Categories
News

When was the first UK coronavirus case?

Over recent days the mainstream media have been vying with each other to reveal the identity of the United Kingdom’s Covid-19 “patient zero”.

According to The Guardian on June 1st:

In the UK, the first confirmed cases of coronavirus came on 31 January when two Chinese nationals staying in a hotel in York tested positive. But as the crisis has rolled on, and the virus’s range of distinctive symptoms become more widely known, many – some in letters to the Guardian – have asked themselves if they or their loved ones could have had it earlier.

The article reports that:

A day before the first confirmed fatality from coronavirus outside mainland China was reported on 2 February this year, the death of the influential guitarist and musician Andy Gill was announced. The 64-year-old, who fronted the post-punk band Gang of Four, died of pneumonia after two weeks in St Thomas’ hospital in London.

The trajectory of Gill’s illness, which took medics looking after him in January by surprise, is now familiar – sudden deterioration, low oxygen levels and organ failure. He had fallen sick after his band returned from a trip to China in late November.

Then on June 8th The Sunday Times published an article by their chief foreign correspondent, Christina Lamb describing her own Covid-19 like symptoms in early January and reporting that:

“Thousands of people have emailed me with classic Covid symptoms from late December and January,” said Professor Tim Spector, a leading epidemiologist at King’s College London, who runs the Covid-19 Symptom Study app to which 3.8 million people have signed up.

“Either there was another virus behaving in a similar way which has since disappeared or these were early cases.”

If so, why was it not reflected in a spike in hospital admissions or deaths? “That’s the medical mystery,” said Spector.

There were, he said, possible explanations. “People who got it were young and healthy and didn’t transfer it to the elderly, obese and so on. Many of those early cases were skiers coming back from holidays. Or the virus was in some way different and didn’t have that final stage which attacks the immune system.

Christina points out that:

Officially, the first case involving a Briton was Steve Walsh, 53, a businessman from Hove… On February 6 he was diagnosed and transferred to Guy’s Hospital in London.

Before suggesting that:

It now seems likely that Walsh was not the UK’s “patient zero”. A month earlier, Susannah Ford… had fallen ill after flying back from a skiing holiday in Austria. [She] became ill on January 6, two days after her return from a new year trip.

Ford had spent a week in the resort of Obergurgl, near the Italian border, with her husband and two teenage daughters, flying back into Gatwick on January 4. She was the only one in the family who fell ill and assumed it was something she had picked up on an earlier trip to Trinidad.

Last week Ford paid for a test that shows whether the patient’s blood contains the antibodies that form when a person successfully fights off the disease. It came back positive, confirming that she had had Covid-19, although not when.“I’m convinced it’s when I was ill in January,” she said. “I can’t prove it was then but I haven’t been ill since or come into contact with people with it.”

Is there any advance on early January? Not as far as I am aware in the UK, but there have been several reports that European athletes who attended the Military World Games in Wuhan, China in October 2019 fell ill with symptoms resembling those of Covid-19.

According to an article in The Times on May 8th:

A French athlete who fell ill after competing in Wuhan in October says she has been told by doctors that Covid-19 was the likely cause of her ailment.The claim by Élodie Clouvel, an Olympic silver-winning pentathlete, has bolstered speculation that the coronavirus may have been present in the Chinese city several weeks before it was declared and then carried around the world by those who had taken part in an international competition there.

However according to the Global Times on February 24th:

A Wuhan hospital clarified the clinical diagnoses of five foreign athletes at the 7th CISM Military World Games held in Wuhan, Central China’s Hubei Province in October 2019, saying that they contracted malaria and were not infected by the novel coronavirus.

And what of the science? According to a paper published in “Infection, Genetics and Evolution” in early May:

We observe an estimated time to the Most Recent Common Ancestor, which corresponds to the start of the COVID-19 epidemic, of 6 October 2019–11 December 2019 (95% CIs). These dates for the start of the epidemic are in broad agreement with previous estimates performed on smaller subsets of the COVID-19 genomic data using various computational methods.

It seems that it’s not beyond the bounds of possibility that several athletes brought the SARS-CoV-2 virus to Europe from Wuhan in late October 2019.

Categories
News

Covid-19 Messaging in the United Kingdom

With apologies to Neil Henderson here is a sequential set of “front page news” headlines from the Great British mainstream media over the past four days:

When the Danse Macabre is over and the inevitable “second wave” of Covid-19 invades “This royal throne of kings, this sceptred isle” who do you suppose will take the blame?

Here is our glorious government’s alleged message du jour:

Plus some creative alternative messages gleaned from Twitter this morning:

[Edit – May 11th]

Here is the Daily Telegraph’s version of Boris Johnson’s speech to the once United Kingdom, pre-recorded then broadcast at 19:00 hours British Summer Time:

The mainstream media’s response this morning, via Helena Wilkinson for a change:

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

Wear homemade masks when you venture outdoors

The Guardian repeats today what we have been saying for quite some time:

The public should wear homemade masks when they venture outdoors to help reduce the spread of coronavirus, according to scientists who claim Britain’s masks policy does too little to prevent infections.

Prof Sian Griffiths, who led the Hong Kong government’s investigation into the 2003 Sars epidemic, said Britain should adopt the same approach as the US, where people are advised to make their own “cloth face coverings” and wear them in public spaces.

Trish Greenhalgh, a professor of primary care health sciences at Oxford University who recently completed a review on face masks, also advocated the use of masks in public and suggested an old T-shirt combined with kitchen paper would suffice.

The Guardian has some suggestions on how to make your own face mask, as indeed do we. Take a look here.

However some would have you believe that wearing a face mask is not such a great idea. The New Scientist for example. According to Jessica Hamzelou in a possibly paywalled article:

As cases of covid-19 continue to rise, many people are choosing to wear a face mask when out in public – but do they work?

Some have also been using cloth face coverings, but these aren’t up to the job, says Raina MacIntyre at the University of New South Wales in Sydney.

In 2015, MacIntyre and her colleagues ran a clinical trial pitting cloth masks against medical ones. The team provided 1607 healthcare workers at 14 hospitals in Hanoi, Vietnam, with either disposable medical masks or reusable cloth ones, which could be washed at home at the end of the day they were worn. Those that wore cloth masks were significantly more likely to catch a virus, the team found.

It seems that I need to point out to Jessica that just because an academic study finds that DIY masks aren’t as effective as pukka medical masks that doesn’t mean that they are useless. She continues:

But what about the rest of us? In an attempt to answer this question, Paul Hunter at the University of East Anglia, UK, and his colleagues looked at 31 published studies on the efficacy of face masks.

Overall, the evidence suggests there may be a small benefit to wearing some kind of face covering. They do seem to prevent sick people from spreading the virus, but the evidence is weak and inconsistent, says Hunter.

“Our view is that there was some evidence of a degree of protection, but it wasn’t great,” he says. “So we still don’t effectively know if face masks in the community work.”

It seems masks “prevent sick people from spreading the virus”. You can spread the SARS-CoV-2 virus before you show any symptoms, so wear a mask to prevent other people possibly catching your bugs!

Scientists say so, and somewhat grudgingly so does the New Scientist. In the current climate I wouldn’t go out in a public place without one:

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