Data, Stats & Daily Numbers started 5th August 2021

[boys3]

This is the DATA thread. We welcome 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
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/
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/
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/

⏭ Our STUDIES Corner ⏮ www.mumsnet.com/Talk/coronavirus/3869571-Studies-corner?msgid=99913434

Sorry, I may have confused you. The most infectious period is early, but people can continue being infectious for some time. PCR tests pick up some dead virus too, so it's hard to know how long and I haven't seen anything conclusive on that. Hopefully you've swerved it though. Or even more hopefully are fully immune.

That research posted by @borntobequiet yesterday evening was interesting on possible natural immunity

WTF on the scotland cases today! 2,538 cases, compared to 1,498 a week ago, and 1,814 yesterday.

Cases and positivity have been creeping up slowly the best few weeks. I wonder if it is running away again, or just school return testing.

@CaptainMerica

WTF on the scotland cases today! 2,538 cases, compared to 1,498 a week ago, and 1,814 yesterday.

Cases and positivity have been creeping up slowly the best few weeks. I wonder if it is running away again, or just school return testing.

Surely that would fit in with return to school testing though, LFTs picking up asymptomatic cases with PCR follow-ups?

Just noticed an update on the Covid dashboard - On Thursday 19 August, headline vaccination uptake by report date for the UK and nations will be updated to include ages 16 and 17 in the denominator.

Yes, looking closer there was a big increase in the number of tests carried out. I thought that school return testing would have worked its way through the system by now - schools are all back, some for over a week. However, you are right that people would need to take an LFT and then schedule a PCR and wait for results.

Scotland also dropped self isolation for vaccinated people a week before England did - that's probably starting to feed into the numbers around now..

If I am reading the Scotland's dashboard correctly, the biggest relative increase in cases occurred in the 15-19 and 20-24 age groups. The former might include some schoolchildren but the latter is likely to be driven by increased socialisation post August 9th re-opening.

Re: testing in Scotland - the week on week numbers have not changed that significantly. 31,653 tests are reported for August 16 with 2,617 positives. The results for August 9 were 33,057 tests and 1,614 cases. The numbers are from the Scotland's dashboard (not the UK one):

public.tableau.com/app/profile/phs.covid.19/viz/COVID-19DailyDashboard_15960160643010/Overview

This is a genuine increase - not just expanded testing.

I am in Scotland and currently know more people with Covid than I did before the vaccinations started . One friend is double jabbed but very unwell . Worrying .

This is a genuine increase - not just expanded testing

And among the 15-25 age group, so the "expected" wave from the end of restrictions that kept pub spreading down?

The reported numbers for Cornwall have really spiked today. I am wondering how much of the increase is driven by Boardmasters. It was an outdoor event but people tend to gather in pubs afterwards.

today's England spec date graphic. Yesterday (first day of reporting) pretty flat; Monday (second and the bulk day for numbers) more clearly up. Again a shame the age breakdown lags behind.

Thanks, boys3. I think Cornwall is one of the biggest drivers for the Monday spike.

Cornwall has so far been shielded from the worst of Covid (the cumulative reported prevalence is only 5,000/100,000 vs 17,000 in Blackburn) so it is not surprising one potential super spreading event might have had a significant impact.

Another big day (relatively) in Sedgemoor. 165 cases so far for Monday as opposed to 119 fully reported for last Monday.

Somerset West and Taunton also up 109 for Monday so far vs 70 in total last Monday.

South Somerset 96 vs 62

Mendip less pronounced 64 vs 53

Like Cornwall Somerset cumulative rate since start one of the lowest in England.

Variant to watch is the AY.3 version of delta. It is most prevalent in the US but is increasing (still in very small numbers) here.

Christina Pagel has a thread about it.

mobile.twitter.com/chrischirp/status/1428014796897652737

Just looking at Monday so far vs last Monday fully reported

Wiltshire 324 vs 219

east Devon 150 vs 75

Mid Devon 81 vs 32

Rother 59 vs 12

Thanet 109 vs 54

Broadland 60 vs 21

Chichester 90 vs 49

Cornwall as highlighted by winter 553 vs 364

Interesting, boys3, several of these LAs might now be seeing the impact of Boardmasters (if it was indeed the big super spreading event as hypothesised on SM).

A little more on the AY.3 from Henk-Jan Westeneng:
The graph shows raw sequencing data in UK on a logit scale.
"Please note the downward deflection of B.1.617.2 which indicates that 'something else' is growing faster than B.1.617.2. This is most likely AY.3."
mobile.twitter.com/HJWesteneng/status/1427738574326321153

What’s a logit scale please?

I'm not a mathematician, so someone please correct me if I'm wrong, but I think it is the same as a log scale where it is easier to spot exponential growth.

Logit scale of the inverse of the logistics function. It's used usually where probabilities are very small so they can be added up to identify a trend very early.
Two thoughts:

1. We've all seen what tiny does, which is grow; distribution elsewhere needs to be taken just as seriously.
2. It might need a longer timeframe to account for our wobbly up and down cases, because the dip is tiny right now and testing of all travellers means there could be slants from USA that wasn't fully taken over by Delta but has cases rising is many places regardless.

I haven't looked into this variant's global distribution yet, will have a look later and interested in anything else people see about it.

IS the inverse (not "of")

This may is useful on global distribution (map at the bottom) but beyond my scientific understanding!
nextstrain.org/groups/neherlab/ncov/AY.3?c=gt-S_417&f_clade_membership=21A%20%28Delta%29&label=clade:21A%20%28Delta%29

UNISON have sent some very pertinent questions to Gavin Williamson asking how contact tracing is going to work in schools from September, has this been risk assessed, etc:

www.unison.org.uk/content/uploads/2021/08/UNISON-letter-to-Secretary-of-State-18-August-2021.pdf?fbclid=IwAR3hzmu4VUvHv_iQNajlpfmXlpAdLICh3OUx4s0X-gDbI-fE8-DlwbxhmRE

Cases per 100,000 using a three day lag for the past four weeks, with first column showing the rank for the most recent week (for the council tables). Last but one column shows the 7 day rate to 16th August, so using a two day lag, with any where the rate is higher than the rate to 15th Aug orange highlighted. Final column shows the ranking based on this final two day lag rate.

For each table the England and median rate shown at the top.

Overall English regions first (so no rankings, and no median on this table)

To follow councils (England) by region and sorted by highest rate within their region. Conditional formatting across the four weeks shown is against all councils in England.