Data, Stats and Daily Numbers started 18th January 2022

[boys3]

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/

From Tim Spector:
"While the U.K. official figures and ⁦*@BBCNews*⁩ say cases in U.K. have plateaued- the reality is that they have been increasing for the last two weeks based on the Zoe data . Now at 176000 cases per day - thanks for logging !"

mobile.twitter.com/timspector/status/1487414741274402817

[quote lonelyplanet]From Tim Spector:
"While the U.K. official figures and ⁦**@BBCNews**⁩ say cases in U.K. have plateaued- the reality is that they have been increasing for the last two weeks based on the Zoe data . Now at 176000 cases per day - thanks for logging !"

mobile.twitter.com/timspector/status/1487414741274402817[/quote]
Do you think this is because some people LFT then don't necessarily register a positive (or confirm with a PCR)?

In which case our daily figure could be hugely inaccurate.

Do you think this is because some people LFT then don't necessarily register a positive (or confirm with a PCR)?
Yes and others don't test at all.

I think the difference between Zoe and the reported cases in the last few weeks may be partly down to reinfections - I think these are included in Zoe aren't they? We'll find out tomorrow what the reported cases look like with them added in, but my prediction is that reinfections will have been increasing steeply in they last few weeks, enough to make the current "plateau" turn into an upward trend, as seen in Zoe (and probably to be seen in the next ONS report too, given the lag there is with that one).

On the plus side, higher than we realised case rates will mean that the proportion of cases ending up in hospital and mortality rates will both become lower.

Why is this not also true for people in their teens, 20s and 30s?

It is, but the risks to those groups are higher, so there may be a different trade off.

Also the decision to vaccinate those came before the low effectiveness of the vaccine at preventing infection was known - although there were many "scientists" saying it.

It's always a trade-off, the vaccine deaths and injury are deemed to be worth it, because of the overall benefit (even though different individuals are harmed versus getting the benefit).

Israel decided second booster, but have suspended it, but Denmark still pressing on, the trade-offs are risk, there is not established unequivocal evidence, just risks vs benefits. Vaccines so far have been absolutely pushing towards uncertain benefit but low risk so jab more, now the benefit is more known, and less beneficial (you get lots of protection against serious outcomes without the booster) even the low risk might not be enough.

Especially when the vaccine hoarding is preventing vulnerable people even getting a first dose still.

Surely we should have some reasonable data to test out whether people who've caught one strain are better protected than vaccinated people against a different strain?

We do, don't we? The infection info on omicron, vaccinated people more likely to be infected than non-vaccinated people, and non-vaccinated people more likely to have been infected up until that point (both from less protection, and because one of the reasons to be vaccinated was prior infection either too recently or because the personal trade-off decision felt the vaccine less beneficial)

@sirfredfredgeorge

Surely we should have some reasonable data to test out whether people who've caught one strain are better protected than vaccinated people against a different strain?

We do, don't we? The infection info on omicron, vaccinated people more likely to be infected than non-vaccinated people, and non-vaccinated people more likely to have been infected up until that point (both from less protection, and because one of the reasons to be vaccinated was prior infection either too recently or because the personal trade-off decision felt the vaccine less beneficial)

You're right that was shown in reported cases, but that data is all very confounded by the likelihood of different test-seeking behaviour between vaccinated and unvaccinated. A common reason for adults to be unvaccinated is not considering covid to be a serious disease, and often resenting the entire response to it including testing - so they may be less likely to test (there are also some issues around population numbers making it hard to calculate accurate figures on the proportion of unvaccinated who test positive)

The ONS study or React study might be better for removing the testing differences. And I'd like to see the infection rate for people who've actually definitely had covid, rather than just assuming the unvaccinated are more likely to have had it.

Firefliess why was it not seen in delta then? I agree their could be confounding, but not to the level required to adjust the unvaccinated not testing.

And I don't really think the idea that ONS or React would be better if the argument is that unvaccinated are not co-operative with other measures, when ONS/React require loads of co-operation! You'd be less likely to invest the time in that surely?

@sirfredfredgeorge

Firefliess why was it not seen in delta then? I agree their could be confounding, but not to the level required to adjust the unvaccinated not testing.

And I don't really think the idea that ONS or React would be better if the argument is that unvaccinated are not co-operative with other measures, when ONS/React require loads of co-operation! You'd be less likely to invest the time in that surely?

I think a lot of unvaccinated people would be uncooperative with testing, but obviously not any who are involved with the ONS or React studies, which is why they would be better sources.

Vaccines worked better against Delta, as well as there being fewer previously infected people around to catch it again, so hard to separate out these two things from the data.

I accept that the difference between Zoe and reported could be re infections. I don’t buy it’s the sudden lack of testing caused by the pcr change and still think the data just isn’t there to support it, despite it being a very common theory on mumsnet and on Twitter!…ultimately the U.K. has reported over a million test results every day since 4 December…throughout October and November (when pcr confirmation was always required) it was usual to have a million tests on one or two days in any week but not every day. It’s true that there has been a fall off from the high level of testing just before Christmas but then all sources support there was a fall off in the number of actual cases ..and cases drive testing as a lot of testing is for symptoms and there are less symptomatic infections around now than then.

Ultimately to date case numbers have shown to be a reasonable guide to infection trends and followed ons etc very closely. If that has changed it is interesting to ask why but while I can but reinfection (more common with omicron than delta) I cannot buy changes in testing without much bigger falls in the numbers of tests reported, historically these remain very high!!…do people remember when the government was fudging the figures to convince us we were doing a 100,000 tests a day?!..sometimes I think people forget how far we have come!

but obviously not any who are involved with the ONS or React studies, which is why they would be better sources

But I don't buy that anyone who is not co-operative would be in those studies? Why would you co-operate with those but not testing? I'd test if I ever had symptoms (I won't bother asymptotically) but I certainly wouldn't bother with ONS or React.

@sirfred. That's my point. Those studies would only include people who're cooperative with testing. Therefore if you compare the rate of infections in them between vaccinated people and unvaccinated people who've had previous infections, it ought to be reasonably good data. But the reported cases data isn't so good because the unvaccinated might well be less likely to test (or maybe not, we don't know, but the point is we know that not everyone tests and there's good reason to think that testing behaviour might differ across the general population)

Oh I see, yes, but the problem with that is the ONS and REACT people both adjust based on assumptions of the uncooperative people, so it would need to be raw data for that analysis, and they've not published that so far, I also don't think the unvaccinated in the group would as representative - as they would by virtue of their engagement - taking other NPI's maybe, or being quite different.

ie my hypothesis is someone involved with ONS would be less likely to have tested positive before regardless of vaccination status, which would under-report re-infections. The only people I knew in the ONS study even took extra precautions over their normal just before they expected the ONS testers to arrive because of the risk of being forced to all isolate.

I'm on the ONS study and don't make any particular lifestyle changes before testing, nor do my family (which now represents three separate ONS study households).

twitter.com/john_actuary/status/1487823920736710660?s=21

Hospitalisations rising again in SE

twitter.com/tuliodna/status/1487816624497311744?s=21

Paper on a SA HIV patient, infected for long period, develops 20 mutations...

Hope they'll be lots of here after the new "inclusive of reinfections" figures are published!

@JanglyBeads "millions of cases in the UK today"

Well… without re-infections, UK has got one of the lowest transmission levels in Europe (of course, Indie Sage will never mention it). Let us see how the data changes post today.

@wintertravel1980

Well… without re-infections, UK has got one of the lowest transmission levels in Europe (of course, Indie Sage will never mention it). Let us see how the data changes post today.

Incredible. Thanks for posting, good to see

Is there a sweepstake for when the dashboard may be updated today. 20:00 is my starter. 20:00 today that is.

I presume alongside making sure everything is updating as it should, although presumably testing should have sorted that, one or more what has changed downloads may also be being provided. For those who can remember back to autumn 2020 they published tables to show the reallocation of uni student cases. Of course that is not really comparable with the scale of change coming in today.

I do wonder though what prevents other core components of the dashboard - testing, healthcare, vaccinations - being updated.

Yes I must admit I don't really see that we should have expected delays today, they've been preparing for this for at least a month.... but I guess it's to the wire every day, and this complicates things?

Or maybe they're all just watching BBC Parliament....

6.34 and no update on ETA still....
9pm?

10.30

Could be right lonely!

Still says "An estimated time will be provided when available.".... as it did at 4pm.