John Bye Profile picture
1 Jan, 15 tweets, 9 min read
The latest Test & Trace report is out, covering the week before Christmas.

Cases in London and the South East were soaring, and an outbreak of coronavirus at the Lighthouse Lab in Milton Keynes caused further issues in the testing system as demand for tests rapidly increased.
There was another big increase in testing as demand rose, with increasing numbers of quick but less sensitive Lateral Flow Tests being used to screen asymptomatic people.

In total 2.6 million tests were done. But a higher percentage than last week were positive.
If you separate Lateral Flow (which are ONLY used on asymptomatic people) and PCR (which are used on both symptomatic and asymptomatic people) tests, positivity for PCR is back to the peak last seen at the beginning of November, while positivity for LFTs is rising fast now too.
Meanwhile a coronavirus outbreak at the Milton Keynes Lighthouse Lab caused issues, forcing some staff to self-isolate.

With demand rising rapidly and a lab that should handle 70,000 tests a day not running at full capacity, the system was overstretched.

news.sky.com/story/covid-19…
As a result, the time from taking a test to getting your result increased sharply again.

There's a target to deliver results from all in person tests (at drive in, walk in and mobile test sites) within 24 hours.

This week only 17% of tests met that target.
Turnaround times for home test kits and tests at satellite sites such as care homes also increased sharply.

With demand surging, the outbreak at Milton Keynes, and reagent shortages reported the week before that, the last couple of weeks have reversed two months of improvements.
Void rates (where a sample was leaking, damaged etc, or didn't give a clear result) barely changed, but the number of tests "not completed" (where a sample was processed but the person it's from hasn't received their result yet) also rose significantly before Christmas.
Despite a sharp rise in cases referred to contact tracers, they managed to reach 86% of them (only a slight drop on last week's 88%), and mostly within 24 hours.

A new tab in the spreadsheet also means we now have complete data on HOW cases were reached all the way back to June.
When it comes to reaching the close contacts identified by those cases, most are counted as reached because the person who tested positive is now told to notify everyone in their household to self-isolate.

But performance for non-household contacts isn't improving.
The impact of the change in procedure is dramatically illustrated by another piece of new data, showing how contacts were reached.

Over 80% are now "reached" by the person in their home who tested positive. 10% follow a link to a website for advice. Only 8% are reached by phone.
Comparing the numbers before and after the change, it looks like at least 100,000 less phone calls were needed in the week before Christmas than would have been the case under the old system, where contact tracers tried to reach every member of a household individually.
It's also striking how much the percentage of contacts where no contact details were given dropped when this change was first introduced, from 20% to 4%.

This suggests many people testing positive were refusing to give out contact details for other members of their own family.
Of course, we don't know if they're actually telling other members of their household to self-isolate, or giving them accurate information on what they need to do.

But it does at least stop families being bombarded by multiple calls from contact tracers, as happened in the past.
This week's (cut down) Test & Trace report and accompany data can be found here.

gov.uk/government/pub…
And here's my analysis of last week's report for comparison.

Note: I've swapped the columns around in the Summary table now, as I felt it makes more sense to show Last Week's numbers first, then This Week's numbers, and finally the change between them.

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More from @_johnbye

28 Dec 20
It's sad we still need to say this, but false positives are NOT driving rising cases.

In the summer the False Positive Rate (FPR) at lots of labs was below 0.1%.

For example, Milton Keynes' FPR for the ONS Infection Survey was less than 0.04% in July.

ons.gov.uk/peoplepopulati…
In fact, when prevalence was low, labs all over the world had less than 0.1% of tests give a positive result.

So their FPR (the % of people they tested who didn't have the virus but got a positive result) must also have been less than 0.1% at the time.

So there's nothing fundamentally wrong with PCR. It doesn't conjure up lots of false positives out of thin air when nobody has the virus.

Any false positives would mostly come from cross contamination or errors, either when the sample is taken or at the lab when it's processed.
Read 26 tweets
26 Dec 20
This week's Test & Trace report covers the week to December 16th, when cases in London and the South East were surging and falls in the North and Midlands levelling off.

There were also issues in the Lighthouse Lab system, apparently caused by a shortage of reagents. Image
As demand soared, almost 2 million tests were done in a week in England, which is amazing when you consider we struggled to test a few thousand people 9 months ago.

Despite this, the number of positive results rose much faster than testing, with positivity rates climbing again. ImageImageImageImage
Breaking it down by type of test done:

The new Lateral Flow Tests are still only being used on people without symptoms, so positivity is very low but rose sharply this week.

Some (but not all) PCR tests are used on people with symptoms so have higher positivity. Over 10% again. Image
Read 19 tweets
24 Dec 20
The interim report on the Liverpool community testing trial is now out, with more complete results for the sensitivity of the tests, as well as lots of additional information and data about the trial.

h/t @angelaraffle and @scb909

liverpool.ac.uk/coronavirus/re…
Firstly, more results have been released, showing the Innova LFTs only found 40% of people who were PCR positive.

More relevantly, they missed 17.6% of people positive at Ct 20 or lower, and 45.5% at Ct 20-25.

So overall they missed a third of people with "higher viral load". Image
Interestingly though, when they went back and reassessed test results based on photos of the devices (with a third person checking if the result differed from the initial one), their performance improved significantly. Finding 83% of PCR positives at or below Ct 25. Image
Read 13 tweets
22 Dec 20
2,800 lorries are now stranded in Kent, with many drivers not even having access to basic facilities. The government appears to have done nothing to help them.
Meanwhile a Sikh charity that's more used to aiding victims of wars and natural disasters is stepping in to provide bottled water and hundreds of hot meals for stranded drivers.

The good news is France has agreed to reopen the border.

The bad news is this only applies to EU nationals and residents, and they must have had a negative PCR test within the last 72 hours.

So it may be a couple of days before things get moving.

Read 6 tweets
21 Dec 20
In case you wonder why everyone's so alarmed, daily case numbers in London, the South East and the East of England are rising VERY rapidly.

Much faster than the second wave in the North and Midlands in the autumn.

And the rest of the country seems to be edging up again now too. Image
Hospital admissions in those areas are now rising rapidly as well, with the East of England actually seeing the most new admissions when you adjust for population. Image
Both the East of England and South East have now passed the number of covid patients they had in hospitals at the peak of the first wave.

London is half way to its first wave peak and rising rapidly.

And the first wave was in the spring, when hospitals are generally quieter. Image
Read 4 tweets
12 Dec 20
The full results of the Liverpool LFT trial have been released.

False positives are much lower than expected, but false negatives much worse.

Liverpool has now paused plans to use the tests on care home visitors, following Sheffield and Manchester.

gov.uk/government/pub…
The good news is the LFTs only gave 2 false positives out of 3,199 tests checked by PCR. That gives a false positive rate of 0.07%, far less than the 0.38% reported in initial tests.

The bad news is they missed 23 of the 45 PCR positives, giving a 51% false negative rate!
We already knew the Innova LFTs were less sensitive than PCR, but they were meant to catch 95% of people with "higher viral load".

In the Liverpool trial though they missed 15% of people who were positive at below 20 cycles on PCR, and 47% of people positive at 20-25 cycles!
Read 16 tweets

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