Coronavirus - worldwide spread and control

[Adrian]

may also be of interest

The quality of the code does worry me. Refactoring the code will add bugs but the fact he won't release the original suggests that it isn't well written and so could have bugs.

The important thing is what steps he took to verify the code runs the model as expected and this can include subtleties like ensuring that the random number generator is adequate for the task (things like sequential correlation can be an issue). I would hope that there was a series of unit tests of overall testing to check it does what it says but I don't have much faith in the process by which research software at universities is produced.

But from a modelling perspective there are issues of how he validated the modelling techniques and model. Models aim to be a sufficient abstraction of the situation without over complication. But they basically play out a set of assumptions (either as distributions, things like spread values or structural features contained in the model) so there is always the question do they capture the situation. In this case this is a model of influenza spread so are the assumptions all valid for a corona virus model (for example, with the spread patterns).

I've not seen these things discussed but I've not had time to really look and dig.

 

[Keela Too]

A friend of a friend shared this on Facebook. I thought it a good read about the relative risks of different types of transmission.

Basically it explains how increasing time in an area with airborne viral particles increases the risk of reaching infection threshold. Makes sense.

It ends by suggesting mask wearing in enclosed spaces to reduce the number of airborne viral particles.

https://www.erinbromage.com/post/th...cM0dNbr4QmTuRNtCXGcmvHImLOu27o9vzwnDzD_QYou7k

 

[lunarainbows]

The Scientific Advisory Group on Behavioural science (SPI -B) are not happy...the govt published the SAGE scientific reports but redacted a lot of the behavioural science report...

https://theguardian.com/world/2020/may/08/revealed-uk-scientists-fury-over-attempt-to-censor-covid-19-advice?

“Large blocks of text in the report, produced by SPI-B, the Sage subcommittee providing advice from behavioural scientists on how the public might respond to lockdown measures, were entirely blanked out.

Several SPI–B members told the Guardian that the redacted portions of the document contained criticisms they had made of potential government policies they had been formally asked to consider in late March and early April.

One SPI-B adviser said: “It is bloody silly, and completely counterproductive.” A second committee member said: “The impression I’m getting is this government doesn’t want any criticism.”

here’s the heavily redacted report:

https://assets.publishing.service.g...ncing-comments-suggestions-spi-b-01042020.pdf

 

[Cheshire]

The World Doesn’t Yet Know Enough to Beat the Coronavirus

The urge to reopen society far outpaces scientific discovery. Ten scientists offer a plan to close the gap.

The United States and many other nations are launching a life-threatening experiment. They are rapidly and perhaps prematurely easing restrictions on businesses and social activity—even as the novel coronavirus, SARS-CoV-2, is still prevalent and much of the population remains susceptible to the disease it causes, COVID-19. The understandable desire to restore normal life quickly has raced ahead of the scientific knowledge necessary to do so safely. The result could be mortality rates that exceed even those occurring now, in the first wave of the pandemic.Since late last month, I have been meeting frequently online with a group of nine colleagues: David Baltimore, Mike Brown, Don Ganem, Peggy Hamburg, Richard Lifton, Marc Lipsitch, Dan Littman, Shirley Tilghman, and Bruce Walker. All are well known for their work in areas such as virology, immunology, genetics, and epidemiology. All have served in one or more leadership roles: as presidents of universities or other academic institutions, as heads of government agencies, as advisers to drug or biotechnology companies, or simply as pioneers and mentors in their field. All have sought solutions to the great medical problems of our time. None of us can recall a crisis as stark as COVID-19.

https://www.theatlantic.com/ideas/archive/2020/05/lack-testing-holding-science-back/611422/

 

[Adrian]

This looks like an interesting story about members of a choir in the UK who all came down with Covid-19 like symptoms late December and January. There is also an association with Wuhan as someone came back from a business trip with a cough.

https://www.bbc.co.uk/news/health-52589449

 

[FMMM1]

There's still a lot of focus on herd immunity in the Swedish media... Tom Britton and others from Stockholm University and Nottingham University are now claiming/speculating that "herd immunity can be obtained already at 40%" (earlier models say 60%), which they say could mean that "the spread of infection could stop in Stockholm in the middle of June". Chief epidemiologist Tegnell agrees, saying that it is "definitely possible".

https://omni.se/britton-flockimmunitet-kan-nas-vid-40-procent/a/LA7dBx

https://www.dn.se/nyheter/sverige/tegnell-flockimmunitet-betyder-inte-att-faran-ar-over/

Yes regarding the focus on herd immunity.

I was a bit concerned to hear this on BBC Radio 4* Any Questions "put measures in place too early"---"perhaps would not have got the maximum benefit". Surely the only possible "benefit" would be more people becoming immune i.e. herd immunity. The problem, with herd immunity, is that the death toll would be greater that 500,000 in UK (anyone got data on death toll/herd immunity?). Surely the logical thing would have been to test (or diagnose on symptoms), trace and isolate; then we would have fewer cases. Would you rather have 4000(?) new cases day UK or 1000(?) day France?

Someone posted here that this approach (aiming for peak incidence/not overwhelming the health service) misses the point i.e. that the number of cases would have been lower if they had initiated measures (lockdown, test & trace --) earlier. Someone posted previously regarding act earlier and the peak is lower --- grateful if someone could point me to that post.

Other issue is more cases of infection --- equals more opportunity for the virus to mutate.


*Dr Michael McBride Chief Medical Officer (CMO) for Northern Ireland.

time "4.38" [https://www.bbc.co.uk/sounds/play/m000hwsx]

 

[lunarainbows]

Yes regarding the focus on herd immunity.

I was a bit concerned to hear this on BBC Radio 4* Any Questions "put measures in place too early"---"perhaps would not have got the maximum benefit". Surely the only possible "benefit" would be more people becoming immune i.e. herd immunity. The problem, with herd immunity, is that the death toll would be greater that 500,000 in UK (anyone got data on death toll/herd immunity?). Surely the logical thing would have been to test (or diagnose on symptoms), trace and isolate; then we would have fewer cases. Would you rather have 4000(?) new cases day UK or 1000(?) day France?

Someone posted here that this approach (aiming for peak incidence/not overwhelming the health service) misses the point i.e. that the number of cases would have been lower if they had initiated measures (lockdown, test & trace --) earlier. Someone posted previously regarding act earlier and the peak is lower --- grateful if someone could point me to that post.

Other issue is more cases of infection --- equals more opportunity for the virus to mutate.


*Dr Michael McBride Chief Medical Officer (CMO) for Northern Ireland.

time "4.38" [https://www.bbc.co.uk/sounds/play/m000hwsx]

Yes.. I posted something about this a while ago - is it this? https://www.s4me.info/threads/coronavirus-worldwide-spread-and-control.13287/page-130#post-255097

My worry now is they are still possibly following herd immunity. Otherwise, changing the messaging and lockdown strategy right now while cases are high and people are flouting lockdown already, doesn’t make sense. They can’t possibly be aiming for elimination if they’re doing this.

 

[Sasha]

Basically it explains how increasing time in an area with airborne viral particles increases the risk of reaching infection threshold.

This idea of an infection threshold still confuses me. I don't see why you'd need more than one viral particle (which will replicate in your body) to get infected.

 

[lunarainbows]

Croydon in London the worst affected in London in terms of number of cases that have been recorded (see: https://www.cityam.com/coronavirus-worst-affected-london-boroughs/ )
And within that borough - Thornton Heath is one of the worst affected areas. It is also a deprived area with overcrowded housing.

https://www.thorntonheathchronicle.co.uk/covid-cluster-as-widespread-disregard-for-lockdown/
“In a letter to MP Steve Reed, Thornton Heath police have said a lot of residents don’t believe Covid-19 exists. Officers have issued multiple fines over the last few weeks and issued warnings to shopkeepers flouting government guidelines.

In a recent Twitter post Thornton Heath MPS, wrote: “More fines issued by the teams for breaching Covid regulations. Lots of advice given. Unfortunately still a lot of people who think that Covid-19 does not exist. Very frustrating.

In a letter to MP Steve Reed, in response to a residents complaint about street drinkers ignoring the lockdown, Thornton Heath’s new sergeant Andy Smith said: “The issue with Thornton Heath at the moment is there seems to be a pretty widespread disregard for the directions given by the government. We have spoken to a number of shops about social distancing and that the onus sits with them to manage the crowds that are drawn to their shops.”

In another post Sgt Smith pictured in Grangewood Park says: “Took a bike ride out on the ward today, still lots of people out and about so lots of advice given. Also a house party dispersed.”

Throughout the lockdown street drinkers have continued to gather and drink outside the Clocktower, Tesco and on Ambassador House forecourt. A half hearted attempt was made to tape off the seats at the Clocktower but the tape was removed.“

I’m finding it really hard not to despair. I’m seeing the number of cars on the main road going up - today it looks like a normal Sunday daytime. I believe that in London at least, the coronavirus is going to continue to spread at a high rate

 

[Mithriel]

Herd immunity is a worrying concept. It only works in diseases that give long term immunity and do not mutate much but colds don't fit that very well. Years ago I read that the problem with the highly populated cities we live in is that a virus infects everyone living in one place then spreads out but every time it passes through a person it mutates slightly. By the time it passes through thousands it is so different that the first people infected have no immunity to the changed virus so they get sick again.

There is a biological phenomenon called the Wallace Effect where species change slightly as you travel round the globe so that it becomes a new species unable to interbreed by the time it reaches the start again so the idea of the same thing happening with viruses is not far fetched.

Also infections which are too aggressive kill off their hosts so that only the ones which are milder persist in the population. But that only works when there is limited availability of hosts. In our modern world the population is so large there is no evolutionary pressure to become less lethal.

Historically, populations of hosts become more resistant to diseases. Europeans tend to have mutations which make them more resistant to TB because only people with them lived to reproduce.

So herd immunity often involves large numbers of people dying in the initial stages of a novel microbe and may not work very well in modern societies with large population densities.

My hopes are for a treatment, only then will I feel secure going out the way I used to.

 

[spinoza577]

I think this is pretty interesting, and possibly important:
https://www.web24.news/u/2020/04/ac...conditions-could-lead-to-corona-immunity.html My bold.

When examining defense cells in pre-pandemic samples, the researchers had seen that 34 percent of the patients had reactive T cells – i.e. blood cells – that to a certain extent recognized certain parts of the new coronavirus. So-called reactivity can be expected when the disease is behind – however, these patients have had no contact with Sars-CoV-2, according to Drosten. The fact that there were still reactive T cells could be due to infections with human cold coronaviruses.

 

[Keela Too]

This idea of an infection threshold still confuses me. I don't see why you'd need more than one viral particle (which will replicate in your body) to get infected.

So if my understanding is correct, it goes like this.

1 virus particle will have a doubling time, before it becomes 2 particles. Then another doubling time elapses before there are 4 particles.

Potentially this will carry on like this: 1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048 etc etc.

Once established the virus will keep replicating until either the individual’s immune system overcomes the virus and stops (or slows) it replicating, or the virus becomes uncontrolled and the infected individual dies. (Treatment at the moment I understand, is all about giving the patient time to over come the virus themselves, as we don’t yet have a means of artificially stopping the virus multiplying in an infected individual.)

So in the above series there have been 11 units of time between the receipt of 1 viral particle and the number 2048 being reached. (Each unit being the doubling time of a viral particle). I don’t know the doubling time for the coronavirus but really it’s not relevant to this discussion. It’s just important that each additional unit of time gives the immune system time to mount a response.

If an individual receives 1000 viral particles at inoculation instead of only one, then from 1000 to 2000, there is only 1 doubling time to reach approximately the same viral load (2048) as the example above.

Timing is everything with an exponentially increasing infection, the sooner a response can be mounted the better. The later the immune system gets the message to start the response, the greater the opportunity for the virus to get ahead, and so the harder the infection will be to control.

This means that the person receiving only 1 or 2 viral particles has substantially more time to respond to and knock-out the infection, than the person receiving 1000 viral particles all at once. Basically the greater the initial inoculation the greater the headstart the virus gains.

So keeping exposure as low as possible is vital.

This may also be why those with greater exposure might also have a more severe experience of the disease, because their own body’s response has not managed to reduce the effects of the virus to a more manageable level.

 

[FMMM1]

Yes.. I posted something about this a while ago - is it this? https://www.s4me.info/threads/coronavirus-worldwide-spread-and-control.13287/page-130#post-255097

My worry now is they are still possibly following herd immunity. Otherwise, changing the messaging and lockdown strategy right now while cases are high and people are flouting lockdown already, doesn’t make sense. They can’t possibly be aiming for elimination if they’re doing this.

Yes I can't see that it makes sense to allow the infection rate (R naught) to increase; we really need to reduce it and maintain that. I heard something on the Radio about "we can't stay in lock down forever"; however, suppressing the outbreak seems to be the best way of getting the economy back to something like normal. Maintaining infection levels seems to be a recipe for shutting down your economy for longer.

Heard a joke (form a planning officer) along these lines "garden centres --- most of them don't have much floor area devoted to selling plants --- general retail, coffee shop ---". So if they are re-opening garden centres --- can I go fishing (sorry, should have a more acceptable hobby)?

 

[JaneL]

I found the minutes from the meetings of The New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG). NERVTAG are one of the expert groups advising the UK government on the Covid-19 response.

The minutes are quite enlightening - it looks like NERVTAG had a significant role in shaping the government’s response. In the meetings they discuss PPE, port health, modelling, epidemiology and surveillance, treatments etc.

You can access the minutes to these NERVTAG meetings here:
https://m.box.com/shared_item/https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/browse/103551854721

I’ve reviewed the advice they gave on air travel into the UK which I will try to summarise in a separate post.

 

[JaneL]

As mentioned, I have reviewed the advice that The New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) gave on air travel into the UK which I have attempted to summarise in this post.

The topic of “port of entry screening” was discussed at the very first Covid-19 NERVTAG meeting on 13 January and the following conclusions were reached:

5.8 NERVTAG noted that the body of scientific evidence and previous experiences indicate that port of entry screening, whilst not having zero effect, has very low efficacy and the benefit is very unlikely to outweigh the substantial effort, cost and disruption.

They referred to this modelling study by Pitman et al (2005) which I noticed has some significant limitations. That was the only study from the “body of scientific evidence” relating to port screening that was referred to at this meeting. There was no discussion about the possibility of introducing quarantine or immigration restrictions (which would have overcome the limitations of port of entry screening).

By the time of their next meeting on 21 January, The Department for Health and Social Care (DHSC) asked NERVTAG to reconsider the issue of port health screening in light of the changing epidemiological picture. The same conclusions were reached and they continued to advise against port of entry screening. There was still no consideration given to quarantine or immigration restrictions (no mention of either). NERVTAG did however agree that information leaflets and broadcasting messengers to passengers on flights as well as posters in airports would be “worthwhile”.

Although there did not appear to be any indication that NERVTAG would ever advise port of entry screening for those coming from Wuhan, the DHSC still wanted to know at what point NERVTAG would advise discontinuing such a policy if it were to be introduced in the UK. This was the response:

NERVTAG noted that one trigger would be the epidemic being brought under control and case numbers declining. The other would be self-sustaining transmission in either the UK, or cities outside of Wuhan, which would make screening redundant or unfeasible.

Toward the end of the minutes of this meeting it was stated that:

DHSC planned to review these issues using advice from NERVTAG alongside information from other organisations involved in port health/travel to finalise policy.

I was surprised to see that the issue of port health/travel was not raised again in any of the following 10 NERVTAG meetings which took place between 28 January and 27 March...

There are more details in the minutes of the meeting - here again is the link to access them:
https://m.box.com/shared_item/https://app.box.com/s/3lkcbxepqixkg4mv640dpvvg978ixjtf/browse/103551854721

 

[Jonathan Edwards]

A friend of a friend shared this on Facebook. I thought it a good read about the relative risks of different types of transmission.

Basically it explains how increasing time in an area with airborne viral particles increases the risk of reaching infection threshold. Makes sense.

https://www.erinbromage.com/post/th...cM0dNbr4QmTuRNtCXGcmvHImLOu27o9vzwnDzD_QYou7k

I doubt there is any basis to this story. The contact time was introduced to give a guide to probability of being infected, not degree of infection. If you were less than two metres away for ten minutes someone estimated the chance of infection was high enough to warrant quarantine.

You only need one virus particle to be infected. They do not help each other (much). One virus particle enters a cell and either produces about a million more or fails to. Thos million float about and next time other cells multiply by a million, sometimes and sometimes not.

I suspect the dose effect that has been suggested depends on whether you rub your face with a hand so that one or two virus particles happen to reach cells or you inhale a fresh droplet containing ten billion virus particles. Time does not come in to it.

The other thing is that the immune system will get triggered once a certain number of cells are sending out danger signals - maybe you need 1000 or 10,000. So to some extent the number of particles at the start does not matter. The immune system gets going at the same level of particles.

What may also be important is whether virus comes in via mouth and pharynx, where tonsils provide a strong door keeping function, or goes straight in to lung.

I don't think we actually know that dose is that relevant anyway.

 

[Adrian]

As politicians talk about relaxing lock down and how that relates to R0 it strikes me as R0 is not a useful concept but is rather confused because it is both a function of the natural spread rate of the virus along with the effect of all the mitigations. That can lead to confused thinking or messaging where R0 seems to be a value that allows change rather than a reflection of the effectiveness of mitigations so that with any change you need to reason through how a change will keep R0 low - for example by tracing and isolating when the numbers are low enough to enable such a system to work.

I think it may also encourage thinking that it is a value rather than an average of a spread situation that can vary a lot with location and situation (for example high in care homes). Wouldn't it also be better to talk of a spread value and the varience of the value over the country (perhaps a heat map).

The problem is if R0 becomes the thought tool and it rolls so many concepts in together then those who are not used to talking of the details of disease spread will use it as their thought tool and can be lead down the wrong path.

 

[Jonathan Edwards]

The problem is if R0 becomes the thought tool and it rolls so many concepts in together then those who are not used to talking of the details of disease spread will use it as their thought tool and can be lead down the wrong path.

Absolutely. Johnson appeared to give completely inappropriate analysis of R (as he called it) and its role in allocating warning levels this evening.

As I understand it warning levels should reflect relative risk of the virus being spread. That will be a function of both R and the current infection rate - in particular the presymptomatic infection rate. So R is the wrong variable to use to allocate warning level and is, anyway, as you suggest, dependent on regulations and very likely on warning level. So we have an opaque indicator. Johnson indicates that he is happy to tell people what is going on without himself having any understanding of the mathematics - i.e. no understanding of the real situation.

Unfortunately, I have heard epidemiologists making what seem to be similar mistakes. It is easy to give clumsy explanations when interviewed in response to skewed questions when you do actually understand. But it is also easy to give clumsy explanations when you do not understand.

I get the impression we are progressing towards July much as I had expected - with false starts in Germany and maybe Korea and an imaginary start in the UK feeding in to what is likely to be a gradual convergence on reality by then. In June I suspect professionals will start making noises about having had enough. Ultimately people are going to have to do what it takes to get case numbers way down. Unless you live in a country where that simply isn't government policy even now...

 

[spinoza577]

...In June I suspect professionals will start making noises about having had enough. ...

Here in Germany it was a professional who began to promote R0 as a relevant indicator, interestingly without explaining anything, just conveying something. Interesting also that it was the director of the CDC. Even more interesting only then, that he is a vet.
The original strategy was to flatten the curve so that hospitals won´t be overburdened.

@Adrian has got it rightly, I would say. Although Germany has done well so far, this lack in understanding and clear communication in combination with a not anymore declared strategy leads people to confuse around. Discussions become fairly one sided, which is dangerous, if anyone agrees.

The courts [have to deal with] that there is in a democracy not the possibility to cut fundamental rights if it doesn´t prevent a catastrophe. [The BVerfG did an verdict (PSPP) on Mai 5th, to declare and show the danger in relation to the measurements.]

 

[Leila]

There have been protests all over Germany over the weekend with thousands of people protesting against social distancing rules/for civil rights.

They were legal and mostly peaceful but I'm worried they will push more infections causing more of the very same measures they are protesting against.

It's up to every district/county now to keep infections at bay and go back to implementing stricter measures when there are >50 cases per 100.000 citizens per week. So more of a localized rather than nationwide approach.

Not sure how well that can work. If one county closes their stores again people might just drive to the surrounding counties and spread the infection even further..