COVID-19 Coronavirus Containment Efforts

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Boris Johnson is holding a press conference amid rising Coronavirus infections. Some info about the mutation and its effect on current and future containment methods.
 
Biology news on Phys.org
Regarding the new N501Y mutation in the spike protein of SARS-CoV-2 identified in the UK, here's a press release from the scientific consortium that identified the mutation: https://www.cogconsortium.uk/news_i...ant-and-how-cog-uk-tracks-emerging-mutations/

The variant described today in the House of Commons contains a novel set of mutations associated with a lineage spreading rapidly in the South East of England (and more widely) that is the subject of ongoing investigations by the UK Public Health Agencies, coordinated by Public Health England and supported by COG-UK. This variant carries a set of mutations including an N501Y mutation in the receptor binding motif of the Spike protein that the virus uses to bind to the human ACE2 receptor.

Efforts are under way to confirm whether or not any of these mutations are contributing to increased transmission. There is currently no evidence that this variant (or any other studied to date) has any impact on disease severity, or that it will render vaccines less effective, although both questions require further studies performed at pace. We will provide further updates as our investigations proceed.
 
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A severe variant of Coronavirus has been detected in South Africa which could explain the rapid spread of a second wave affecting younger people, the health minister said today.

Known as the 501.V2 Variant, it was identified by South African researchers and details have been sent to the World Health Organization, Zwelini Mkhize said in a statement.
https://www.rte.ie/news/world/2020/1218/1185398-south-africa-covid/

As of December 18, 2020 , South Africa had recorded 892,813 known cases of Covid-19 with 24,000 known deaths.
https://www.theeastafrican.co.ke/te...rus-variant-confirmed-in-south-africa-3233502

Looking at the picture from Soweto, it seems like an large proportion of folks are not wearing masks.
 
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so far, more than 400,000 patient courses of both the monoclonal therapies from Eli Lilly and Regeneron have been allocated to the states, and more than 250,000 have been delivered -- but very little of what has been distributed is actually being used. ABC News confirmed the findings of a new U.S. Department of Health and Human Services report which shows that only 5-20% of that available supply has been used -- strikingly low uptake of what could be a “lifesaving intervention” for some COVID-19 infections as case counts surge across the country.
https://www.msn.com/en-us/health/medical/why-are-authorized-monoclonal-antibodies-rarely-being-used-to-treat-covid-19/ar-BB1c2QUn

Data for December 18, 2020
Currently hospitalized 113,955
Currently in ICU 21,745
Currently on ventilator 7,786

Deaths 305,127
Date, Deaths (cumulative), New Deaths
Dec 18, 2020305,1272,866
Dec 17, 2020302,2613,438
Dec 16, 2020298,8233,448
Dec 15, 2020295,3752,971
Dec 14, 2020292,4041,358
Dec 13, 2020291,0461,494
Dec 12, 2020289,5522,494
Dec 11, 2020287,0582,749
 
Further discussion by Trevor Bedford on antigenic drift.
- Some variants like mutations at position 501 (one of the features in the new UK variant) may be emerging independently in different part of the world, perhaps consistent with weak selection pressure
- In spite of the antigenic drift, he still estimates that if the vaccine will need to be updated, it will still be on the time scale of a few years (~ 3 years, is mentioned for the antigenic drift of other coronaviruses)
 
Here is the paper from Rachel Eguia and colleagues from group of Jesse Bloom, the basis of the ~3 years of other coronaviruses to escape immunity by antigenic drift. They've also tweeted is a very readable summary.

A human Coronavirus evolves antigenically to escape antibody immunity
https://www.biorxiv.org/content/10.1101/2020.12.17.423313v1
 
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It looks as though the UK is being heavily isolated this morning.



I noticed an upswing in deaths here in my state of Oregon last month, that is continuing. Even Vermont has an upswing. Not sure if these are due to the cold weather or this the new English mutant. From the following graph I made, it looks like it may have originated in France.

England.being.isolated.today.2020-12-21 at 5.21.10 AM.png

Deaths/million/day
 
OmCheeto said:
It looks as though the UK is being heavily isolated this morning.

It's a trifle harsh to close the English Channel to haulage (between the UK and mainland Europe), given the relatively low risk of letting haulage through and the huge impact this is having. But, if you elect a government that openly boasts contempt for our soon-to-be-ex European partners, then perhaps we can't complain if they put the boot in given the chance.

We are an Island Nation once more!
 
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PeroK said:
We are an Island Nation once more!
Well, you can't change geography. The resulting isolation, however, is self-imposed. Eire is an island, too, but ...

As far as the new strain is concerned, the current actions are pure populism and can only slow down spread. It is merely the assurance against a later "they knew and haven't done anything"-complaint. AFAIK it is already in Italy, Belgium, the Netherlands, and some I have forgotten. It is the kind of political marketing which brought you the Brexit. I guess it is a natural consequence of evolution: the virus adjusts its genome to his main host.
 
OmCheeto said:
I noticed an upswing in deaths here in my state of Oregon last month, that is continuing. Even Vermont has an upswing. Not sure if these are due to the cold weather or this the new English mutant. From the following graph I made, it looks like it may have originated in France.
In a world where the virus is almost everywhere you don't need a specific source for a new larger outbreak. Just poorer control in the existing place is sufficient. The precise timing will depend on many things - local holidays, weather, end/begin of government intervention, ...
 
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mfb said:
In a world where the virus is almost everywhere you don't need a specific source for a new larger outbreak. Just poorer control in the existing place is sufficient. The precise timing will depend on many things - local holidays, weather, end/begin of government intervention, ...
Well, I'll be interested in reading the paper on why Germany, Oregon, and Vermont tracked so closely, for this current period.
They were all previously doing exceptionally well, and then, all hell seemed to break loose.
 
OmCheeto said:
Well, I'll be interested in reading the paper on why Germany, Oregon, and Vermont tracked so closely, for this current period.
They were all previously doing exceptionally well, and then, all hell seemed to break loose.
Luck? Selection bias? The fact that they were doing well increased the likelihood of doing poorly?
 
OmCheeto said:
Well, I'll be interested in reading the paper on why Germany, Oregon, and Vermont tracked so closely, for this current period.
They were all previously doing exceptionally well, and then, all hell seemed to break loose.
I doubt that you can formulate a hypothesis which survives any statistical test, means I assume this is independent from a random coincidence.

Informally and personally I assume that people who got away with a controlled environment became sloppy in their efforts due to the illusion of a false safety. Moreover there have been holidays between March and October, so people took the chance to get infected somewhere else! A second wave was likely from the beginning. And we should not forget that this is a highly dynamic system. The virus learns to adapt to his main host.
 
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fresh_42 said:
...The virus learns to adapt to his main host.
Idiots?
 
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OmCheeto said:
Well, I'll be interested in reading the paper on why Germany, Oregon, and Vermont tracked so closely, for this current period.
They were all previously doing exceptionally well, and then, all hell seemed to break loose.
Exponential growth and critical mass. Like a Uranium bomb?
 
I can't speak to Germany and Oregon, but here in Vermont the various outbreaks around the state mostly trace back to an outbreak in a hockey league:

https://vtdigger.org/2020/11/30/is-there-a-skater-zero-tied-to-central-vermonts-covid-outbreak/

The recent uptick in deaths stems from outbreaks in nursing homes. As the virus became more prevalent in the community, asymptomatic spread increased and naturally trickled into those vulnerable places.

Luckily, it seems like we've plateaued in terms of daily case numbers (if not decreased slightly since the peak). If folks can follow the guidelines, which is challenging during the holidays, maybe we can get back to the levels we enjoyed over the summer and early fall.
 
OmCheeto said:
Well, I'll be interested in reading the paper on why Germany, Oregon, and Vermont tracked so closely, for this current period.
They were all previously doing exceptionally well, and then, all hell seemed to break loose.

Spurious correlation? There are 50 states in the US and ~200 countries in the world. Make enough comparisons and you're almost certain to find some that correlate by chance. For example:
chart.png

https://www.tylervigen.com/spurious-correlations
 
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OmCheeto said:
Well, I'll be interested in reading the paper on why Germany, Oregon, and Vermont tracked so closely, for this current period.
They were all previously doing exceptionally well, and then, all hell seemed to break loose.
The only thing I see in common there is "roughly exponential rise for a while" with a time constant that's not too different. With 50 US states and 50 European countries, and with the same disease and winter as common factor influencing most of them, I'm not surprised to see such a pattern.
 
fresh_42 said:
As far as the new strain is concerned, the current actions are pure populism and can only slow down spread. It is merely the assurance against a later "they knew and haven't done anything"-complaint. AFAIK it is already in Italy, Belgium, the Netherlands, and some I have forgotten. It is the kind of political marketing which brought you the Brexit. I guess it is a natural consequence of evolution: the virus adjusts its genome to his main host.

You need to ban yourself for making political comments! Also, are you sure it's the sort of populism you are thinking of, and not the EU's brexit negotiating strategy (border closures a minor foretaste of what may happen to goods when reverting to WTO rules)? OK, you can ban me when you ban yourself. Anyway, I believe that at this stage the possibility remains the UK variant under discussion has become more common simply by chance (ie. Johnson's statements about increased transmissibility are not solidly founded).

https://www.sciencemag.org/news/202...om-sets-alarms-its-importance-remains-unclear
"Christian Drosten, a virologist at Charité University Hospital in Berlin, says that was premature. “There are too many unknowns to say something like that,” he says. For one thing, the rapid spread of B.1.1.7 might be down to chance. Scientists previously worried that a variant that spread rapidly from Spain to the rest of Europe—confusingly called B.1.177—might be more transmissible, but today they think it is not; it just happened to be carried all over Europe by travelers who spent their holidays in Spain. Something similar might be happening with B.1.1.7, says Angela Rasmussen, a virologist at Georgetown University. Drosten notes that the new mutant also carries a deletion in another viral gene, ORF8, that previous studies suggest might reduce the virus’ ability to spread."
 
I don't think that I made a comment I cannot prove. Containment simply doesn't work in our free societies. I did not in the first wave, so why should it work now? And yes, I had Drosten's interview (heard, not read) in mind as I wrote that those measurements would be in vain. Why politics decided otherwise anyway was an assumption, but knowing the political scenarios here, not far fetched. And my remark about the Brexit is also provable, i.e. that it has been driven by politicians using marketing strategies rather than facts.
 
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atyy said:
increased transmissibility
My wife and I were listening to a news program last night and heard Boris Johnson's rationale, and we were wondering how one would measure 'increased transmissibility'. Is measured in the laboratory or in the field? If the latter, is it actually a calculation, e.g., greater R0? Or is it really just a matter of some portion of the population congregating and not wearing masks, which I think would increase R0?
 
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Astronuc said:
If the latter, is it actually a calculation, e.g., greater ##R_0##? Or is it really just a matter of some portion of the population congregating and not wearing masks, which I think would increase ##R_0##?
As usual, such facts are left out in the news, whether interviews or trailers. It is a shame. But someone said "increase by 70%" and since this number is all over the place. They don't even say 70% of what!?
 
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Astronuc said:
My wife and I were listening to a news program last night and heard Boris Johnson's rationale, and we were wondering how one would measure 'increased transmissibility'. Is measured in the laboratory or in the field? If the latter, is it actually a calculation, e.g., greater R0? Or is it really just a matter of some portion of the population congregating and not wearing masks, which I think would increase R0?
You just calculate some R values for the old and the new strands from some statistics. Doesn't matter what R-value. For all different kinds of R-values the ratio of the two R-values should be the same:

## R_{new} / R_{old} = 1.7 ##Like for example, if speedometers of all cars have an unknown but same error of x% , then if the speedometer of car1 reads 100km/h and the speedometer of car2 reads 170 km/h, then we don't know how fast the cars move, but we know that car2 moves 70% faster than car1.

Those different kinds of R-values are measurements of transmissibility, with possibly a large error, that error doesn't matter in this case.
 
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jartsa said:
Those different kinds of R-values are measurements of transmissibility, with possibly a large error, that error doesn't matter in this case.
It matters if it doesn't cancel in the ratio.
To make things worse, measuring R1 in one place and R2 in another won't lead to any useful ratio.
 
36 people on a research station. Luckily exchange between research stations isn't that common, so the other stations are probably still fine.
 
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