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/

[quote JanglyBeads]Yes @vera99 I saw that… haven’t seen anyone factoring hospital-acquired infections at that new high rate either. Crikey.

This thread is good on what will perhaps happen when we hit testing capacity. Many on here will appreciate Oliver Johnson’s reply….

twitter.com/kallmemeg/status/1471597408949874695?s=21[/quote]
I was going to post this too I love his reply!

Do not overlook that one aspect of lag is that numbers testing positive is updated daily, and reflects the numbers up to the cut off point that day.

Numbers admitted to hospital is usually at least 4 days older. So as well as taking about a week from start to need for hospital, there's a further 4 day lag in publication. Yesterday's big rise won't show in the figures for another 10 days or so

And if it comes to it that, the accounts of excessive strain on hospitals will be about 4 days ahead of the worst of the figures

Numbers admitted to hospital is usually at least 4 days older

London numbers do not lag that much, but your general point is still sound.

The UK wide hospital numbers often lag more because they're aren't calculated until the data is in from all 4 nations. English admissions (or anything beneath that, eg London) is usually only a day or two old.

I love this chart. Biggest increases: London followed by the East of England, South East then North West.

Follow this thread but don’t usually post. So my son tested positive on Lateral flow test yesterday morning. Flowflex nasal only faint positive line. Did PCR yesterday afternoon which has just come back negative. Others at his work have had positive lft and negative PCR. They have repeated lft using the nose/throat type which is negative. Is it false positive lft’s or have they done PCR too early.
Supposed to be having family meet up tomorrow. Most of us have had our boosters but some haven’t. Don’t know what to do

Some new data on hospital fatality rate just come out of South Africa twitter.com/michaelzlin/status/1471749391585214465?t=3eior1x7G79rdRR_kZvasg&s=19

Fatality rate of hospital admissions with Omicron only about a third of what it was previously. Uncertain whether that's because most had some immunity due to prior infection, or because Omicron is inherently less deadly.

Or if you wanted to be pessimistic about the lower fatality rate in SA it could also be down to 'survivorship bias' - ie those who were vulnerable to dying from covid have already died. This would be the explanation least likely to be useful in the UK though as we have had a lot less people dying from covid (SA excess mortality around twice what ours is, despite a much younger population).

Booo @Firefliess

(I think you make a valid point, I just don’t like it! As you were data peeps).

@MidtoLon

Follow this thread but don’t usually post. So my son tested positive on Lateral flow test yesterday morning. Flowflex nasal only faint positive line. Did PCR yesterday afternoon which has just come back negative. Others at his work have had positive lft and negative PCR. They have repeated lft using the nose/throat type which is negative. Is it false positive lft’s or have they done PCR too early. Supposed to be having family meet up tomorrow. Most of us have had our boosters but some haven’t. Don’t know what to do

Does he have any symptoms? Hard to know but he could keep doing daily lfts and another pcr if still symptomatic?

Has anyone at work (or elsewhere he goes) had positive PCR?

Well it gets stranger as he has now received a second email stating his PCR is positive. So we are taking that as definitive and him and his family won’t be coming to meet up but it’s really strange that he received email saying negative and then one saying positive.
He is going to report that to 119
He is asymptomatic at present. Another workplace colleague has now also tested positive

Sorry to hear that and yes very strange to get a second email.

Hmmm. I have two colleagues who have pos LFTs and neg PCRs too (and are close contacts of a PCR positive). I do hope that isn't starting up again...

www.bbc.co.uk/news/health-59696499

Not the best news. The booster looks as though it could provide 85% protection against severe infection. Is it also likely that immunity will wane as with earlier vaccines? Add in the large number yet to have any vaccine plus immunosuppressed and under 12s. Could be worse with no booster I suppose

@mrshoho

www.bbc.co.uk/news/health-59696499

Not the best news. The booster looks as though it could provide 85% protection against severe infection. Is it also likely that immunity will wane as with earlier vaccines? Add in the large number yet to have any vaccine plus immunosuppressed and under 12s. Could be worse with no booster I suppose

Seems plausible - we know boosters are less effective at stopping you catch Omicron than they are with Delta, so you'd also expect a comparable loss of efficacy against severe disease. I'd treat it as a bit of an educated estimate though as it's just modelling the level of protection based on laboratory tests of antibodies - not real world data with people.

So WTF is going on in the dashboard, the 7 day "R" and "Growth Data" have been updated for the first time since omicron is out.
coronavirus.data.gov.uk/details/healthcare?areaType=nhsRegion&areaName=London

And for the week between the 10th and 17th they predict an R of 1.1 to 1.3 and a growth rate between 2 and 4%

This is in a time when the positive tests had ~10,000 cases on the 10th to todays maybe an "optimistic" 35,000

Nothing unexpected in todays stats I'd say, London hospitalisation again shows little evidence that omicron is milder in those that present at hospital, admissions to in-patients still higher than before and ventilation slightly up - but of course still within normal bounds, and the numbers presenting at hospital is not growing as fast as cases.

I am a bit skeptical about the imperial research to be honest. The estimate that previous infection protection is as low as 19 percent.

The problem is something is going on in South Africa there simply are not as many people in hospital as in previous waves and by now there should be. So that is either this is inherently milder (which no one seems to believe) or there is immunity in the population kicking in, but in South Africa that is mainly prior infection immunity which suggests a lot higher than 19 percent. I am assuming it must be a T cell thing and they are looking at antibodies but I wouldn’t be surprised if real world data gives different results since otherwise South Africa doesn’t make sense.

90,000 today

I'm sorry to be dense but what occasions the WTF ? What is odd about the figures ?

Usual caveat - no need to respond ,I'm unable to process numbers .

@mrshoho

www.bbc.co.uk/news/health-59696499

Not the best news. The booster looks as though it could provide 85% protection against severe infection. Is it also likely that immunity will wane as with earlier vaccines? Add in the large number yet to have any vaccine plus immunosuppressed and under 12s. Could be worse with no booster I suppose

The Israelis are already reporting waning after the booster against Delta so it makes sense it would happen even more so against Omicron. You need a high level of neutralising antibodies to combat it.

London hospital admissions clearly growing quite fast, though if you want something more positive, the numbers in ICU are much flatter. Could of course be a greater lag of people taking more time to get very sick, but also possible that a fair number of the growing "admissions" for covid are admitted for some other reason and incidentally positive for covid, or that it's going round the hospital wards - we'd expect to see the numbers of incidentally positive hospital patients rising in line with cases (no lag) so when cases are rising very fast, they would be likely to account for a growing proportion of hospital "admissions".

I'm not a medical doctor, but Firefliess could it not also be due to patients coming in sooner (so not in such need of ICU level oxygen etc.) and maybe better early treatment options than in the more distant past?

Oh sorry, that's what you said, isn't it!?

@moimichme

I'm not a medical doctor, but Firefliess could it not also be due to patients coming in sooner (so not in such need of ICU level oxygen etc.) and maybe better early treatment options than in the more distant past?

I'm not a doctor either (though have friends who do work in healthcare) But I'm not aware of any reason why patients would have started coming in sooner. The NHS isn't exactly full of spare beds and crying out to take people in who don't strictly need to be there. There's a new pill they're trialling which can help stop covid becoming severe - but it's taken at home. People don't need to go into hospital for it.