Coronavirus Sars-CoV-2/Covid-19 Megathread

[Iormlund]

Given the amount of colds I catch every season I should probably donate my plasma to mankind.

I have one right now. Can I be: immune? 

[Valmy]

We have been doing a massive Corona Virus outdoors experiment that last couple days. I guess we will have lots of data about how contagious this thing is outdoors very soon.

[Tamas]

We have been doing a massive Corona Virus outdoors experiment that last couple days. I guess we will have lots of data about how contagious this thing is outdoors very soon.

.

Yeah we also had thousands pile up in a protest in London yesterday. Judging by the pictures the police strategically didn't turn up because if they did they would have had to disperse it, what's with there being more than 6 people and no social distancing. Would have been bad PR.

[Maladict]

Latest figures seems to suggest 5.5% of the population now has antibodies. This herd immunity strategy is really paying off, we should get there by 2025 or so

[celedhring]

Spain is releasing the second wave of the antibody survey later today. My guess is the data won't change much from the first one.

[jimmy olsen]

Yikes
https://twitter.com/guardiannews/status/1268500051455852544

St Petersburg death tally casts doubt on Russian coronavirus figures
City issues 1,552 more death certificates in May than last year, but Covid-19 toll was 171

[Sheilbh]

Interesting piece in the FT on data issues in Spain - I imagine every country has similar issues around data quality especially with so many factors and issues with something very new. In a way, it's like the scientific knowledge about this, in a way it's incredible how much of a challenge it is to know anything about something that's utterly changed our lives, in another way it's incredible we know anything about something that didn't really exist 6 months ago:

Flawed data casts cloud over Spain's lockdown strategy
Erratic numbers create uncertainties for policymakers and the public
Daniel Dombey in Madrid and John Burn-Murdoch in London 7 HOURS AGO

This week Spain reported what should have been cause for huge celebrations: according to the official coronavirus statistics, there were no new deaths in the 48 hours to midday on Tuesday.

Yet on the same day, at least two regions — Madrid and Castile-La Mancha — reported 17 deaths from the virus between them. The health ministry insisted it had not been informed of any death that had taken place in the previous 24 hours.

The confusion, in one of the countries worst hit by the pandemic, underlines what experts say is a big challenge as Spain relaxes its lockdown: a misleading impression that the coronavirus threat is past, which could encourage people to behave recklessly.

 "The figures are driving us crazy," said Jeffrey Lazarus, head of the Health Systems Research Group at the Barcelona Institute for Global Health.

"[The number] zero has a lot of power . . . It's causing a false sense of security among the population."

Speaking in parliament on Wednesday, Pedro Sánchez, Spain's prime minister, hailed the zero deaths figure as "an achievement of everyone". His government says it is a vindication of Spain's harsh lockdown and its success in bringing down the daily death toll from a peak of 950 two months ago.

But some researchers say the government figures are deeply compromised because of revisions in ways the ministry of health counts the data.

"In real time, changes in detection or reporting can make it harder to work out the actual shape of the current epidemic," said Adam Kucharski, an epidemiologist at the London School of Hygiene and Tropical Medicine. 

The Spanish government has stopped explicitly listing how many deaths have been reported in the last 24 hours, switching to a contentious measure of how many people have died in the past seven days. Nor is it updating the overall tally of deaths as frequently or completely as before.

Breaking with its past practice, the ministry's new policy adds new deaths to the running total only if they occur in the 24 hours before each daily bulletin. All other deaths are only added once a week, when the figures are revised.

After the changes were introduced in May, the death rates recorded by the health ministry plummeted. Its cumulative tally of deaths since the beginning of the outbreak also fell by almost 2,000.

"There is 100 per cent for sure a data problem," said Mr Lazarus.

In the latest confusion, on Wednesday the ministry of health figures increased the tally of people who had died over the past seven days from 34 to 63. But at the same time the cumulative total they gave for all those who had died since the outbreak only went up by just one, to 27,128.

The problems with the figures are all the more serious since they come as the country is phasing out its lockdown measures.

"To come out and say there are zero deaths when deaths are taking place can create a lot of misunderstanding," said Rafael Bengoa, a former Basque region minister for health and director at the World Health Organization. 

"We are improvising at a moment when the population needs clear information."

He said that Spain was bringing the pandemic under more control than other hard hit European countries and discounted any suggestion of political manipulation of the figures. Despite the problems with the Spanish data, the country's death counts are an order of magnitude smaller than those in Italy and UK, which have averaged 85 and 247 a day respectively over the last seven days.

One problem is that the country's regions — which run autonomous health systems under Spain's decentralised government — have on several occasions provided late or inaccurate death numbers.

Lags are all the more important as the the government has pledged to focus on up-to-speed information. Late data falls outside the ministry of health's criteria for the main coronavirus figures it produces, bringing totals down.

The Spanish government argues its focus on detecting infections as rapidly as possible — rather than concentrating on how many people are hospitalised or have died — fits the current stage of the epidemic. 

"We are interested in the cases that are active now, that can infect people today, where symptoms have developed over the last one or two weeks," said a senior Spanish health official.

Officials say that since the start of the outbreak, the typical notification time of new cases after the emergence of symptoms has come down from two-three weeks to 24-48 hours.The senior health official said there was now only a "very small number of cases" where information from the regions was arriving with a lag. 

But Spanish data has been more volatile than that of any other rich country. Just a week ago, the country increased its overall tally of people dying from all causes during the pandemic to 43,000 — up by 12,000.

The overnight change — due to revisions rather than a sudden surge in deaths — briefly gave the country the world's highest excess mortality rate, the measure most widely used to compare the pandemic's toll across countries. 

Asked at the weekend about the data revisions, Mr Sánchez, said the country could be proud of its "absolute transparency".

But he acknowledged that, "until some months pass and the virus is definitively overcome . . . we are not going to know exactly what the number of deaths is".

[Legbiter]

We've not found any new cases for over a week now. Only 2 people have an active infection in the entire country. Bookings are exploding from tourists eager to vacation... We might get small, localized outbreaks in the future but that will be handled at the lowest municipal level.

[Valmy]

We've not found any new cases for over a week now. Only 2 people have an active infection in the entire country. Bookings are exploding from tourists eager to vacation... We might get small, localized outbreaks in the future but that will be handled at the lowest municipal level.

Recent news on the pandemic is very encouraging I think. I mean I guess I am not totally plugged in on how things are going today in my country.

[celedhring]

The changes in reporting will make the Spanish data eventually better, since they are now collecting much more particular data of each case that before was only being collected piecemeal. The change between systems, however, has been a mess and communicated poorly. They should have kept the old one running alongside the new one until it was fully validated.

One of the issues our health care system had is the fragmentation of reporting systems given health care is devolved to the regions (all 17 of them). Heck, even within the regions data systems are still fragmented (in Catalonia, for example, my GP still can't access some of my tests unless I collect the results and physically take them to her).

Now, I think, in part, the reporting change has been communicated poorly intentionally. "No deaths today" (the crux is that deaths are now anotated on the actual day of them happening instead of the day of notification, and there's a lag that artificially deflates the "deaths yesterday" figure until it is updated in the following days) is too tempting a headline to put an asterisk after. This has sown confusion and thrown doubts about the numbers, but the numbers themselves will be fine once they finish the transition.

[Sheilbh]

The changes in reporting will make the Spanish data eventually better, since they are now collecting much more particular data of each case that was only being collected piecemeal before. The change between systems, however, has been a mess and communicated poorly. They should have kept the old one running alongside the new one until it was fully validated.

Now, I think, in part, it has been communicated poorly intentionally. "No deaths today" (the crux is that deaths are anotated on the actual day of them happening instead of the day of notification, and there's a lag that artificially deflates the "deaths yesterday" figure until it is updated in the following days) is too tempting a headline to put an asterisk after. This has sown confusion and thrown doubts about the numbers, but the numbers themselves will be fine.

Yeah it does seem a little complex and kind of needing both systems running at once. The FT data journalist, John Burn-Murdoch did a really interesting thread on this on Twitter along with the article, I actually think the thread explains the issues a little bit more:

NEW: much has been made this week of Spain recording zero new Covid deaths for two successive days.

Spanish Prime Minister Pedro Sanchéz called it "A success for all".

Unfortunately it's also nonsense.

Story by me & @danieldombey
: https://ft.com/content/77eb7a13-cd26-41dd-9642-616708b43673

Thread follows:
1/ On Sun, Mon & Tues Spain's total cumulative number of Covid deaths remained flat on 27,127.

This was widely reported as zero new deaths for two days in a row, and indeed that line was trumpeted by the Prime Minister

EL PAÍS
@el_pais
· Jun 3
TV en Directo | Sánchez: "Hoy tenemos 0 fallecidos en España como consecuencia del covid. Es un éxito de todos" http://bit.ly/3cqMXkf

2/ But if you look at the Spanish govt's daily data releases, you'll spot a new footnote that appeared around a week ago: https://mscbs.gob.es/profesionales/saludPublica/ccayes/alertasActual/nCov-China/documentos/Actualizacion_125_COVID-19.pdf
"Only the cases in which the date of death is the day before the time of writing this report are added to the total on a daily basis"
3/ So Spain is only adding deaths that took place the day before the report is published (!)

Not *registered* the day before, *happened* the day before.

Given how long it takes deaths to be registered, especially in a system with autonomous regions, this is absurd.
4/ And what's more, they don't go back later on and say "okay some more deaths have been processed from earlier in the week, let's add those to the total".

They just ... don't add those deaths in.
5/ e.g on Mon & Tues when Spain was celebrating zero deaths, Madrid actually recorded 11 and then 12 new deaths, but since they hadn't occurred the day before the report, they were ignored: https://abc.es/sociedad/abci-simon-admite-datos-sobre-numero-fallecidos-esta-dando-problemas-202006021827_noticia.html


They still haven't been added to the cumulative total.
6/ The situation is nothing short of ridiculous, and these ... incredible ... zero deaths figures come at a critical time when Spain is coming out of lockdown.

As @JVLazarus
told me, "The figures are driving us crazy" and "causing a false sense of security among the population."
7/ To be clear, this is what Spain's data for daily deaths looks like over the last week or so

Guess when they introduced the counting method change...
8/ Now, it's not as though other countries haven't done things with Covid deaths data.

This week UK reported 111 new deaths while quietly increasing overall total by 556. Not good, but it's standard practice when new info emerges, and doesn't paint artificially rosy picture
9/ To give an idea of what Spain's "method" does: if England adopted the same approach, yesterday NHS would have reported 20 new deaths, not 179. A nice little reduction of 90%.

England would have reported deaths in the teens and 20s all week. 152 for the week, instead of 995.
10/ Now, nobody is suggesting Spain is secretly seeing hundreds of deaths per day. Its numbers were lower than the UK's last time we could trust them, and were trending down.

But we don't know what the true number is. We have no idea.
11/ Spain says it will fully revise its total once a week to include the deaths it's ignoring on a daily basis, but a) this will give us a new type of number that no other country is publishing, making comparability impossible, and b) it makes Spain's own historical data useless.
12/ We cannot say this is a deliberate move by the government to massage the figures downwards at a critical time, but we do know two things:
• Government health officials know the problem with the daily numbers
• The government has loudly hailed zero deaths as a success
13/13 Finally, I'm unimpressed with Johns Hopkins, ECDC etc who take Spanish data at face value and re-publish (we stopped using Spanish data a week ago).

It's increasingly clear these orgs just launder dodgy data. Add a badge of reliability to junk figures. Zero due diligence.
14/13 End note: everyone should follow @kikollan
, who has been tirelessly reporting on the mess that is Spanish Covid data for weeks now (and does consistently great work on other topics too).

He published a great round-up of all the problems here
https://elpais.com/politica/2020/05/31/actualidad/1590937360_892099.html

[celedhring]

Kiko Llaneras - the twitter account they recommend in the article - is a fantastic data guy on all things Spanish. That's actually who I get my info from... Sadly I don't think he publishes in English.

[Iormlund]

12/ We cannot say this is a deliberate move by the government to massage the figures downwards at a critical time...:

Oh yes, yes we can.

That's exactly what is happening.

[Sheilbh]

Really interesting analysis of the non-covid excess deaths by the ONS. Basically they think these excess deaths have five explanations:
1. COVID was present but undiagnosed, particularly in the presence of other co-morbidities and the absence of a positive test
2. Reluctance to seek care or a delay in receiving care for people with serious health conditions
3. Reduced hospital capacity affecting ongoing care for people with underlying conditions
4. An increase in stress related causes due to lockdown
5. An increase in death registration efficiency introducing a process effect

There's been an increase in non-covid excess deaths in the areas that were worst hit by covid and a significant portion basically seem to have been displaced from hospitals to care homes and homes. Covid was less likely to be mentioned in the deaths of the very eldest and this possibly partly explains that these deaths were mainly in men until mid-April at which point they became more predominant in women (this reflects the UK deaths - twice as many men seem to be dying in age groups until you get to about 80 when it switches to women, reflect the underlying demographics).

In the undiagnosed covid category there's been a very sharp increase in dementia, alzheimers and old age/frailty. Given the sharp increase they think this is likely to include a large number of undiagnosed covide cases because often these are patients who aren't necessarily able to communicate their symptoms.

There's also been a big uptick in deaths related to sepsis, asthma and diabetes - these are ones they think are probably due to people not going to hospitals. There was an increase in strokes too but that's now reverted to normal. There is a minor uptick in deaths that are likely related to disrupted cancer care (renal failure and cancer survival rates are dropping), but this is probably going to be a long term thing. Increases in suicides and drugs won't be visible yet because they need coroners inquests so take time, but there's been an increase in deaths related to hypertension which could be linked to stress.

One interesting point is that so far in May all excess deaths are accounted/attributable to covid as we're returning to average levels of mortality.

[crazy canuck]

Amongst all the horror, a feel good story - NYT tribute to Dr. Henry, our Provincial Health Officer

https://www.nytimes.com/2020/06/05/world/canada/bonnie-henry-british-columbia-coronavirus.html?action=click&module=Editors%20Picks&pgtype=Homepage