Data & analysis thread, started 9th April 2022

[Jenasaurus]

Welcome to another instalment of the DATA thread.

Our preference is for factual, data driven and analytical contributions.
Please try to keep discussion focused on these

UK govt press conferences slides & data www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history
UKHSA Variants of Concern Technical Briefings www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefing
UKHSA Vaccine efficacy www.gov.uk/guidance/monitoring-reports-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
UKHSA 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/

And in most myocarditis cases it's mild, not even requiring hospitalisation.

So maybe it can explained in terms of: 'even if you're the unlucky one in a million that gets a mild heart effect after the vaccine, it's still worth it to prevent a bad Covid infection which would see you ten times more likely to get heart problems' - ?

Interesting: why omicron symptoms start earlier and why five days isolation is not enough now:

twitter.com/michaelmina_lab/status/1561927371711807489?s=21&t=AVv8tVyKmycVR2k1ZcRQkw

An analysis of excess deaths:

mobile.twitter.com/jburnmurdoch/status/1562004612172873728

I was about to post the same thread. Here's a link for non twitter people:
threadreaderapp.com/thread/1562004612172873728.html

It’s a grim read isn’t it @Lonelyplanet ?

summary for anyone just glancing through, current excess deaths are convincingly down to a failure of health and social care funding over the past decade. The author accounts for heat, covid and covid related illnesses. Interestingly he points out that numbers of people attending A&E and calling for ambulances haven’t risen dramatically if at all compared to the five (I think it was) year average.

It is an excellent thread, possibly his best yet, and possibly the most worrying. It is well worth the time to read through. I found it more easy on the threadreaderapp.com link that lonely posted

This is the summary in JBM's words

(1/4)
• Excess deaths are currently over-stated in many countries due to a failure to age-standardise
• But in England there remains a significant non-Covid excess which cannot be explained by extreme heat, unlike other countries

(2/4)
• Delays in urgent & emergency care are almost certainly a large factor
• These stem from a shortage of capacity elsewhere in the hospital system
• Which in turn stems from under-investment in social care, IT and other infrastructure, plus other issues with patient flow

(3/4)
• This is not an exhaustive list, either on the global excess death picture or on the pressures facing the NHS
• Please let me know if I’ve missed anything, or if there are other areas I should be digging into
• I’m now going to lie down for approximately a week

(4/4)
• To state the obvious, in the weeks of work that went into this, I’ve not encountered any evidence for either vaccines or lockdowns playing any role in this excess mortality
• This is not to dismiss wider impact of lockdowns (cc @snj_1970), just saying no clear role here

Oh, and to pre-empt what I suspect may be an FAQ:
After searching high and low, I don’t believe US publishes sufficiently granular all-cause mort data to allow for full age-standardisation. I ideally need weekly deaths by 5-year age-group, 2015 to now. Any pointers appreciated!

• @NHSEngland & @NHSDigital, for putting out so much granular data on so many facets of the NHS. Just like with @UKHSA @ONS during pandemic, I’m astonished at how much NHS data is available to UK public. We may be in a crisis, but at least we can see what’s happening.

^^and yet still we do nothing meaningful about it (my most damning takeaway).

and a certain small group of people truly believe Liz Truss is the answer. [head hanging in despair emoji]

Thank you for keeping these stats ticking over. I want to get up to speed before autumn and winter creep up on us.

Respectfully most of that is a load of old cobblers. You seem to be blaming lockdown for covid in most cases.

The only commentators blaming lockdown for excess deaths seem to be those who are keen to blame lockdown any chance they get, like people who blame immigration for everything..

It's not logical, it's because they have a bias that skews their thinking.

I supported most of the England lockdowns @RadioRouge, you asked for reasoning so I linked you to those who argued against lockdown and summarised the position. Then you asked for how lockdown had longer term impact on deaths and so I gave them to you. That does not mean those are the biggest factors in all excess deaths now, just that they are factors. I presumed you knew covid caused deaths as you were coming at the other side of the argument. If you want a balanced view, then you ought to see all facts as important, if not then "respectfully" don't waste time asking questions.

"But in England there remains a significant non-Covid excess which cannot be explained by extreme heat, unlike other countries"

Maybe we're drastically underestimating how many people are actually in the country? Some issues with the census were raised recently including problems with the questions, and the fact that not everyone completes it. The consequences are that we don't have a clear picture of how many people are here, ages, lifestyle, health problems etc. If that information has not been accurate for several years, how could anyone have used this to accurately to predict how many people would die this year, pandemic or not? The more people there are, the more people will die of all causes surely? Just my thoughts - happy to be wrong.

Did you read this thread?

It attributes the excess deaths in the U.K. largely to under investment in the NHS.

twitter.com/jburnmurdoch/status/1562004612172873728?s=21&t=xGqpVNIBdpae5tLnAG8IOw

I always take a balanced view and I thank you for outlining the blame it on lockdown position,

But I can't characterise it as reasoning when it isn't logical and bears little relation to reality.

Yes. Both can be true.

Yes, I have a lot of respect for him and his analysis capabilities. In fairness he calls out NHS IT spend and adult social care.

I do think he missed a few things:

1. The UK has a higher level of humidity than Spain or Portugal, the rise started in mid June alongside the temperature rise. It is harder for the human body to keep cool in humidity as sweat doesn't evaporate as quickly. So we can't just take a temperature at 40 and say that's where heat causes excess death equally in all countries.
2. IT isn't an easy fix; older CT scanners for example use old Microsoft operating systems, MRI use a range of Linux - it isn't always possible to upgrade without international effort through manufacturers (who would much prefer that you just buy a new one please) and huge updates to vital, expensive and highly utilised equipment that can't afford to go offline or it increases waiting list time. It isn't as simple as even just throwing money at the problem, because NHS capacity is so poor. Slow and steady is the way of NHS local management, but the speed of technology updates outstrips their project speed. So, try national projects for speed and try to get those managers to agree you can take something offline for a project they don't personally run - no chance at all!! I have some sympathy with their fears, my local hospital lost all letter printing for many weeks due to an upgrade failure. It still needed to happen though, for security and for longer term process improvement!
3. Adult social care - he's bang on that it's causing enormous ripple issues through the NHS. He doesn't call out the disparate broken nature of the services. Again, it isn't just money but people in disparate services being able to just decide not to take the "difficult" patients. I don't know how it can be fixed, but some of the provider choice aspect really needs to change.
4. Mismanagement - it isn't always IT being slow; loads of shit managers and shit admin staff get in the way frequently too. If they were performance monitored as closely as the medical staff then perhaps HR could start getting rid of the worst of them, and getting in people who have some ideas and passion for the roles.

Just to clarify - I don't think the heat is the only reason for the excess deaths, I think there are issues with bed space as outlined, and also contributed to by covid. Age factors affect most Europeam countries, but covid disproportionately affects elderly as does heat, so it shouldn't be a simple rule-out for Spain nor Portugal either. I suspect most countries have some covid lag that will affect deaths. (They don't all have the same adult social care issues though, that is the unique UK bit.)

I thought I'd share this but think boys should have had a mention too!!

osr.statisticsauthority.gov.uk/an-army-of-armchair-epidemiologists/

ONS update:
The ONS have changed their methodology to postal rather than doorstep engagement so there is a lag of about 13 days in August rather than 9 days previously.

There are continued falls in the % of people testing positive for Covid in all 4 countries. Changes since last week:
E: 2.6% to 2.2%
W: 2.4% to 2.2%
NI: 2.0% to 1.4%
S: 3.1% to 2.6%

Decreases in all regions of England, Yorksire and Humber is the highest at 2.6.
Also falls in all age groups, except there is uncertainty in 25 to 34 group. Thankfully with schools returning soon, children are currently the lowest.

With the soaring energy costs and no cap or help for schools I do worry about whether there will be pressure to keep windows shut this winter. This won't help with ventilation and keep cases down.

Think you're right about schools @Lonelyplanet

oops dashboard did its Wednesday update and I must have got sidetracked elsewhere.

Health metric graphs for England - positive direction of travel still. Admits now slightly below that seen this time last year; number in hospital still slightly above, although regional variations on both.

Admits first

number in hospital

vents

deaths within 28 days of a positive test by date of death

finally comparator graph for the ONS survey (England only again)

Are we not now in the situation where hospitals have stopped routine testing at admission for coincident infections and hence admissions should start dropping rapidly? Or did I misread that?

(and thanks everyone, especially boys, for keeping the thread going, I have been reading!)