Daily numbers, graphs, analysis thread 21

[BigChocFrenzy]

Welcome to thread 21 of the daily updates

Resource links:

Uk dashboard deaths, cases, hospitals, tests - 4 nations, English regions & LAs
R estimates UK & English regions
Imperial UK weekly LAs, cases / 100k, table, map, hotspots
UK School statistics Attendance
Modelling real number of UK infections February to date
NHS England Hospital activity
MSAO Map of English cases
Cases Tracker England Local Government
ONS MSAO Map English deaths
CovidMessenger live update by council district in England
Scot gov Daily data
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t
PH Wales LAs, tests, ONS deaths
NI Dashboard
Zoe Uk data
UK govt pressers Slides & data
ICNRC Intensive Care National Audit & Research reports
NHS t&t England & UK testing Weekly stats
PHE Surveillance reports & LA Local Watchlist Maps by LSOA
ONS England infection surveillance report each Friday
Datasets for ONS surveillance reports
ONS Roundup deaths, infections & economic reports
ECDC rolling 14-day incidence EEA & UK
Worldometer UK page
Our World in Data GB test positivity etc, DIY country graphs
FT DIY graphs compare deaths, cases, raw / million pop
Alama Personal COVID risk assessment
Local Mobility Reports for countries
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery

⏭ Our STUDIES Corner ⏮

We welcome factual, data driven and analytical contributions
Please try to keep discussion focused on these
📈 📉 📊 👍

@sirfredfredgeorge

There was a detailed report for Sage that explained you can run a different test

Yes, so it has to be a different test - I'm not convinced how a PCR test can randomly report wrong, something had to bind to the DNA for it to multiply, so if the something is in the sample (as opposed to contamination) then it would bind again. As noted a false positive due to remains of the covid RNA hanging around, but it could be any RNA similar enough that the DNA binds to it. The assumption being a different test will bind in a different way, in any case I certainly can't imagine they are truly independent enough that running the same test again rules out a false positive.

Not that I think it matters an awful lot given the number of false positives, but I think they're over-egging the chance removal.

..... I'd need a genuine expert with recognised qualifications & experience in the field to state it's "over-egging" Are you going to challenge the Crick guy about that on twitter ?

I doubt that there is anything like a significant number of false positives after a procedure of 2 tests, carried out by the Crick or ONS labs

A regular lurker here (DH is a statistician) but may I ask a stupid question, as I think this is beginning to irritate me?

• DH is a statistician, but I'm a writer... words matter.

Media reports say that "cases jump by 7k" but on looking at the data dashboard, in fact the daily number of positive cases by specimen date has been fairly consistent for around 10 days. What appears to be happening is that test results seem to be lagging and then catching up a few days later in fairly significant quantities.

The eventual numbers being the same, of course, but it isn't quite the same as 7k people presented simultaneously as positive in one tranche. If that's the correct reading of that data....?

Merkel's chief virologist adviser, Drosten, recently answered if the test he developed for Covid (back in January) reacted to other things:

Christian Drosten@c_drosten

Diejenigen, die öffentlich behaupten, unsere SARS-CoV-2 PCR sei nicht gegen menschliche Coronaviren und Erkältungsviren validiert, sollten sich einfach mal die Mühe machen, die Publikation zu lesen.
Auch Herr #Wodarg und Frau #Kämmerer. Tabelle 2.

https://eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.3.2000045#html_fulltext

(transl: Those who publicly claim that our SARS-CoV-2 PCR is not validated against human coronaviruses and cold viruses should simply take the trouble to read the publication)

@Cattermole

A regular lurker here (DH is a statistician) but may I ask a stupid question, as I think this is beginning to irritate me?

• DH is a statistician, but I'm a writer... words matter.

Media reports say that "cases jump by 7k" but on looking at the data dashboard, in fact the daily number of positive cases by specimen date has been fairly consistent for around 10 days. What appears to be happening is that test results seem to be lagging and then catching up a few days later in fairly significant quantities.

The eventual numbers being the same, of course, but it isn't quite the same as 7k people presented simultaneously as positive in one tranche. If that's the correct reading of that data....?

.... It's why in addition to naturally following the daily figures, I always recommend looking at the 7-day rolling average: this smooths out reporting blips, weekend effects, public holidays etc

Also, consider the hospitalisation rates, ICU and the latest R numbers and daily growth rates - link in OP tom the latter 2.

All the data together gives a more complete picture
and following these over a period of time gives the trends

Very true Cattermole and BCF < waves pompoms>. Some of the news reporting of stats makes my teeth itch.

I also find it very irritating that people keep talking about how 71 or whatever people have died in the last 24 hours when probably none of them did - deaths are clustered 2 to 4 days before the day of reporting so you really need to wait a few days to see the trend, hence the value of the weekly rolling average for all stats.

I am however pleased to see that London still doesn't seem to be 2-4 days behind the North East, looking at hospitalisations if not tests.

I think the bottleneck is the testing. I am wondering whether there are huge piles of samples in the labs and we get a burst of results when they make some headway with the processing.

I note that the testing data refers to PCR capacity on the home screen of the dashboard. The capacity is 296,812 today, which is an increase isn't it. Is that old news or a recent thing?

Merkel pushing fresh air & ventilation strategy nationwide, in a speech yesterday

Slogan AHA (space, hygeine, masks) ==> AHACL - added on the App (C) + ventilation (L)

Fresh air is not really new here
Even during lockdown, singletons were allowed unlimited outdoor exercise (except in a few epicentres), people could sunbathe, sit on benches etc
However, now officially being pushed nationwide

We still need to keep SD outdoors though, remembering how outdoor carnivals were early epicentres

@cathyandclare

I note that the testing data refers to PCR capacity on the home screen of the dashboard. The capacity is 296,812 today, which is an increase isn't it. Is that old news or a recent thing?

.... The capacity in the past has been highly theoretical, more a fond hope than reality

I gather capacity includes about 100k tests for regular testing of NHS staff, plus this month an unknown number allocated for care staff - so all in Pillar 1
Then the Pillar 3 & 4 tests for PHE surveillance, ONS etc

So Pillar 2 test capacity - the tests ordinary bods get - are way below the headline capacity of nearly 300k atm
Looking at the dashboard, the number oscillates around 150k

However, not so long ago it turned out only 62k Pillar 2 tests were actually being processed daily in the UK, despite the claimed 200k+ capacity
and some tests had been sent to Italy & Germany for processing, as UK labs couldn't cope

• that outsourcing facility will eventually go, as cases are rising there too, allbeit slowly.

@Cattermole - Crick might use two test types, I'm not certain from what's been said that they don't do so.

My issue with Scotland's numbers is that double testing everyone makes no sense for reducing false positive tests, you would only retest the 800 or so positive tests. If it's false negative issues then which do you take to be correct, only any positive - but then why test twice for a positive. Also, test totals declared are 2.5* the number of first time tests, whereas first time tests seem to be what's then used. I can see SOME tests on covid patients to declare when they're clear, double the positive results to avoid false positives, some inconclusive leading to retesting... I'm still coming up short by many thousands of tests. The only explanation I can see is the "we're idiots who are only counting people (NHS/ care home staff, shop workers etc) on the first test they ever had and haven't yet noticed this is having a huge unexpected impact on figures".

@herecomesthsun

I think the bottleneck is the testing. I am wondering whether there are huge piles of samples in the labs and we get a burst of results when they make some headway with the processing.

I don't know if you're right, but what I'm worried about is the (possibly) huge numbers of infected, symptomatic people who aren't even getting to the testing stage.

@BigChocFrenzy love that Merkel is pushing fresh air and ventilation and masks.

It really annoys me how there is lack of clarity of message and is not getting through. My DS school still think if they sit apart in the same classroom and wipe down tables that is adequate. Whereas everyone breaths the same air. Same with workplaces. My brother even was worried about people meeting up outside the gardens of his work in groups of 6, but inside his workplace there are 10 to a room and he doesn’t see one is more risky than the other. Ventilation is not getting through at all.

The interpretation of evidence based risk is not being communicated.

@MRex

Actually she's reporting half the.number of tests assigned to Scotland on the PHE coronavirus board. 11.5% would mean 7008 tests. Now look: www.gov.scot/publications/coronavirus-covid-19-update-first-ministers-speech-29-september-2020/.

Bloody nonsense.

Agreed @MRex The number of test being down is crazily low now. 17k at the beginning of Sept today just over 6k

I note that the testing data refers to PCR capacity on the home screen of the dashboard. The capacity is 296,812 today, which is an increase isn't it

The site administrators have changed the presentation of the dashboard (once again!). Their initial default view was the total number of tests including antibody Pillar 3 which was misleading and gave an artificially high number of 375k.

They then switched to Pillar 1 and 2 which, in my opinion, was the right thing to do. This gave a capacity of roughly 240-260k which made sense.

They have made another change today and they are now reporting total PCR capacity (including Pillar 4) - 297k. It might be technically correct but if the ONS tests are "ring fenced" for their purpose, the number of tests including Pillar 4 is not particularly interesting. I still think capacity and tests across the first two pillars are the most relevant numbers.

By the way, anecdota - anyone in Oxford who has a quick panic soon about a massive increase (and @littleowl1 on their behalf), huge numbers of students have tested positive and been confined to flats. Better flats than halls, but of course it increases the risk of cross-infections.

Hospitalisations

England
Hospitalisations rise to 308
(graph by UK COVID-19 @UKCovid19Stats)

France

• 650 new hospitalizations
• 135 new ICU admissions
• 64 new deaths

15,629 new tests were recorded today in Scotland.
6230 new people were tested.

From the coronavirus dashboard:

• Antibody / serology test capacity staying flat at 120k/day, but only about 5k tests being done per day on average
• PCR swab / Covid infection test capacity has recently had a low point of 200k, high point 288k and looks to be regularly 230k-260k per day on average
• Pillar 1 NHS portion varies 55k-80k typically 73k weekday results and 57k weekend results
• Pillar 2 general public tests 130k-185k per day, typically about 160k
• Pillar 3 antibody 1k - 6k per day
• Pillar 4 surveillance tests have gone as low as 4k age had catch-ups, but usually about 23k per day.

Now, we know there is some retesting of inconclusives and rechecking in case of false positives - but should still be about 120k general public tests in that (finger in the air, please anyone else to analyse and adjust that number).

Ah Mrex I see what your issue is. I'm a bit slow today. Need a new positive count, rather than newly tested person count.

Exactly @Perihelion. Are you Edinburgh based and can ask your local MSP to challenge the maths? (Apologies if not, I may have confused you with someone else.)

I just spotted this and it made me gasp. Does this mean the amounts of asymptomatic cases in general could actually be far higher than previously estimated?

Covid: 170 test positive at Cornwall meat plant www.bbc.co.uk/news/uk-england-cornwall-54361824

Head of armed forces says both China and Russia trying to undermine cohesion in west

Beware of false info being spread deliberately, especially about vaccines

https://www.theguardian.com/uk-news/2020/sep/30/russia-spreading-lies-about-covid-vaccines-says-uk-military-chief