COVID-19

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raven
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Re: COVID-19

Post by raven » Sun Dec 20, 2020 4:58 pm

shpalman wrote:
Sun Dec 20, 2020 8:01 am
raven wrote:
Sat Dec 19, 2020 6:16 pm
raven wrote:
Sat Dec 19, 2020 5:12 pm


See, I would've thought that adding 0.4 to R made it 40% more infectious. (You know, 10 people who would've infected 10 more at R=1 for the old strains, now infect 14 more.)
What Johnson said, if I heard it right, was 70% more transmissable. (That's ability to spread between hosts.) Infectivity is ability to infect more hosts, which according to Wikipedia is subtly different. Somehow. I am a bit confused as to how.

Just caught the Naked Scientist guy on Al-Jazeera, and he says the mutation makes it 'stickier'. So more likely to stick to cells and infect someone. And that it's accounting for 60% of cases in London, which seems rather dramatic if correct.
I suspect that if it's 'stickier' from a more effective spike protein then they should be talking about its infectivity, because transmissibility would relate to how well it can aerosolize or survive on external surfaces or something, but what do I know, I'm not the moron who invented "four weeks behind Italy".
That's what I thought too. Sounds like the distinction between infectivity and transmissability is more theoretical than practical (ETA I mean it's not pratically feasable to work out which it is from the data we've got). But anyone with sense is caveating all statements with 'maybe', as you'd expect, and I think right now we don't know anything for sure other than it seems to be out-competing other strains in the SE.

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Re: COVID-19

Post by jdc » Sun Dec 20, 2020 7:44 pm

Millennie Al wrote:
Sun Dec 20, 2020 2:52 am
lpm wrote:
Sat Dec 19, 2020 4:27 pm
Official statement is 70% more infectivicity and adds 0.4 to R
Taken at face value, that means R was 0.57 and became 0.97 (0.97 is a 70% increase over 0.57).

But I think what it really means is that the official statement reveals a lack of understanding by whoever compiled it. The handling of covid-19 reveals ongoing failure caused by linear thinking meeting an exponential reality.
I might be being thick here, but if this is one of a number of strains of covid doing the rounds won't it mean that you can't translate the 70% increase in infectivity of this particular strain into a 70% increase in the overall R - doesn't a calculation of R have to take into account the other strains?

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Re: COVID-19

Post by Martin Y » Sun Dec 20, 2020 8:32 pm

lpm wrote:
Sat Dec 19, 2020 2:30 pm
Wait wait, Tier 4 fears, has anyone done that yet? Geddit? Tier 4 fears? Well, OK, you're probably too young but there used be a band and this is a good joke honest.
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Re: COVID-19

Post by Millennie Al » Mon Dec 21, 2020 2:00 am

jdc wrote:
Sun Dec 20, 2020 7:44 pm
Millennie Al wrote:
Sun Dec 20, 2020 2:52 am
lpm wrote:
Sat Dec 19, 2020 4:27 pm
Official statement is 70% more infectivicity and adds 0.4 to R
Taken at face value, that means R was 0.57 and became 0.97 (0.97 is a 70% increase over 0.57).

But I think what it really means is that the official statement reveals a lack of understanding by whoever compiled it. The handling of covid-19 reveals ongoing failure caused by linear thinking meeting an exponential reality.
I might be being thick here, but if this is one of a number of strains of covid doing the rounds won't it mean that you can't translate the 70% increase in infectivity of this particular strain into a 70% increase in the overall R - doesn't a calculation of R have to take into account the other strains?
You're right, but it's complicated.

The new and the old strains are each a barrier to the other, but if the proportion of those infected is small enough this does not matter - each spreads independently. Each spreads exponentially. Since a bigger exponent will always catch and surpass (by any fixed amount) a smaller exponent, in theory the new strain will overwhelm the old one. In practice, they may run out of population to infect before then.

To give a concrete, but simplistic, example, suppose the old strain has R=2 and has been running for 16 generations from the first case, then there are now 65536 cases. If the new strain has R=3 then after 27 more generations the R=3 has caught up. Of course that's unrealistic for a disease as by then there are 11,228,112,530,963 cases, so everyone in the world would have been infected by both strains. For actual diseases the exponential model only applies until enough people have caught it that the nature of the population changes - then it has to be modelled as a logistic or something more complex.

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Re: COVID-19

Post by Woodchopper » Mon Dec 21, 2020 7:07 am

I set up a specific new variant thread over here: viewtopic.php?t=2011

Shall I move the discussion here over there?

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Re: COVID-19

Post by lpm » Tue Dec 22, 2020 4:20 pm

UK daily deaths: 691.

With deaths this high at this stage of the second wave upswing, Boris Johnson has the ability to make the first wave look like a ripple.
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Re: COVID-19

Post by shpalman » Tue Dec 22, 2020 5:28 pm

lpm wrote:
Tue Dec 22, 2020 4:20 pm
UK daily deaths: 691.

With deaths this high at this stage of the second wave upswing, Boris Johnson has the ability to make the first wave look like a ripple.
Italy's number is similar but its trend has been gently downwards for a while now (apart from in Veneto). Daily cases have come down a lot since the peak.
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Re: COVID-19

Post by bolo » Tue Dec 22, 2020 6:22 pm

This week's run of the U of Virginia model is that Virginia cases won't peak until early February, at 13x the summer peak. Yikes.

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Re: COVID-19

Post by Woodchopper » Tue Dec 22, 2020 6:42 pm

lpm wrote:
Tue Dec 22, 2020 4:20 pm
UK daily deaths: 691.

With deaths this high at this stage of the second wave upswing, Boris Johnson has the ability to make the first wave look like a ripple.
sh.t. Hasn’t been that high since early May.

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Re: COVID-19

Post by KAJ » Tue Dec 22, 2020 7:06 pm

Looking at deaths by date of death (rather than by date of publication) I see no evidence that numbers are increasing ... yet :(
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Given the clear rises in numbers of cases, hospital admissions, patients in hospital, and patients in mechanical ventilation beds I'm afraid it's only a matter of time until deaths follow.

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Re: COVID-19

Post by dyqik » Tue Dec 22, 2020 8:40 pm

Is there sign of an increase in the lag between spikes in cases, hospitalizations and deaths as the treatment options become better understood?

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Re: COVID-19

Post by dyqik » Tue Dec 22, 2020 8:42 pm

Oh, and CoVID has now made it to Antarctica.

Story

Fortunately the various Antarctic bases are fairly well isolated from each other (except say Amundsen-Scott and McMurdo, for example, where one is the stopping off point on the way to the other), and this is only in the Chilean base for now.

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Re: COVID-19

Post by sTeamTraen » Tue Dec 22, 2020 8:45 pm

dyqik wrote:
Tue Dec 22, 2020 8:40 pm
Is there sign of an increase in the lag between spikes in cases, hospitalizations and deaths as the treatment options become better understood?
I've been asking people who understand modelling of time series data way better than me (and that list includes Priti Patel, frankly) to try and work out what the best estimate of the lag is, and they all come up with different estimates, But my guess would be that if treatment improves, the number of deaths would be what came down. The ICU doctor with whom I wrote this blog post considers that to a first approximation, once you're in the ICU you're typically there for three weeks, regardless of whether you're going to leave head- or feet-first.
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Re: COVID-19

Post by shpalman » Tue Dec 22, 2020 9:08 pm

sTeamTraen wrote:
Tue Dec 22, 2020 8:45 pm
dyqik wrote:
Tue Dec 22, 2020 8:40 pm
Is there sign of an increase in the lag between spikes in cases, hospitalizations and deaths as the treatment options become better understood?
I've been asking people who understand modelling of time series data way better than me (and that list includes Priti Patel, frankly) to try and work out what the best estimate of the lag is, and they all come up with different estimates, But my guess would be that if treatment improves, the number of deaths would be what came down. The ICU doctor with whom I wrote this blog post considers that to a first approximation, once you're in the ICU you're typically there for three weeks, regardless of whether you're going to leave head- or feet-first.
Does it take more than a week to get the to ICU? The stats only consider deaths within four weeks of the positive test.

The weekly deaths "with COVID-19 on the death certificate" have been slowly decreasing too though, but we only have not-recent data.
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Re: COVID-19

Post by KAJ » Tue Dec 22, 2020 9:37 pm

shpalman wrote:
Tue Dec 22, 2020 9:08 pm
Does it take more than a week to get the to ICU? The stats only consider deaths within four weeks of the first positive test.

The weekly deaths "with COVID-19 on the death certificate" have been slowly decreasing too though, but we only have not-recent data.
ETA an important word

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Re: COVID-19

Post by shpalman » Tue Dec 22, 2020 9:56 pm

The ONS stats don't suggest that there's a significant number of excess but not-officially-covid deaths on top of the significant number of excess covid deaths in the second wave.

Image

Up until the 11th of December, anyway.
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Re: COVID-19

Post by sTeamTraen » Tue Dec 22, 2020 10:53 pm

shpalman wrote:
Tue Dec 22, 2020 9:08 pm
sTeamTraen wrote:
Tue Dec 22, 2020 8:45 pm
The ICU doctor with whom I wrote this blog post considers that to a first approximation, once you're in the ICU you're typically there for three weeks, regardless of whether you're going to leave head- or feet-first.
Does it take more than a week to get the to ICU? The stats only consider deaths within four weeks of the positive test.

The weekly deaths "with COVID-19 on the death certificate" have been slowly decreasing too though, but we only have not-recent data.
I should have written my comment much more clearly. Some people just die on the ventilator; the main point the doctor made was that whether or not someone is going to survive does not become clear until they have survived three weeks. At that point they typically turn off the ventilator and see if your lungs have enough function to stop you drowning. And UK protocols may be different.

That said, among the kinds of people who end up in the ICU, I would expect a week from the first test to be reasonable. I'm assuming that older people are, typically, getting their first test mostly because they have symptoms, rather than swinging down to the health centre because they need the all-clear for a short break in Croatia.
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Re: COVID-19

Post by sTeamTraen » Tue Dec 22, 2020 10:57 pm

shpalman wrote:
Tue Dec 22, 2020 9:56 pm
The ONS stats don't suggest that there's a significant number of excess but not-officially-covid deaths on top of the significant number of excess covid deaths in the second wave.
I've done something similar with data from the Netherlands (the five-year average deaths are standardized to zero). In wave 2, most of the excess deaths are COVID-positive. In week 33 there was a heatwave which killed a few older people. But you can see that back in March-April a lot of people were very probably dying from COVID without getting a test.

Deaths in the 0-65 age range are very slightly below normal, although probably within fluctuation range. I guess this corresponds to some reduction from road traffic deaths and other accidents outside the home, offset by some COVID deaths in the upper third of that age range.
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Re: COVID-19

Post by shpalman » Tue Dec 22, 2020 11:09 pm

These people have done something similar for Italy https://www.scienzainrete.it/articolo/n ... erra/paola
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Re: COVID-19

Post by Squeak » Tue Dec 22, 2020 11:26 pm

dyqik wrote:
Tue Dec 22, 2020 8:42 pm
Oh, and CoVID has now made it to Antarctica.

Story

Fortunately the various Antarctic bases are fairly well isolated from each other (except say Amundsen-Scott and McMurdo, for example, where one is the stopping off point on the way to the other), and this is only in the Chilean base for now.
That's going to give the logistics folk the willies. I know the UK has already been running three sets of plans for this summer for several months now and even their best case scenario involved a massive reduction in fieldwork. Everyone's worked so hard to keep it out of Antarctica because it's so hard to do complicated health care down there. :(

And there's a nasty little covid gift brewing for oceanographers and climate modellers in coming years, both in Antarctica and globally. People can't get on ships to deploy gear and service moorings so there are going to be big observational holes in the next few years. :(

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Re: COVID-19

Post by PeteB » Wed Dec 23, 2020 9:45 am

Oh dear

My gut feel is close schools or 1000s a day dying by end of Feb

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Re: COVID-19

Post by lpm » Wed Dec 23, 2020 3:16 pm

Hancock:

"The tier system doesn't work with the new variant... but we have to take action... so I am carrying on with the tier system by moving areas up a notch"
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Re: COVID-19

Post by shpalman » Wed Dec 23, 2020 3:23 pm

lpm wrote:
Wed Dec 23, 2020 3:16 pm
Hancock:

"The tier system doesn't work with the new variant... but we have to take action... so I am carrying on with the tier system by moving areas up a notch"
Well, tier 3 worked. It was tiers 1 & 2 which didn't work.

COMPLETELY UNEXPECTED that having tier 2 London right next to tier 3 Kent caused London to f.ck it.
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Re: COVID-19

Post by Bird on a Fire » Wed Dec 23, 2020 3:28 pm

I'm in Hampshire. We've just gone from 2 to 4. ETA Well, from boxing Day.

I was isolating anyway, but now everyone else is too. ETA well, will be from boxing Day.

Merry Christmas.
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Re: COVID-19

Post by shpalman » Wed Dec 23, 2020 4:32 pm

Congratulations on your 39237 new covids.

How were the scotch eggs?
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