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/

I thought, only a few days ago, Javid said the rates were twenty times what the confirmed figures suggest?

Yes, that was for Omicron transmissions due to delays in genomic sequencing, i.e. it was a very different estimate.

Re: Javid’s comments - I have noticed he is actually good with numbers but he clearly picks and chooses which data to quote. The “200,000 infections per day” is probably the very upper end of the MRC-BSU estimate that might be very wide (e.g. 120,000-200,000 or something like this).

Doubling every two days is partially based on the case dynamics in the 20-29 age group. Here is the latest graph from Alex Selby.

South Africa’s data is very noisy and there was a large number of aged cases added yesterday but Gauteng and specifically Tshwane might be slowing down (based on adjusted data):

twitter.com/lrossouw/status/1470290407946956804

@wintertravel1980 The Guardian asked for clarification regarding the 200,000 daily infections figure, and apparently had a response indicating that 200,000 refers to the number of people believed to be currently infected with Omicron.

It's been picked up by French news sites though as 200,000 daily Omicron infections.

lonely This thread explains how it is currently 1.7. However he is often bleak so happy for it to be disputed

Thanks for that thread, if that thread is correct then the number of (supposed) cases at the beginning of that time must've been way less than was claimed at the time, and that makes the stats just about fit, but I still struggle to square it with only 40% of the cases in London (only a few other MSOA's are growing at any rate - Coventry being the main one, but not enough to make a huge portion of the out of London omicron cases) It will all become clear in a few days though as it won't be able to hide any longer.

South Africa’s data is very noisy and there was a large number of aged cases added yesterday but Gauteng and specifically Tshwane might be slowing down (based on adjusted data)

The data drop doesn't seem to have reduced the slowdown estimates in Gauteng, which is good, although western cape was revised upwards - but it had seemed even lower than reasonable.

Zoe estimating 1,136,247 people currently infected so 20% of that is approximately 200,000.

lonely This thread explains how it is currently 1.7. However he is often bleak so happy for it to be disputed

Thanks for that thread, if that thread is correct then the number of (supposed) cases at the beginning of that time must've been way less than was claimed at the time, and that makes the stats just about fit, but I still struggle to square it with only 40% of the cases in London (only a few other MSOA's are growing at any rate - Coventry being the main one, but not enough to make a huge portion of the out of London omicron cases) It will all become clear in a few days though as it won't be able to hide any longer.

South Africa’s data is very noisy and there was a large number of aged cases added yesterday but Gauteng and specifically Tshwane might be slowing down (based on adjusted data)

The data drop doesn't seem to have reduced the slowdown estimates in Gauteng, which is good, although western cape was revised upwards - but it had seemed even lower than reasonable.

With figures like that and a short doubling time how swift will this be?

When have we all had it by

@MarshaBradyo

With figures like that and a short doubling time how swift will this be?

When have we all had it by

In a purely mathematical exponential model we will all have it by the end of January. However, that is not quite how it works and it will flatten out.

Confirmed Omicron cases in England and Scotland - daily and cumulative -from the UKHSE daily tweets.

some of the regional figures from the Sanger date updated today - with the caveat that its latest week is that to 4th December.

These are London Inner and Outer boroughs

East and South East

East Midlands, North West , and Yorks & Humber

Apologies if this is a stupid question but if the doubling time is 1.7 days, is there ny point in pushing boosters hard? It takes 2 weeks for the effect of the booster to kick in for any individual. Isn't the wave moving so fast that it will have gone through the population before boosters given next week have done much of anything at all?

Happy to be told I'm wrong!

@Motorina

Apologies if this is a stupid question but if the doubling time is 1.7 days, is there ny point in pushing boosters hard? It takes 2 weeks for the effect of the booster to kick in for any individual. Isn't the wave moving so fast that it will have gone through the population before boosters given next week have done much of anything at all?

Happy to be told I'm wrong!

I think it's more like one week for boosters to kick in. So the ones done this week may be really helpful. January ones, less so.

Yes, the PHE/UKHSA research suggests boosters become effective in 7 days.

The period may hypothetically be slightly shorter for younger people with stronger immune response.

London on 3 December (specimen date) was 5,000. A week later (10th, almost complete) it's 10,000. If Omicron was 40% of those that would be 4,000. Back on the 3rd Omicron would have been around 350 of the 5000 daily cases (3 and a bit doubling times before the 10th). So the case rate growth in London looks more than high enough for Omicron to be doubling every 2 days to me. If it goes on doing that while Delta is roughly flat, case rates by 17th December specimen date will be around 50,000 per day, which is like nothing we've seen before. And most of those people will be contacting it over the next 2-3 days. Whether cases will be mild enough to enable hospitals to cope, it's hard to know. But I'm struggling to see how society will function with that many people off sick at once.

And for the national (England) picture, see twitter.com/AlastairGrant4/status/1470491762296827909?t=rfhcxUWDX4ZyidwlUpOh4Q&s=19
Suggests that Omicron was 19% of cases with specimen date of 10 December. So that's 19% of the 39,000 cases in England that date - around 8,000 cases. That data shows doubling also in around 2 days, which would make Omicron cases around 90,000 per day by 17th - plus the 30,000 odd Delta cases.

Back on the 3rd Omicron would have been around 350 of the 5000 daily cases (3 and a bit doubling times before the 10th). So the case rate growth in London looks more than high enough for Omicron to be doubling every 2 days to me

Surely that requires the 8th to be under 7500 (as that was more than one doubling change from your 5000 total omnicron cases) but it was well over 9000? And we have similar problems on the previous doublings, delta can't both have been flat throughout to hit the intermediate days, but needs to be flat to hit the last day.

@sirfred - But we know there's always day to day fluctuations between days of the week don't we?

@Firefliess I agree it’s hard to see how society will function if everyone is sick, but also worth remembering a large proportion of people are only mildly poorly or completely asymptomatic. They would not be able to work due to isolation rules but hypothetically if they got it over the biggest uk holiday of the year perhaps we would enter next year stronger?

How stronger: at least 1% of those hospitalised; long covid affecting ?3% or similar: a currently unknowable number dead.

And reinfection much more likely than with previous variants.

I'm just popping on to say that there must surely be a lag of more than 2 or3 days between people catching covid and getting a ppositive result .

Anecdotally ,in the young ( 20s ) I know they often know when they were in contact ( their mate with whom they socialised at a particular event tells them of a positive ) but daily LFT's don't turn positive for 5 or 6 days later .Then add on 2 days for PCR .And longer for testing for omricon .

And in London ,where I live ,I think an awful lot are not reported .

Remember a couple of weeks ago, when some of us were saying to look for the nonverbal signals of those in leadership?

Keir Starmer has broadcast to the nation tonight, talking about our patriotic duty to get boosted.

Embedded in this article
www.bbc.co.uk/news/uk-59639007

The big questions are around % of hospitalisations / long Covid numbers and deaths.

The latest report from Denmark does not look great (hospitalisations are estimated at 1%) but there is the perennial question of “with Covid” vs “due to Covid”.

I have always thought that distinction does not really matter because the percentage of hospitalisations “with Covid” remained constant (at around 25%) so the hospitalisation trends were still useful and relevant data points.

However - if SA data is right and hospitalisations “with Covid” may indeed reach 70%, we should re-visit our assumptions and models.

I guess we will know soon.

Presumably the "with covid" or "of covid" question matters more when you have very fast exponential growth and a large percentage of the population infected. It would look like covid hospital admissions are going up sharply even if no one was actually being hospitalised "of covid" because a higher percentage of the population and therefore of hospital admissions is infected each day. Same for deaths given how we record them.