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Coronavirus - Modelling Aspects Only

The home for all non-political Coronavirus (Covid-19) discussions on The Lemon Fool
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This is the home for all non-political Coronavirus (Covid-19) discussions on The Lemon Fool
zico
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Re: Coronavirus - Modelling Aspects Only

#320910

Postby zico » June 23rd, 2020, 11:13 pm

dealtn wrote:
zico wrote:
I've assumed an average daily deaths figure of 160, but what will happen in practice is that the figure as of today's date will be lower than that, and gradually increase as lockdown measures are lifted, so government will have plenty of time to take measures to combat increases in infections.



All quite reasonable, but I will just focus on this bit.

I don't think we know what will happen to the R number (which in itself isn't perfect at low numbers) or the daily deaths as a result of lockdown changes.

Partly this will depend on how those different (age) groups (and other groups of differing outcomes if infected) respond. In fact if those least affected actually acted speedily and unwisely it might even be of benefit to the other groups, so long as they weren't affected.

As one of the scientific advisors very early on put it (can't remember who, and the exact quote), if everyone who was likely to die were isolated together in say the Hebrides, and everyone else mingled freely such that the virus spread as fast as possible, but only amongst that "unaffected" group, the virus would run its course quickly and no lives would be lost.



You're right. For simplicity, I've ignored the issue of whether the R number will rise - personally I think it will, and we'll probably need a 2nd lockdown around Oct or Nov unless a vaccine is available then or the vulnerable group are being properly shielded (or self-shielding).
The big problem is that there isn't an easy way to stop the "unaffected" group mingling with the "affected" group.

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Re: Coronavirus - Modelling Aspects Only

#321180

Postby johnhemming » June 24th, 2020, 7:46 pm

https://www.the-scientist.com/news-opin ... dies-67650

A pair of studies published this week is shedding light on the duration of immunity following COVID-19, showing patients lose their IgG antibodies—the virus-specific, slower-forming antibodies associated with long-term immunity—within weeks or months after recovery.

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Re: Coronavirus - Modelling Aspects Only

#321185

Postby Lootman » June 24th, 2020, 7:52 pm

zico wrote: I've ignored the issue of whether the R number will rise - personally I think it will, and we'll probably need a 2nd lockdown around Oct or Nov unless a vaccine is available then or the vulnerable group are being properly shielded (or self-shielding).

The mortality rate is 0.3%. That is less than one person in 300.

Do we stop the world again or just accept the loss? If we stop it again then how do we know there won't be a third wave when we re-open for the second time?

At some point the voters are going to say: "Screw the science, screw the 0.3%, let's just get back to normal life and let the very weakest succumb".

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Re: Coronavirus - Modelling Aspects Only

#321201

Postby Mike4 » June 24th, 2020, 9:27 pm

Lootman wrote:The mortality rate is 0.3%. That is less than one person in 300.


How do you know that please? A link or a reference perhaps?

And what is the definition of "mortality rate'..? Is it the same thing as the infection fatality rate (IFR)? Or the case fatality rate (CFR)? The thing about the IFR is no-one knows what it is, because we still don't know how many people get infected asymptomatically.

Thanks

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Re: Coronavirus - Modelling Aspects Only

#321214

Postby Lootman » June 24th, 2020, 10:21 pm

Mike4 wrote:
Lootman wrote:The mortality rate is 0.3%. That is less than one person in 300.

How do you know that please? A link or a reference perhaps?

And what is the definition of "mortality rate'..? Is it the same thing as the infection fatality rate (IFR)? Or the case fatality rate (CFR)? The thing about the IFR is no-one knows what it is, because we still don't know how many people get infected asymptomatically.

It is (if I am to believe the cited stats) the probability that if you catch the bug you will die of it. Hence the term mortality rate rather than (say) infection rate.

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Re: Coronavirus - Modelling Aspects Only

#321217

Postby Alaric » June 24th, 2020, 10:31 pm

Lootman wrote:It is (if I am to believe the cited stats) the probability that if you catch the bug you will die of it.


There seems empirical evidence that the probability of dying from the infection is age dependent. At younger ages, the combined risk of catching the virus and then dying of it may be at around the same level as being involved in a fatal motor accident or a victim of knife crime,

Much higher for older sufferers and those at risk with other conditions though.

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Re: Coronavirus - Modelling Aspects Only

#321224

Postby Mike4 » June 24th, 2020, 11:18 pm

Lootman wrote:
Mike4 wrote:
Lootman wrote:The mortality rate is 0.3%. That is less than one person in 300.

How do you know that please? A link or a reference perhaps?

And what is the definition of "mortality rate'..? Is it the same thing as the infection fatality rate (IFR)? Or the case fatality rate (CFR)? The thing about the IFR is no-one knows what it is, because we still don't know how many people get infected asymptomatically.

It is (if I am to believe the cited stats) the probability that if you catch the bug you will die of it. Hence the term mortality rate rather than (say) infection rate.


So mortality rate is the same thing as IFR.

Now as you accurately explain, it is the likelihood of you dying if you catch it. But given we had no idea how many catch it, how can you (or anyone) define it as 0.3% with such apparent certainty?

Hence my request for a reference.

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Re: Coronavirus - Modelling Aspects Only

#321332

Postby Backache » June 25th, 2020, 11:36 am

Mike4 wrote:
Lootman wrote:
Mike4 wrote:How do you know that please? A link or a reference perhaps?

And what is the definition of "mortality rate'..? Is it the same thing as the infection fatality rate (IFR)? Or the case fatality rate (CFR)? The thing about the IFR is no-one knows what it is, because we still don't know how many people get infected asymptomatically.

It is (if I am to believe the cited stats) the probability that if you catch the bug you will die of it. Hence the term mortality rate rather than (say) infection rate.


So mortality rate is the same thing as IFR.

Now as you accurately explain, it is the likelihood of you dying if you catch it. But given we had no idea how many catch it, how can you (or anyone) define it as 0.3% with such apparent certainty?

Hence my request for a reference.

Generally speaking when epidemiologists talk about mortality rate they are referring to the number of people who have dies as a proportion of the population as a whole , Though casually mortality is sometimes used both in respect of case fatality rate infected fatality rate or virtually any other proportion of deaths to some population, maybe ventilated mortality or itu or hospital or whatever.
So if talking about a cancer it may be 10 per 100,000 annually
In an epidemic the mortality will climb until the epidemic is over. So currently it is around 50-60,000 out of a population of 65M or whatever.
The Case fatality rate is the number of people who have dies out of the cases identified.
The Infected Fatality rate is the number of people who die per case infected.

None of these numbers are precisely known and all will vary from place to place according to the ability to identify the numbers and the underlying health and age structure of the population, access to medical facilities etc.

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Re: Coronavirus - Modelling Aspects Only

#321369

Postby Lootman » June 25th, 2020, 1:14 pm

Backache wrote:
Mike4 wrote:
Lootman wrote:It is (if I am to believe the cited stats) the probability that if you catch the bug you will die of it. Hence the term mortality rate rather than (say) infection rate.

So mortality rate is the same thing as IFR.

Now as you accurately explain, it is the likelihood of you dying if you catch it. But given we had no idea how many catch it, how can you (or anyone) define it as 0.3% with such apparent certainty?

Hence my request for a reference.

Generally speaking when epidemiologists talk about mortality rate they are referring to the number of people who have dies as a proportion of the population as a whole , Though casually mortality is sometimes used both in respect of case fatality rate infected fatality rate or virtually any other proportion of deaths to some population, maybe ventilated mortality or itu or hospital or whatever.
So if talking about a cancer it may be 10 per 100,000 annually
In an epidemic the mortality will climb until the epidemic is over. So currently it is around 50-60,000 out of a population of 65M or whatever.
The Case fatality rate is the number of people who have dies out of the cases identified.
The Infected Fatality rate is the number of people who die per case infected.

None of these numbers are precisely known and all will vary from place to place according to the ability to identify the numbers and the underlying health and age structure of the population, access to medical facilities etc.

The mortality rate as a percentage of the population is known. It is a little under one in a thousand even if we take your higher estimate there of 60,000 deaths. Because the population is known, 65 million or so.

I think what most people want to know is what is the percentage chance that they will die. That is a combination of the risk of catching the virus, and the rate at which those who are infected do not recover.

So the 0.3% number cited above is on the high side, but then this isn't over yet so might be a reasonable rule of thumb for the stated purpose, which is deciding how much personal risk to take with the reopening. And personally I am comfortable with that 0.3% risk. I will remain conscious of situations where I consider the risk to be elevated such as being in a crowded, enclosed place with a lot of people shouting, e.g. watching a football game in a pub.

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Re: Coronavirus - Modelling Aspects Only

#321445

Postby Backache » June 25th, 2020, 3:55 pm

Lootman wrote:The mortality rate as a percentage of the population is known. It is a little under one in a thousand even if we take your higher estimate there of 60,000 deaths. Because the population is known, 65 million or so.

I think what most people want to know is what is the percentage chance that they will die. That is a combination of the risk of catching the virus, and the rate at which those who are infected do not recover.

So the 0.3% number cited above is on the high side, but then this isn't over yet so might be a reasonable rule of thumb for the stated purpose, which is deciding how much personal risk to take with the reopening. And personally I am comfortable with that 0.3% risk. I will remain conscious of situations where I consider the risk to be elevated such as being in a crowded, enclosed place with a lot of people shouting, e.g. watching a football game in a pub.


The trouble with this is two fold one 0.3% is someones guess no one really knows at the moment. Furthermore we do not know what the guess even refers to which population? Young Germans returning from skiing holidays, UK as a whole, a cruise ship. The number is utterly meaningless without context.

The other problem is that if you are looking at this and trying to extrapolate it to yourself you cannot because virtually no ones individual apparent risk will be the same as the populations. Even looking at it simplistically most people are either male or female but men have about twice the risk of women so you will either have a risk about 60% greater than average or 20% below average. The difference is binary . The age strata of the population means that many people will have a risk that is significantly higher or lower than the average risk.

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Re: Coronavirus - Modelling Aspects Only

#321535

Postby johnhemming » June 25th, 2020, 7:49 pm

The really big issue is that the risk varies from person to person on a primarily predictable basis (age and/or other vulnerablities - COPD etc). Hence regardless of the IFR itself there is a tactical question as to whether for the people who are more vulnerable it is best for everyone else to have had the disease so they can go about their daily lives without too much worry or whether trying to reduce the general rate of infection in the population as a whole is best.

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Re: Coronavirus - Modelling Aspects Only

#321542

Postby Nimrod103 » June 25th, 2020, 8:08 pm

https://www.telegraph.co.uk/news/2020/0 ... ki-resort/

It is reported that nearly half (42.4%) of the population of Ischgl, one of the disease epicentres, have developed antibodies. I believe there are also quite a few people who have enough natural immunity that infection never gets a foothold. I think the herd immunity threshold has been reached.

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Re: Coronavirus - Modelling Aspects Only

#321616

Postby servodude » June 26th, 2020, 12:36 am

Nimrod103 wrote:https://www.telegraph.co.uk/news/2020/06/25/highest-coronavirus-immunity-found-austrian-ski-resort/

It is reported that nearly half (42.4%) of the population of Ischgl, one of the disease epicentres, have developed antibodies. I believe there are also quite a few people who have enough natural immunity that infection never gets a foothold. I think the herd immunity threshold has been reached.


That's a really interesting nugget, thanks!

I'm trying to reconcile it with the arguments I've seen that very low antibody presence within a population implies that many others fought off the disease using only T-cells, and hence did not develop antibodies.

Taking that sample at face value it would suggest to me that this is unlikely; or at very least they are unlikely to be significantly more than those people who do get antibodies.

Also, I think that 42% of a population would be considered a high proportion to have been infected with something (flu is estimated to get 3 - 11% of the US in a year) ; especially considering there have been arguments that you only require around 20% to achieve "herd immunity".

Obviously this sample might be an outlier, but I'll need to find myself a good reason to discard it.
-sd

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Re: Coronavirus - Modelling Aspects Only

#321671

Postby johnhemming » June 26th, 2020, 9:23 am

The interesting question about Ischgl is to what extent there was so much infection going around that pretty well everyone who could get it got it. That would imply a localised infection rate of potentially 90-95% of the susceptible population. If we take the working assumption that about half of people are not susceptible or don't generate antibodies that would be a fair conclusion.

I think there have been a similar level of antibodies (over 40%) generated in medics in some areas.

The point about herd immunity is it is a probabilities thing which relies on not having that many opportunities for infection. If you have a lifestyle that has a lot of opportunities for infection then herd immunity would only kick in at a higher percentage.

Ishgl also tends to endorse an IFR in the range of 0.2-0.3%.

Hence on a broad brush basis we are talking about susceptibility being about 50% and IFR being 0.2-0.3%.

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Re: Coronavirus - Modelling Aspects Only

#321674

Postby Alaric » June 26th, 2020, 9:30 am

johnhemming wrote:The point about herd immunity is it is a probabilities thing which relies on not having that many opportunities for infection. If you have a lifestyle that has a lot of opportunities for infection then herd immunity would only kick in at a higher percentage.
.


Ischgl in the Ski season would also share with meat plants the feature of being cold, crowded and noisy.

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Re: Coronavirus - Modelling Aspects Only

#321678

Postby johnhemming » June 26th, 2020, 9:35 am

Alaric wrote:Ischgl in the Ski season would also share with meat plants the feature of being cold, crowded and noisy.

Drunken singing is particularly infectious. More so than meat plants. Infection rates may go down below 5c, but the bars would be warmer than that.

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Re: Coronavirus - Modelling Aspects Only

#321710

Postby Mike4 » June 26th, 2020, 10:26 am

servodude wrote:
Nimrod103 wrote:https://www.telegraph.co.uk/news/2020/06/25/highest-coronavirus-immunity-found-austrian-ski-resort/

It is reported that nearly half (42.4%) of the population of Ischgl, one of the disease epicentres, have developed antibodies. I believe there are also quite a few people who have enough natural immunity that infection never gets a foothold. I think the herd immunity threshold has been reached.


That's a really interesting nugget, thanks!

I'm trying to reconcile it with the arguments I've seen that very low antibody presence within a population implies that many others fought off the disease using only T-cells, and hence did not develop antibodies.

Taking that sample at face value it would suggest to me that this is unlikely; or at very least they are unlikely to be significantly more than those people who do get antibodies.

Also, I think that 42% of a population would be considered a high proportion to have been infected with something (flu is estimated to get 3 - 11% of the US in a year) ; especially considering there have been arguments that you only require around 20% to achieve "herd immunity".

Obviously this sample might be an outlier, but I'll need to find myself a good reason to discard it.
-sd


It's not a million miles from that early study of the population of the small town of Vò where every resident was tested, and where one third of the population was found to have antibodies (IIRC).

So Ischgl is another straw in the wind suggesting a very high level of infectivity in parallel with a very high level of asymptomatic infection.

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Re: Coronavirus - Modelling Aspects Only

#321953

Postby Itsallaguess » June 27th, 2020, 6:18 am

Earlier in this thread we were discussing the potential for improved hospital outcomes over time, as methods and approaches to treating hospitalised patients improved, as our understanding of this virus got better.

The BBC now have an article on this subject that seems to confirm that this is indeed happening -

Coronavirus patients in hospital in England are dying at a slower rate now than they were at the peak of the epidemic, analysis suggests.

University of Oxford researchers found the proportion of coronavirus patients dying each day in England fell from 6% to 1.5% between April and June.

Improvements in treatments, changes in the patient population and seasonal effects could all play a role.

The data emerged as the government prepares to ease lockdown restrictions.

Around the height of the outbreak, on 8 April, there were 15,468 people in hospital in England with coronavirus of whom 899 died (6%).

By 21 June there were 2,698 hospitalised coronavirus patients, 30 of whom died (1%), according to the most recent data compiled University of Oxford's Centre for Evidence-Based Medicine.

Hospital case fatality is a measure used since the beginning of the outbreak, providing consistent figures and enabling researchers to look for trends.


Image

Source - https://www.bbc.co.uk/news/health-53192532

Cheers,

Itsallaguess

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Re: Coronavirus - Modelling Aspects Only

#321958

Postby GoSeigen » June 27th, 2020, 8:09 am

Itsallaguess wrote:Earlier in this thread we were discussing the potential for improved hospital outcomes over time, as methods and approaches to treating hospitalised patients improved, as our understanding of this virus got better.

The BBC now have an article on this subject that seems to confirm that this is indeed happening -


What about harvesting/displacement as an explanation? It might even be the predominant factor -- but the trend is good of course.

GS

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Re: Coronavirus - Modelling Aspects Only

#321961

Postby Itsallaguess » June 27th, 2020, 8:27 am

GoSeigen wrote:
Itsallaguess wrote:
Earlier in this thread we were discussing the potential for improved hospital outcomes over time, as methods and approaches to treating hospitalised patients improved, as our understanding of this virus got better.

The BBC now have an article on this subject that seems to confirm that this is indeed happening -


What about harvesting/displacement as an explanation? It might even be the predominant factor -- but the trend is good of course.


Some theories behind the clearly downwards trend, which has also been seen in other countries too, are covered in the linked article -

Although the researchers were unable to determine exactly what was behind the trend, they put forward a number of reasons.

One is that, as more is understood about the disease, healthcare staff have been better able to treat it using existing drugs, even without any major breakthrough in new treatments.

For example, doctors are now primed to expect patients with blood clotting and overactive immune responses, whereas in the early days they were looking to treat the symptoms of what was seen as primarily a respiratory disease.

And in critical care patients, the common steroid dexamethasone is now being used to dampen down the out-of-control immune reactions that can cause organ damage. This is likely to be a key factor, but is unlikely to completely explain the falling death rate, according to Prof Heneghan.

It may also be down to changes in the types of patients admitted to hospital.

As strain on the NHS has eased, the researchers say it is possible that there is room to admit patients who would not have met the stricter threshold for hospital care at the height of the epidemic. And these patients may be slightly less vulnerable and therefore less likely to die.

More sombrely, it's also possible that the virus, having torn through the most vulnerable populations, has left behind people who were at lower risk to start with.

A further possibility is that there could be a group of patients in hospital for long periods, not being discharged but also not succumbing to the virus.

Summer might also be playing a protective role: there are fewer other illnesses in circulation to compromise people's immune systems, and more sunlight means more Vitamin D.


https://www.bbc.co.uk/news/health-53192532

It's likely that it's a combination of many of these factors coming together to benefit outcomes, but whilst that may be the case, I think the overwhelmingly positive aspect is that it's happened, and it's happened during a time where lock-down protocols have been eased, so unless the specifically warmer weather is a highly prominent factor, which of course might impact any future spikes during the coming colder months, it's good to know that there is a 'protocol level / treatment level' that can maintain very low mortality rates from hospitalised patients...

On an ongoing basis, that's likely to be very important in terms of any future spikes and how they are handled, given that we can perhaps start to draw lines in the sand in terms of how far back we might need to reverse any lockdown protocols to 'get back to where we are now'...

Overall then, and given that the more strenuous lockdown protocols were predominantly in place to protect the NHS capacity issue, it may be starting to look like those much harsher lock-down protocols may not have to be revisited - surely a boost for the wider economy in general, and healthcare capacity too -

While both the number of people in hospital and the number of hospitalised people dying are falling, deaths are falling at a faster rate.

The number of people in hospital with Covid-19 is halving every 29 days, while deaths are halving every 16 days.

Prof Carl Heneghan, who carried out the analysis, said the pattern of falling death rates in hospitals was also being seen in other countries, including Italy,


Cheers,

Itsallaguess


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