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Data, Stats Thread June 11

986 replies

PatriciaHolm · 11/06/2021 15:05

UK govt pressers Slides & data

www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history

Data Dashboard coronavirus.data.gov.uk/
Covid 19 Genomics www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
Covid 19 Variant Mapping Sanger Institute covid19.sanger.ac.uk/lineages/raw
NHS Vaccination data www.england.nhs.uk/statistics/statistical-work-areas/covid-19-vaccinations/
Global vaccination data ourworldindata.org/covid-vaccinations
R estimates UK & English regions www.gov.uk/guidance/the-r-number-in-the-uk
Imperial UK weekly LAs, cases / 100k, table, map, hotspots statistics imperialcollegelondon.github.io/covid19local/#map
NHS England Hospital activity www.england.nhs.uk/statistics/statistical-work-areas/covid-19-hospital-activity/
NHs England Daily deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/
Cases Tracker England Local Government lginform.local.gov.uk/reports/view/lga-research/covid-19-case-tracker
ONS MSAO Map English deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/
CovidMessenger live update by council area in England www.covidmessenger.com/
Scot gov Daily data www.gov.scot/publications/coronavirus-covid-19-daily-data-for-scotland/
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t www.travellingtabby.com/scotland-coronavirus-tracker/
PH Wales LAs, cases, tests, deaths Dashboard public.tableau.com/profile/public.health.wales.health.protection#!/vizhome/RapidCOVID-19virology-Public/Headlinesummary
ICNRC Intensive Care National Audit & Research reports www.icnarc.org/Our-Audit/Audits/Cmp/Reports
NHS t&t England & UK testing Weekly stats www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports
PHE Surveillance reports & LA Local Watchlist Maps by LSOA (from last summer) www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports
ONS England infection surveillance report each Friday www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/coronaviruscovid19infectionsurveypilot/previousReleases
Datasets for ONS surveillance reports www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/datasets/coronaviruscovid19infectionsurveydata/2020
ONS Roundup deaths, infections & economic reports www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/coronaviruscovid19roundup/2020-03-26
Zoe UK data covid.joinzoe.com/data#interactive-map
ECDC (European Centre for Disease Control rolling 14-day incidence EEA & UK www.ecdc.europa.eu/en/cases-2019-ncov-eueea
Worldometer UK page www.worldometers.info/coronavirus/country/uk/
Our World in Data GB test positivity etc, DIY country graphs ourworldindata.org/coronavirus/country/united-kingdom?country=~GBR
FT DIY graphs compare deaths, cases, raw / million pop ig.ft.com/coronavirus-chart/?areas=eur&areas=usa&areas=bra&areas=gbr&areas=cze&areas=hun&areasRegional=usny&areasRegional=usnj&areasRegional=usaz&areasRegional=usca&areasRegional=usnd&areasRegional=ussd&cumulative=0&logScale=0&per100K=1&startDate=2020-09-01&values=deaths
PHE local health data fingertips.phe.org.uk/profile/health-profiles
Alama Personal COVID risk assessment alama.org.uk/covid-19-medical-risk-assessment/
Local Mobility Reports for countries www.google.com/covid19/mobility/
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery www.centreforcities.org/data/high-streets-recovery-tracker/

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We welcome factual, data driven and analytical contributions
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OP posts:
Thread gallery
125
lonelyplanet · 17/06/2021 20:49

@JanFebAnyMonth

Er no one else is lucky enough to have an Operation Moonshot....
😄
Piggywaspushed · 17/06/2021 20:49

Our local dashboards show positivity rates. The comments on Facebook do rather reveal that people don't understand them though.

DamnYouAutoCatRectal · 17/06/2021 23:31

I didn't exist in the 2021 census data and I'm a fairly law abiding citizen. I left the census form at my old flat for the new owners, as the date hadn't passed yet, the previous owners had already sent off the one for our new house with their details.

I can see how hard it is to keep track of lots of people who have nothing to hide, but just use the wrong date or make another simple error. Who knows how you begin to estimate the people who don't want to be found, as well as the people who just don't fill in the form correctly.

JanFebAnyMonth · 18/06/2021 08:26

A lot to look at in this Telegraph article, which claims that in one week (the week schools returned) 60% of school LFTs come back with a negative PCR:

Covid testing in schools is hugely disruptive and should be suspended, experts have said, as it emerged that up to 60 per cent of "positive" tests a week are coming back negative when checked.

Under plans to keep schools open, more than 50 million lateral flow tests have been carried out on youngsters, leading to thousands of pupils and their social bubbles being forced to self-isolate for 10 days.

But an analysis of NHS Test and Trace data by The Telegraph shows that, in secondary schools, one-third of lateral flow tests checked against the gold-standard Polymerase Chain Reaction (PCR) test have come back negative. In one week in March, that rose to 60 per cent.

In an interview with The Telegraph, Prof Sir Andrew Pollard, who led the Oxford vaccine programme, warned that mass testing was leading to such huge disruption in schools that it may be worth vaccinating youngsters to stop the chaos.

"If children are not severely affected, if they're not major drivers of transmission, the testing itself is picking up lots of cases – causing classes to be sent home and so on – we've got to get to a point where we're not impacting on education," he said. "And I think that impact on education could be a reason for vaccination.

"If children aren't very much affected, then the testing is obviously not protecting them as they're not very affected. So is the testing being done to protect other people?"

The Joint Committee on Vaccination and Immunisation (JCVI) is deciding whether to recommend jabs for children amid fears that the risks may outweigh the benefits.

Children and teenagers have been disproportionately impacted by measures to control the pandemic despite being largely unaffected by the virus.

Many have seen exams cancelled and been forced to homeschool for months, putting their mental health and socialisation at risk.

On Thursday, 23 British academics from universities including Oxford, Cambridge and University College London wrote to Gavin Williamson, the Education Secretary, to warn that lateral flow testing posed a danger for schools.

They are concerned that ongoing contact tracing trials could spark a wave of new infections and have called for them to be suspended.

Currently, 170 schools and colleges across England are taking part in the trials, in which students no longer need to self-isolate when a close contact tests positive if they test negative themselves using a lateral flow test.

But there have been concerns that as well as throwing up false positives, lateral flow devices miss large numbers of true positives. A pilot in Liverpool last year found they failed to spot positive cases around 50 per cent of the time

The letter, published in the BMJ, reads: "It is undisputed that lateral flow tests (LFDs) cannot detect the lower levels of virus among individuals in early infection. There is a high chance that infected contacts in a classroom may be infectious before they are detected as positive by a LFD test."

The scientists said they were also concerned that the US Food and Drug Administration (FDA) had recently banned the Innova lateral flow test currently being used in schools, citing risk to health and "further spread of the virus". The FDA also said Innova had not provided evidence for efficacy of the tests.

On Thursday, the Medicines and Healthcare products Regulatory Agency (MHRA) said it had reassessed the Innova test following the FDA ban and had extended approval until August this year.

Graeme Tunbridge, the MHRA Director of Devices, said: "We have now concluded our review of the risk assessment and are satisfied that no further action is necessary or advisable at this time."

However, the Royal Statistical Society (RSS) warned that the regulator's assessment of test safety needed to extend beyond physical safety to the consequences of false positives and false negatives for those tested, saying in a report: "The full range of consequences, from liberalised behaviour to deprivation of liberty, should be considered."

Analysis by The Telegraph shows that lateral flow tests are giving large numbers of false positives, leading to needless disruption in classrooms and beyond.

Around 19,000 infections were picked up by lateral flow devices in secondary school pupils between March and June – but despite new guidelines saying cases must be confirmed with a PCR test, only half were actually checked.

Of the 9,546 checked, nearly one third came back negative – meaning almost 3,000 tests had to be removed from the daily reported figures. In June alone, more than 2,000 positive tests were quietly erased from the daily government dashboard, primarily because of problems with lateral flow testing.

The percentage of tests coming back negative in secondary schools reached 60 per cent in the week of March 4 to March 10, when 379 of the 624 positive tests were found to be wrong. It has since fallen to around one third.

If the negative rate holds true for the 9,500 unchecked tests, it suggests thousands more should be removed from the daily figures.

Experts warned that false positives not only caused disruption in schools but also made tracking the pandemic much harder.

Prof Carl Heneghan, the director of the Centre for Evidence Based Medicine at the University of Oxford, said: "What concerns me here is the idea that we are picking up such high numbers of false positives with lateral flow. And there seems to be a growing strategy of just using lateral flow for testing.

"It means we are getting a problem of inaccurate data. In evidence-based medicine we call this a problem of noise, and it's difficult to see what is really going on amid this noise. At this point I would be ignoring lateral flow testing and be focusing on PCR positivity to get a true picture of the pandemic, and that shows cases are only going up in small incremental measures."

A spokesman for the Department for Education said daily contact testing as a replacement for self-isolation would be reviewed at the end of June. The Department of Health was contacted for comment.

MarshaBradyo · 18/06/2021 09:05

"If children are not severely affected, if they're not major drivers of transmission, the testing itself is picking up lots of cases – causing classes to be sent home and so on – we've got to get to a point where we're not impacting on education," he said. "And I think that impact on education could be a reason for vaccination.

"If children aren't very much affected, then the testing is obviously not protecting them as they're not very affected. So is the testing being done to protect other people?"

I agree entirely. This is such a pain right now. Disproportionate

EasterIssland · 18/06/2021 10:24

The UK has reported 33,630 new cases of the Delta coronavirus variant in the last week, taking the total number of confirmed cases to 75,953, Public Health England said in a data release this morning.

According to the figures, as of 14 June, a total of 806 people have been hospitalised with the Delta variant, an increase of 423 since the previous week. Of these, 527 were unvaccinated, and only 84 of the 806 had received both doses. That implies that 195 people who had received one dose were hospitalised. The data doesn’t appear to show how recently people had received their vaccine.

www.gov.uk/government/news/confirmed-cases-of-covid-19-variants-identified-in-uk

sirfredfredgeorge · 18/06/2021 10:42

It also doesn't say if they were hospitalised for covid or not, which is really even more important than the number of doses.

strangeshapedpotato · 18/06/2021 10:43

@JanFebAnyMonth

Nope - it's the Telegraph - all it is capable of doing is lying and manipulating. I wondered what had happened to the fraud Heneghan who disappeared into the woodwork after his grand claims last Autumn that the UK had herd immunity and that rising numbers were entirely due to flaws with PCR tests.

LF's are associated with a number of false +ve's - before we started using them it was thought this could be around 3 per 1000. It's turned out to be lower than 1 per 1000 - possibly as few as 3 per 10k. This is unconnected to the actual number of +ve's.

So if you test 1 million kids, when infection rates are extremely low, you get ~300 false +ves and say 100 true positives.

Test 1 million kids when infection rates are very high and you get ~300 false +ves and 3000 true positives.

So while you could argue that continuing to use them as cases fall is unhelpful, to do so as cases rise, on the cusp of a new wave, is dumb and completely unjustified.

NannyAndJohn · 18/06/2021 10:44

So that's almost half the cases and over half the hospitalisations concentrated in one single week.

Eek.

wintertravel1980 · 18/06/2021 11:07

The weekly PHE technical briefing is out:

assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/994839/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

I have only had a quick look and not seen any major surprises. The good news is that the estimated secondary attack rate for households has been revised down (consistently with the secondary attack rate for all close contacts):

The estimate of secondary attack rate for household contacts of cases with Delta has fallen over the last 4 weeks of reporting, from 16.8% (95% CI 15.1% to 18.7%) for exposure events in week commencing 26 April 2021 to 11.8% (95% 11.3% to 12.3%) for exposure events in week commencing 17 May 2021. Over the period presented, secondary attack rates for both household and non-household contacts of cases with Delta remain higher than for Alpha (or other cases). A peak in secondary attack rates from cases with Delta was seen in both household and non- household contacts exposed during the week commencing 26 April 2021, while secondary attack rates from cases with Alpha were stable compared to earlier and later weeks.

If Delta fluctuated significantly in comparison to Alpha over the same period, it is unlikely that the change can be explained by increased vaccinations. We hypothesised that the initial SAR estimates for Delta may be overstated due to environmental factors and I think the new report might be confirming that.

Having said that, a 40 to 50% transmission advantage is still very significant.

strangeshapedpotato · 18/06/2021 11:18

@wintertravel1980

The weekly PHE technical briefing is out:

assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/994839/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

I have only had a quick look and not seen any major surprises. The good news is that the estimated secondary attack rate for households has been revised down (consistently with the secondary attack rate for all close contacts):

The estimate of secondary attack rate for household contacts of cases with Delta has fallen over the last 4 weeks of reporting, from 16.8% (95% CI 15.1% to 18.7%) for exposure events in week commencing 26 April 2021 to 11.8% (95% 11.3% to 12.3%) for exposure events in week commencing 17 May 2021. Over the period presented, secondary attack rates for both household and non-household contacts of cases with Delta remain higher than for Alpha (or other cases). A peak in secondary attack rates from cases with Delta was seen in both household and non- household contacts exposed during the week commencing 26 April 2021, while secondary attack rates from cases with Alpha were stable compared to earlier and later weeks.

If Delta fluctuated significantly in comparison to Alpha over the same period, it is unlikely that the change can be explained by increased vaccinations. We hypothesised that the initial SAR estimates for Delta may be overstated due to environmental factors and I think the new report might be confirming that.

Having said that, a 40 to 50% transmission advantage is still very significant.

The obvious explanation would be that Delta was originally seeded mainly in households with a greater than average likelihood of secondary attack (sociological factors), but now it's spreading in the same way as the Alpha variant, so that initial distinction is being ironed out.
JanFebAnyMonth · 18/06/2021 11:28

@strangeshapedpotato yes, agreed, but where on earth does the Telegraph get a 60% false positive rate for that week in March?

JanFebAnyMonth · 18/06/2021 11:29

*how on earth rather than where...

sirfredfredgeorge · 18/06/2021 11:35

but where on earth does the Telegraph get a 60% false positive rate for that week in March?

That was pretty much the data in the coronavirus dashboard for all LFTS, legit positives were so low. Most of March and April had ratios were close to that, so I'm sure it's possible that school only tests were there - not the I know of any sources of data for school only.

wintertravel1980 · 18/06/2021 11:38

...yes, agreed, but where on earth does the Telegraph get a 60% false positive rate for that week in March?

The 60% is probably the accurate number.

We had a few weeks this year when Covid prevalence was very low - 1 in 1,000 in the general population and perhaps 1 in 2,000 in secondary school kids (I am quoting numbers off top of my head but we can go back to ONS surveys if we double check this).

LFTs have got 50-60% sensitivity and 0.03% specificity. Let us look at an example where we test 10,000 children:

  • 5 of them will have Covid
  • 3 of those 5 will be correctly flagged as positive (60% x 5)
  • 3 out of 10,000 will be false positives (0.03% x 10,000)

In total, we will end up with 6 reported positive cases, including 3 (50%) true positives and 3 (another 50%) false positives.

This calculation is correct but it only works when cases are very low. With the current prevalence, the picture will be very different.

I think it is reasonable to argue that LFTs are less useful when there is very little community spread. We might have been there in March but, unfortunately, we are not there now.

JanFebAnyMonth · 18/06/2021 11:46

Thanks @wintertravel1980. I’ve never fully understood the thing about false positivity rates at low prevalence, but accept that it’s true! So do the numbers work for a current rate of 30% among school children?

Let’s hope someone eminent challenges the Telegraph!

sirfredfredgeorge · 18/06/2021 11:52

So do the numbers work for a current rate of 30% among school children?

Possibly, likely a little high by now across the whole country, but it massively depends on the area, lots of areas in the UK the chance of a positive being more likely a false positive is quite high still.

wintertravel1980 · 18/06/2021 11:57

Assuming prevalence of 0.5% (from last week ONS), we would end up with approximately 10% of false positives (10,000 children tested, 28-33 positive results, including 3 false positives).

The 30% might be based on the number of people who decide to get the follow up PCR. People with positive LFTs who believe they might actually have Covid (e.g. if they feel a bit off without classic symptoms) will just accept the test result and not bother with re-testing.

JanFebAnyMonth · 18/06/2021 12:17

Thank you

ILookAtTheFloor · 18/06/2021 12:45

What was the peak attack rate for Alpha? Hasn't that been going down as well?

Any explanations for this? The Alpha was going down before the vaccine effect, right?

ILookAtTheFloor · 18/06/2021 12:49

The January technical briefing had the Alpha attack rate at 12% here, it's been revised down now.

assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/959426/Variant_of_Concern_VOC_202012_01_Technical_Briefing_5.pdf

Surely this makes it hard to accurately assess transmissibilty?

TruelyonelastSchlep · 18/06/2021 14:10

Apparently AZ supplied the EU with moreAZ than they were obliged to do not less

EU loses legal case against AstraZeneca over vaccine supplies

The European Union has lost its legal fight against AstraZeneca over claims it failed to deliver on its vaccine commitments for the bloc, the pharmaceutical firm has said.

EU officials took AstraZeneca to court after it underdelivered on its promise to produce 300 million COVID vaccine doses for member states by the end of June.

They only managed to produce 100 million doses due to production constraints.

The cut in supplies delayed the EU's vaccination drive in the first part of this year, when the bloc was relying on AstraZeneca to deliver the largest volume of jabs.

It led to a bitter dispute and EU legal action to get at least 120 million doses by the end of June.

But the judge today ruled that the company should only have to deliver 80.2 million doses by 27 September, AstraZeneca said.

MarshaBradyo · 18/06/2021 14:12

Truely well spotted, do a thread we can get all the old posters together ; - all of us who hoped they wouldn’t lose

TruelyonelastSchlep · 18/06/2021 14:16

@MarshaBradyo

Truely well spotted, do a thread we can get all the old posters together ; - all of us who hoped they wouldn’t lose
😂😂😂

I would get massacred by the UK hating UK posters. Not to mention the European posters and the AZ critics from the I hate AZ threads😱

You are welcome to start a thread yourself thoughGrin

MarshaBradyo · 18/06/2021 14:17

Ha I feel the same Grin

Just spotted Easter started one on good news thread - braver than me