Data, Stats and Daily Numbers started 5 December 2021

[JanglyBeads]

Welcome to the DATA thread.

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

Our links below probably need a refresh ready for the festive season,. so all reasonable suggestions welcome.

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/

Sometimes I really hate the way newspapers word things the Guardian linked says

Scientists find ‘stealth’ version of Omicron not identifiable with PCR test

which gives the impression PCRs dont work but actually the article states

The variant is still detected as coronavirus by all the usual tests, and can be identified as the Omicron variant through genomic testing, but likely cases are not flagged up by routine PCR tests that give quicker results.

Definitely something going on in Greenwich, Lewisham and Southwark.

That's from here:

archive.uea.ac.uk/~e130/R.html

[quote manolantern]This from earlier says we have a current "worst case scenario of ~2500 cases so far and an R-value of 3.47 (CI 2.75 - 4.40)":

twitter.com/AlastairGrant4/status/1468151959957950466[/quote]
From The Telegraph

"Citing unpublished data collated by the UK Health Security Agency, Prof Alastair Grant of the University of East Anglia said omicron now made up two per cent of PCR swabs in England.

“This gives a worst case scenario of about 2,500 cases so far and an R-value of 3.47,” he said in a viral Tweet on Tuesday. “[This] would correspond to a doubling time of around 3 days.”

Re vaccine passes - the Scottish government have changed the criteria for entry to events etc and now you can show a negative test taken 24hrs before - not just your vaccine status. The flaw is that it only applies to over 18s so totally pointless when most of the cases are in kids. The only way I can see LFTs helping would be supervised on-the-door testing for everybody but that would be a practical and logistical nightmare.

as health metrics got mentioned earlier update 2020 v 2021 comparison graphs for England.

This one though is all three plus cases in a simple, so not a comparative, timeline. Primary y axis is for cases and hospitalisations and the secondary for admissions and deaths within 28 days (by date of death)

and just cases in England, seven day average as with all these graphs, before getting into health.

admissions in England for both the full year, and then just for Oct-Dec

ditto for hospitalisations

and deaths within 28 days by date of death - with the average calculated up to one week ago to account for reporting delays.

then for NHS England regions admissions for the full year

and just for Oct-Dec

full year for hospitalisations for NHS regions

and just Oct-Dec

then rates per million for admissions by region - from start October, and then from 15th November - which shows the more recent upward drift in London and the South-East

same for hospitalisations

finally something I forgot to post earlier - today's England spec date graphic

@containsnuts

Re vaccine passes - the Scottish government have changed the criteria for entry to events etc and now you can show a negative test taken 24hrs before - not just your vaccine status. The flaw is that it only applies to over 18s so totally pointless when most of the cases are in kids. The only way I can see LFTs helping would be supervised on-the-door testing for everybody but that would be a practical and logistical nightmare.

The flaw is there are no checks on the LFTs, so you just scan the QR code and mark it as negative.

A quicker test to enter places would be the answer, and if not available now this is something I think we should be working towards in the future.

Checking in

It doesn't even make much sense as an infection prevention measure - the reason to exclude the unvaccinated is that they are more likely to be infected by any covid that is at the venue, not that they are more likely to have it surely?

Latest data analysis from John Burn-Murdoch:
mobile.twitter.com/jburnmurdoch/status/1468310548609744904

During Delta we divided Covid ICU by all for-Covid admissions, but now we’re dividing Covid ICU by for-Covid and a bunch of other people who didn’t know they had Covid. Inflate denominator -> deflate severity

But if that's the case, for proportionately more people arriving with co-unknown incidental covid, that requires that the community case rates of unknown covid must be proportionately much higher - otherwise the same random sampling of unrelated issues would've turned up last time. So is this analysis correct? (of course it suggests that the case rates need to be even higher and the detection rates are lower in the community)

First, if a chunk of Covid+ patients are not in for Covid and would have been admitted anyway, then they are not adding to hospital pressure. Say 70% are admitted for Covid, creating additional load, but maybe 30% are not

This assumes the coincidental covid does nothing to impact their treatment - this is surely not sustainable for all of the cases, even if it is some, and even those with simply a broken arm or similar would still need different treatment due to hot/cold ward issues.

Looks like the update to allow people in England to have their booster sooner has hit the website, it allowed me to bring my appointment forward by a week. Not sure if it has opened to under 40s yet.

Thanks @kittykarate, I've been able to bring forward DH's.

@sirfredfredgeorge

It doesn't even make much sense as an infection prevention measure - the reason to exclude the unvaccinated is that they are more likely to be infected by any covid that is at the venue, not that they are more likely to have it surely?

That's funny you've assumed that - I'd assumed precisely the opposite! That vaccine passports are to ensure that people with covid are less likely to enter an event and so everyone is safer. If it were about the protection of the individual it would make a lot more sense to ban everyone over 60 from indoor gatherings, as they are many, many times more likely to get really ill than 20 somethings, jabbed or not jabbed.

I could see an argument for vaccine passports if the vaccine really did make people very, very unlikely to be contagious, as it could benefit the small number of people who can't have the vaccine or with weak immune systems who need to be kept safe. However I don't think the data support that being the case, even with Delta - I know huge numbers of people who've caught covid post vaccination, and the HSA data also show most (reported) cases as being among the vaccinated - they're only a bit less likely to be infected and infectious than unvaccinated people. And it's an even weaker argument with Omicron.