What is the evidence supporting the Government’s claims that Innova LFT detects infectious cases?

There are no real studies at all which directly show how well Innova +ve detects infectious people and Innova -ve indicates non-infectious people.

No direct data at all.

The data come from studies of PCR with inferences made by linking PCR proxy “viral load” Ct values to the viral load levels we know that Innova detects.

Ct values are not standardised and depend on how much biological matter on a swab. They have high measurement error

Evidence on infectiousness comes from studies linking Ct values with rates of (a) secondary cases and (b) the ability to culture the virus. Neither are perfect – but are the best we can do. They will both most likely underestimate infectiousness.

Innova has been shown to be able to detect viral loads when Ct <25, both in Porton Down studies (left) and in real application in the Liverpool pilot (right).

And SAGE has advised the Government that Ct<25 indicates those people most likely to be infectious.

So what is the evidence from these studies that people with high viral loads detectable by Innova (Ct=<25) are infectious and that those with lower viral loads (Ct>25) are not? First two studies are of viral culture rates, second two studies are of secondary attack rates.

#1 PHE Colindale n=324 - symptomatic and asymptomatic. Clear trend that higher Ct values (lower viral load) less likely to have culturable virus. Culture rate Ct<25 is 85% but Ct>25 is still 34% - just less that half so lots of “infectious” cases would be missed by Innova.

#2 is regional lab in Marseille n=3790, probably largely symptomatic but not clearly stated.

The viral culture rate below Ct=25 is 85%, above it is 24% - just less that a third the value. Again a substantial proportion that would be missed by Innova could be cultured.

#3 secondary cases in contacts tested at t=0 & 14 days with PCR. Conversion from viral load back to Ct value is done from linked publication.

Secondary case rate 20% for Ct<25 & 13% for Ct>25. Case rates in those likely to be missed by Innova more than half of those found

#4 secondary case in UK Test-and-Trace system. No actual numbers are in the report - data from graphs.

Secondary case rate 7.4% for Ct<25 and 3.4% for Ct>25 roughly half the value. Again secondary cases in those Ct likely to be missed by Innova not negligble.
So clear evidence that

infectiousness has a continuous trend, no step change
anywhere so higher Ct values linked with high chances


viral culture rates and secondary attack rates in those likely to be missed by Innova are concerningly high and
definitely matter.

Governments are using models rather than real world evaluations to predict how well LFT testing will work. Some of these include “infectiousness functions” to show the chances that somebody with a Ct value is infectious. How well do these match with these real data?

Red shows the household infectiousness function from study #4 Test-Trace data household contacts

This function is a reasonable first approximation …

But this one (Blue) from Mina’s key study excludes the possibility that anybody could be infectious at Ct values above 22, nowhere near the patterns in any of these studies. Clearly will lead to overoptimistic predictions of how well LFTs would work.

Data from these 4 studies show high risk that Innova -ves can infect others.

This is why many scientists are expressing reservations about their use – particularly where they are to be used as a green light test - when a negative test is used to start activities.

If people stop socially distancing with a negative test (e.g. nightclubs, theatres, workplaces) then mixing with some infectious people will occur, increasing risk of transmission.

But remember, nobody has provided any data actually using the LFTs – most are from model predictions, some of which might be very wrong.

Good studies and real world evaluations are needed.

If you want to hear this presentation in 9 minutes you can access it here

Please don’t bother posting abuse stating I don’t understand statistics, biology, virology, public health, have an agenda, have shares in a PCR company or am intentionally misleading the world. It harms your reputation too. This is about facts and data, not what I think.

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More from @deeksj

21 Jan
@TomChivers has taken on the challenge of trying to understand the disagreements over LFTs. We had a good chat, but unfortunately the final article mispresents some of my views. I explain more below.

What Covid tests can we trust? @UnHerd unherd.com/2021/01/what-c…
Read 7 tweets
18 Jan
Context matters … I am aware that people outside the UK are reading my tweets and papers, and influencing their thinking about lateral flow testing. It’s really important that you understand the context I am writing from, and why it probably is different where you are.

The situation and issues in the UK (particularly in England), is almost certainly unlike where you are. The UK Government are unique in many ways and that is impacting on how tests are being used. (As a Brit I am also prone to understatement and being overpolite).

Our Government have staked their reputation on the Moonshot idea “to get our lives back to normal” using LFTs before there was evidence to see whether it would work. It doesn’t make sense to decide policy before evaluating the technology. Decision-making is now politicised.
Read 11 tweets
16 Jan
Testing in schools saga - again

What is the explanation behind this from @educationgovuk? Why has the @MHRAgovuk said DfE does not need regulatory approval for daily “assisted testing” given it does not approve daily “self testing” of contacts of infected cases in schools?
Daily self-testing of contacts was not approved because MHRA considered that the test misses too many cases, allowing infected and infectious individuals to remain in class. The MHRA would have come to this decision based on a forensic and balanced assessment of the evidence.
Hopefully somebody can help answer why this does not also apply to “assisted testing”. I can think of three different explanations. There may be more.
Read 7 tweets
15 Jan
Great summary and we really need to take the toxicity out of this. Agree with >95% of what is here. Thx for taking time to do this. The big challenge is how we make quick progress without being able to get a ref std for infectiousness. Cluster RCTs great but hard to do.
Part of my 5% disagreement arises in whether we are making a mistake in trying to force “infectiousness” into the test accuracy paradigm, or whether we could do better considering it in a different way. It is a probabilistic rather than binary concept which causes the problem.
We can classify people as more or less likely to infect others, but I don’t think we will ever successfully put people into two groups of those who do or do not infect somebody else from a test. That is unlike our ability to say that people do or not have detectable virus.
Read 9 tweets
15 Jan
The testing in schools story is still unfolding.

@DHSCgovuk told journalists today that yesterday's Guardian story was "not true".

But then the @MHRAgovuk have come and said the opposite.

The MHRA has now confirmed to Schools Week it has “not issued an Exceptional Use Authorisation for that self-test device for ‘serial testing’ for school pupils who have been exposed to a confirmed positive COVID case that would enable them to attend school as normal”.
MHRA: “continues to advise that close contacts of positive cases identified using the self test device continue to self-isolate in line with current guidelines. Discussions with Test and Trace regarding any future exceptional use cases are ongoing.”

So - contradicting DfE policy
Read 6 tweets
7 Jan
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.
Read 7 tweets

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