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/

ZOE estimates still falling nicely.

there’s a definite increase in reporting as well when you check their heat map.

A new variants of concern technical briefing has been published.

Here is a thread by Meg Kall summarising the main points:

twitter.com/kallmemeg/status/1551325004079534080

www.nature.com/articles/d41586-022-02026-x

No evidence that people are infectious for less than ten days on average.

Large study on:
Long-term cardiovascular outcomes of COVID-19 | Nature Medicine

that was reported by the BMJ:
Covid-19: Even mild infections can cause long term heart problems, large study finds | The BMJ

(Apologies if already posted earlier.)

Thread from Deepti Gurdasani on excess deaths:
pingthread.com/thread/1553102316139601920

And Stuart McDonald's views on this thread:
twitter.com/ActuaryByDay/status/1553286968225792000

Thanks @Lonelyplanet, neither make nice reading.

I think the rise in excess deaths is going to be multi-factorial but having witnessed recent NHS admission and ambulance usage in the household for serious illness I can’t ignore the obvious that the healthcare system we sought to protect has broken. Pretty much completely.

‘The end of covid’ never had any investment of any kind to adjust provisions and we’re suffering for it. It’s a scandal but not one people realise is happening until they need it.

She is a total nutjob, why would anyone still be quoting her? Genuinely confused!

Absolutely @Cornettoninja. Interesting that the actuary identifies rising excess deaths in hospitals and care homes.

She's a respected professional, not a "nut job"....

I think the rises in hospital deaths is going to be partly due to the fact people don’t get near inpatient care until they’re in a life threatening situation. There’s no preventative care going on at any level.

My DP recently had pneumonia (not covid but I’m not convinced we didn’t miss it). Was an inpatient for a week and sent home with his o2 levels hovering around 50 to late 70’s (I’ve no doubt he stupidly pushed for this or slyly discharged himself). He’s had a couple of rock bottom level reading resulting in ambulances which on average took two hours. He’s lucky his own stupidity (possibly unfair considering he was hypoxic) didn’t kill him.

With ambulances taking so long I’m unsurprised deaths are rising. direct or indirect consequence of covid it’s still all connected.

Wow @Cornettoninja! But yes, that'll be a main factor. Also in care home deaths, plus ambulance times.

Deepti Gurdasani is the zero Covid equivalent of Carl Heneghan. She is not a "nut job" (I would save this definition for someone like Denise Dewald, an "MD" who suggests that we all pour bleach into toilets to prevent Monkeypox) but she has got a strong confirmation bias, refuses to admit mistakes, completely dismisses alternative opinions and tends to re-write history. However, just like Carl Heneghan, she also occasionally gets things right.

At the same time, being Deepti, she always presents information from a single angle. There is another potential explanation of excess deaths she has not included - and it is (i) lack of preventive care that we have been experiencing over past 2+ years in combination with (ii) deteriorating health due to restrictions/lack of physical activity.

It is too early to draw conclusions and, of course, the increase should be investigated.

FWIW, the excess death numbers for the week ending July 23 are going to be scary. We may see ~800+ extra deaths on a single day - July 19 - the peak of the heat wave.

I realise Deepti has a strongly angled views ('nut job' is frankly a rude, ignorant and unnecessary way of describing someone that you don't agree with), which is why I posted an alternative viewpoint on the same data.

Whether or not you agree with Deepti's angle, her conclusion is valid - that the large numbers of excess deaths needs further investigation.

Further comment on this from James Ward:
twitter.com/JamesWard73/status/1553323292131459072

health metrics all heading in the right direction in England.

However starting with deaths - within 28 days of a positive test by date of death.

Very significant spike on July 19th - biggest day on day increase seen over the pandemic in absolute numbers, and if low numbers days are excluded biggest day on day percentage increase too. July 20th less marked; although that was when the 40 degree mark was broken.

year on year views

number in hospital most recent day has dropped back below 10,000 - although lets not see close to 10,000 in hospital as a particular cause for celebration. Downward trajectory is of course very much welcomed.

number on mechanical ventilator beds still well below this time last year, and again starting to fall.

finally admissions

Thanks @boys3 . Wow that spike in deaths on 19 July!

Today's ONS survey downward trend continues; aside from Northern Ireland where the trend is uncertain

Graph just for England.

No survey publication next week

The results in this bulletin are based on data collected from study workers. We are now moving to an online data collection method and postal returns for swabs and blood samples. As a result of this change, there will be a pause to the publication of our weekly bulletin on Friday 12 August 2022

next one therefore Friday 19th August.

The ZOE estimates in all regions are showing a similar dramatic fall to this image.

I think that feeds into the theory that schools are a massive driver in infection. I don’t think it would be received well, but I do think that testing and vaccinations should be targeted on this group and their households if there’s no relief on the horizon for current NHS pressures.

Schools might also be a factor in why Scotland tends to be a few weeks ahead in each wave. Scottish schools go back a few weeks earlier after summer so the subsequent chain of events is set in motion earlier.

There doesn't seem to be much appetite to manage this though. Ventilation could help but there doesn't seem to be any realistic plan for this. Sigh.

Zoe’s numbers are useful to identify turning points (peaks and troughs) but I wouldn’t use them for serious analysis. ONS is much more reliable and it shows that:

• Infections in children during the BA.5 were lower than in older groups; and
• Prevalence in children had peaked before schools closed (July 7 for 2 y/o - Yr 6 and July 10 for Yr 7-11).

Of course, schools amplify the spread but so far every single new wave has been started within young adults. This effect was particularly visible in winter with Omicron.

On vaccinating children - Denmark initially recommended vaccinations for 5-11 year olds to “slow down spread at the population level”. They have recently reversed this decision after reviewing real-life data. Vaccines for kids didn’t appear to make any meaningful impact on Denmark’s Covid transmission.

And here is another illustration of the importance of age stratified vaccine coverage.
Country A vaccinated 87% of its population and achieved an excellent uptake in younger age groups (including children).
Country B vaccinated 82% with a very high coverage in the elderly.
Both countries have got a strong culture of mask wearing. Compliance with voluntary and non-voluntary NPIs is also very high.
The differences in Covid death numbers are striking.

In fact, if we look at excess deaths, the picture is even more striking.
By focusing on wrong age groups, Hong Kong managed to surpass the UK (relative to the size of population) in the number of excess deaths.
Japan, however, continues to do well. It is now going through a big BA.5 wave but it is quite clear its death numbers are not going to spike as much as they did in HK.