COVID-19

[AMS]

So this is frightening...

What the 1918 flu's hidden history can teach the coronavirus era

https://flip.it/7._14u

While I don't want to be complacent about what might be coming, I suspect today's epidemiologists are well informed about the time course of the 1918 flu. I had heard of its second deadlier wave, and this is not my field at all.

A big difference now is how fast the science community can properly understand the virus and share that information. I think there are already crystal structures solved of some of the viral proteins, and there are fast-tracked clinical trials underway with some of HIV therapies that show promise for blocking the virus' protease. I suspect there will also be work going on with antibody sequences from recovered patients.

On the other hand, the public information strategy is hostage to the idiot in the White House.

[Fishnut]

I think it's important to remember one big difference between 1918 and now - we have antibiotics. And ICUs. And all sort of other medical advances that mean that people have a greater chance of surviving any illness than they did over 100 years ago.

[basementer]

I think it's important to remember one big difference between 1918 and now - we have antibiotics. And ICUs. And all sort of other medical advances that mean that people have a greater chance of surviving any illness than they did over 100 years ago.

Quite. And I trust people will know damn well that in mentioning antibiotics, you are referring to treating the secondary infections or existing conditions that the virus can exacerbate.

[AMS]

I think it's important to remember one big difference between 1918 and now - we have antibiotics. And ICUs. And all sort of other medical advances that mean that people have a greater chance of surviving any illness than they did over 100 years ago.

I was actually wondering, after posting, what proportion of the 1918 victims could have been saved by 2020 medical knowledge and equipment.

[raven]

True, but the data is so detailed, they're giving very specific location data, alongside age, sex, nationality. Can't imagine it would be hard to dig out identities with only a little bit of detective work.

Their data dashboard is at https://experience.arcgis.com/experienc ... fe67bd8b89. It's very impressive from the point of view of a public health tool. But not an equivalent that can be made publicly available in the UK.

Yeah, that level of detail is not going to fly here in the UK. Thanks for that link. (MrRaven is meant to be changing planes in Singapore in a week or so, and it's good to see that graph isn't going up too fast.)

On the 1918 flu, afaik the unusual numbers of young, fit patients it killed is thought to be partly due to cytokine storm, which is something that is better understood today. I have no idea if coronaviruses in genreal have the potential for that, but I haven't seen anything to suggest this one is causing it.

If anyone wants to know what Whitty said this morning, you can download the transcript here
here or watch it here

[Herainestold]

True, but the data is so detailed, they're giving very specific location data, alongside age, sex, nationality. Can't imagine it would be hard to dig out identities with only a little bit of detective work.

Their data dashboard is at https://experience.arcgis.com/experienc ... fe67bd8b89. It's very impressive from the point of view of a public health tool. But not an equivalent that can be made publicly available in the UK.

Yeah, that level of detail is not going to fly here in the UK. Thanks for that link. (MrRaven is meant to be changing planes in Singapore in a week or so, and it's good to see that graph isn't going up too fast.)

On the 1918 flu, afaik the unusual numbers of young, fit patients it killed is thought to be partly due to cytokine storm, which is something that is better understood today. I have no idea if coronaviruses in genreal have the potential for that, but I haven't seen anything to suggest this one is causing it.

If anyone wants to know what Whitty said this morning, you can download the transcript here
here or watch it here

Whitty is very good. Thanks for this.

[bmforre]

Looking at shpalman big cat avatar made me wonder if zoos and suchlike (stables?) take part in breeding and spreading this virus.

No, they don't.

Turns out that a dog has a ‘low-level’ coronavirus infection in first known human-to-animal transmission:
https://www.seattletimes.com/nation-wor ... nsmission/

How long will other animals stay safe?

[basementer]

Looking at shpalman big cat avatar made me wonder if zoos and suchlike (stables?) take part in breeding and spreading this virus.

No, they don't.

Turns out that a dog has a ‘low-level’ coronavirus infection in first known human-to-animal transmission:
https://www.seattletimes.com/nation-wor ... nsmission/

How long will other animals stay safe?

"Weak positive" was a phrase quoted, and politely dismissed, by John Campbell about 17 min into here
https://youtu.be/cmIRMHzBZdU
... is it the same case?

[shpalman]

If I want to model this slowdown I could reduce the susceptible population to some number which isn't several orders of magnitude greater than the number of cases, i.e. 6000 instead of 60 million. But to get the same exponential increase in the first week or so I need to increase the contact parameter so R_0 is now 11.3.

Figure_1.png

Reducing the susceptible population fudges the idea of quarantine and travel restrictions, so that the virus can't actually reach the entire population of Italy.

It predicts that we'll have 2625 active infections by the end of today.

(ETA I think https://www.corriere.it/salute/malattie ... 09c8.shtml is a more comprehensive source of information, for example, that 25856 swabs have been taken).

As someone who is no stranger to this kind of ecological modelling, I wouldn't worry too much about points falling a little bit away from the line. This is partly because of measurement issues meaning that the number of cases is never precisely known, but mostly because the numbers you're using to generate those curves are not known precisely.

You desperately need some kind of sensitivity analysis. Try running a large number of scenarios where each parameter varies within a reasonable range, then plot the 95% CIs. Because IME nothing involving living organisms ever falls precisely onto a trend line, and by manipulating your equations to fit the most recent points you're risking overfitting.

I will bet a small sum of money that, if you use official estimates of R_0 and susceptible population, but include uncertainty in the modelling, you'll find that the points fall within the CIs.

The number of cases keeps going up, and I could increase by susceptible population to deal with that, but after a few days of data it seems simpler to just say that we still have the number of total cases increasing exponentially but that we've gone from a doubling time of 2.1 days, to 3.4 days.

Just about anything which involves groups of people here is shut down until the 3rd of April at this point.

[Pucksoppet]

If anyone wants to know what Whitty said this morning, you can download the transcript here
here or watch it here

My thanks too. Very interesting and informative reading.

I have one minor irritation that has nothing to do with the virus outbreak: the transcript is a Microsoft Word document. I thought the government were meant to be using open standards, and for non-editable documents, they should really have used PDF.

GOV.UK : Guidance : Publishing government documents Updated 19 February 2020

GOV.UK : Press release : Open document formats selected to meet user needs Published 22 July 2014

[calmooney]

Interesting article on liver injury in COVID-19
https://www.thelancet.com/journals/lang ... 1/fulltext

[lpm]

China is no longer the worst affected country, on a per capita basis.

Vatican City is now the hottest of hot spots, with 0.1% of the population infected.

[El Pollo Diablo]

There's been some commentary about how when the weather warms up it might help halt the spread of coronavirus, but then you just think, "Singapore though".

[FlammableFlower]

Interesting article on liver injury in COVID-19
https://www.thelancet.com/journals/lang ... 1/fulltext

The Lancet has made all of its COVID-19 stuff free to access in a COVID-19 Resource Centre.

To assist health workers and researchers working under challenging conditions to bring this outbreak to a close, The Lancet has created a Coronavirus Resource Centre. This resource brings together new 2019 novel coronavirus disease (COVID-19) content from across The Lancet journals as it is published. All content listed on this page is free to access.

So dive in everyone.

[shpalman]

There's been some commentary about how when the weather warms up it might help halt the spread of coronavirus, but then you just think, "Singapore though".

Here's something on the temperature stability of the SARS virus, however it's in a Hindawi journal.

https://www.hindawi.com/journals/av/2011/734690/

I also remember hearing that rhinoviruses do indeed prefer cooler temperatures, which is why they mainly inhabit your nose, and generally another reason having a fever helps. (SARS-CoV-2 can also inhabit your lungs.)

I'm not sure if that's this: https://www.longdom.org/open-access/ina ... 000170.pdf

[El Pollo Diablo]

Singapore is very air-conditioned, I guess.

[shpalman]

It's currently 27°C in my lab because the heating is a bit all-or-nothing. It will probably be cooler than that in here during the summer because the airconditioning is similarly overenthusiastic.

[JQH]

So this is frightening...

What the 1918 flu's hidden history can teach the coronavirus era

https://flip.it/7._14u

The best we can do is not be as complacent as the people of 1918 — and choose leadership that offers reality-based responses.

Looks like we're f.cked then. Trump gutted the CDC and claims it's a hoax. Over here, Matt Hancock's claims to have been working with the supermarket chains to guarantee the food supply have been denied by the industry.

[El Pollo Diablo]

tell you what though, you can get a flight to Milan for £40 and a good hotel in the city centre from £55 per night for two adults. Plus you get to work at home for two weeks when you get back.

[Gentleman Jim]

Looks like we're f.cked then. Trump gutted the CDC and claims it's a hoax. Over here, Matt Hancock's claims to have been working with the supermarket chains to guarantee the food supply have been denied by the industry.

Or to quote the BBC (for once) -

A leading supermarket executive has told the BBC he is baffled by Health Secretary Matt Hancock's comments the government was working with retailers to ensure uninterrupted food supplies.

His exact words were: "Matt Hancock has totally made up what he said about working with supermarkets."

[lpm]

Before I spend as much as £4.99, can someone tell me if this will be fully BSL-4 compliant?

[TopBadger]

While I don't want to be complacent about what might be coming, I suspect today's epidemiologists are well informed about the time course of the 1918 flu.

Add to which...

Todays Astronomers are well informed about the asteroid that wiped out the dinosaurs
Todays Historians are well informed about the causes of World Wars I and II
Todays Economists are well informed about what caused the depression

The thing is - epidemiologists, astronomers, historians, economists etc aren't calling the shots... we're to rely on PM Dick and Matt "I'll do or say anything you want just let me keep my job" Hancock.

[AMS]

Today's epidemiologists have a lot more influence on medical responses to Covid (eg through the WHO sharing data and clinical guidance) than astronomers have over random bits of rock zipping through space.

[dyqik]

Today's epidemiologists have a lot more influence on medical responses to Covid (eg through the WHO sharing data and clinical guidance) than astronomers have over random bits of rock zipping through space.

I'm not entirely sure that's the case in the US.

[mikeh]

Looks like we're f.cked then. Trump gutted the CDC and claims it's a hoax. Over here, Matt Hancock's claims to have been working with the supermarket chains to guarantee the food supply have been denied by the industry.

Or to quote the BBC (for once) -

A leading supermarket executive has told the BBC he is baffled by Health Secretary Matt Hancock's comments the government was working with retailers to ensure uninterrupted food supplies.

His exact words were: "Matt Hancock has totally made up what he said about working with supermarkets."

Ah man. Hancock was doing so well, when he basically repeats what Chris Whitty tells him to say. The moment he lapses into Tory-politics mode, he's back into panicked-based lying.

Today's epidemiologists have a lot more influence on medical responses to Covid (eg through the WHO sharing data and clinical guidance) than astronomers have over random bits of rock zipping through space.

Agreed. We could quite literally not have Johnson, Hancock and co around, and the response to the outbreak would be barely affected (and given the above supermarkets story, it would prob be a positive impact if politicians went and hid for a few weeks). It is the experts that are overwhelmingly calling the shots here (in the UK).

I'm not entirely sure that's the case in the US.

I am willing to believe this is the case.
I was having a conversation today with a colleague in Thailand. They were saying there is so much government-led misinformation (and criticism of the government can rebound on you), and a health service that demands you pay the equivalent of average 2-4 weeks salary for tests and follow-up. Therefore, people are uninformed (at best, more likely ill-informed) and not getting tested because public health is disorganised and costs are passed onto the general public.
Remarkably similar to Stateside.

In all seriousness, the UK is doing pretty well on the whole, in this public health emergency. There are a lot worse places to be.