Data & analysis thread, started 9th April 2022

[Jenasaurus]

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/

South East, where numbers around 3.5 times higher than early October last year

South West

Several of those regions are having a fairly dramatic upswing by the look of it. Blimey. Here we go again.

But does it matter? Most people are just putting themselves to bed for a couple of days. 70% of the uptick in hospital admissions are not for Covid. Of the 30% most are over 85, who would probably be admitted for other different respiratory illnesses if not Covid.

It matters in that it's additional pressure on NHS. Also the longer term impacts matter - covid is not just about the initial symptoms, it's about the havoc it can create on your body, even in a mild case - numerous studies on organ damage, 2.3m with long covid in UK.

I thought hospitals weren't routinely testing for covid now unless there are symptoms?
Where can I see the data that shows what proportion are admissions with covid v covid admissions? (even better if it's by region as my df was asking for his area)

It does also matter because 2 days in bed (and then a few more days of feeling rough and not up to par) also effects the healthcare workers. I know two people who have had urgent operations cancelled in the last month due to their surgeon testing positive. One of them has been given a new date in February 2023 apparently that's the first free date. They're hoping for a cancellation before then though.

If you are trying to run a hospital, or want treatment in a hospital or an ambulance if you need one, yes it matters.

Where are your 70% and 30% stats from? I'm not sure the admissions data or a comparison with the number patients hospitalised with resp infections at this time of year pre-covid would support those stats.

I saw something on Twitter about 30% the other day but can't find it now. But I thought that was the percentage of Covid hospitalisations which were "for Covid", however.

I found it. @JanglyBeads. I think it’s the figure for the number of people admitted to hospitals or ICU with covid as the primary reason they were admitted between June and August this year. But it varies widely regionally from much lower that 30% in London to just over 50% in the SW. It also comes with the usual caveats about covid as a secondary cause not necessarily being straight forward.

I suspect that significant variation might go a long way to explaining the different experiences of NHS staff tbh.

Thanks @RafaistheKingofClay

Screenshot from the latest Indie Sage broadcast shows number of people in hospital with covid as primary cause in red.

The covid 19 actuaries response group do a weekly report on hospitals:

twitter.com/COVID19actuary/status/1577956776506544128

Headlines:
"Hospital admissions with COVID are still rising sharply.

7-day average for England is up 33%.

Regionally growth is consistently high, with increases between 22% (South West) and 47% (the East).

The number of beds occupied by patients where COVID is the Primary Diagnosis is up by 25%.

So the proportion of patients with COVID where it is the primary diagnosis has fallen back to 35% after rising slightly last week.

Much of the increase seems to be people acquiring COVID while in hospital. Likely hospital acquired cases now account for 40% of all COVID admissions!

This may be a consequence of routine testing on admission being reduced as this allows COVID to spread more freely in hospitals."

It matters because catching covid in hospital when you are already sick is likely to be a problem. You might need extra care, stay in longer or be more likely to die. This will not help overstretched hospitals.

Then there is also a knock on effect with staff getting sick and needing time off. Lots of staff needing to put themselves to bed for 2 days is not going to help overstretched hospitals either.

It feels like a race to half term now. That'll drop numbers for the start of Nov, DS has mocks so I don't want him poorly.

Great easy to follow variant update from Tom Wenseleers:

threadreaderapp.com/thread/1580701680840024065.html

"the estimated growth rate advantage of level6+ variants (BQ.1.1, XBB, etc) over resident type BA.5.2 is in excess of 10% per day. All this means a resurgence is likely later in November, even if cases currently start to flatten a bit..."

Are these level variants a type of omicron or something entirely different?

My understanding (which is limited) is that they are descendants of Omicron. Because so many different variants have recently appeared, he has grouped similar ones to make it visually easier to see what is happening.

The technical briefing last week said, "They have varying Omicron backbones but some convergent receptor-binding domain (RBD) mutations (notably at S:346) which are likely to produce a degree of escape from current immunity in the UK (MODERATE confidence due to predictive and laboratory data)."

Warrior - here's a little diagram from Daniele Focosi, if you want to see how they're all linked!

Blooming 'eck! Thanks, fascinating.

I had O end jan and in the summer so guessing I may possibly have some immunity to "typhon!"🤞

@Lonelyplanet love the diagram! Although I'd obviously prefer that it was not needed in the first place of course.

ONS survey, main points below, plus comparative graph for England

The following points are for the week ending 3 October 2022 for England, and the week ending 29 September 2022 for Wales, Northern Ireland, and Scotland.

The percentage of people testing positive for coronavirus (COVID-19) continued to increase in England and Northern Ireland, increased in Wales, and the trend was uncertain in Scotland.

In England, the estimated number of people testing positive for COVID-19 was 1,513,700 (95% credible interval: 1,428,900 to 1,604,500), equating to 2.78% of the population, or around 1 in 35 people.

In Wales, the estimated number of people testing positive for COVID-19 was 74,900 (95% credible interval: 60,700 to 90,900), equating to 2.47% of the population, or around 1 in 40 people.
^^
In Northern Ireland, the estimated number of people testing positive for COVID-19 was 45,100 (95% credible interval: 35,300 to 56,100), equating to 2.46% of the population, or around 1 in 40 people.

health graphs for England

7 day average for admissions still rising but at a considerably slower rate,up just under 4. Number in hospital 20% increase, again slower as compared with a week earlier.

In absolute terms of absolute number both around double this time last year, although quite a bit of regional variation.

admissions in England

The shorter term graph (as with all that will follow) cover 1st Sep to 25th Dec

regional rates - going back to last November and then just the past month

regional admissions daily figures and the seven day average

East of England

London