Data, Stats, Daily Numbers started 22nd October 2021

[boys3]

This is the DATA thread.

Our preference is for factual, data driven and analytical contributions.

Please try to keep discussion focused on these.

The links below cover a range of data sources. Ideas for additions or deletions always welcome. PHE probably should be referenced at UKHSA.

UK govt press conferences slides & data www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history
PHE Variants of Concern Technical Briefings www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201
PHE Vaccine efficacy www.gov.uk/government/publications/phe-monitoring-of-the-effectiveness-of-covid-19-vaccination
SAGE : Minutes and Models www.gov.uk/government/collections/scientific-evidence-supporting-the-government-response-to-coronavirus-covid-19
Data Dashboard coronavirus.data.gov.uk/ includes R estimates
PHE Weekly Flu & Covid Surveiilance Reports 2021-22 Season www.gov.uk/government/statistics/national-flu-and-covid-19-surveillance-reports-2021-to-2022-season
Dashboard Vaccine Map to MSOA level coronavirus.data.gov.uk/details/interactive-map/vaccinations
Covid 19 Genomics www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
Sanger Genome Maps & Data covid19.sanger.ac.uk/lineages/raw
UCL Virus Watch ucl-virus-watch.net/
NHS Vaccination data www.england.nhs.uk/statistics/statistical-work-areas/covid-19-vaccinations/
Sewage www.gov.uk/government/publications/wastewater-testing-coverage-data-for-19-may-2021-emhp-programme/wastewater-testing-coverage-data-for-the-environmental-monitoring-for-health-protection-emhp-programme.
Sewage reports www.gov.uk/government/publications/monitoring-of-sars-cov-2-rna-in-england-wastewater-monthly-statistics-june-2021
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 MSOA Map English deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/

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/

⏭ Our STUDIES Corner ⏮ www.mumsnet.com/Talk/coronavirus/3869571-Studies-corner?msgid=99913434

49,298

Last Friday, that is.

@NoisyBrain ok thank you - technically still going down then!

Down 12.7% last 7 days

Looks like the immensa scandal has also caused a rise in hospital admissions.
mobile.twitter.com/VictimOfMaths/status/1454094507738271753

@lonelyplanet There's an obvious correlation that the areas with most positive people would also be most impacted (as the problem is false negatives) and also have more hospitalisation ('cos more people have it)

They've identified "areas most affected, by looking purely at cases missed and comparing it to others in the southwest, but if those others in the southwest were also using the same lab (which I understood they were?) then they genuinely had different patterns of covid during this period, otherwise they would also have been highly affected.

We need to compare with similar areas with and without the testing failures, we cannot identify causation in that data.

@sirfredfredgeorge

But what is happening? You say the ONS is accurate, then R is 1.1, but if R is 1.1 then there are huge mitigations going on, R of delta covid without mitigations is estimated at over 8, but even if it's 3 the mitigations are having a massive impact.

I'd imagine the "mitigations" are mostly that those who have been behaving as though Covid is over (or have been forced to by virtue of their jobs) have largely been infected over the past year and so have substantial immunity, whilst those who remain cautious aren't giving themselves the same opportunities to catch it.

@ThereIsAGreenHillFarAway

Snapshot of figures from Worldometer yesterday showing reported +ve cases / deaths

UK - 39,842 / 165 = 1 death per 241 +ve cases
Germany - 26,610 / 122 = 1 death per 218 +ve cases
France - 6,461 / 33 = 1 death per 196 +ve cases
Italy - 4,866 / 50 = 1 death per 97 +ve cases
Spain - 2,212 / 33 = 1 death per 67 +ve cases

Obviously i'd rather we had a much lower number of deaths, but other countries +ve rates look very low by comparison to reported deaths so is it possible there's a more general European problem with PCRs giving false negatives?

It’s because the uk is testing way more than any other nation.

I agree that more cases lead to more hospitalisations. The issue is that the 13 areas involved have sky high rates because of the failures. People assuming they were negative continued their daily business and infected many others. This caused the rise in hospitalisations. Other areas in the SW (not the 13 that were affected) didn't have this happen so people isolated and cases didn't rise in the same way. It is perfectly reasonable to compare these areas as they both had similar levels prior the the cock up.

As the thread stated, "it isn't definitive proof of causality", however it goes on to say, " It certainly looks to me that the data supports the idea that incorrectly telling lots of people with COVID in these Local Authorities has led to more people getting COVID, and more people being hospitalised as a result."

Then to sum up, "This also seems like pretty basic common sense, but apparently common sense is in short supply these days."

Other areas in the SW (not the 13 that were affected) didn't have this happen so people isolated and cases didn't rise in the same way

They have not published the areas where the tests were being sent to the bad lab though, we don't know exactly which areas it was do we? Only those which had a high number of failed tests - you're assuming that the other "south west" councils went to a different lab, but there's no evidence of that, just that they didn't have a large number of failed tests - but they wouldn't've if they didn't have much covid there to detect.

@Bizawit - that makes no sense. A higher percentage of cases discovered would lead to lower deaths per case.

I tried to find the breakdown of the 43,000 false negative PCRs by local authority but I was unsuccessful.

Intuitively, of course, it makes sense that missed positive cases increased transmission but it is also reasonable to acknowledge that the lower level of acquired immunity in many of the boroughs of SW/WM and Wales was the perfect ground for the virus to spread.

False negatives in Barking and Dagenham or Blackburn would have had a very different impact.

[quote Stilltalkstotrees]@Bizawit - that makes no sense. A higher percentage of cases discovered would lead to lower deaths per case.[/quote]
Yes which is what the data greenhill posted is showing? Uk = 1 death/ 241 cases, which is the lowest deaths per case ratio? Spain having the highest death ratio at 1/67? Or am I having a brain freeze?

No, you are absolutely right, Bizawit.

@wintertravel1980 thank you 😅 thought I was going mad there for a second.

The problem with the case/death data (not that I don't think the general thrust is true, the UK almost certainly detects a higher proportion of cases) is the timing difference in deaths and cases, we need to find some way to account for the lag in deaths in the comparisons. Perhaps looking at totals over a longer time period rather than snapshots? (cases over the previous 60 days ignoring the last 20 and deaths in the last 40 say?) as daily rates would over state cases in a country undergoing a significant rise in cases as the deaths wouldn't've happened yet.

Where the detected cases matter too, if a country rarely tests under 18's, then they'll be completely different death/case rates than one which mass tests them.

lower level of acquired immunity in many of the boroughs of SW/WM and Wales was the perfect ground for the virus to spread.
Do you have data to back this compared with similar areas not using the Immensa lab?

[quote Bizawit]@wintertravel1980 thank you 😅 thought I was going mad there for a second.[/quote]
I wondered too as it made sense to me

Do you have data to back this compared with similar areas not using the Immensa lab?

Well… both of my statements are based purely on intuition since we do not have secondary attack rate (SAR) estimates at the local authority level. However, at the regional level, SW has always had the lowest SAR in the country according to MRC-BSU modelling.

The closest comparison may be Trafford, an affluent area that was hit by Covid in the past but nowhere as hard as its more deprived neighbours. It had a major Covid wave in the middle of October (1,000+ cases/100,000 people over 7 days) without any tailwinds from Immensa failings.

FWIW, of course, I think Immensa fiasco accelerated the spread but I do not think it was the only factor. As we know, “for every complex problem there is an answer that is clear, simple, and wrong.”

@wintertravel1980

Do you have data to back this compared with similar areas not using the Immensa lab?

Well… both of my statements are based purely on intuition since we do not have secondary attack rate (SAR) estimates at the local authority level. However, at the regional level, SW has always had the lowest SAR in the country according to MRC-BSU modelling.

The closest comparison may be Trafford, an affluent area that was hit by Covid in the past but nowhere as hard as its more deprived neighbours. It had a major Covid wave in the middle of October (1,000+ cases/100,000 people over 7 days) without any tailwinds from Immensa failings.

To say Trafford is more affluent than its neighbours is not completely accurate. There are some parts of South Manchester that are more affluent than parts of Trafford and even some parts of Salford that are more affluent than the poorest parts of Trafford. It is mixed really, though on average it is more affluent than Salford I guess. At one time last year it was the exception to the rapidly rising rates in Greater Manchester but iirc it then got a lot higher in the GM "league table" even last year. I have no idea why it got so high more recently though but the likes of Stroud and Cheltenham which have been badly affected by the PCR problem are now massively higher than Trafford at its peak

Are there any studies for the amount of false positives on lateral flow tests? I ask because one of my DC’s has had three strong positives on a lateral flow but his PCR was negative. We’ve done another PCR and are awaiting the result but a relative is telling me that they were false positives as “40 per cent of positives on lateral flow are false”.

A false positive in my DC’s case seems unlikely given that there were seven cases in their class last week, they have a dry cough and have said that their chest hurts and I have tested positive on a PCR myself this week. However, I would be interested in seeing any studies/data that look at false positives on lateral flows.

Noted on Trafford’s mixed demographics. I have always thought of Trafford as an “affluent area” but I accept I can be completely wrong (Londoners often are when it comes to the rest of the country).

Re: infection levels - Trafford would be more comparable to places like Bath that had Covid spikes in the past (up to 500/100,000 prevalence) but never went “really high” (over 800/100,000 threshold). Delta wave in both LAs peaked at 1,000/100,000.

Covid historic prevalence in places like Cheltenham or Strout was particularly low (under 400/100,000 in their highest week). As a result, they got hit hard and fast, similarly to NE earlier this summer and climbed all the way to 1,500/100,000. Immensa failures clearly added fuel to fire.

… in places like Cheltenham or Stroud…, sorry.

Bunsy some studies had 40% of LFD negatives as false, I think your relative has misremembered. It’s about .5% of positives which are false.