Categories
News

Covid-19 in the UK in June 2020

Today is a Tuesday, which means that The Office for National Statistics have just released their latest weekly “death certificate” data, which brings us up to May 22nd. The “main points” are:

  • A total of 43,837 deaths involving COVID-19 were registered in England and Wales between 28 December 2019 and 22 May 2020 (year to date).
  • In England, including deaths that occurred up to 22 May but were registered up to 30 May, of those we have processed so far, the number involving COVID-19 was 42,210; the comparative number of death notifications reported by the Department of Health and Social Care (DHSC) on GOV.UK was 32,666 and NHS England numbers, which are deaths in hospitals only, showed 25,875 deaths.
  • In Wales, including deaths that occurred up to 22 May but were registered up to 30 May, of those we have processed so far, the number involving COVID-19 was 2,122; the comparative number of death notifications reported by the DHSC on GOV.UK was 1,260 and Public Health Wales (PHW) numbers, which come from the same source as the DHSC figures but are continuously updated, showed 1,275 deaths.
  • In England, the number of deaths involving COVID-19 in care homes that were registered by 22 May was 12,142, while in Wales the number of deaths was 591.
  • The Care Quality Commission (CQC) provides numbers of deaths involving COVID-19 in care homes in England that were notified between 10 April and 29 May, which showed 11,186 deaths, of which 531 occurred in the week up to 29 May.
  • The Care Inspectorate Wales (CIW) provides the number of deaths involving COVID-19 in care homes in Wales that occurred between 17 March and 29 May, which showed 462 deaths, of which 35 occurred in the week up to 29 May.

Here’s the “graphic” representation of those numbers:

Here is an alternative view on weekly “death occurrences in England and Wales” over recent years from EuroMOMO:

Publishing the number of death occurrences is outside EuroMOMO’s terms of reference, but their “Z-scores” provide a graphic illustration of how badly England in particular has been doing over the course of the 2020 Covid-19 epidemic.

[Edit – June 9th]

The latest weekly data from the ONS has been released:

  • The number of deaths registered in England and Wales in the week ending 29 May 2020 (Week 22) was 9,824; this was 2,464 fewer than in Week 21 but 20.2% (1,653 deaths) higher than the five-year average.
  • Of the deaths registered in Week 22, 1,822 mentioned “novel coronavirus (COVID-19)”, the lowest number of deaths involving COVID-19 in the last eight weeks; this accounts for 18.5% of all deaths and is 767 deaths fewer than in Week 21.
  • People aged 90 years and over continued to have the highest number of COVID-19 deaths in Week 22.
  • In Week 22, the proportion of deaths occurring in care homes decreased to 25.5% while deaths involving COVID-19 as a percentage of all deaths in care homes decreased to 28.2%.
  • In Week 22, the number of deaths in care homes was 819 higher than the five-year average, while in hospitals the number of deaths was 30 fewer than the five-year average; the total number of excess deaths involving COVID-19 continued to decrease.

Here’s a graphic representation of the overall “excess death” numbers:

By way of explanation:

The number of deaths was around or below the five-year average up to Week 12. The number of deaths increased between Weeks 13 and 16 before decreasing between Weeks 17 and 22, with the exception of Week 20 where the deaths increased.

The number of death registrations in Week 20 was impacted by the early May Bank Holiday, which took place on Friday 8 May 2020 (in Week 19). The number of deaths registered on the early May Bank Holiday fell to 88 deaths compared with 2,950 deaths registered on the previous Friday (Friday 1 May 2020). Trends seen in Week 19 and Week 20 should therefore be interpreted with caution, as deaths not registered on the early May Bank Holiday were likely registered in the following week (Week 20). Week 22 also included the late May Bank Holiday but as this was on a Monday, we have seen less of an effect on death registrations.

The number of death registrations involving the coronavirus (COVID-19) decreased from 2,589 in Week 21 to 1,822 in Week 22. Of all deaths registered in Week 22, 18.5% mentioned COVID-19; this is down from 21.1% in Week 21.

Similar patterns can be seen for England and Wales separately, with the number of deaths in England decreasing from 11,586 in Week 21 to 9,228 in Week 22, which was 1,621 deaths higher than the Week 22 average. Of the Week 22 deaths, 18.6% (1,715 deaths) involved COVID-19 in England.

In Wales, the number of deaths decreased from 692 deaths in Week 21 to 587 deaths in Week 22, 41 deaths higher than the Week 22 average. Of these Week 22 deaths, 17.9% (105 deaths) involved COVID-19 in Wales.

[Edit – June 10th]

Today’s Downing Street Briefing was somewhat unusual. Boris Johnson was master of ceremonies, and what’s more he was accompanied by some scientists! Boris began by referring to “the progress we as a country have made against our 5 tests for adjusting lockdown”

Instead of listening to what was said, let’s take a look at some of the data that was referred to shall we?


The overall aim is evidently to “reduce the rate of infection to manageable levels” whilst “not risk[ing] a second peak of infections that overwhelms the NHS”. Boris hopes that the latest lockdown “adjustments” will be “underpinned by NHS Test and Trace”, so let’s also see how that’s coming along shall we? As luck would have it the Independent Sage committee also reported this yesterday:


Categories
Testing

Covid-19 testing in the UK

On April 2nd 2020 (not the first!) the UK Government’s web site published a press release stating that:

The UK will carry out 100,000 tests for coronavirus every day by the end of this month, Health Secretary Matt Hancock pledged today.

Increased testing for the NHS will form part of a new 5-pillar plan, bringing together government, industry, academia, the NHS and many others, to dramatically increase the number of tests being carried out each day.

Professor John Newton the Director of Health Improvement for Public Health England, has been appointed to help deliver the new plans and bring together industry, universities, NHS and government behind the ambitious testing targets.

So how is Matt’s pledge and John’s delivery plan looking at the end of April? According to the Department of Health and Social Care‘s latest daily update:

As of 9am 30 April, there have been 901,905 tests, with 81,611 tests on 29 April.

Not quite there yet then, though there is still one more April update to come! Much more recently another Government press release on April 28th announced that:

Anyone in England with symptoms of coronavirus who has to leave home to go to work, and all symptomatic members of the public aged 65 and over, will now be able to get tested, the government has announced today.

This will mean people who cannot work from home and those aged 65 and over can know for sure whether they have coronavirus and need to continue isolating.

Members of their households with symptoms – a new continuous cough or high temperature – will also be eligible for testing.

Anyone eligible can book a test using an online portal.

The government also announced that NHS staff, care home staff and care home residents will be eligible for testing whether or not they have symptoms.

How’s that coming along do you suppose? I’m over 65 and I’d very much like to know for sure whether I have had coronavirus. I even have some of the symptoms! However there is evidently a problem. The Government’s online testing portal told a familiar tale yesterday evening:

Today I discovered via Twitter that somebody else managed to get further through the process than I did, only to discover:

I myself am also forced to wonder why on Earth a United States credit checking agency such as TransUnion should be involved in the process of obtaining a long overdue test for a UK citizen suffering from the symptoms of Covid-19?

Answers on a virtual postcard in the space provided for that purpose below! Should I receive an answer to that question I’ll pose another one:

What does the UK Government make of this proposal in the British Medical Journal for “Mass periodic testing” of the citizens of this sceptred isle?

At the end of (say) 3 weeks of lock-down all households and care homes would return self-taken swabs taken on that date from all residents. All residents would test negative in most homes, so most people could resume normal life within a month of starting the lock-down.

Meanwhile on the NHS front line:

[Edit – May 1st]

Here is the BBC’s video of this evening’s Covid-19 daily briefing from Downing Street, hosted by Matt Hancock:

Fast forward to 36:40 where Channel 4’s Victoria Macdonald asks:.

There was a report in the HSJ that a sample would only be counted once it had been processed, but that testing has been changed and it’s counted once it’s been posted out. Is that the case?

Matt swiftly passed that buck to Professor John Newton, and it’s not until 38:40 that Victoria receives an answer:

There’s been no change to the way that tests are counted. As we’ve developed new ways of delivering tests we’ve taken advice from officials as to how this should be counted.

So, the tests that are within the control of the programme, which is the great majority, are counted when the tests are undertaken in our laboratories. But any test which goes outside the control of the programme, they’re counted when they leave the programme, so that is the tests that are mailed out to people at home and the tests which go out in the satellite. So that is the way they are counted, have always been counted, and the way we were advised to count them by officials.

So that’s the way they are counted, have always been counted, and the way we were advised to count them by officials.

According to Matt Hancock:

That’s all set out on gov.uk

Whilst according to the BBC:

The total testing figure includes 27,497 kits which were delivered to people’s homes and also 12,872 tests that were sent out to centres such as hospitals and NHS sites. However, these may not have been actually used or sent back to a lab.

According to my hasty mental arithmetic:

122,347 – 27,497 – 12,872 = 81,978

Those mysterious “official” bean counters have a lot to answer for!

[Edit – May 8th]

The UK Government’s Covid-19 “contact tracing” smartphone app created by NHSX is now available to residents of the Isle of Wight as part of an initial trial. Here’s an initial review of the app:

Isi’s Dad’s thoughts? Here’s a brief summary:

The app is named NHS COVID-19, and is described by the NHS as “an automated system for rapid symptom reporting, ordering of swab tests, and sending targeted alerts to app users”. It’s one of three parts of the trial which has just started here, the other two being:

  • “web-based Contact Tracing and Advisory Service (CTAS) and increased capacity to provide tailored alerts to all contacts by phone.”
  • “widespread availability of rapid swab testing kits to make sure confirmed cases remain in isolation, and support rapid detection and isolation of higher-risk contacts.”

This is quite different from what has been generally reported: the NHS sees the app primarily for rapid symptom reporting and the ordering of swab test kits.

Installing and configuring the app is simple, provided that you have an iPhone running iOS 11 or later, or a compatible Android phone, about which I will say no more…

Early indications here are that this app protects the user’s privacy, doesn’t track users at all, doesn’t flatten batteries, and is unobtrusive to the point where you can’t even tell whether it is detecting contacts. It doesn’t appear to be the contact tracing app which was expected, though: it’s not ‘track and trace’ so much as ‘diagnose and test’, and may explain where Boris Johnson intends sending his promised 200,000 test kits a day.

Categories
News

Covid-19 in the UK in May 2020

We’re starting this thread a couple of days early, because here in the United Kingdom a variety of things have changed regarding the reporting of Covid-19 “statistics”.

First of all the daily reports from the Department of Health and Social Care: now include “all deaths where a positive test for COVID-19 has been confirmed”, not just those “in hospital”. As the explanation on the DHSC web site puts it:

From 29 April 2020, DHSC are publishing as their daily announced figures on deaths from COVID-19 for the UK a new series that uses improved data for England produced by Public Health England (PHE). These figures provide a count of all deaths where a positive test for COVID-19 has been confirmed, wherever that death has taken place. Figures for Scotland, Wales and Northern Ireland have already begun to include deaths outside hospitals, so this change will ensure that the UK-wide series has a shared and common definitional coverage. This updated statement explains what the new data are and how they differ from both the data series previously published by DHSC and the figures produced by the ONS.

Separately, to improve the timely availability of data on deaths in care homes involving COVID-19, the ONS and the Care Quality Commission (CQC) agreed to publish from 28 April 2020 provisional counts of deaths in care homes, based on statutory notifications by care home providers to CQC. A separate explanatory statement about these new data has been published jointly by the ONS and CQC.

In addition to that change there is now a new section of the UK Government web site devoted to “National COVID-19 surveillance reports“. The most recent report at the moment:

Summarises the information from the surveillance systems which are used to monitor the Coronavirus Disease 2019 (COVID-19) pandemic in England.

The report is based on week 16 (data between 13 April and 19 April 2020) and where available daily data up to 22 April 2020.

COVID-19 is the disease name and SARS-CoV-2 is the virus name.

The report includes sections devoted to UK “Community surveillance”, “Primary care surveillance”, “Secondary care surveillance”, “Virological surveillance” and “Mortality surveillance”. In the latter section it points out that:

In week 16 2020 in England, statistically significant excess mortality by week of death above the upper 2 z-score threshold was seen overall, by age group in the 15-64 and 65+ year olds and sub nationally (all ages) in all regions (North East, North West, Yorkshire & Humber, East & West Midlands, East of England, London and South East & West regions) after correcting GRO disaggregate data for reporting delay with the standardised EuroMOMO algorithm (Figure 18). This data is provisional due to the time delay in registration; numbers may vary from week to week.

The recent “spike” appears to be statistically significant! However despite that, this report and the rest of the virtual paperwork emanating from the UK Government still fail to address the question we posed last week:

How will the UK Government build on the amazing community solidarity we have seen in the past few weeks and reassure the citizens of the nation that lifting the lockdown won’t result in further out-of-control outbreaks?

Whilst we continue to wait for an answer, here are the new “positive test” daily death numbers from the DHSC:

They do of course beg the question of how many “untested” deaths due to Covid-19 are occurring. Regular readers will be aware that we have been following the modelled future death projections of James Annan. Here’s his first update using the DHSC’s new numbers:

[Edit – May 5th]

The Office for National Statistics have released their latest weekly “death certificate” data. Here are the “main points” from their report:

  • The provisional number of deaths registered in England and Wales in the week ending 24 April 2020 (Week 17) was 21,997, a decrease of 354 deaths registered compared with the previous week (Week 16); this is the first decrease in the number of deaths since the week ending 20 March 2020 (Week 12) but is 11,539 more than the five-year average for Week 17.
  • Of the deaths registered in Week 17, 8,237 mentioned “novel coronavirus (COVID-19)”, which is 37.4% of all deaths; this is a decrease of 521 deaths compared with Week 16 (39.2% of all deaths).
  • The number of deaths in care homes (from all causes) for Week 17 was 7,911, which is 595 higher than Week 16. The number of deaths in hospitals for Week 17 was 8,243, which is 1,191 lower than Week 16.
  • In London, over half (50.5%) of deaths registered in Week 17 involved COVID-19; the North West and North East also had a high proportion of COVID-19 deaths, accounting for 38.8% and 38.0%, respectively, of deaths registered in these regions.
  • In Wales, there were 413 deaths registered in Week 17 involving COVID-19, accounting for 36.7% of all deaths registered in Wales.
  • Of deaths involving COVID-19 registered up to Week 17, 71.8% (19,643 deaths) occurred in hospital with the remainder mainly occurring in care homes (5,890 deaths), private homes (1,306 deaths) and hospices (301 deaths).

Here are those numbers in graphic detail:

[Edit – May 12th]

The latest weekly Covid-19 update has been issued by the Office for National Statistics. Here’s the summary on Twitter:

33,337 / 21,647 = 1.54

[Edit – May 19th]

The latest weekly update from the ONS has been published:

Plus some additional detail:

Deaths in care homes made up 36.0% of all deaths in Week 17, 35.7% in Week 18 and 33.6% in Week 19 (Figure 7). Between Week 18 and Week 19, the number of deaths in care homes decreased by 33.7% to 4,248. However, the proportion of care home deaths that involved COVID-19 continued to increase, and 39.2% of all deaths in care homes involved COVID-19 in Week 19.

Watch this space!

Categories
News

Covid-19 in the United Kingdom

Nassim Taleb is fond of one pagers these days, but he’s also into the precautionary principle, fat tails and “black swans”. Based on those principles he has argued for action on “climate change”:

We have only one planet. This fact radically constrains the kinds of risks that are appropriate to take at a large scale. Even a risk with a very low probability becomes unacceptable when it affects all of us – there is no reversing mistakes of that magnitude.

By way of a change, here’s an extract from a recent COVID-19 “note” of his:

The general (non-naive) precautionary principle delineates conditions where actions must be taken to reduce risk of ruin, and traditional cost-benefit analyses must not be used. These are ruin problems where, over time, exposure to tail events leads to a certain eventual extinction. While there is a very high probability for humanity surviving a single such event, over time, there is eventually zero probability of surviving repeated exposures to such events. While repeated risks can be taken by individuals with a limited life expectancy, ruin exposures must never be taken at the systemic and collective level. In technical terms, the precautionary principle applies when traditional statistical averages are invalid because risks are not ergodic.

Cartoon by John Farmer

I’m more used to posting the the University of Washington’s Polar Science Center’s modelled Arctic sea ice volume graphics, but here’s the UoW’s Institute for Health Metrics and Evaluation‘s UK COVID-19 death projections for a change:

Here in the once Great Britain we won’t have to wait a few decades to get a feel for how good Chris Murray’s coronavirus model is:

Here are the current official statistics from the United Kingdom’s Department of Health and Social Care:

As of 9am on 7 April, 266,694 tests have concluded across the UK, with 14,006 tests carried out on 6 April. Some individuals are tested more than once for clinical reasons.

213,181 people have been tested, of whom 55,242 tested positive. Today’s figure for people tested does not include Manchester and Leeds due to a data processing delay. The tests concluded figure excludes data from Northern Ireland.

As of 5pm on 6 April, of those hospitalised in the UK who tested positive for coronavirus, 6,159 have died.

and Office for National Statistics:

The provisional number of deaths registered in England and Wales in the week ending 27 March 2020 (Week 13) was 11,141; this represents an increase of 496 deaths registered compared with the previous week (Week 12) and 1,011 more than the five-year average.

A total of 150,047 deaths were registered in England and Wales between 28 December 2019 and 27 March 2020 (year to date), and of these, 647 involved the coronavirus (COVID-19) (0.4%); including deaths that occurred up to 27 March but were registered up to 1 April, the number involving COVID-19 was 1,639.

For deaths that occurred up to 27 March, there were 1,568 deaths in England registered by 1 April involving COVID-19 compared with 1,649 deaths reported by NHS England for the same period in a newly published dataset.

Of the deaths registered in Week 13, 539 mentioned “novel coronavirus (COVID-19)”, which is 4.8% of all deaths; this compared with 103 (1.0% of all deaths) in Week 12.

This is slightly lower than the figures reported by the Department of Health and Social Care (DHSC) for Week 13 (739) as it takes time for deaths to be reported and included in Office for National Statistics (ONS) figures.

Of deaths involving COVID-19 in Week 13, 92.9% (501 deaths) occurred in hospital with the remainder occurring in hospices, care homes and private homes.

Please note, where Easter falls in previous years will have an impact on the five-year average used for comparison.

[Edit – April 8th PM]

Here’s the current Kings College COVID Symptom Tracker map for South West England, dated April 1st:

For some strange reason North Devon is even more of a hot spot than Cornwall. Second home owning surfers down from London for the weekend?

Here’s the symptom tracker explanatory webinar:

Meanwhile, and only marginally off topic, whilst Donald Trump berates the World Health Organization for being too China-centric:

the IHME projects peak COVID daily deaths in the once United States will occur in a mere 4 days time:

P.S. James Annan, a “climate modeller though probably doing more epidemiology in the last couple of weeks”, has published a pertinent article on his blog entitled “Dumb and dumber“:

All these people exhorting amateurs to “stay in their lane” and not muddy the waters by providing analyses and articles about the COVID-19 pandemic would have an easier job of it if it wasn’t for the supposed experts churning out dross on an industrial scale.

The article describing [the IHME] method is here, it’s some sort of fancy curve fitting that doesn’t seem to make much use of what is known about disease dynamics. I may be misrepresenting them somewhat but we’ll see below what a simple disease model predicts.

James goes on to present the outputs of his “simple disease model” for the UK:

My model predicts a total of 8k deaths next week, with a 5-95% range of 4-19k. Yes it’s a wide uncertainty range, I think my prior on Rt is probably still too broad as I don’t really expect to see a value lower than 0.5 or higher than 1.5 (and these are just the 1sd spread limits in the above). But I am very optimistic that the median estimate generated by this method is better than the experts have provided, and they don’t seem to believe that anything in the lower half of my range is possible at all.

It will be exceedingly interesting to discover how all the numbers look on or about April 16th!

[Edit – April 9th]

Today let’s take a look at the “official” UK novel coronavirus death forecasts from Neil Ferguson’s team at Imperial College, with the help of James Annan’s latest article. He covers a variety of countries, but sticking with the United Kingdom for the moment:

Here is the current UK forecast…before today’s figure comes out.

This is the IC forecast for the UK for this week again (pink plume again, below). The data were already outside their range by yesterday. What on earth were they thinking?

What indeed! The Imperial College model seems to habitually “over forecast” the number of deaths due to COVID-19 here in the UK. Of course time will tell how much “under reporting” there has been during the pandemic.

[Edit – April 12th]

James Annan has produced an animation showing how his model evolves over time as more data becomes available:

His current forecast looks like this:

[Edit – April 14th]

Another week’s worth of COVID-19 mortality data has been released by the ONS. Included in the news release is this graph:

As suspected:

Nick Stripe, head of health analysis and life events at the ONS said:

“The latest comparable data for deaths involving COVID-19 with a date of death up to 3 April, show there were 6,235 deaths in England and Wales. When looking at data for England, this is 15% higher than the NHS numbers as they include all mentions of COVID-19 on the death certificate, including suspected COVID-19, as well as deaths in the community.

“The 16,387 deaths that were registered in England and Wales during the week ending 3 April is the highest weekly total since we started compiling weekly deaths data in 2005.”

[Edit – April 15th]

James Annan has submitted a paper about his Covid-19 epidemic model to medRxiv:

What’s more the R Markdown source code is available via GitHub!

https://github.com/jdannan/COVID-19-operational-forecast

[Edit – April 18th]

I discovered something deeply disturbing today. Whilst I happily admit to being an old sceptic, I generally subscribe to the “cock up” theory of history.

However today I noticed that my surfing tweet in the comments below, and retweeted at the time by Andrew “Cotty” Cotton, looked rather strange. I clicked through the link to Twitter, only to discover this:

Now I didn’t delete that Tweet, and Cotty wouldn’t have been able to do that even if he wanted to. Which does rather beg a question or two:

Who did delete my (subversive?) surfing images? And what are they so concerned about?

[Edit – April 21st]

The latest batch of weekly death certificate data has been released by the ONS. Would you like to play “spot the difference”?

  • The provisional number of deaths registered in England and Wales in the week ending 10 April 2020 (Week 15) was 18,516; this represents an increase of 2,129 deaths registered compared with the previous week (Week 14), is 7,996 deaths more than the five-year average and is the highest weekly total since Week 1 in 2000.
  • Of the deaths registered in Week 15, 6,213 mentioned “novel coronavirus (COVID-19)”, which is 33.6% of all deaths; this compares with 3,475 (21.2% of all deaths) in Week 14.
  • In London, over half (53.2%) of deaths registered in Week 15 involved COVID-19; the West Midlands also had a high proportion of COVID-19 deaths, accounting for 37.0% of deaths registered in this region.
  • Total deaths registered by place of occurrence between Week 11 (when first COVID-19 deaths were registered) and Week 15, the number of deaths in care homes has doubled by 2,456 deaths (99.4% increase); whilst we have seen a 72.4% increase (3,603 deaths) in hospitals, and 51.1% increase in private homes (1,392 deaths).
  • Of deaths involving COVID-19 registered up to Week 15, 83.9% (8,673 deaths) occurred in hospital with the remainder occurring in care homes, private homes and hospices.
  • Week 15 included the Good Friday bank holiday; the five-year average does show a decrease in registrations over the Easter holiday; however, the Coronavirus Act 2020 allowed registry offices to remain open over Easter, which may have reduced any drop in registrations for Week 15 2020.

[Edit – April 28th]

The ONS have released their latest weekly “death certificate” data:

  • The provisional number of deaths registered in England and Wales in the week ending 17 April 2020 (Week 16) was 22,351; this represents an increase of 3,835 deaths registered compared with the previous week (Week 15) and 11,854 more than the five-year average; this is the highest weekly total recorded since comparable figures begin in 1993.
  • Of the deaths registered in Week 16, 8,758 mentioned “novel coronavirus (COVID-19)”, which is 39.2% of all deaths; this compares with 6,213 (33.6% of all deaths) in Week 15.
  • In London, over half (55.5%) of deaths registered in Week 16 involved COVID-19; the North West and North East also had a high proportion of COVID-19 deaths, accounting for 42.3% and 41.1% respectively of deaths registered in these regions.
  • Of deaths involving COVID-19 registered up to Week 16, 77.4% (14,796 deaths) occurred in hospital with the remainder occurring in care homes, private homes and hospices.
  • The number of overall deaths in care homes for Week 16 was 7,316; this is 2,389 higher than Week 15, almost double the number in Week 14 and almost triple the number in Week 13.
  • Week 16 included the Easter Monday bank holiday, and the five-year average shows a decrease in registrations over the Easter holiday; however, the Coronavirus Act 2020 allowed registry offices to remain open over Easter, which may have reduced any drop in registrations for Week 16 2020.

Here’s the cumulative totals graph

Continued over here:

Covid-19 in the UK in May 2020