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/

It might be useful for you to look up some articles with actual signatories if you want to understand the thinking, the declaration itself has names: gbdeclaration.org/. It was after the first wave, which is where many excess deaths had already occurred and included a hope to rely on vaccines, not just infections. For example, Sunetra Gupta in the UK has said her numbers for expected deaths were slightly low, and commented that the reinfection timeframe is much shorter than she had expected (data: she had expected IFR 5 in 10,000, 3-6 months instead of 2 years). She still believes that the negative impact of general lockdowns should be and should have been taken into greater account; the financial, social and practical impacts for different communities. The negative impact on poor people in Africa and parts of Asia such as India can be extreme where there is no financial buffer. See here for an example article with her views: unherd.com/thepost/sunetra-gupta-how-have-my-covid-hypotheses-held-up/.

There are several strands to unpick - Was lockdown ever a useful tool? Was shielding ever a more useful tool? To what extent have lockdowns impacted on cost of living now? What's the actual final excess death comparison between policies and what measures should be used for that? How to separate the excess death impacts of older populations, poverty, poor healthcare, varying policies over time, vaccine rates etc?

For figures, I find the economist to be the most useful in identifying and comparing excess deaths, see this article: www.economist.com/graphic-detail/coronavirus-excess-deaths-estimates. The difficulty however is that you could pick and choose countries to support any argument by leaving out critical factors. Australia and NZ = lockdown works, but only possible due to being affected so much later. Sweden vs Spain = better not to lockdown, but lower population density in Sweden had a huge effect. Peru = random draconian rules without support really don't work, Brazil = deny it exists doesn't work, Russia = deny anyone actually died doesn't work. Looking globally, some level of lockdown and some level of shielding certainly seem to have been useful tools, but only where countries could afford them or for managing peak healthcare demands where healthcare availability was literally collapsing. Comparing deaths across Europe quickly brings a need to balance figures for age of population and population density; after that it isn't just spend on healthcare but sophistication of healthcare that appears to have had the highest impact. The actual difference between excess death rates of the various European countries doesn't appear to reflect who had the most draconian lockdowns. We have not yet seen the impact of the cost of living crisis/ depression and there will undoubtedly be detailed assessment of the extent to which lockdowns created it.

But surely you will not know the overall impact for many years?

the current excess death rate is worrying.

@BeethovenNinth the GBD didn't model the effect but Kit Yates et al have here, showing how the plan would never have been workable:

https://journals.plos.org/globalpublichealth/article?id=10.1371/journal.pgph.0000298

Here's his Twitter thread on it:

https://twitter.com/kityatessmaths/status/1519013611661926400?s=21&t=Jseg2fRu-QyC2pRTBU3jA

Sorry that should have been to @RadioRouge

Impact of what? Great Barrington was stating that lockdown is damaging, but recommended distancing, shielding etc. Have you changed topic?

Excess deaths compared to what other possible outcome? Look at the figures for excess deaths, they are so much lower than the first two big waves. If you're comparing with other countries the rates are similar to say Germany this wave, half Australia and double USA - but Britain certainly isn't an outlier. We can't just wish away covid, so what are you suggesting that you think should be happening here that isn't - another lockdown?

Latest ONS infection survey released after the gap last week.

www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/coronaviruscovid19infectionsurveypilot/19august2022

The percentage of people testing positive for coronavirus (COVID-19) continued to decrease in England, Wales and Scotland; and decreased in Northern Ireland.

In England, the estimated number of people testing positive for COVID-19 was 1,432,900 (95% credible interval: 1,339,600 to 1,524,800), equating to 2.63% of the population, or around 1 in 40 people.

In Wales, the estimated number of people testing positive for COVID-19 was 72,600 (95% credible interval: 54,800 to 93,000), equating to 2.39% of the population, or around 1 in 40 people.

In Northern Ireland, the estimated number of people testing positive for COVID-19 was 36,600 (95% credible interval: 25,100 to 50,200), equating to 2.00% of the population, or 1 in 50 people.

In Scotland, the estimated number of people testing positive for COVID-19 was 164,100 (95% credible interval: 137,400 to 193,700), equating to 3.12% of the population, or around 1 in 30 people.

Graph is just England and based on publication date - to avoid a gap on the graph figure added for 12th August when there was no report

The excess death rate is high, but I wonder how many are due to previous infection of covid.

For example on the site I'm looking at with English excess mortality, one of the higher excess death is for: ischemic heart disease (the term given to heart problems caused by narrowed heart arteries-the most common reason being a blood clot). In fact there's only 14 weeks since the end of March 2020 where that hasn't been had excess deaths.
So what needs to be looked at here is whether the people in these categories have had a previous covid infection, and if they have avoided or been refused medical care.

To counter that cancer has 55 weeks, so approaching half where there haven't been excess deaths and, if you take out the first wave, a good number of the excess death weeks are only small numbers.
Now this is one which does give the argument that will increase as obviously it takes time, so this is something you're potentially looking at 5, even 10 years later before you can see how big a risk factor delaying may turn out to be.

Diabetes, again a known risk factor with covid, only has 5 weeks in that time where they aren't into excess deaths, and only one of those is over 100 people, whereas several of the excess deaths are over 1000, and one is over 2000.

So what I'm saying is that you can't look at the excess deaths now and necessarily say that means lockdown = bad. It looks to me that there would be a lot more unpicking of the figures before that is a definite conclusion.

what I'm saying is that you can't look at the excess deaths now and necessarily say that means lockdown = bad
I was just answering a question, I hadn't at any point given an opinion that in all cases "lockdown = bad". For my opinion, lockdown has both positives and negatives, while lockdown forever is economically and practically impossible; possibly there are charts somewhere to explain both points, but I think they are obvious enough that we can agree. There are situations where lockdown appears to be a useful tool, and the start of the pandemic plus Kent (now Alpha) wave were both fairly clear cut. Stopping travel, social distancing and ventilation appear to have the highest benefits in reducing transmission, particularly for those who are unable to lock themselves away due to hospital appointments etc. Lockdown as such was more incremental on top. Then there are times when the downsides of lockdown outweigh the benefits; no schools, loss of work, low tax revenue with higher government expenses, restrictions on hospital or care home visitors, restrictions on local in-person support services, restrictions on funerals, missed milestones and activities, etc etc etc.

There are many possible actions to reduce deaths from covid (more vaccines, different vaccines, more testing, bringing back distancing etc) - but whatever those are, even lockdown, there will still be some deaths from covid. It comes down to balance; how much economic cost (cost of restrictions, vaccines, tests etc) and social cost (damaged education, stress etc) do we take for how many excess deaths.

If you want to advocate for more lockdowns then ok, make the case; but I have questions. Who is deciding the new excess deaths target, how long are we locking down for, how do we know we've met the new target if you think metrics don't work to measure the old figures, in what countries should this happen, who is paying for this, and how will government get the population to comply?

one of the higher excess death is for: ischemic heart disease (the term given to heart problems caused by narrowed heart arteries-the most common reason being a blood clot)
Undoubtedly there will be some of these that are directly due to covid, though I don't know how they can be proven. The indirect ones due to healthcare overwhelm and procedures are interesting too: ambulances slow to arrive, delays in accessing consultants, GP appointment not in person for those who need it, delays in heart bypass operations, issues with getting hold of doctors in care homes, people delaying seeing doctors due to covid exposure fear etc. I have no idea how the figures can be unpicked into different categories without so many assumptions they might as well be opinion. I presume someone is working on that.

@MRex

I'm not trying to make a case for more lockdowns, and I'm not sure why you got that idea.

I'm saying that the current excess death figure would need to be looked at in a lot more depth before condemning the lockdowns we already have had.

It may be that if we hadn't locked down at all that we wouldn't be looking at excess deaths now, or we could be looking at higher numbers of excess deaths now. We can't tell that just by the excess death numbers. It's something that needs to be looked into by someone with far greater knowledge of the ins and outs of the situations.
Keeping an open mind is what I would advocate for. And, as I said, I don't think we'll know the full picture for 5-10years or longer. But I hope it will be investigated thoroughly, and not by someone with a political agenda of proving they were right, whichever side of the debate. In that way we will be better prepared if the situation arises again. Which obviously we all hope that it won't.

I understand how ambulances arriving too late or having to sit in hospital car parks is leading to people dying who shouldn't be.

I understand how the staffing shortages and staff burnout in the NHS is leading to poorer care and things being missed, leading to more deaths.

I understand how waiting lists at an all time high because hospitals have had to shift resources to dealing with covid is causing deaths through treatments and operations not being offered on time.

I understand how covid has had long term effects on people's organs and cardiovascular systems which is leading to more covid-related deaths not directly attributed to covid.

How is a lockdown from years ago killing people now?

Why was there a gap in ons reports?

@MargaretThursday - yes, it would be good for it to be looked into, unpicking the impacts of policy differences between waves, population density, age of population, vaccines etc will be very hard to do.

How is a lockdown from years ago killing people now?

1. Delays in accessing preventative medical care, which can shorten lifespans. It's the waiting lists you mention, as well as for example; cancer treatment being requested late, doctors not visiting care homes and so not seeing required updates to medication, people delaying going to GPs (say they don't go for pain and have a mild heart attack, even if recovered that weakens the heart forever). I know someone personally who delayed going to the optician because of a new wave (we didn't know the issue at the time), and that delayed starting treatment so the eye has more permanent damage than if they had gone in earlier. It's not life threatening in that case, but it is life limiting.
2. Impact of lockdown itself on health; more sedentary lifestyle making people fatter and therefore healthier, certain drugs not available due to reduced factory outputs globally (some alternatives might cause issues for some people), failed businesses (stress for staff and owners), reduction in community nursing and social care visits increasing risk for those in need.
3. Cost of living; it's likely that inflation will lead to a global recession in the best case, a depression is more likely. The reduced output from lockdown across so many industries coupled with increased government spending leaves a deficit to be paid for. Even without lockdown in one country, it's a global economy so for example; no mining in our country leads to no raw material for chips in another leads to stalling computer manufacture, no forestry in one country leads to furniture shortage in another. Russia attacking Ukraine has exacerbated it all, perhaps they thought other countries would just let them out of self interest because it was so clearly going to be another economic shock. Recessions lead to higher child mortality rates and for adults lead to significantly higher death rates for up to 10 year following. Here's an article with some research: www.bis.org/publ/work910.htm.

Sorry but I disagree that lockdown is the primary reason for long waiting lists - rather the reverse - high sickness rates, over full hospitals are at least partly result of covid infection that causes longer waiting lists and other hospital problem - which is saying that without lockdown waiting lists could be worse

there are going to be a lot of factors involved regarding waiting lists/treatments/ambulance times, but imho, the largest factor is that this government has basically declared covid as ‘over’ without tackling the fact that covid can and does continue to cause significant immediate and long term health issues and essentially requires it’s own speciality and associated resources. ‘Living with covid’ never included the conversation about how it would be accommodated within existing framework.

waiting times were awful before covid and now we have a new disease that will always require a share of resources. We didn’t have the staff or resource before covid and now it’s exacerbated. I can’t say whether the government can’t (probably as the staff required just don’t exist even with a bottomless wallet) or won’t address it but they do appear to be desperate not to admit it.

Here is Stuart MacDonald's thread on the DT headline, including actuarial analysis:

twitter.com/actuarybyday/status/1560527181637472256?s=21&t=nhdSvVWNL3NPUVkAO3n8jA

I'll post his summary of likely causes of excess deaths as a screen shot.

He says that analysis is ongoing, and important.

The break in ONS figures was because of a move to the new data collection system.

Here we are

Interesting: Eric Topol says we need to (and could) achieve respiratory mucosa immunity via nasal vaccines:

twitter.com/erictopol/status/1560709149335650304?s=21&t=nhdSvVWNL3NPUVkAO3n8jA

@JanglyBeads

I'd had a very similar thought process to that Stuart McD's thread, so I found that an interesting link, thanks for posting it.

I also found Stuart McDonald's thread a much better analysis of the death situation than the DT article.

Some of the comments on the DT article inevitably point to the vaccine as another factor.

presumably this has been thoroughly debunked? If the excess is largely cardiovascular events presumably they can see that it’s not an impact of the vaccine itself?

it would be a real shame if people were put off having their boosters of this wasn’t properly explained

Throughly debunked.

Much more detail on excess deaths caused by ambulance wait times. Shocking:

twitter.com/shaunlintern/status/1561260078984052737?s=21&t=VW5FebzYR4JAwhR-xAWwRA

7/9

"But transparency over coroner deaths is lacking - The Sunday Times has learned publication of 'prevention of future death' reports has been quietly suspended by @MoJGovUK since May. A new website is blamed but publication is not expected to start til later in the autumn."

www.judiciary.uk/related-offices-and-bodies/office-chief-coroner/https-www-judiciary-uk-subject-community-health-care-and-emergency-services-related-deaths/

Thanks Jangly! Do you know where I can find that debunking. Interesting debate with my elderly mum today and want to reassure her.

https://www.bhf.org.uk/informationsupport/heart-matters-magazine/news/coronavirus-and-your-health/coronavirus-vaccine-your-questions-answered/covid-19-vaccines-and-myocarditis-should-you-be-worried

The risk exists, but is tiny, especially for older people - and the same as with having a flu jab, which people in general don't fear.

A scientific study here

twitter.com/chrischirp/status/1470845540548104194?s=21&t=nDV4Me60r5_9-3UvNbTpHg

From that Twitter thread

"there would be an extra 1-2 cases of myocarditis per million patients due to the vaccines and
6 per million due to Covid infection within 28 days. After 28 days an extra 40 per million in Covid infection group.

Plus >incidence of arrhythmias & pericarditis"