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/

But thats the point

We were told x would happen, we did nothing and x didn't happen.

Hence why when we are now told that x will happen we are more sceptical.

So how does UKHSA believe that cases are 20times the detected, what's the mechanism for a detection rate in Omicron that is orders of magnitude less than Delta or Alpha, and given the time period required to get to 10,000 cases, how are there no hospital detected cases (I believe hospital positives are sequenced at a higher rate than community?) How is it spreading only in communities who are doing no LFD's etc. ? And how did it get to 10,000, the doubling time and the "first here" time in the consensus statement are incompatible unless it was "first here" by hundreds of cases at the same time. (This would require it to be extremely common outside the UK and for the travel pcr to fail to catch it in all the cases)

And why if they have that data, has it only been provided to the Guardian, rather than mentioned in their briefing.

Maybe the 10,000 is true, but it does match any of the other data they chose to publish....

does NOT

SAGE minutes from Tuesday

www.gov.uk/government/publications/sage-98-minutes-coronavirus-covid-19-response-7-december-2021/sage-98-minutes-coronavirus-covid-19-response-7-december-2021

Done nothing?

Think I may have lost the plot but things are always changing

Although it's observation not data you see behaviour change at the first reports of anything

and the Telegraph take (with some good graphs)

www.telegraph.co.uk/news/2021/12/09/charts-ministers-think-could-hit-million-omicron-cases-day-christmas/

Yeah I only didn’t post the Telegraph article as it’s paywalled.

Excellent graphs, I agree!

@bordermidgebite

Done nothing?

Think I may have lost the plot but things are always changing

Although it's observation not data you see behaviour change at the first reports of anything

But we didn't do anything when the claims were made.

We were told when we removed restrictions that cases would rise to 100k a day and they didn't. Various models were produced showing various scenarios with cases and admissions which were wildy over stating what would happen.

Do you really not remember this for example?

This is my whole point, a lot of people no longer believe these predictions as they've been wrong in the past.

[quote herecomesthsun]and the Telegraph take (with some good graphs)

www.telegraph.co.uk/news/2021/12/09/charts-ministers-think-could-hit-million-omicron-cases-day-christmas/[/quote]
I'm just trying to work this out in my head.

Taking SA as a yardstick, if they are seeing a massive increase in detected cases, how many actual cases do they have - still 20x as estimated for the UK?

So if we reach 1 million cases a day, in just over a 2 month period every single person in the UK will either have it or have just recovered from it.

Sounds like it will be fairly swift

Depending on what happens around it

Boosters a priority then it’s ramping up fast

We confirmed about 250 cases of Omicron today, presumably via sequencing so tests from around 8 data ago. We sequence around a third of PCRs and have previously estimated that around half of all infections are detected. So that would suggest that 8 days ago there were in fact around 1500 new Omicron infections. With a doubling time of 2-3 days that would give around 12-24,000 infections beginning today, but if incubation and time-to-get-tested period is about 5 days, that could give two further doublings - which would be up to 100,000 people catching it today Could that be how they've reached their 100,000 figure? A lot of guesswork in there though.

@amicissimma

So if we reach 1 million cases a day, in just over a 2 month period every single person in the UK will either have it or have just recovered from it.

Not quite, if it's doubling in 2-3 days. But there will reach a point not long after when that would be the case. I think this may be the first wave we see in the UK where we get to see how it reaches a natural end, having run out of people to infect and dying down naturally. Previously, the two big waves were brought down via lockdowns.

So that would suggest that 8 days ago there were in fact around 1500 new Omicron infections. With a doubling time of 2-3 days that would give around 12-24,000 infections beginning today

But the problem with that, is Delta would've needed a precipitous drop in infectiousness to maintain the R=~1 that overall the country has had during that time. And it would also be seen in regional changes - the places where delta was rampant would've needed to drop precipitously previously (R

siralfred if you have the time could you expand on your post above ?
I'm having trouble understanding ,no certainty that I'll understand even with further explanation so feel free to scroll on by

[quote sirfredfredgeorge]So that would suggest that 8 days ago there were in fact around 1500 new Omicron infections. With a doubling time of 2-3 days that would give around 12-24,000 infections beginning today

But the problem with that, is Delta would've needed a precipitous drop in infectiousness to maintain the R=~1 that overall the country has had during that time. And it would also be seen in regional changes - the places where delta was rampant would've needed to drop precipitously previously (R

Here's the link to the S gene dropout twitter.com/theosanderson/status/1468657703056723971?t=YUZDL2UCUpUXaoL2Wh0z6A&s=19
Note the log scale. The latest dot is at 8% which is easier to see on the non log scale, but I can't seem to find a link to that any more

peridito R in the UK has been broadly 1 for months now, some times a bit above, some times a bit below, but basically 1, and it's all been delta where the next generation appears 4 days later.

Omicron is said to have a large advantage - increasing R, and a shorter time to infection. So if Omicron is present in significant numbers, then the only way that the data could've carried on with R basically 1 and same generational growth is if something inexplicable happened to delta to reduce it.

Otherwise, you would've seen R going upwards as the Omicron cases rose up the percentage of cases (as they appear quicker), it would've also required a big change in location of cases - the cases would've needed to become more clustered around the omicron infections, having other areas fall.

There's no evidence of this in any of the stats.

Of course this doesn't change any of the future direction of omicron, it just says about where we are today, it just moves the dates a couple of weeks.

The model showing cases doubling every 2.5 days to 1.1 million cases a day by Christmas do look alarming, but are they assuming an unfettered and unchecked spread in that scenario? Because between isolating, WFH, social distancing, masks, vaccinations, and previous infections I don't see that Omicron would have easy access to much of the population, as it were, and although I would not be surprised to see high cases I would be very surprised to see case numbers that high. I don't think assuming doubling every X days is a reliable real world scenario. But I'd be interested to be told otherwise.

Well yes it kind of assumes doesnt it that it sticks with that doubling rate - and looking at South Africa it seems to have slowed. Which the other waves have tended to as well.

I agree I think we could see 6 figures cases but not convinced it will hit 7

I am wondering, if we have between 500k- 1 million people getting infected per day, what the death rate is likely to be with that, even with the boosters? and what would people be willing to tolerate?

It still comes down to though the healthcare system @herecomesthsun I think. Because as long as that is working and people can seek care then all anything else is doing is managing the numbers to make sure that happens. Its why it has to be the key metric because if that does get overloaded you do start to have avoidable deaths because people cant access the care that they need.

It is also the easiest metric to clearly manage and get data from as well.

@sirfredfredgeorge thank you so much ,that does indeed help!
I do hate not understanding ,though I have a cut off point and know when I've reached a level (significantly below many on these threads) where I have to accept defeat .

@herecomesthsun

I am wondering, if we have between 500k- 1 million people getting infected per day, what the death rate is likely to be with that, even with the boosters? and what would people be willing to tolerate?

Well given that rate is 10- to 20-times our current (known) case rates then I'd say multiply the current deaths per day by 10 or 20 and add a bit more for the lag between infection and death.

However, it is believed that Omicron presents with a milder illness (whether through to inherent capability or because of immunity levels in the population) so this is a very very general estimate.

I do not personally believe it would be possible to hit quite that many cases a day in the UK for a sustained period of time given our vaccination levels, previous infection levels, and reduction measures such as Plan B.

As for what people would be willing to tolerate, well that I can't answer.