Data, Stats and Daily Numbers started 18th January 2022

[boys3]

Welcome to another instalment of the DATA thread.

Our preference 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/

bit of a statement of the not wholly unexpected

This is the cumulative case rate per 100,000 for every English council as at 31st Aug 2021 plotted against the Dec 2021/Jan 2022 percentage increase in cases as a result of re-infections now being included.

Clearly this could be run with varying data parameters and geographic areas - end Sept 2021 position and just the Jan 2022 (to 25th or thereabouts) for example.

Noted re negs reported.

See comments here from Fiona O'Leary re reinfection counting!

twitter.com/dgurdasani1/status/1488445667185987586?s=21

Can ignore the latter part of my 10:08 . It would have helped if I’d have looked at the dashboard properly first.

Laurence Gilder's noticed something odd about early reinfection date

twitter.com/lawrencegilder/status/1488618580564492296?s=21

But it's not just 90 days, it's 90 days or 4 successive negative tests, there's a couple of obvious ways that miscoding of tests can happen, perhaps not testing the same people but all be coded as the same person (more likely in the early days I suspect) or with unreliable tests / methodology someone being tested often and going in and out of positivity.

I think that's the most likely thing, not some case actually pre Wuhan infection.

[quote JanglyBeads]Laurence Gilder's noticed something odd about early reinfection date

twitter.com/lawrencegilder/status/1488618580564492296?s=21[/quote]
Quite a few oddities in today’s release as compared with what was released yesterday. Who knows what tomorrow may bring.

I noticed yesterday that Greece had overtaken us on the deaths per million front, and Russia was just a couple of points behind. This morning we have shot ahead 10 points or so, which means around 6800 deaths have been added to the total retrospectively, somewhere. Did anyone else notice this? The total deaths dont seem to have gone up so I’m wondering what has happened with the stats!

Ignore me - 10 “points” would be 680 deaths not 6800. I still can’t see in the data when it was added but my mind is at rest!!

@SecretKeeper1

Ignore me - 10 “points” would be 680 deaths not 6800. I still can’t see in the data when it was added but my mind is at rest!!

www.economist.com/graphic-detail/coronavirus-excess-deaths-tracker

This is oft posted, but Russia is way up there, in third place globally. We are somewhere in the middle now, below Italy and Spain and most of Eastern Europe.

I heard that the inclusion of reinfections has increased the reported deaths within 28 days - though I don't quite understand why as someone who dies within 28 days of a test which found a reinfection would still have died within 28 days of a test wouldn't they, even if not their first test?

@Firefliess

I heard that the inclusion of reinfections has increased the reported deaths within 28 days - though I don't quite understand why as someone who dies within 28 days of a test which found a reinfection would still have died within 28 days of a test wouldn't they, even if not their first test?

It must be something to do with that. It’s the Worldometers stats I’m looking at and Russia was due to “overtake” us on the deaths per million today/tomorrow, putting us in 32nd place. We’re now back at #30.

Seems to have been a big correction in deaths being reported today after the 2 recent low days. @RP131 has plotted them by date and the trend still seems to be down thankfully!

It’s the way deaths within 28 days have been revised - there’s something specifically about it on the dashboard.

This is just England but taking the file published 30th Jan there were for example 4439 deaths with date of death between 1st and 21st Jan. in yesterday’s file the same period now has 4632.

Taking the full 2021 year net increase of 534.

2020 net increase 130

I’ve not looked at today’s update yet to see if amends have been further amended.

Sky News reporting that daily stats will cede to be published from Easter at the latest.

*cease

That seems unwise if we are due another wave in early summer.

Preliminary results from the human challenge trial run by Imperial:

www.imperial.ac.uk/news/233514/covid-19-human-challenge-study-reveals-detailed/

I thought the two things were particularly interesting:

• Only 50% of the participants were infected. It confirms the hypothesis that susceptibility to Covid is not homogenous - some of us are much more likely to catch it than others.
• LFTs did a good job in identifying viable virus / infectious individuals.

Ons headlines for England:
The percentage of people testing positive for COVID-19 aged 2 to school Year 6 at 13.09%. That's 1 in 8.

Anecdotal but in my Year 6 class this week it has been 1 in 2.6. Pretty high considering most of them had it in November and December.

@wintertravel1980

Preliminary results from the human challenge trial run by Imperial:

www.imperial.ac.uk/news/233514/covid-19-human-challenge-study-reveals-detailed/

I thought the two things were particularly interesting:

• Only 50% of the participants were infected. It confirms the hypothesis that susceptibility to Covid is not homogenous - some of us are much more likely to catch it than others.
• LFTs did a good job in identifying viable virus / infectious individuals.

I saw a headline about this which was that it showed that symptoms wear earlier than previously thought-2 days after infection not 5/6. The accompanying article gave no indication which variant was used though -presumably delta?

@wintertravel1980

Preliminary results from the human challenge trial run by Imperial:

www.imperial.ac.uk/news/233514/covid-19-human-challenge-study-reveals-detailed/

I thought the two things were particularly interesting:

• Only 50% of the participants were infected. It confirms the hypothesis that susceptibility to Covid is not homogenous - some of us are much more likely to catch it than others.
• LFTs did a good job in identifying viable virus / infectious individuals.

Also notable that there was high Viral Load despite asymptomatic infection.

The accompanying article gave no indication which variant was used though -presumably delta?

"The virus used in this study was a ‘pre-Alpha’ strain of SARS-CoV-2.

It was obtained very early in the pandemic from a swab of a hospitalized patient in the ISARIC4C study."

@herecomesthsun

That seems unwise if we are due another wave in early summer.

Why would we be due another wave in the summer? We may have another wave of course, but I'm not sure why one would be "due"?

but I'm not sure why one would be "due"

If boosters have been effective and reduced infection now, but wane in line with other vaccine experience, then yes most models would have a wave due in summer. Waning immunity decides waves.

Interesting M Mina study on workers possibly returning to workplace on day 5...

TL:DR NOT a good idea, especially if they're boosted!

twitter.com/michaelmina_lab/status/1488988413948829696?s=21

That Challenge study is really interesting - surprising that the incubation period appears much shorter than was thought. Also suggests that LFTs work well to identify the most likely infectious people, so find for people to end isolation sooner if they test negative, but not if they don't