Coronavirus - worldwide spread and control

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lunarainbows said:
I thought the Independent SAGE press conference was really good! I sincerely hope the govt take it all on board.
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Yes, I haven't watched all of it yet but they seemed to fire off a series of excellent points well directed at the general journalists asking questions. It is all just common sense. I think the government will gradually move to all these suggestions, much as it already has trailed behind other sensible ideas like a grumpy child. The only question is when - maybe July.
 
Interesting article by Tom Chivers on Simpson’s Paradox. It explains how, counterintuitively, the R value could go up as a consequence of reducing the transmission rate in the community through lockdown.

Not a great sub-heading but the content of the article is very good:

”We should be very wary of the R value”:
https://unherd.com/2020/05/what-the-headline-covid-figures-dont-tell-you/
 
Robert 1973 said:
Interesting article by Tom Chivers on Simpson’s Paradox. It explains how, counterintuitively, the R value could go up as a consequence of reducing the transmission rate in the community through lockdown.

Not a great sub-heading but the content of the article is very good:

”We should be very wary of the R value”:
https://unherd.com/2020/05/what-the-headline-covid-figures-dont-tell-you/
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Could it not just simply be that care home (and other) cases are now being included into the figures where before they were not, so it will look like more cases have been spawned from fewer earlier infectious individuals than is actually the case? i.e. It was actually from a larger number of earlier cases.
 
Barry said:
Could it not just simply be that care home (and other) cases are now being included into the figures where before they were not, so it will look like more cases have been spawned from fewer earlier infectious individuals than is actually the case? i.e. It was actually from a larger number of earlier cases.
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It could, although I would hope and assume that this is taken into account by those calculating the R values.

Regardless of the true values, it is still interesting (to me at least) to note that the R value in the whole population can go up when the R value both in care homes and outside of care homes is going down.

I remember being fascinated by Simpson’s paradox when I first learnt about it but I had forgotten it, and I hadn’t considered that it could apply to transmission rates.
 
This blog post seems to be getting a lot of hits online, and includes this statement:

In order to get infected you need to get exposed to an infectious dose of the virus; based on infectious dose studies with MERS and SARS (and this one), some estimate that as few as 1000 SARS-CoV2 viral particles are needed for an infection to take hold. Please note, this still needs to be determined experimentally, but we can use that number to demonstrate how infection can occur. Infection could occur, through 1000 viral particles you receive in one breath or from one eye-rub, or 100 viral particles inhaled with each breath over 10 breaths, or 10 viral particles with 100 breaths. Each of these situations can lead to an infection.​

The author is a Professor Erin Bromage, a Comparative Immunologist and Professor of Biology (specializing in Immunology) at the University of Massachutsetts Dartmouth and here is a short bio she gives about her relevant credentials for talking about coronavirus.

So once again I am confused! She is saying that there is a number-threshold of viral particles that you need for an infection, but @Jonathan Edwards's explanation that you only need one viable particle to enter your body (where the particle then replicates) for an infection to occur makes sense to me.

@Jonathan Edwards, is this a controversial concept in virology? Would different principles apply to different kinds of virus, for example?
 
I would imagine it's a statistical/probability thing.

Only one viral particle needs to be successful at entering a cell to replicate, but presumably not all are successful, even before the host immune system becomes active.

I'm thinking it's much the same thing as why plants can produce millions of seeds, only a very few are able to find a suitable environment to replicate successfully.

Only one viral particle is needed to infect someone, but it needs to be 'lucky' and most aren't, which may be why there are threshold numbers, a guesstimate at how many viral particles would be needed in order for it to be a virtual certainty that one will find a hospitable environment, manage to get inside a suitable cell, and start replicating.

Just a reflection of the odds I suspect, and not a 'being exposed to 1 less than whatever the number is means you're not going to get infected until the next one comes along' situation.
 
Fortfarande långt kvar till 100 000 tester
https://www.svd.se/fortfarande-langt-kvar-till-100000-tester

Still far to 100,000 tests
The number of coronate tests increased minamally last week - despite the government's ambition to reach 100,000 tests a week by mid-May.
Sweden still only tests about a third of its capacity.

"In many regions, people have come a long way and done very well, while others are still in their starting pits," says Harriet Wallberg, the government's new test coordinator.

The number of tests for ongoing corona infection increased by 600 last week, from just over 28,800 to almost 29,400, according to new statistics from the Public Health Authority. This means that far fewer tests are carried out than the government wants and for which there is analytical capacity.

Social Minister Lena Hallengren (S) has signaled dissatisfaction with how the regions are conducting the testing and last week appointed Harriet Wallberg to remove bottlenecks and get the regions to start testing more.

The purpose of extended testing is partly to prevent the spread of infection and thus save lives, and partly to make society work again by allowing uninfected persons to return to work.

In the future, the focus of the testing will be on three groups, says Harriet Wallberg.

The first is healthcare and care personnel. In some places, this work has not yet come so far.

The other group is the elderly and the elderly care staff - and there the plan is to test widely, that is, not just those with symptoms.

- There I think that you can actually test everyone. If you have someone in a retirement home who has the infection and does not have symptoms, that is devastating for the others living there that can get infected by that person, says Harriet Wallberg.

The third group they want to start testing is staff in other socially important professions, ranging from police and preschool staff to drivers and food transporters.

TT: How is this going to happen? Should they call 1177 and get a referral and then a self-test kit sent home?

- This is something that the Public Health Authority must now quickly plan and draw up the guidelines for.

According to Emma Spak, section manager at Sweden's Municipalities and Regions, it may take several weeks before the target of 100,000 tests is reached.

- The regions are currently gearing up when it comes to testing. The important thing here is to ensure that we have a well-functioning sampling chain, that it is patient-safe and that you actually get samples that you use correctly so that they become useful, she says.

What is especially lacking in order to extend the testing is logistics.

- Someone has to press a start button, say "this person should be tested". Possibly some form of referral must be written. Then, sampling materials must be distributed to different locations, either to drive-in stations, or a car that comes to one's home. Then the samples must be sent to a laboratory, and then there must also be feedback, says Harriet Wallberg.

Testing must not turn into a stick hunt, she points out.

- There is probably a risk of that happening and it would be unfortunate. If we are to test, it must be relevant and it should provide information that we benefit from.

Facts:
The number of people being tested
Analyzed samples for the virus that causes covid-19 in Sweden:

Week 19: Nearly 29,400

Week 18: Just over 28,800.

Week 17: Nearly 24,600.

Week 16: Just over 20,000.

Week 15: Nearly 19,900.

Week 14: Just over 17,700.

Week 13: Just over 12,300.

Week 12: Just over 10,300.

Week 11: Nearly 9,000.

Week 10: Just over 4,300.

In total, almost 148,500 individuals' samples have been analyzed since the diagnostics were set up in Sweden.

Source: Public Health Authority
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"TT: How is this going to happen? Should they call 1177 and get a referral and then a self-test kit sent home?

- This is something that the Public Health Authority must now quickly plan and draw up the guidelines for.

According to Emma Spak, section manager at Sweden's Municipalities and Regions, it may take several weeks before the target of 100,000 tests is reached."


It seems to me that Sweden is very behind with regards to testing and not very well prepared. Shouldn't plans and guidelines for this already have been made and just be ready to set in place by now?

There are a number of countries that have been very successful in their testing, they could have reached out to them for guidance and information on how to set it up.

The low numbers of tested individuals also makes me question the accuracy of the reported number of infected.

I am thoroughly underwhelmed by the Swedish government's way of handling this....
 
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Sasha said:
@Jonathan Edwards, is this a controversial concept in virology? Would different principles apply to different kinds of virus, for example?
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I have never heard of Erin Bromage but he seems to some sort of self-styled expert on viruses who works on fish or something - relatively junior.

I don't know how anyone can know that you need more than one virus particle - which is the logical assumption since if ten particles can infect one can infect and that will lead to replication.

The statement is 'as few as 1000'. In other words not more than 1000 - which includes 1.

There may be literature on minimum dose but as Wonko says and I have said before it seems much more likely to be statistical thing. The probability of one virus particle hitting you and getting going is small and for 1000 the probability that some will grow is bigger but that does not mean that you need 1000 to be infected. The seed analogy seems very good to me.

Remember that all sorts of junior scientists set themselves up as 'communicators' these days to sell themselves. Dartmouth immunology is quite good on some things but not all.
 
Robert 1973 said:
It could, although I would hope and assume that this is taken into account by those calculating the R values.

Regardless of the true values, it is still interesting (to me at least) to note that the R value in the whole population can go up when the R value both in care homes and outside of care homes is going down.

I remember being fascinated by Simpson’s paradox when I first learnt about it but I had forgotten it, and I hadn’t considered that it could apply to transmission rates.
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Yes I'd never encountered Simpson’s paradox as such, though I'm familiar with the notion that percentages (implying ratios generally therefore) can become skewed in such situations, where the absolute numbers might shift drastically. And of course R is a ratio.

Basically ratios and % should always come with warning flags.
 
Sasha said:
I would say that 'as few as' means 'as few as, but no fewer', so greater than or equal to 1000. I think he really is saying this is a minimum threshold.
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Yes, that's what I generally take "as few as" to mean - is in it could be as few as.
 
Sasha said:
I would say that 'as few as' means 'as few as, but no fewer', so greater than or equal to 1000. I think he really is saying this is a minimum threshold.
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I agree that that I what he is wanting to mean. And it is what English usage generally does with the phrase.
But there is a paradox in using as few if that is to include more in this context. It has to mean 'no more than 1000 may do the trick', which means that you don't need more than 1000. More than 1000 is excluded from the threshold. But logically it does not exclude less. And if it is evidence based it will not exclude less. 'Experiments have shown that as few as 1000 will do the trick' is no evidence that 10 will not (absence of evidence is not... and all that) but it is evidence that more than 1000 is not always needed.

I think he is fitting the evidence to a mis-learned assumption. I may be wrong, and sometimes am - but that is my hunch.
 
Jonathan Edwards said:
I agree that that I what he is wanting to mean. And it is what English usage generally does with the phrase.
But there is a paradox in using as few if that is to include more in this context. It has to mean 'no more than 1000 may do the trick', which means that you don't need more than 1000. More than 1000 is excluded from the threshold. But logically it does not exclude less. And if it is evidence based it will not exclude less. 'Experiments have shown that as few as 1000 will do the trick' is no evidence that 10 will not (absence of evidence is not... and all that) but it is evidence that more than 1000 is not always needed.

I think he is fitting the evidence to a mis-learned assumption. I may be wrong, and sometimes am - but that is my hunch.
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Yes, I could say as little as 500 horse power will make my car go, but actually the same is true with significantly less than 100 HP. And if it had a 500HP engine it would 'go' spectacularly.
 
lunarainbows said:
Im just re quoting this post.. was wondering if anyone here who is computer or code savvy has an opinion / understanding of this app & code? I am interested since we will all be asked to download it in a few days or weeks - Mid May apparently!
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Television and movies give a very misleading view of how to assess somebody else's code. It makes for good TV when someone glances at some code for 5 seconds and marvels at its brilliance but that's not a real thing. Not even close, in fact. It takes serious efforts and basically a complete audit of the code to really get a good analysis. As in read it once in full. Then again. Then with proper debugging tools to follow execution paths. It's a slog. By the way that's why the Y2K bug was so expensive to fix. You can't just glance at some code and know what it does, especially since code tends to be spread around in various parts of the code base.

So this kind of review would be done by a team with ample resources and time. Anything less is just a cursory glance that should be ignored. If there's anything bad in there it would be hard to find as it's easy to hide stuff within a large code base.

It's good to have it open source, though. Great, in fact. This is how it should be done. But a proper audit is still professional work that requires as much skill as it takes time.
 
Here's some data from Sweden to follow up on my earlier posts on whether loose advice/recommendations are more sustainable over time than stricter lockdown measures enforced by laws etc:
Google Translate said:
In the survey, more than 5,000 people were asked questions about how they changed their behavior since the beginning of the corona crisis. Until last week, there was a steady increase in respondents who stated that they changed their behavior due to the pandemic. But the latest survey shows a trend break. Among other things, the proportion who state that they have avoided public transport and refrained from social activities.

Some examples:
  • "Less participation in social activities outside the home" has decreased from 74 to 66 percent.
  • "Avoiding public places where there are many people" has decreased from 72 to 65 percent.
  • "Using less public transport in everyday life" has decreased from 50 to 42 percent.
Read the full survey on msb.se.
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https://www.krisinformation.se/nyheter/2020/maj/sifo-matning-farre-anger-andrat-beteende

(I'm sharing these data in an attempt to help dispel the mis-/disinformation that is currently being spread on social media and elsewhere about "the Swedish situation".)

Not directly related, but here's an article by prof Lenny Jason and others on "quarantine fatigue":

Inverse: 3 experts explain how you can combat quarantine fatigue
“We just kind of have to roll with it and keep trying to make the adjustments that will help us withstand it all.”

https://www.inverse.com/mind-body/how-to-overcome-quarantine-fatigue
 
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