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Data, Stats and Daily Numbers started 17th December

997 replies

boys3 · 17/12/2021 21:17

Welcome to the DATA thread.

Best wishes for the festive season to all contributors and lurkers

The preference for this thread 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/

OP posts:
Thread gallery
158
sirfredfredgeorge · 31/12/2021 20:05

Indicating Delta confers good short term immunity?

I think we have lots of anecdotal evidence that infection of all sorts is superior to vaccine alone for immunity against omicron, but nothing concrete, it would be so nice if the NHS data could be crunched to show it!

The original "characteristics of omicron" implied it, the german data on omicron I posted yesterday implies it, the South African wave size shows it but what we don't know is the scale, and it would be really good to know the scale as it will help imply upper bounds on infections.

(Thanks for pointing out the mistake @firefiles, I couldn't find anything to indicate how much or when it might be widely available)

sirfredfredgeorge · 31/12/2021 20:11

I'm just trying to recall where we were with RATs/LFTs and PCRs this time last year and if we were detecting volume of overall cases accurately

Low supply of LFD's used in healthcare settings only finding

IWannaWishYouANutNutsChristmas · 31/12/2021 20:17

@sirfredfredgeorge

*Omicron's done that in about a month in a highly vaccinated population.

So I would say that's bad*

But it depends how much of it is coincidental, we know that the ratio of admissions to in-patients are lower than in the alpha wave, this implies either that those presenting at hospital are much less ill so spend considerably less time in hospital, or they're more incidental - the actual levels of infection in the community are much higher than during the alpha wave. Because we don't know the exact numbers or the nature of admissions, I think focusing on in patient demand is a better comparison between the waves.

Not that much of it is coincidental.

And also, some of the "coincidentals" are there because having covid gave them a new health problem or made an old one worse.

From a hospital bed pressure point of view, does it matter if one covid patient is in a hospital bed for a month or of it is occupied by ten people for three days each if in both cases there are more people who need to be admitted than there are beds available?

Data, Stats and Daily Numbers started 17th December
sirfredfredgeorge · 31/12/2021 20:51

Not that much of it is coincidental

I'm going to repeat it again, can we stop quoting statistics of "people in hospital" with ratios of admissions, it is not, if 90% of admissions are coincidental but they all stay in 1 day, but the 10% of covid patients stay in 3 weeks, then you get a graph like yours.

Everything you say about beds is true, but quoting misleading statistics helps no-one.

sirfredfredgeorge · 31/12/2021 20:52

We have no data on how much is coincidental, none at all.

JanglyBeads · 31/12/2021 20:55

Fred, how are you defining coincidental? Because we obviously do have data on those not admitting primarily for covid....

sirfredfredgeorge · 31/12/2021 21:00

Fred, how are you defining coincidental? Because we obviously do have data on those not admitting primarily for covid....

We don't, we have data on people IN HOSPITAL and being treated primarily for covid. That doesn't say anything about admissions, because we know nothing about discharges.

If 99% of people arrive at hospital with a primary covid diagnosis. But their average stay is shorter than the average stay of coincidental people, then the percentage of in-patients at 8am being treated primarily for covid will decline despite 99% of people being admitted with it.

Some of the in-patients are the same people every day, and some change, and lots of the admissions never become in patients, none of that is published in detail so we can't know what happens.

JanglyBeads · 31/12/2021 21:50

Sorry I thought by definition an admission becomes an inpatient? Is the 'for observation' wards which create the problem?

I read an interesting Twitter thread this morning by a consultant explaining how HAIs are classified, will try and find it.

And I thought discharges could be worked out from the various sets of figures? But I appreciate you've looked at it in far more detail than I have, and I'm probably being no help at all!

JanglyBeads · 31/12/2021 22:01

Here we are, from an anaesthetist/intensivist

twitter.com/doctimcook/status/1476256967274471431?s=21

Summerofcontent · 01/01/2022 07:44

Sorry to interject, is there any information on protection after 3 jabs and a natural infection?

peridito · 01/01/2022 08:00

That's really interesting JB .

I don't understand why FFP3 masks aren't being provided .At a micro level wouldn't the cost of provision be less than paying for agency staff? Or are hospitals not using /affording agency staff ?

And surely better outcome on a much wider level ?

www.theguardian.com/world/2021/dec/27/give-ffp3-masks-to-nhs-staff-omicron-doctors-say

Words · 01/01/2022 08:05

.

sirfredfredgeorge · 01/01/2022 08:08

Sorry to interject, is there any information on protection after 3 jabs and a natural infection?

Not enough, but that's reported to be absolutely the best (not surprisingly) Which means it must be well over 90% chance reduction, or about the same as the vaccine alone at preventing delta.

Jangly You can't work out discharges as you don't know if it's someone who spent the night for observations after being worried about covid symptoms or someone who's spent a month in hospital that disappeared from the data. And no, not all admissions become in-patients in the data. There's even a time difference (midnight-midnight 24 hours reporting for admissions, although I bet some trusts differ) vs "in patient at 8am".

It's just a mess of data, and the two figures just need not be confused.

sirfredfredgeorge · 01/01/2022 08:21

On the Warwick Model that was shown yesterday, Pagel pointed out they thought they were following a particular part. Like any model though, now we're later on in the process we can look at the assumptions, and if the assumptions turned out invalid, then the conclusions have to also be.

www.medrxiv.org/content/10.1101/2021.12.30.21268307v1.full.pdf

One of the biggest points on the forecasting outcome is
Throughout we have assumed that Omicron has the same generation time distribution as Delta - essentially the same latent and infection periods. However, the rapid increase of Omicron relative to Delta could partially be due to a shorter generation time; Omicron would still need to have a competitive advantage over Delta but this would be magnified by a shorter generation time. As such, if the generation time of Omicron was half that of Delta (so around 2.5-3 days instead of approximately 5-6 days), once the model is recalibrated to match the growth of SGTF, this would approximately halve the predicted peak outbreak sizes

We now have a lot of confidence that the generation time for omicron is less - although I've not heard a prediction that specifically says it's managed to be halved, but either way, their model would say lower peak than the graph offered.

They also assume length of hospital stay is the same between delta and omicron, however hospitalisation -> in patient ratios so far have come down considerably implying a shorter average stay here, and explicit evidence on shorter average stays is available.

Another thing of note, their model predicts no change in wave size if NPI's are introduced on the 4th of Jan, so no reduction from locking down.

As you know, I don't have much truck with modellers (not because they don't do a good job, it's just too hard a job where small assumptions cause huge impact!) but that's good news, all the assumptions I could find would change their results towards a smaller wave.

peridito · 01/01/2022 08:26

Lovely post for a New Year SirFred ,Thank you for your analysis .

sirfredfredgeorge · 01/01/2022 08:29

Which means it must be well over 90% chance reduction, or about the same as the vaccine alone at preventing delta

We should be able to start identifying the size in the data from Wales, Welsh case data has re-infections in, so they should grow faster and to a higher level than similar areas in England proportional to the size of re-infections. Of course the fines for going to the office etc. will have a confounding effect.

JanglyBeads · 01/01/2022 08:56

twitter.com/drtomlinsonep/status/1476971511613382662?s=21
Thought these points,one from an American medic and one from a UK one, were both important to bear in mind re hospital capacity.

JanglyBeads · 01/01/2022 09:01

That is helpful, and hopeful re Warwick model Fred, thanks.

Probably a basic question but why is it that

if the generation time of Omicron was half that of Delta .... this would approximately halve the predicted peak outbreak sizes ?

Summerofcontent · 01/01/2022 09:25

Thanks very much @sirfredfredgeorge

Firefliess · 01/01/2022 09:28

If you overestimate the generation time then you end up assuming that the fast growth you see is due to a higher r rate than it actually is. For example a generation time of 6 days and an r rate of 4 would mean 4 times as many cases in 6 days. But if the generation time is in fact 3 days, an r of 2 would produce this same result (doubling in 3 days, so 4 times as many after 6 days). But as soon as the epidemic starts to decline (which could be due to behaviour changes or running out of people to infect) the growth rate will fall more quickly. Once r is below 1 it'll decline twice as fast if the generation time is only half what it was.

Motorina · 01/01/2022 09:42

Absolutely endemic in hospitals due to zero air changes in a regular bay. Yet still determined nosocomial with IPC practices scrutinised…cleaning, HH, distancing etc called into question. Without airborne acceptance, hospitals will continue to unfairly deemed plague pariahs

This really stood out at me from the twitter thread that @JanglyBeads linked to.

I'm getting increasingly frustrated that, every time we get staff to staff transmission at work we're told that we must have messed up. That we must have slipped in following the infection control procedures.

No, we're getting staff to staff transmission because it's a highly infectious disease and it's hanging in the air. Stop blaming individuals for this!

JanglyBeads · 01/01/2022 09:48

That's ridiculous Motorina, am so sorry to hear HCPs are being blamed!

Firefliess · 01/01/2022 10:11

I'm not sure how you can even know that staff are catching it off other staff - it's so widespread everywhere! Yes really unhelpful to be blaming staff when they're unavoidably breathing the same air

Piggywaspushed · 01/01/2022 10:14

The same thing has happened repeatedly in schools, too. Teachers were blamed routinely for spread amongst adults in schools. Mainly for drinking coffee and sitting down. This was both at macro and micro level as it were. It's very draining on morale.

containsnuts · 01/01/2022 10:16

Question. Why did they cut the isolation time in response to Omicron while there was still Delta in circulation? Could this compromise the elimination of Delta as infectious people with this strain are coming out of isolation too early and continuing to spread (albeit to a lesser extent?).

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