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/

Wales had no cases on Saturday and then nearly 4.5k today. Was there a data issue there?

@BonneMaman15 and @BigWoollyJumpers with vaccines I think the 80% or whatever refers to protection against infection .

So, for example, let’s imagine a vaccine with a proven efficacy of 80%. This means that – out of the people in the clinical trial – those who received the vaccine were at a 80% lower risk of developing disease than the group who received the placebo

www.who.int/news-room/feature-stories/detail/vaccine-efficacy-effectiveness-and-protection

Anyone have any insight into Belgium - they appeared to have introduced lockdown restrictions and cases starting falling from peak - however no restrictions loosened and they're climbing again and as fast as before and at over 1000 per 100k which is apparently shocking in just a single age group in the UK.

We know Omicron is there, but is it really there in large enough numbers in just a short time - or had it been there longer than expected?

Yes re Belgium
www.pbs.org/newshour/world/omicron-was-in-netherlands-days-earlier-than-first-thought

I've seen a tweet with a (horizontal) bar chart showing something like 5% of cases in either the Netherlands or Belguim (or maybe both?) are now omicron. Will try and find that.

@weddingguesttbc

Wales had no cases on Saturday and then nearly 4.5k today. Was there a data issue there?

That quite often happens with the Welsh data. Some days they fail to update it and then the following day is a big number. It's usually better just to look at the English data by reporting date and compare it to 7 days ago. (Unless you're particularly interested in Scotland, Wales or NI)

@JanglyBeads

Yes re Belgium www.pbs.org/newshour/world/omicron-was-in-netherlands-days-earlier-than-first-thought

I've seen a tweet with a (horizontal) bar chart showing something like 5% of cases in either the Netherlands or Belguim (or maybe both?) are now omicron. Will try and find that.

5% of all sequenced cases wouldn't be enough to cause a big upturn overall though would it? Unless there's a lag to it and it's actually gone to to 50% or something in the last week or so since whenever they took the samples that they sequenced.

Here’s the tweet with the chart, which is from OurWorldinData and dated 4 Dec:
twitter.com/annaalbecka/status/1467573788900564996?s=21

Although it seems it only represents 4 sequenced samples (see in replies). So does Belgium not do their own sequencing - seems that only 80 samples sent for sequencing??

@JanglyBeads

Here’s the tweet with the chart, which is from OurWorldinData and dated 4 Dec: twitter.com/annaalbecka/status/1467573788900564996?s=21

Although it seems it only represents 4 sequenced samples (see in replies). So does Belgium not do their own sequencing - seems that only 80 samples sent for sequencing??

That's not a big sample is it? And if they're not doing their own sequencing then there might well be quite a lag. Not on our red list though are they?

I don't believe Belgium does much sequencing, and Belgium has always been a bit fluctuating in cases, but the lockdown (which I think is not that limited as hospitality is still open with "2G" covid passes) turned cases initially, but have recently stopped working. If it is omnicron then that implies WFH and Mask mandates (including in schools whilst at desks) is not enough a mitigation even with 75% vaccine, which implies the restrictions required will need to be extensive.

But of course it could be something else we're missing?

Wales don't report on Saturdays and haven't done for quite some time.

@sirfredfredgeorge

Larger increase than recently - will be interesting to see the geographic distribution

London - not exclusively of course.

The other thing is that for England reporting last Monday just under 4500 of the cases came from Spec dates for Friday and Thursday of the week past. Today the figure is just over 10,000. Around 175 last week going back five days or more, today just over 900.

the spec date graph for England.

Not wholly convinced too much should be read into the day 1 (Sunday) spec date number in England (lower than day 1 reporting for last Sunday)

@Firefliess and @sirfredfredgeorge that’s a really helpful explanation thank you.

Only 30-35% of Pillar 2 (normal pop testing, that’s2 isn’t it?) samples can be checked for S gene drop out, and the figures have about a week’s lag

www.theguardian.com/world/2021/dec/06/patchy-monitoring-means-uk-omicron-numbers-unclear-say-officials?CMP=Share_iOSApp_Other

[quote JanglyBeads]Only 30-35% of Pillar 2 (normal pop testing, that’s2 isn’t it?) samples can be checked for S gene drop out, and the figures have about a week’s lag

www.theguardian.com/world/2021/dec/06/patchy-monitoring-means-uk-omicron-numbers-unclear-say-officials?CMP=Share_iOSApp_Other[/quote]
The S Gene dropout is detected during normal PCR testing so there's not much lag on that - and looking at the proportion of s gene dropout is definitely the way to see trends. It's the full sequencing that takes another few days - so "confirmed cases" could be a week behind. I think that's way Sajid Javid was saying today that they believe there's been over 1000 cases in the UK but only 300 odd confirmed.

Yes indeed

twitter.com/apsmunro/status/1468194662548660234

Hospitalisations and ventilation beds in England are tilting up the last few days. 6 days still until the booster programme moves into the new faster pace. I nervously suspect a pause for booster increases is on the way.

Mrex, do you mean plan B?

No idea, plan X? London is going up much too fast; the numbers look knife edge, just a few weeks to get boosters in could tip the balance. If we knew early Omicron testing results it would really help.

manolantern That just shows what has been often reported in young age groups the hospitalisations are generally with covid not because of covid, we don't have specific data collected of reason for hospitalisations, but other similar indirect measures have been shown, it's still good news of course on the reflecting the low severity of covid in the young.

And of course shows again that RSV immunity is purely infection acquired.

Not sure I really agree with the "tilting up" on hospitalisations, still looks like normal variability particularly on vent. beds.

@MRex crikey! Do you think they'll go in with harsher restrictions in the next week or so? Skip plan b totally?

Which chart are people looking at for this fast increase?

To me, the total number in hospital looks like it's decreased recently? A long way to go until we're back at Oct / Early Nov levels again

Children I suspect would rarely be hospitalised with covid because no one would know beforehand what they had. If your toddler suddenly has a very high temperature, or is struggling to breathe, you wont know what it is, just that they need to go to hospital.