Coronavirus Sars-CoV-2/Covid-19 Megathread

[Sheilbh]

This is interesting - and it's really important to understand the cause:
https://www.theguardian.com/world/2020/jul/13/nhs-data-reveals-huge-variation-in-covid-19-death-rates-across-england

NHS data reveals 'huge variation' in Covid-19 death rates across England
Exclusive: hospital mortality rate varies from 12.5% to 80% in different trusts around country
Denis Campbell and Niamh McIntyre

Mon 13 Jul 2020 12.53 BST
Last modified on Mon 13 Jul 2020 15.35 BST

A wide disparity in coronavirus mortality rates has emerged in English hospitals, with data seen by the Guardian showing that one hospital trust in south-west England had a death rate from the disease of 80% while in one London trust it was just 12.5%.

[DGuller]

As a data scientist, I feel like poor quality of data collection is really impeding the ability of everyone to zero in on what matters and what doesn't.  Poor data science practices really do kill in this case.  I feel like so many Covid mysteries would not be mysteries anymore, or at least would be narrowed down usefully, if data collection were uniform and detailed.  The public datasets available are nearly useless for solving any Covid mystery.

[Sheilbh]

As a data scientist, I feel like poor quality of data collection is really impeding the ability of everyone to zero in on what matters and what doesn't.  Poor data science practices really do kill in this case.  I feel like so many Covid mysteries would not be mysteries anymore, or at least would be narrowed down usefully, if data collection were uniform and detailed.  The public datasets available are nearly useless for solving any Covid mystery.

The full article covers some of the data issues. But one of the virtues of a centralised health system is it does allow for fairly consistent data and studies (I think some of the data the NHS collects is the world's largest sort of collections medical data, which means it does quite a lot of interesting analysis):

NHS data reveals 'huge variation' in Covid-19 death rates across England
Exclusive: hospital mortality rate varies from 12.5% to 80% in different trusts around country
Denis Campbell and Niamh McIntyre
Mon 13 Jul 2020 12.53 BST
Last modified on Mon 13 Jul 2020 17.53 BST

A wide disparity in coronavirus mortality rates has emerged in English hospitals, with data seen by the Guardian showing that one hospital trust in south-west England had a death rate from the disease of 80% while in one London trust it was just 12.5%.

The figures, which NHS England has compiled but never published, show the age-standarised mortality rates that all of the country's 135 acute hospital trusts have recorded during the pandemic. Doctors regard age as the single biggest predictor or risk factor for dying from Covid-19.

They cover the period from the start of the coronavirus crisis in March, through its peak in late March and April, up until 15 May, by which time 42,850 – or 85% – of the 50,219 deaths so far in all settings had occurred in England and Wales.

It is the first such data to emerge about how many people have lived or died in each trust after being treated there because they had been left critically ill by the disease. They are based on patients who were treated in an intensive care or high-dependency unit or on a ward.

Senior doctors said the dramatic gap in death rates of 67.5 percentage points between the trusts with the highest and lowest rates was notable and may mean that some hospitals needed to learn lessons from others.

"That is a huge variation, a huge range. I'm surprised at the degree of variation. A spread between 12.5% and 80% is quite stark," said Dr Alison Pittard, the dean of the Faculty of Intensive Care Medicine. It represents the intensive care specialists who have played the lead role in treating what is now more than 100,000 people hospitalised in England with Covid-19.

Dr Nick Scriven, a former president of the Society for Acute Medicine (SAM), said: "The range does look larger than you would expect and should prompt further analysis and thought as to why this may appear as it does, which for the general population will be concerning."

However, both Pittard and Scriven cautioned that the data did not give a full picture of differential death rates between hospitals because it did not take account of four other key factors for risk of death from Covid-19, namely gender, ethnicity, deprivation and underlying health problems. All four have been found to significantly increase a patient's chances of dying.

NHS England has plotted each trust's death rate, and the number of patients with Covid-19 each of them admitted, on a graph which it has shared with some senior doctors. Crucially, though, it has not identified the trusts on it. It has only disclosed which of the NHS's seven regions the trust is in.

The five trusts with the highest death rates are in the south-west (80%), north-west (68%), south-west (62%), east of England (60%) and London (54%).

The five trusts with the lowest death rates are in: London (12.5%), Midlands (13%), London (14%), London (15%) and the south-east (15%).

Doctors pointed out that some trusts' apparently high mortality rates could be skewed because they were based on them having treated fewer than 100 patients by 15 May, which makes their rates less reliable. But other trusts with notably high or low mortality had treated up to 2,350 patients over the same period, so their rates are more likely to be reliable.

Research published by the Intensive Care National Audit and Research Centre shows that of 9,995 patients treated in intensive care units with known outcomes, 5,985 (59.9%) have been discharged and 4,010 (40.1%) have died, while 426 others are still receiving critical care.

Mortality among such patients in intensive care has improved from 50% early in the pandemic to 41% now, reflecting in part medical teams' better understanding and treatment of Covid-19.

There is no suggestion that a high or low death rate indicates that patients have received a worse or better standard of care at any particular hospital. The makeup of the local population that a trust serves is the single biggest factor underlying a high or low death rate, Pittard said.

"We know that poorer communities and BAME communities have a higher risk of mortality, so if a trust is in an area of higher-risk individuals you woud expect that trust's Covid-related mortality rate to be higher," added Pittard.

NHS England's data shows that 26 of the 135 trusts had a death rate between 12.5% and 25%. "That's reassuring, absolutely. It's positive that 26 trusts had that low mortality," said Pittard.

However, at least half of patients treated at 11 trusts died. "Eighty percent does seem an extremely high number," she added.

Dr Sue Crossland, the president of the SAM, said hospitals' use of non-invasive ventilation, the early involvement of critical care teams and lying ventilated patients on their front – "proning" – have saved patients' lives as doctors have better understood how to deal with Covid-19.

An NHS spokesperson said: "We do not recognise these figures, which appear to be experimental analysis of unverified data. But there is now a wide range of published data on the role that health inequalities, including pre-existing conditions and other health factors, have played when it comes to the impact of Covid, including from the ONS and Public Health England.

"The NHS is accelerating work to tackle health inequalities, and will shortly be providing local services with a range of actions they should build in to their plans for the coming months."

[Zanza]

Germany has just 1.3% of the population with antibodies and the first infected from January have much less antibodies than before now. Both signs that herd immunity will likely not happen.

[Admiral Yi]

So we're going to mask and not go to bars until (if) there's a vaccine.

[merithyn]

Is a vaccine possible under these circumstances?

[Barrister]

Is a vaccine possible under these circumstances?

We won't know until we have a vaccine.  There are various different kinds of vaccines under development so it is quite possible that even if exposure to the live virus doesn't cause immunity, that a vaccine will.

This is just one data point, but because it's me I think it's relevant: as a child I caught chicken pox twice.  For the huge majority of people that doesn't happen, but it did for me.  And of course that didn't mean that they couldn't ultimately develop a chicken pox vaccine.

[viper37]

So we're going to mask and not go to bars until (if) there's a vaccine.

My favorite bar is reopening this Saturday  the mask part though, 

Is a vaccine possible under these circumstances?

yes.  I don't understand all of it, but what I've read is they are targetting T-cells inside the body with the newest vaccines candidates and this has the probability or developping an immune response inside our cells, i.e. our immune system would recognize the virus and start shooting on sight - I mean, start developping antibodies as they need it.  Or something like that.

Bad news: this will be longer to develop than other kind of vaccines.

[Sheilbh]

We won't know until we have a vaccine.  There are various different kinds of vaccines under development so it is quite possible that even if exposure to the live virus doesn't cause immunity, that a vaccine will.

This is just one data point, but because it's me I think it's relevant: as a child I caught chicken pox twice.  For the huge majority of people that doesn't happen, but it did for me.  And of course that didn't mean that they couldn't ultimately develop a chicken pox vaccine.

I was speaking to a medical researcher friend about this and he said it doesn't really indicate that. It's rare that vaccines don't in some way leverage a natural immune response - but it's not the same as the natural immune response so it will often be prompting a stronger immune response.

So we're going to mask and not go to bars until (if) there's a vaccine.

The more it's under control and you can isolate outbreaks the less restrictive things probably need to be. But otherwise I think yeah social distancing etc is likely in some way or other until there's a vaccine or treatment - maybe at some point people just stop caring enough to do that stuff but I think don't we're anywhere near there yet.

[Zanza]

Is a vaccine possible under these circumstances?

Some of the mechanisms tried for vaccines now are completely new like targeting the messenger RNA. No one knows yet if it will work.

[DGuller]

Do we know for sure that Covid parties actually exist?  The sociopathic stupidity described sounds a little too perfect to be true, and more like a useful cautionary tale, but I've seen a story or two claiming that they do exist.  I haven't been able to find a fact check on that.  Does anyone know if someone did fact check this?

[The Minsky Moment]

It appears it is a real guy but whether the particulars are true is another story

he Times could not independently verify Dr. Appleby's account. On Monday, the San Antonio health department said its contact tracers did not have any information "that would confirm (or deny)" that such an event had happened there.

In recent days, the hospital distributed video of Dr. Appleby describing the case, along with a press statement. She did not say when or where the party took place, how many people attended or how long afterward the man was hospitalized with Covid-19, the disease caused by the coronavirus. She said she was sharing the story to warn others, especially in Texas, where cases are surging.

The hospital, citing patient confidentiality rules, declined to publicly identify the man. His family did not respond to several interview requests passed along through the hospital.

[Zanza]

Do we know for sure that Covid parties actually exist?  The sociopathic stupidity described sounds a little too perfect to be true, and more like a useful cautionary tale, but I've seen a story or two claiming that they do exist.  I haven't been able to find a fact check on that.  Does anyone know if someone did fact check this?

With the current level of infections in some parts of the US, every party is potentially a Corona party.  That's why experts call for social distancing.

[celedhring]

AI-14 of Spanish regions. As you can see, the trouble spot remains the border between Catalonia and Aragon. Yesterday the Catalan government finally attempted to lock down the affected area, but it was shot down by a local court. They have circumvented it via decree - which is constitutionally pretty dubvious. The whole "who can order people to remain in their houses and how" is still pretty murky.

[Sheilbh]

Is there any theory why those regions?

I know in Germany it was meatpacking, in England it was the fast fashion sweatshops. Something similar there, or is it less clear?