Data, Stats, Daily Numbers started 14th November 2021

[boys3]

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/

Recent update for Exeter university just for interest. Large spike post half term, so students bringing infection back into University having been home, and also being asked to test upon return. Since then back to pretty level infections, indicating not much transmission on campus. This cohort also being most recently vaxxed probably helps. Higher percentage incidence seen in staff.

@BigWoollyJumpers

Recent update for Exeter university just for interest. Large spike post half term, so students bringing infection back into University having been home, and also being asked to test upon return. Since then back to pretty level infections, indicating not much transmission on campus. This cohort also being most recently vaxxed probably helps. Higher percentage incidence seen in staff.

The university closest to me has apparently had just 240 cases, total, amongst students in the past 14 months. And just over 100 cases amongst staff.

The small print says the figures are for cases that have been reported to the university's health and safety team.

So the conclusion I'd draw is that that students, unlike staff, do not bother telling the university when they get Covid!

@manolantern I can't verify obviously, but a note at the bottom of the page, states data comes from PHE England.

[quote BigWoollyJumpers]@manolantern I can't verify obviously, but a note at the bottom of the page, states data comes from PHE England.[/quote]
PHE England has been renamed/abolished. But I wouldn't be surprised if it was the case that they were reliant on the university (and therefore on students self reporting) providing them with the figures.

In previous waves deprivation was blamed for many differences, we now know there are genetic differences that predispose to severe illness and they are common in those of south asian ancestry and not rare in european ancestry. It is unlikely that all such differences have been identified. So caution is wise in interpreting data from other countries.

We also know that being exposed to high viral load is more likely to lead to severe illness. So it is possible that differences in severe illness and deaths between areas would be more closely related to mask wearing than case numbers.

Dont look only for the explanation you want to be true, consider all the data.

Testing way up still, but cases only barely up, so overall positivity falling significantly (of course if the extra testing is because of the worried person who's not left the house in a week or seen anyone then it might not mean much, but if it's targeted testing then that is good news that it's not finding loads of extra cases)

Positive data for me here.

Now to go see if I can find out @Mrex's south london wave.

Guildford wave seems to be over. Falling in all age groups, and last seven day count down 18%. My ludicrously high MSOA down 39%.

16.7%drop in my MSOA - figures here are up and down all the time.

@BigWoollyJumpers

Recent update for Exeter university just for interest. Large spike post half term, so students bringing infection back into University having been home, and also being asked to test upon return. Since then back to pretty level infections, indicating not much transmission on campus. This cohort also being most recently vaxxed probably helps. Higher percentage incidence seen in staff.

But staff will also be vaccinated?

Conversely, Brentwood which is just up the road is UP by 80%, which would tie in with the omicron testing I guess?

@sirfredfredgeorge

There's something very strange going on with the NICD data 1st of November as age/case data of admissions www.nicd.ac.za/wp-content/uploads/2021/11/NICD-COVID-19-Daily-Sentinel-Hospital-Surveillance-report-National-20211101.pdf as does 1st of December www.nicd.ac.za/wp-content/uploads/2021/12/Datcov19_National_Export-20211201.pdf

The problem is there's not enough extra admissions in the age breakdown in the whole of November to account for the stated numbers of admissions.

In the data there 2.6% of all admissions were under 10's up to Nov 1st vs 18% of the breakdown on the November cases - but the problem is the November cases claimed total 750 odd, which is nothing like the sum of the daily admissions. I'm getting very annoyed with scientists making statements based on data, when they don't provide the source of the data they're using so we can actually look.

Quite a big decrease in secondary school, which is lovely to see, presumably they have at last had some vaccinations, which are finally taking effect. 3.5% positive

Or with the average size of school being much bigger, it's simply gone through all the schools, which I actually hope, as otherwise we just get a whole new wave in 3-6 months once the vaccine (and booster) has waned.

Have you seen the report that suggests omicron is twice as likely to cause re-infection as alpha and delta?

"The [preprint] estimates Omicron could be twice as likely to cause a re-infection than earlier variants.

Prof Juliet Pulliam, from Stellenbosch University and one of the researchers, said: "These findings suggest that Omicron's selection advantage is at least partially driven by an increased ability to infect previously infected individuals." "

www.bbc.co.uk/news/health-59520945

However, there have been very positive reports about the vaccines and boosters this week, so much room for optimism there.

Have you seen the report that suggests omicron is twice as likely to cause re-infection as alpha and delta?

Yes, it's hugely positive news! Means re-infection won't drive much - remember 10 million odd cases and only 100,000 odd re-infections, just doubling them doesn't impact "herd" immunity much at all.

I'm sure they'll wane of course, but presumably not as fast as the vaccine immunity.

@sirfredfredgeorge

Have you seen the report that suggests omicron is twice as likely to cause re-infection as alpha and delta?

Yes, it's hugely positive news! Means re-infection won't drive much - remember 10 million odd cases and only 100,000 odd re-infections, just doubling them doesn't impact "herd" immunity much at all.

I'm sure they'll wane of course, but presumably not as fast as the vaccine immunity.

Yes, doubling of a small number is still a small number.

This is one of the tricks used by the media to hype up & overstate dangers.

For example if your chance of being killed by an block of ice falling from an aircraft toilet on any given day is 1 in 2,000,000,000, but then there's an increase in air traffic and it increases to being 1 in 1,000,000,000.... The number has DOUBLED but the risk is still negligible!

The problem is there's not enough extra admissions in the age breakdown in the whole of November to account for the stated numbers of admissions.
Could it be people being admitted more than once? We had duplication at one point if admitted to one hospital then moved to another. Possible too that doctors are getting a bit bullish about sending people home who then deteriorate and need to go back in.

I wondered if Omicron originating from Alpha means the vaccine might end up more effective than for Delta, but the number of mutations seems to have scientists suggesting the opposite. The variant individuals were infected with might make some difference though in terms of reinfection.

New VOC report out. Megan Kall goes through the main points here:
mobile.twitter.com/kallmemeg/status/1466807245056970753

To be fair fred, that also happens the other way round.

There is lots about the rising number of cases with SGTF in the report:
"Omicron VOC-21NOV-01 (B.1.1.529) has a deletion at position 69/70 of the spike
protein which allows it to be tracked through S gene target failure (SGTF) in some
polymerase chain reaction (PCR) tests. SGTF is also observed in a very small
fraction of test results from lineages lacking this deletion, including the Delta lineage
and sub-lineages. The proportion of test results with SGTF has been low over the
past 90 days, but in the past week has increased. The logistic growth rate of SGTF
has fluctuated between approximately -50% and +50% over the past 90 days but in
the past week has climbed to +141%. This finding indicates that SGTF is growing
faster, and can be considered a strong early signal. However, the number cannot be
interpreted as a change in transmissibility or an increase in the absolute number of
cases of the variant."

Young children being infected in the uk now is potentially good if they get Delta. Then if Omicron turns out to affect children worse they have a little protection from reinfection.

@alreadytaken

Young children being infected in the uk now is potentially good if they get Delta. Then if Omicron turns out to affect children worse they have a little protection from reinfection.

What a dreadful thing to say. It is never good that a child is sick. My school currently has so many cases. Yes most are mild but children miss at least 10 days of school. Some are really poorly. One child in my class has had 5 weeks off because she has been really ill. My colleague caught it and passed it to her 2 year old who ended up in hospital.

@sirfredfredgeorge

Have you seen the report that suggests omicron is twice as likely to cause re-infection as alpha and delta?

Yes, it's hugely positive news! Means re-infection won't drive much - remember 10 million odd cases and only 100,000 odd re-infections, just doubling them doesn't impact "herd" immunity much at all.

I'm sure they'll wane of course, but presumably not as fast as the vaccine immunity.

I'm sure they'll wane of course, but presumably not as fast as the vaccine immunity.

Well, I guess we 'll soon find

• how waning of post-infection immunity compares with vaccine waning for protection where omicron is concerned

and we are still waiting to see whether natural immunity wanes further after 2 years or so - we just don't know yet

quite keen for my kids to stay well, really

Although the UKHSA report says there are 22 omicron cases, Cog-uk (which is doing daily updates again) is reporting 66 cases in the UK up to Wednesday.

@lonelyplanet

Although the UKHSA report says there are 22 omicron cases, Cog-uk (which is doing daily updates again) is reporting 66 cases in the UK up to Wednesday.

66 sounds more likely to me. We were at 22 at least 2 days ago. Bound to be more found since then even if it were just the last of the imported cases before they made the new red list

What a dreadful thing to say. It is never good that a child is sick.

I'm not sure, yes of course it is dreadful if children are sick, however our government have decided to leave them unvaccinated, even the 12+ were not eligible for vaccination before October. If a future strain is more of a concern for children I would be grateful that a previous infection gave them some antibodies. The uncontrolled spread through school was and is a political decision, they gaslit for months saying children do not spread it, and then without any fuss everyone has accepted they do.
I see daily what this unmitigated spread has done to children's futures. If this cavalier attitude has a surprising benefit I would be glad.

Aside not provable (well it is but I can't share) our area rates have dropped and school cases have remained stable to great delight locally. However no reports about the large number of children and indeed whole age groups that are currently working from home.

Meanwhile, teachers continue to fall ill apace...