here.

4/n
This paper goes through 8 key points, and gives details relevant to Covid test studies. Brief summary below, much more detail and examples in the paper.

5/n
#1: Define the intended use of the test
Many evaluations do not provide accurate estimates of because the relation between the purpose of the test, the selection of the study population, and the selection of the reference standard have not been carefully mapped out

6/n
#2: Define the target condition—that is, what the test aims to detect. Potential target conditions include viral infection , covid-19 disease, infectiousness, immune response, viral clearance, past or recent infection, and immunity.

7/n
#3: Define the population in which the test will be evaluated. Clinical performance studies should be conducted in individuals sampled from the population in which the test will be used, as determined by the intended use in step.

8/n
#4: Describe the index test strategy
This may be one test, the same test repeated, or a combination of different tests. The entire testing pathway should be evaluated.

9/n
#5: If applicable, describe which tests are compared and why
Decisions need to be made regarding the comparative performance of different tests. The comparison can be between different forms of testing, different tests of the same form, or different testing strategies.

10/n
#6: Define the reference standard
The reference standard needs to clearly separate individuals who have the target condition from those who do not; those who have or have had the infection from those who do or have not, those who are infectious from those who are not

11/n
#7: Analysis and presentation of results
Poor reporting of studies evaluating SARS-CoV-2 tests has been a common methodological concern in the studies to date. Reports should follow the STARD reporting guidelines for diagnostic accuracy studies.

12/n
#8: Prospectively register the study protocol
Prospective registration is a sign of quality, provides evidence that the study objectives, test procedures, outcome measures, eligibility criteria, and data to be collected were defined prospectively, and supports transparency.

13/n
We hope that this guide will help us get better evidence so that we can make informed to help use the right tests at the right times in the right patients.

14/n

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More from @deeksj

26 Mar
ONS just announced weekly infection rate in secondary school aged children is 0.43%.

Yesterday Test-and-Trace data showed 0.047% of LFTs were positive.

How can we get an estimate of the sensitivity of LFTs from this? I’ve come up with sensitivity=10%

Here are my workings
Three issues

#1 0.047% will include LFT false positives – 0.03% according to DHSC, so 0.017% will be LFT true positives.

#2 0.43% will include PCR false positives – lets go for 1 in 1000 (probably less) to be conservative. So 0.33% will be true cases
#3 ONS data are based on number of children, LFT on number of tests. If assume two tests per week (but only ever one positive per child) then double the rate to 0.034%

So sensitivity seems to be about 0.034/0.33 = 10%

Anybody else want to present a version of these figures?
Read 5 tweets
25 Mar
LFT test results for week to 17th Mar

Flatlining – few cases in schools - costing tons of money - causing many FPs

7.6M tests week, up from 6.3M
@£5 per test=£38M
@£20 (real cost reported from Wales)=£152M

To get 8279 +ve results (0.108% yellow line) many of which will be FP
What happened in secondary schools?

3.9M tests in students, 1805 positive results.

1 in 2140+ve (previous week 1 in 2070).

Would expect 1160 false+ve if 99.97% specificity (Government’s new claim)

64% of +ves were false+ve with kids+bubbles+families isolating unnecessarily
Overall we’ve been above 1000 tests to find one true positive for the past fortnight using the 99.97% specificity figure,

and for 3 weeks using the slightly 99.9% specificity figure.

“Finding needles in haystacks”
Read 5 tweets
24 Mar
Updated @cochranecollab review of Rapid Tests for Covid-19 is here

Rapid, point‐of‐care antigen and molecular‐based tests for diagnosis of SARS‐CoV‐2 infection - @jacdinnes @deeksj - 2021 | Cochrane Library

cochranelibrary.com/cdsr/doi/10.10…

1/12
Update included electronic searches to end of Sept, and other resource up to mid Nov 2020. Next update is already underway. Many thanks to the great crowd of people involved in putting this together.

2/12
Included both lateral flow antigen tests – data on 16 tests (of 92 with regulatory approval) in 48 studies (n=20,168)

And rapid molecular tests – data on 5 tests (of 43 with regulatory approval) in 30 studies (n=3,919)

3/12
Read 12 tweets
22 Mar
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%
Read 4 tweets
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
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

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