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How many will die of Covid19 in the 2020s directly and indirectly

Less than 10,000
10 (14.7%)
10,000-100,000
9 (13.2%)
100,000-1,000,000
9 (13.2%)
One to ten million
13 (19.1%)
Ten to a hundred million
14 (20.6%)
Hundred million to one billion
9 (13.2%)
Over a billion
4 (5.9%)

Total Members Voted: 60

Voting closed: March 03, 2020, 12:39:52 AM

Author Topic: COVID-19  (Read 547039 times)

Rodius

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Re: COVID-19
« Reply #10350 on: December 22, 2020, 01:25:36 AM »
Concerning my question on viral load.

Firstly, thanks for the content so far, I learned more, which is always a good thing.

My understanding is now:
 - the new strain carries more virus in the mucus
 - this allows it to spread more easily
 - the amount of virus a person gets when they initially become infected is also higher, which means it is also more likely that their illness will be worse
 - Given it is already in several countries that are not controlling the virus, the new strain is likely to become the dominant strain over the long term.
 - At this point in time, the current vaccine works to stop it.

In effect, this strain is worse but the vaccine works so it isn't a total disaster.

My next line of thinking concerns mutation rate.
Within one year, starting from effectively zero we have one confirmed new strain.
It has jumped species at least once (mink) and back to human in a mutated form, albeit not enough to be of concern.

I read that Covid is a slow mutating virus. I understand that when the number of cases is higher the chances of new strains also increase. So, again, answering the question of mutation rate is not a simple thing.
But, given the events we know about, it appears Covid is capable of mutating faster than we want to believe.
Actually, that isn't a question, just a line of thinking.

Anyway, the myth that herd immunity will stop Covid should be refuted with this information, even though it was never a thing in the first place.

Richard Rathbone

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Re: COVID-19
« Reply #10351 on: December 22, 2020, 01:48:25 AM »
Public Health England report on the new variant

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/947048/Technical_Briefing_VOC_SH_NJL2_SH2.pdf

This is where a lot of the numbers being quoted for effects on R come from. The analysis is rough, and likely moderately overestimates the change in R, but that doesn't change the conclusion that B.1.1.7 is likely to spread faster than other variants.

e.g. James reckons 5 days rather than 6.5 is the appropriate mean generation time to use for this sort of approximate calculation and that would drop the changes in R by about 30%. https://twitter.com/jamesannan/status/1341144372499386371

There's quite a bit more detail on how the PCR tests are affected in the report too if thats something you want to know more about.

vox_mundi

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Re: COVID-19
« Reply #10352 on: December 22, 2020, 02:19:24 AM »
Trevor Bedford @trvrb
https://mobile.twitter.com/trvrb/status/1340409968818671616

There has been an open question to the degree to which SARS-CoV-2 will behave like influenza and require vaccine updates. Emerging evidence suggests that antigenic drift is likely.

First off, we have new studies on antigenic drift in seasonal coronaviruses. Katie Kistler and I have shown abundant adaptive evolution in the spike proteins of viruses OC43 and 229E consistent with antigenic drift ( https://bedford.io/papers/kistler-hcov-adaptive-evolution/  ).



We also now have direct serological evidence of antigenic drift in 229E from @eguia_rachel, @jbloom_lab et al, suggesting that reinfection by seasonal coronaviruses that occurs every ~3 years is in part due to evolution of the virus.

https://mobile.twitter.com/jbloom_lab/status/1339939720558563328

https://t.co/g3RlQXDMNY?amp=1

For SARS-CoV-2, we only expect antigenic variants to spread once enough people have been infected to give these variants a transmission advantage gained by the ability to reinfect some portion of individuals immune to the original variant.

At this point, many countries have had perhaps 10% to 20% of their population infected ( https://medrxiv.org/content/10.1101/2020.12.01.20241539v1 ), and so we expect some weak evolutionary pressure for antigenic drift.



We've now seen the emergence and spread of several variants that may have some antigenic impact. These variants are generally labeled based on the mutation to the SARS-CoV-2 spike protein. For example N439K has a change from asparagine (N) to lysine (K) at site 439 in spike.

This variant N439K is now present in ~5% of recent viruses from Europe (https://nextstrain.org/ncov/europe?c=gt-S_439&f_region=Europe&transmissions=hide) and shows evidence of escape from some monoclonal antibodies and decreased reactivity to some convalescent sera (@emcat1, @robertson_lab et al https://biorxiv.org/content/10.1101/2020.11.04.355842v1 )



Recent announcements have focused on spread of N501Y in the UK ( https://twitter.com/CovidGenomicsUK/status/1338580111986204672 ) and independent emergence and spread of N501Y in South Africa ( https://twitter.com/DrZweliMkhize/status/1339970259332325383 ).

The UK variant in particular has several mutations that are of biological interest and deserves close attention (
@arambaut, @pathogenomenick et al https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 ).

Independent emergence and spread of variants is suggestive of natural selection where in addition to N501Y we see for example S477N emerging independently in Europe (https://nextstrain.org/ncov/europe?c=gt-S_222,439,477) and in Australia

@firefoxx66 is maintaining a list of mutations of interest with associated @nextstrain views and relevant publications at https://github.com/emmahodcroft/cluster_scripts/blob/master/README.md. 14/18

All this said, I'm not concerned that these variants will significantly reduce vaccine efficacy in the 2021 rollout. Most circulating SARS-CoV-2 viruses do not have any mutations in the spike receptor binding domain ( https://nextstrain.org/ncov/global?c=gt-S_439,477,484,501 ). 15/18

Additionally, single mutations will generally have small impacts on polyclonal immune responses and the strong immune response to the mRNA vaccines would suggest that a large antigenic change would be needed to significantly reduce efficacy. 16/18

However, we may see modest reductions in vaccine efficacy due to antigenic drift and will likely need a process in the coming years by which we update the spike variant used in the vaccine to best match circulating viruses.

Going forward, I suggest:
1. Emerging variants should be assayed against sera from recovered and vaccinated individuals to test for antigenic effects
2. Immunization records should be connected to genomic surveillance to identify variants involved in breakthrough infections

---------------------------------------
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late

Rodius

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Re: COVID-19
« Reply #10353 on: December 22, 2020, 02:37:35 AM »
That got me thinking.

The original Covid is less likely to mutate when it is the only one around and nobody has immunity. Why would it change when life is easy.

But as more people get Covid, Covid begins to bump into people who are immune.... in these cases it either dies or a mutation that helps reinfect the person breaks through the immunity.

Again, my line of thinking is that the places with higher numbers of Covid cases and higher levels of immunity are also the places where Covid is more likely to mutate its way around people with immunity.

wili

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Re: COVID-19
« Reply #10354 on: December 22, 2020, 03:46:21 AM »
I haven't been keeping up with the latest, so my apologies if this is a dumb question--Is there any evidence at all at this time that any people getting this new variant had 'natural' immunity to the first one (had already gotten it)?

If not, then your hypothesis, Rodius, interesting as it may be, is un-substantiated speculation at this point, no?

I guess at this early date, speculation is about the best we have; it is after all called: V(ariant)U(nder)I(investigation--202012/01 !
« Last Edit: December 22, 2020, 04:22:17 AM by wili »
"A force de chercher de bonnes raisons, on en trouve; on les dit; et après on y tient, non pas tant parce qu'elles sont bonnes que pour ne pas se démentir." Choderlos de Laclos "You struggle to come up with some valid reasons, then cling to them, not because they're good, but just to not back down."

Rodius

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Re: COVID-19
« Reply #10355 on: December 22, 2020, 05:10:49 AM »
I haven't been keeping up with the latest, so my apologies if this is a dumb question--Is there any evidence at all at this time that any people getting this new variant had 'natural' immunity to the first one (had already gotten it)?

If not, then your hypothesis, Rodius, interesting as it may be, is un-substantiated speculation at this point, no?

I guess at this early date, speculation is about the best we have; it is after all called: V(ariant)U(nder)I(investigation--202012/01 !

As far as I know, nobody who caught the original Covid has been reinfected with the new strain.
But that isn't my point anyway.

My point is that since Covid has a new strain and is jumping to other species and back to humans again, it is going to mutate enough to evade our natural immunity eventually and the immunity the vaccines produce. It is how viruses stay alive.... it isn't speculation, it is what happens every year with the likes of influenza, actually, all viruses.

The speculation is more about how fast/slow it is mutating.... and my point is more along the lines that I think it is mutating faster than expected. (As in, the vaccine we make now should be good for three or four years but I suspect it will be less than that.)
That is my speculation that can only be answered by waiting. Right or wrong, I don't mind personally either way, I am simply saying out loud that I think it will be shorter than 3 years based on what I am seeing. Being a non-expert, I expect to be wrong.


vox_mundi

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Re: COVID-19
« Reply #10356 on: December 22, 2020, 07:57:13 AM »
36 Cases Confirmed In Antarctica – Reports
https://www.abc.net.au/news/2020-12-22/coronavirus-cases-confirmed-in-antarctica/13007596

36 Chileans on an army base in Antarctica have tested positive for coronavirus – which means that the continent can no longer claim to be the only one free of the virus.

Spanish-language media has reported up to 36 people connected with the Chilean Army base General Bernardo O'Higgins Riquelme tested positive for the virus on Monday.

It is located close to the northern-most tip of the Antarctic Peninsula in West Antarctica — far from Australia's bases in East Antarctica — and was described by one travel website as "hard to reach even by Antarctic terms".
« Last Edit: December 22, 2020, 08:03:56 AM by vox_mundi »
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late

sailor

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Re: COVID-19
« Reply #10357 on: December 22, 2020, 02:08:13 PM »
I haven't been keeping up with the latest, so my apologies if this is a dumb question--Is there any evidence at all at this time that any people getting this new variant had 'natural' immunity to the first one (had already gotten it)?

If not, then your hypothesis, Rodius, interesting as it may be, is un-substantiated speculation at this point, no?

I guess at this early date, speculation is about the best we have; it is after all called: V(ariant)U(nder)I(investigation--202012/01 !

As far as I know, nobody who caught the original Covid has been reinfected with the new strain.
But that isn't my point anyway.

My point is that since Covid has a new strain and is jumping to other species and back to humans again, it is going to mutate enough to evade our natural immunity eventually and the immunity the vaccines produce. It is how viruses stay alive.... it isn't speculation, it is what happens every year with the likes of influenza, actually, all viruses.

The speculation is more about how fast/slow it is mutating.... and my point is more along the lines that I think it is mutating faster than expected. (As in, the vaccine we make now should be good for three or four years but I suspect it will be less than that.)
That is my speculation that can only be answered by waiting. Right or wrong, I don't mind personally either way, I am simply saying out loud that I think it will be shorter than 3 years based on what I am seeing. Being a non-expert, I expect to be wrong.

I think it is a fair point. Notice that the mutation rate is proportional to the number of infected people or animals. This number is currently huge, a pandemic out of control worldwide and crossing species and infecting millions of animals as well is at its peak of producing news mutations.

If we are lucky and things get under control in a few months, so it will the number of mutations. Zero viruses produce zero mutations.

TeaPotty

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Re: COVID-19
« Reply #10358 on: December 22, 2020, 02:12:13 PM »
Status quo believers as usual busy downplaying news about the new Covid variant. Such hubris should be shamed out of existence by society.

Most amusing is the fixation on whether current vaccines will still be effective, missing the forest for the trees:
  • Significantly enhanced transmission will significantly enhance spread, likely vhastly outpacing our vaccination efforts.
  • Higher R0 = Higher Herd Immunity Threshold. That means more people will need to have antibodies at the same time to have true Herd Immunity. With current vaccine efficacy and public sentiment, that is going to be a big problem. We'd probably need a higher efficacy vaccine.
  • While UK and SA variants are not identical, they share several spike mutations (btw, also the Denmark mink strain). The data (not models) not only points to enhanced transmission, but also increased infectivity in younger people, including children. There is also talk of higher viral loads, but I'm not up read up on that yet.
  • Data shows the new strains spreading since September, so its likely already spreading out of our control. I wouldn't be surprised if its also partly responsible for the recent insane virus surge in USA. Recent detections in Australia, Belgium, Italy, France, and Netherlands are likely all the tip of the iceberg respectively.

Update: Dr. Anthony Fauci says Americans should assume a new, more contagious strain of Coronavirus is already in the US
« Last Edit: December 22, 2020, 02:32:09 PM by TeaPotty »

sailor

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Re: COVID-19
« Reply #10359 on: December 22, 2020, 02:30:22 PM »
Status quo believers as usual busy downplaying news about the new Covid variant. Such hubris should be shamed out of existence by society.

Most amusing is the fixation on whether current vaccines will still be effective, missing the forest for the trees:
  • Significantly enhanced transmission will significantly enhance spread, likely vhastly outpacing our vaccination efforts.
  • Higher R0 = Higher Herd Immunity Threshold. That means more people will need to have antibodies at the same time to have true Herd Immunity. With current vaccine efficacy and public sentiment, that is going to be a big problem. We'd probably need a higher efficacy vaccine.
  • While UK and SA variants are not identical, they share several spike mutations (btw, also the Denmark mink strain). The data (not models) not only points to enhanced transmission, but also increased infectivity in younger people, including children. There is also talk of higher viral loads, but I'm not up read up on that yet.
  • Data shows the new strains spreading since September, so its likely already spreading out of our control. I wouldn't be surprised if its also partly responsible for the recent insane virus surge in USA. Recent detections in Australia, Belgium, Italy, France, and Netherlands are likely all the tip of the iceberg respectively.

Worst case scenario. Nothing says (yet) spread will outpace vaccination efforts

(crossing the fingers vaccines are as safe as we are told 24/7).


pietkuip

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Re: COVID-19
« Reply #10360 on: December 22, 2020, 02:57:46 PM »
Status quo believers as usual busy downplaying news about the new Covid variant. Such hubris should be shamed out of existence by society.

[...]

Update: Dr. Anthony Fauci says Americans should assume a new, more contagious strain of Coronavirus is already in the US

I am quite surprised by the dismissive attitude of Vincent Racaniello of TWiV (the podcast This Week in Virology). He has a series of tweets about the "uninformed" New York Times at https://twitter.com/profvrr

And now there is this video where he blasts the NERVTAG minutes:
https://www.youtube.com/watch?t=909&v=wC8ObD2W4Rk

What I know is that the ECDC is worried too. One or two virology professors that shout about "completely baseless hype" etc won't take such worries away.

SteveMDFP

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Re: COVID-19
« Reply #10361 on: December 22, 2020, 04:25:21 PM »
Status quo believers as usual busy downplaying news about the new Covid variant. Such hubris should be shamed out of existence by society.

[...]

Update: Dr. Anthony Fauci says Americans should assume a new, more contagious strain of Coronavirus is already in the US

I am quite surprised by the dismissive attitude of Vincent Racaniello of TWiV (the podcast This Week in Virology). He has a series of tweets about the "uninformed" New York Times at https://twitter.com/profvrr

And now there is this video where he blasts the NERVTAG minutes:
https://www.youtube.com/watch?t=909&v=wC8ObD2W4Rk

What I know is that the ECDC is worried too. One or two virology professors that shout about "completely baseless hype" etc won't take such worries away.

The TWIV episode in which this is discussed by the group is at 55 minutes in at:
TWiV 696: Tear down that SARS-CoV-2 manuscript
https://www.microbe.tv/twiv/twiv-696/

In this section, these scientists and clinicians are thinking and speaking as scientists and clinicians.  Assertions that are not strongly supported by good science are garbage to them.  This isn't surprising or disturbing.

But they're not thinking or speaking as public health professionals.  I'm confident that they  may be correct in asserting that the increasing prevalence may most likely be explained by a handful of superspreader events that happened (randomly) with the recently-identified variant.

However, they do acknowledge that the increasing prevalence of this variant is also consistent with increased transmissibility being the cause.  It's going to take some time for researchers to determine whether there's evidence of biologically enhanced transmissibility of this variant.

To a public health professional, scientifically proving assertions is not the point.  As long as there's a reasonable probability that the increased prevalence is due to increased transmissibility, then stronger public health measures are appropriate, while scientists duke it out over interpretation of data.

Personally, I'm a bit more concerned about the South Africa new variant.  There's suspicion of both increased transmissibility and increased virulence in younger people.  These seem to be rough impressions from doctors on the ground, so need to be taken with a grain of salt.

pietkuip

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Re: COVID-19
« Reply #10362 on: December 22, 2020, 04:35:49 PM »
^^

And in Denmark they are a bit worried about 1600 cases of N439K.
https://www.ssi.dk/-/media/arkiv/subsites/covid19/sars-cov-2-spike-variant-n439k_21122020.pdf

The UK and Denmark do a lot of sequencing, much more than other countries. They are the first to see these things. And then they get hit by border closures.

Mutations that would be reason for concern are probably in many more places.
« Last Edit: December 22, 2020, 04:42:19 PM by pietkuip »

Alexander555

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Re: COVID-19
« Reply #10363 on: December 22, 2020, 04:40:28 PM »
A new strain in South-Africa, not the same as in the UK. More hospitalisations and more dead people. That's a bad mutation. https://www.aljazeera.com/news/2020/12/22/south-africa-says-virus-variant-driving-resurgence

harpy

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Re: COVID-19
« Reply #10364 on: December 22, 2020, 05:56:23 PM »
36 Cases Confirmed In Antarctica – Reports
https://www.abc.net.au/news/2020-12-22/coronavirus-cases-confirmed-in-antarctica/13007596

36 Chileans on an army base in Antarctica have tested positive for coronavirus – which means that the continent can no longer claim to be the only one free of the virus.

Spanish-language media has reported up to 36 people connected with the Chilean Army base General Bernardo O'Higgins Riquelme tested positive for the virus on Monday.

It is located close to the northern-most tip of the Antarctic Peninsula in West Antarctica — far from Australia's bases in East Antarctica — and was described by one travel website as "hard to reach even by Antarctic terms".

Welp.  There goes the planet.

TeaPotty

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Re: COVID-19
« Reply #10365 on: December 22, 2020, 06:12:43 PM »
I'm confident that they  may be correct in asserting that the increasing prevalence may most likely be explained by a handful of superspreader events that happened (randomly) with the recently-identified variant.

This is hubris blinding people who should know better. It also shows you didn't read my post seriously.

UK and SA strains are different variants, but they share several of the same spike mutations, and both are rapidly becoming the dominant strain. Its utter nonsense at this point to claim confidence that this is random coincidence, especially when these strains have been ramping up since September. Highly unlikely statistically.

kassy

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Re: COVID-19
« Reply #10366 on: December 22, 2020, 06:14:36 PM »
36 Cases Confirmed In Antarctica – Reports

Welp.  There goes the planet.

A lot of research in Antarctica but also across the seas has been cancelled because they feared something like this might happen. That hurts us overall for missing data.

I suggest using smilies when appropriate so people don´t think that was a serious comment.
Þetta minnismerki er til vitnis um að við vitum hvað er að gerast og hvað þarf að gera. Aðeins þú veist hvort við gerðum eitthvað.

Archimid

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Re: COVID-19
« Reply #10367 on: December 22, 2020, 06:34:53 PM »
There are many factors to the rate of mutation, but I bet one of the most important ones is the copy rate. The more copies are being made, the higher the chance for mutation and the higher pool of available strains.

The "Herd immunity" peddled by Trump et al was a lethal trap.

However, vaccines might save the day.
I am an energy reservoir seemingly intent on lowering entropy for self preservation.

Alexander555

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Re: COVID-19
« Reply #10368 on: December 22, 2020, 06:51:41 PM »
He Kassy, is there a link between the new strain in South-Africa. And the new wave in your country. It started a few weeks later, and there is some traffic between the countries.

TeaPotty

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Re: COVID-19
« Reply #10369 on: December 22, 2020, 07:51:06 PM »
He Kassy, is there a link between the new strain in South-Africa. And the new wave in your country. It started a few weeks later, and there is some traffic between the countries.

The UK and SA strains share several spike mutations, and both are rapidly becoming dominant in their area. This is why confidence is so high, and many are missing the forest for the trees. You can’t hope yourself out of a pandemic with optimistic thoughts and feelings.

I detailed it in my well-researched comment above:
  • Significantly enhanced transmission will significantly enhance spread, likely vhastly outpacing our vaccination efforts.
  • Higher R0 = Higher Herd Immunity Threshold. That means more people will need to have antibodies at the same time to have true Herd Immunity. With current vaccine efficacy and public sentiment, that is going to be a big problem. We'd probably need a higher efficacy vaccine.
  • While UK and SA variants are not identical, they share several spike mutations (btw, also the Denmark mink strain). The data (not models) not only points to enhanced transmission, but also increased infectivity in younger people, including children. There is also talk of higher viral loads, but I'm not up read up on that yet.
  • Data shows the new strains spreading since September, so its likely already spreading out of our control. I wouldn't be surprised if its also partly responsible for the recent insane virus surge in USA. Recent detections in Australia, Belgium, Italy, France, and Netherlands are likely all the tip of the iceberg respectively.

harpy

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Re: COVID-19
« Reply #10370 on: December 22, 2020, 08:36:25 PM »
Hoping our way out of the collapse of society has always been our go-to approach.

Let's introduce 8 billion humans on a planet that never sustained more than a few hundred million before civilization, let's all rely on magical wires supported by dead tree posts for the basic survival functions of 90% of the population.  Let's stop growing our own food, and force ourselves to truck everything across the globe on carbon emitting cargo ships and diesel trucks.

Let's make a magical economy where we trade our time for mysterious digits on a screen and call it a "career".

What could possibly go wrong?   ;D

vox_mundi

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Re: COVID-19
« Reply #10371 on: December 22, 2020, 11:35:48 PM »
Pfizer, Moderna Testing Their Vaccines Against UK Coronavirus Variant
https://mobile.reuters.com/article/amp/idUSKBN28W149

(Reuters) - Pfizer Inc and Moderna Inc are testing their COVID-19 vaccines against the new fast-spreading version of the virus that has emerged in Britain, CNN reported on Tuesday.

Moderna expects immunity from its vaccine to protect against the variants and is performing more tests in the coming weeks to confirm, the company said in a statement to CNN.

Pfizer said it is "generating data" on how well blood samples from people immunized with its vaccine "may be able to neutralize the new strain from the UK," according to the report.

--------------------------------------------

CDC Says New Covid Strain In UK Could Already Be Circulating Undetected In U.S.
https://www.cnbc.com/amp/2020/12/22/cdc-says-new-covid-strain-in-uk-could-already-be-circulating-undetected-in-us.html

The new coronavirus strain that was first detected in the United Kingdom could already be in the United States, the CDC said Tuesday.

While the variant hasn't been found in the U.S. yet, the CDC noted that scientists haven't sequenced the genetic coding for many Covid-19 infections here. The agency said "viruses have only been sequenced from about 51,000 of the 17 million US cases," (< 0.3%) so the new strain could have slipped notice.

"Ongoing travel between the United Kingdom and the United States, as well as the high prevalence of this variant among current UK infections, increase the likelihood of importation," the CDC said in a statement. "Given the small fraction of US infections that have been sequenced, the variant could already be in the United States without having been detected."

The agency said it doesn't know why the new strain of the virus emerged, but it could have been "by chance alone." "Alternatively, it may be emerging because it is better fit to spread in humans," the CDC said

-----------------------------------------------

Life, ah, finds a way ....



----------------------------------------------

Suspicions Grow That Nanoparticles In Pfizer’s COVID-19 Vaccine Trigger Rare Allergic Reactions
https://www.sciencemag.org/news/2020/12/suspicions-grow-nanoparticles-pfizer-s-covid-19-vaccine-trigger-rare-allergic-reactions

Severe allergy-like reactions in at least eight people who received the COVID-19 vaccine produced by Pfizer and BioNTech over the past 2 weeks may be due to a compound in the packaging of the messenger RNA (mRNA) that forms the vaccine’s main ingredient, scientists say. A similar mRNA vaccine developed by Moderna, which was authorized for emergency use in the United States on Friday, also contains the compound, polyethylene glycol (PEG).

PEG has never been used before in an approved vaccine, but it is found in many drugs that have occasionally triggered anaphylaxis—a potentially life-threatening reaction that can cause rashes, a plummeting blood pressure, shortness of breath, and a fast heartbeat. Some allergists and immunologists believe a small number of people previously exposed to PEG may have high levels of antibodies against PEG, putting them at risk of an anaphylactic reaction to the vaccine.

The U.S. National Institute of Allergy and Infectious Diseases (NIAID) is also setting up a study in collaboration with Food and Drug Administration (FDA) to analyze the response to the vaccine in people who have high levels of anti-PEG antibodies or have experienced severe allergic responses to drugs or vaccines before. “Until we know there is truly a PEG story, we need to be very careful in talking about that as a done deal,” says Alkis Togias, branch chief of allergy, asthma, and airway biology at NIAID.

Anaphylactic reactions can occur with any vaccine, but are usually extremely rare—about one per 1 million doses. As of 19 December, the United States had seen six cases of anaphylaxis among 272,001 people who received the COVID-19 vaccine, according to a recent presentation by Thomas Clark of the U.S. Centers for Disease Control and Prevention (CDC); the United Kingdom has recorded two.

https://www.cdc.gov/vaccines/acip/meetings/downloads/slides-2020-12/slides-12-19/05-COVID-CLARK.pdf

... The two vaccines both contain mRNA wrapped in lipid nanoparticles (LNPs) that help carry it to human cells but also act as an adjuvant, a vaccine ingredient that bolsters the immune response. The LNPs are “PEGylated”—chemically attached to PEG molecules that cover the outside of the particles and increase their stability and life span.

PEGs were long thought to be biologically inert, but a growing body of evidence suggests they are not. As much as 72% of people have at least some antibodies against PEGs, according to a 2016 study led by Samuel Lai, a pharmaco-engineer at the University of North Carolina, Chapel Hill, presumably as a result of exposure to cosmetics and pharmaceuticals. About 7% have a level that may be high enough to predispose them to anaphylactic reactions, he found. Other studies have also found antibodies against PEG, but at lower levels.

https://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b03437

... In 1999, while working at the Walter Reed Army Institute of Research, Szebeni described a new type of drug-induced reaction he dubbed complement activation-related pseudoallergy (CARPA), a nonspecific immune response to nanoparticle-based medicines, often PEGylated, that are mistakenly recognized by the immune system as viruses.

https://pubmed.ncbi.nlm.nih.gov/10226097/

Szebeni believes CARPA explains the severe anaphylactoid reactions some PEGylated drugs are occasionally known to cause, including cancer blockbuster Doxil. A team assembled by Bruce Sullenger, a surgeon at Duke University, experienced similar issues with an experimental anticoagulant containing PEGylated RNA. The team had to halt a phase III trial in 2014 after about 0.6% of 1600 people who received the drug had severe allergic responses and one participant died. “That stopped the trial,” Sullenger says. The team found that every participant with an anaphylaxis had high levels of anti-PEG IgG. But some with no adverse reaction had high levels as well, Sullenger adds. “So, it is not sufficient to just have these antibodies.” ...

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vox_mundi

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Re: COVID-19
« Reply #10372 on: December 23, 2020, 12:47:30 AM »
UK: Shortages
https://www.theguardian.com/business/2020/dec/22/tesco-limits-purchases-of-toilet-roll-eggs-rice-soap-and-handwash

Tesco has introduced buying limits on items including toilet roll, eggs, rice, soap and handwash. Customers at the supermarket are now limited to one item per person of toilet roll, and up to three products of eggs, rice, soap and handwash.

It is understood the extra limits are pre-emptive measures to help smooth demand in the coming weeks, rather than a reaction to shortages or a change in buying behaviour. They are on top of a three-item limit on essential items such as flour, dried pasta and anti-bacterial wipes which has been in place for several months.

On Monday supermarkets and wholesalers warned of shortages of lettuce, broccoli and citrus fruit around Christmas as thousands of lorries were stranded in Kent after France closed its borders to the UK.

“If nothing changes, we will start to see gaps over the coming days on lettuce, some salad leaves, cauliflowers, broccoli and citrus fruit – all of which are imported from the continent at this time of year,” a Sainsbury’s spokesperson said.

Tesco previously introduced a buying cap on toilet roll in November in anticipation of a repeat of the panic buying that took place in March, and has encouraged customers to “shop as normal”, saying it had plenty of food up to 25 December. [... not so much after that]
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late

pietkuip

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Re: COVID-19
« Reply #10373 on: December 23, 2020, 12:52:01 AM »
That new variant is growing fast.

This is data up to December 5 https://twitter.com/theosanderson/status/1341048068083466246
In regions where this was at that time, it will have doubled a few times by now.

Rodius

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Re: COVID-19
« Reply #10374 on: December 23, 2020, 04:29:25 AM »
Australia Update

Sydney is breaking even in terms of containing the outbreak.
It could still go either way.

Masks are optional because the State Premier dislikes upsetting people. They are saying masks arent needed unless the outbreak gets worse. The media loves the State Premier (Murdoch media anyway) so she is getting an easy ride. However, non-Murdoch media is attacking the mask-wearing being optional a lot. Sadly, most people refuse to wear masks until it must be done.

State borders have been closed and NSW (New South Wales) is complaining (I mention this because they are being hypocritical about it)

Numbers are still below 30 a day with 30K tests happening daily. My money is on containment being successful.....

.... except the new, more contagious strain has been found in two people. Both are returning from the UK so are not in the community, but given the leaks that NSW is becoming infamous for, there is a chance it reach the community anyway. But not at this point.

https://www.ctvnews.ca/health/coronavirus/australia-confirms-two-cases-of-new-coronavirus-strain-1.5240118

Archimid

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Re: COVID-19
« Reply #10375 on: December 23, 2020, 09:06:58 AM »
Quote
Sadly, most people refuse to wear masks until it must be done.

Sad indeed. Such sacrifice being invalidated for the comfort of a few selfish cowards. No mask is a huge hole in the swiss cheese of protection layers. Masks are simple, effective, cheap and allows interactions that would be too risky without them.

It infuriates me that those purveying mask misinformation often cite the economy as a reason to not wear masks when masks are exactly the opposite. They are good for economic growth.
Masks are and have always been the way out of this frigging nightmare.


"The tongue has the power of life and death" Proverbs 18:21. The misinformation around mask-wearing makes it literally so.
I am an energy reservoir seemingly intent on lowering entropy for self preservation.

vox_mundi

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Re: COVID-19
« Reply #10376 on: December 23, 2020, 12:22:17 PM »
California Health System Buckling Under COVID-19 Pandemic
https://medicalxpress.com/news/2020-12-california-health-buckling-covid-pandemic.html

Top executives from the state's largest hospital systems —Kaiser Permanente, Dignity Health and Sutter Health, which together cover 15 million Californians—said Tuesday that increasingly exhausted staff, many pressed into service outside their normal duties, are now attending to COVID-19 patients stacked up in hallways and conference rooms.

The CEO of the Martin Luther King, Jr. Community Hospital in Los Angeles, Dr. Elaine Batchlor, separately said patients there have spilled over into the gift shop and five tents outside the emergency department.

"We don't have space for anybody. We've been holding patients for days because we can't get them transferred, can't get beds for them," said Dr. Alexis Lenz, an emergency room physician at El Centro Regional Medical Center in Imperial County, in the southeast corner of the state. The facility has erected a 50-bed tent in its parking lot and was converting three operating rooms to virus care.

California is closing in on 2 million confirmed cases of COVID-19. The state on Tuesday reported nearly 32,700 newly confirmed cases. Another 653 patients were admitted to hospitals—one of the biggest one-day hospitalization jumps—for a total approaching 18,000.

State data models have predicted the hospitalizations could top 100,000 in a month if current rates continue



Even more worrying than lack of beds is a lack of personnel. The pool of available travel nurses is drying up as demand for them jumped 44% over the last month, with California, Texas, Florida, New York and Minnesota requesting the most extra staff, according to San Diego-based health care staffing firm Aya Healthcare.

-----------------------------------------





https://covid19.ca.gov/state-dashboard/

--------------------------------------------

Tennessee Hospitals Are Disturbingly Close To Their Breaking Point
https://www.scpr.org/news/2020/12/22/95834/tennessee-hospitals-are-disturbingly-close-to-thei/
https://apnews.com/article/tennessee-coronavirus-pandemic-13be036bc15f7b8575d143ba4baf1645

COVID-19 is hitting a handful states harder than anywhere else — California, Oklahoma, Texas and Tennessee. And in Tennessee, hospitals are having to improvise, as nearly 3,000 people are hospitalized for COVID-19 and treatment is underway for far more COVID patients than ever thought possible.

The state continues to report caseloads at or near levels unmatched in viral spread per capita nationwide. There were 1,785 new cases per 100,000 people in Tennessee over the past two weeks, which ranks first in the country for new cases per capita, according to Johns Hopkins researchers. One in every 104 people in Tennessee tested positive in the past week.

Tennessee Department of Health Commissioner Lisa Piercey said COVID-19 patients now make up 47% of all intensive care unit hospitalizations statewide, about a 7 percentage point increase from Sunday.



Piercey said the state requested National Guard staff in the northeastern system and to the Memphis and Shelby County region to go into the hospitals, not just serve testing services. Five large health care systems across the state have also been given flexibility to allow paramedics to practice inside hospitals.

Workers who have tested positive for COVID-19 and "feel up to the challenge" are now allowed to work in long-term care facilities.
The same doesn't apply to hospitals.

Piercey said the state is running out of options for staffing.

Alternative care sites that were set up months ago, to deal with this kind of patient surge, are empty — rendered useless because there's no staff to run them.

Doctors say they are doing things that feel risky, like sending patients home earlier than they typically would, even when they still need supplemental oxygen to breathe.

Hospitals are also telling more people who show up for care to go home, and only come back if things get worse.

... "All of the money in the world can't buy more staff," Piercey said. "That money will only go so far. We have spent all the money we can spend on staff. There are no more staff to spend money on."

Meanwhile, the worsening scenario has prompted growing scrutiny from critics over Republican Gov. Bill Lee’s refusal to implement a statewide mask requirement, which only a dozen states don’t have. He instead is letting counties decide whether to require masks in public, citing personal responsibility and saying a statewide mandate is “controversial” and reasoning that some who refuse to wear masks rebel against the idea.

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« Last Edit: December 23, 2020, 03:55:50 PM by vox_mundi »
“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

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vox_mundi

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Re: COVID-19
« Reply #10377 on: December 23, 2020, 03:46:29 PM »


--------------------------------------------------

“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

Insensible before the wave so soon released by callous fate. Affected most, they understand the least, and understanding, when it comes, invariably arrives too late

Tor Bejnar

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Re: COVID-19
« Reply #10378 on: December 23, 2020, 07:35:59 PM »
I've been wondering about the relationship (if any) between the British and the South African (SA) strains of the coronavirus that are highly contagious.  For example, were they the same thing.  It appears they are not the same thing.
From Fox News
Quote
UK detects another 'highly concerning' coronavirus variant in cases linked to South Africa travel

Health Secretary Matt Hancock said new [SA] variant is 'highly concerning” because it 'is yet more transmissible'
Arctic ice is healthy for children and other living things.

gerontocrat

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Re: COVID-19
« Reply #10379 on: December 23, 2020, 07:38:02 PM »
https://www.worldometers.info/coronavirus/

UK Data

Deaths this day 744, New Cases this day 39k.
The 7 day trailing average graphs can't keep up when the daily values increase this fast.
& Now we have two new strains - a home grown(?) one, and a one just arrived from South Africa.
Both mutations are believed to allow the virus to spread more rapidly.

Italy Data
At the moment progress in reducing cases and mortality continue.
The graphs show how much harder it is to get the graph down than for it to zoom up.
___________________________________
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etienne

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Re: COVID-19
« Reply #10380 on: December 23, 2020, 07:48:36 PM »
I've been wondering about the relationship (if any) between the British and the South African (SA) strains of the coronavirus that are highly contagious.  For example, were they the same thing.  It appears they are not the same thing.
From Fox News
Quote
UK detects another 'highly concerning' coronavirus variant in cases linked to South Africa travel

Health Secretary Matt Hancock said new [SA] variant is 'highly concerning” because it 'is yet more transmissible'

Well, the SA variant is also in the UK
https://www.theguardian.com/world/live/2020/dec/23/coronavirus-live-news-us-cases-increase-14-in-one-week-france-to-reopen-uk-border?page=with:block-5fe35ef68f08dd27861d08ef#block-5fe35ef68f08dd27861d08ef

And another link
https://www.theguardian.com/world/2020/dec/23/south-african-covid-19-variant-may-be-more-effective-at-spreading
« Last Edit: December 23, 2020, 07:57:28 PM by etienne »

vox_mundi

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Re: COVID-19
« Reply #10381 on: December 23, 2020, 10:51:24 PM »
Northern Ireland has confirmed a case of the new Covid-19 variant that was first detected in Britain. The positive case was found after a genome analysis was conducted on a small number of suspected cases, reports PA.

It’s understood that health officials believe that the variant has been in circulation at a low level in the nation for several weeks now.

The Health Minister Robin Swann has said: “This is sadly the confirmation we had been expecting.

The Irish head of the Covid-19 modelling body has said it is not confident that the restrictions announced this week will bring the R number back below 1.

------------------------------------------------

The UK’s R number has risen to between 1.1 and 1.3, according to the latest figures. https://www.gov.uk/guidance/the-r-number-in-the-uk

Almost nine in 10 people in England will be under tier 4 or 3 restrictions once the changes come into effect, with 42% of the population in tier 4 and 44% in tier 3.

Prof Ferguson said evidence suggests that “almost certainly” this virus has already been introduced to the “great majority if not all” of European countries.


------------------------------------------------

Israel has detected four cases of the new, highly infectious variant of the coronavirus that emerged in the UK, the Israeli health ministry said.

------------------------------------------------

Sinovac Biotech’s Covid-19 vaccine is reported to be 50% effective in late-stage trials, according to the newspaper Folha de S.Paulo on Wednesday. They added that the Chinese company had asked the Brazilian institute who ran the tests to wait up to 15 days before publishing their full results.

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“There are three classes of people: those who see. Those who see when they are shown. Those who do not see.” ― Leonardo da Vinci

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vox_mundi

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Re: COVID-19
« Reply #10382 on: December 23, 2020, 11:44:50 PM »
The U.S. Has Vaccinated Just 1 Million People Out of a Goal of 20 Million for December - 330 Million to Go
https://www.cnbc.com/amp/2020/12/23/covid-vaccine-us-has-vaccinated-1-million-people-out-of-goal-of-20-million-for-december.html

The CDC said just 1,008,025 shots had been administered as of Wednesday at 9 a.m. ET.

That's roughly 19 million doses shy of earlier projections for December.

It leaves public officials a little more than a week — about 8 days — to try to close that gap. 2 (4) of those days are holidays.

The U.S. would need to vaccinate more than 2.1 million people per day through Dec. 31 to meet its goal.

It has been 10 days since the FDA gave its first approval for emergency use of the Pfizer vaccine and then a week later for Moderna

The U.S. has the worst outbreak in the world, with more than 18.2 million cases and at least 322,849 deaths, according to data compiled by Johns Hopkins University.
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Re: COVID-19
« Reply #10383 on: December 24, 2020, 02:36:15 AM »
deaths per million population per worldometers:

11 of top 12 countries are European with USA moving down to 13th.

Top 13 countries now have over 1 death per 1000 people. A couple of weeks ago this was only 3 countries.

UK has 20917 in hospital with covid, The peak 12 April was 21683, but now cases are rising rapidly rather than levelled off by mid April.

https://twitter.com/jamesannan/status/1341482191486902276

suggests we could be heading up to three times the current number of cases per day in the next couple of months. Deaths are going to start increasing more noticeably (cases have been rising rapidly last 3 weeks). James has it going up to 3k per day though maybe the vaccine will have started to help cut the deaths before then. It will take vaccine much longer to help with cases.

Policy measures like post Christmas tier 4 lockdowns not built into that model yet. So hopefully it won't be as bad as shown. Even so, it is a grim outlook. 

Rodius

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Re: COVID-19
« Reply #10384 on: December 24, 2020, 03:46:15 AM »
It appears that some people think Australia is in permanent lockdown with a Govt keeping us under firm control.

Truth is this.... for 4 months one city was in lockdown for about four months. It was not fun, people complained, but we did what was needed. It worked. Melbourne has had zero community transmissions for 55 days in a row and 1 case that came into Melbourne from the cluster in Sydney because the person drove here a few days ago.

The only restrictions we have now are wearing a mask while doing things like supermarket shopping. For the most part, our economy is almost fully open and recovering.

Sydney has targeted lockdowns because of its cluster. It is hard and fast, it will almost certainly work, and within the coming week or two, Sydney will be mostly fully open as well.

This is hardly a dictator state or country, in fact, we are almost back to normal and nobody is dying from Covid and the cases are very, very low.

Not bad for 4 months of misery.

Compared to places likes the US, where Trump bloody mindedly did everything he could to let it rip through, with thousands of deaths per day, an economy that is struggling, job loses, hunger increasing, people living in unstable housing due to rent non payment and a hospital system that is all but collapsed and getting worse, I pick the four months of lockdown every single time.

For the people who think Covid isnt much of a thing, a common cold, or no worse than the flu, if any of those people can provide any evidence of any kind that shows them doing what Covid is doing right now, please present the evidence for us to see. Any information at all will do.

Shit, give any information from the US only... find the worst flu season in the last 100 years and compare it to what is happening in the US right now.
You can even present finding from the 1914 flu if you want as that is the closest you will probably come to Covid.

Melbourne fought hard to remove the virus. Lockdowns are needed, so are masks, testing, tracing and strong political leadership. But it was temporary and no longer in place.
And here is the funny thing, the people in Melbourne are prepared to do it all again should it be required. Most people are aware that when our winter comes around next year we may well have to do it again, and that is okay with most people here because the results show that it is worth it.

I just wanted that to be clearly stated.

I would like to see evidence of a worse disease than Covid to see what pops up.... something that has gone global and has done what Coivd is doing.
MERS and SARS might appear as counters to this, but given MERS and SARS were relatively easy to beat, and isn't global, it isn't really a fair comparison. Ebola isn't either. All three of those diseases could have gotten a lot worse and still been brought into containment as they are today because they only spread with symptoms.

So, please, present the findings of how the flu has done what Covid has done to health care systems globally, show the real number deaths, the real organ damages, lets compare them properly.

If it can be shown that Covid is, in fact, no worse than the flu, then I will change my mind. Until then, if you think Covid is no worse than the flu, either front up with researched evidence or stop saying it.

Rant over.

pietkuip

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Re: COVID-19
« Reply #10385 on: December 24, 2020, 10:24:51 AM »
So, please, present the findings of how the flu has done what Covid has done to health care systems globally, show the real number deaths, the real organ damages, lets compare them properly.

I don't know globally, but in Sweden the number of deaths will be only slightly higher than in 2018.
https://twitter.com/_Kodos_/status/1340432329496539139

Health care is not the sector that was most disrupted. The excess mortality in the last weeks is lower than the number of deaths with covid because there is no flu this year.

Cultural life has been hit much worse.

I suppose bringing in some perspective like this will be giving rise to another rant...

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Re: COVID-19
« Reply #10386 on: December 24, 2020, 11:32:39 AM »
even the fact that the precautions to limit the spread of COVID-19 have crushed this season's flu 'out of sight' while COVID-19 itself continues to run riot says it all .. b.c.
2007 + 5 = 2012 + 4 = 2016 + 3 = 2019 + 2 = 2021 + 1 =  ' if only we could have seen it coming ' ...

vox_mundi

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Re: COVID-19
« Reply #10387 on: December 24, 2020, 12:32:41 PM »
Tennessee averaged nearly 128 new infections per 100,000 people over the last week, the highest of any U.S. state, according to U.S. Centers for Disease Control and Prevention data. California stood second at 111 new cases per 100,000 residents.





By the way, the U.S. just reported its second-highest number of coronavirus-related deaths in a single day — 3,401, according to Johns Hopkins University. That makes five days of 3,000-plus deaths from the virus, all in December. 4000/day by Jan.1?
« Last Edit: December 24, 2020, 03:50:23 PM by vox_mundi »
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TeaPotty

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Re: COVID-19
« Reply #10388 on: December 24, 2020, 01:33:29 PM »
Excellent twitter thread from expert Kai Kupferschmidt on our current understanding of the new Covid Variants from UK & SA (@kakape science journalist. molecular biologist. curious. Contributing Correspondent at @sciencemagazine, reporting on #covid19). My emphasis:

Quote from: Kai Kupferschmidt link=https://twitter.com/kakape/status/1342063459350020097
What do we know about the new #SARSCoV2 variants? How worried should we be? What does it mean? I promised to summarize the main points from my reporting over the last few days. So here is my latest story and a thread (and then it’s Christmas)

First: I’ve said “We don’t know yet” a lot over the last few days and we still don’t know most of what we want to know about these variants. Getting good answers takes times. Science takes time. But we are learning a lot fast and we know a lot more today than three days ago.

The UK variant: I explained how B.1.1.7 caught scientists’ attention in my first story on this and why they were worried (https://t.co/HupLMpgHPt). That worry has only increased. There is now more data available and it points to this variant really being more transmissible.

Initially skeptical scientists like @c_drosten have become more convinced. As @mugecevik told me: “We can’t really rule out the possibility that seasonality and human behavior explain some of the increase. But it certainly seems like there is something to do with this variant.”

This is about transmissibility. For now there is little to suggest it causes more severe disease or evades immunity. Scientists I spoke to can see a variant like this shaving a few points off efficacy of a vaccine but not dramatically reducing it. Experiments will tell us soon.

As @profshanecrotty pointed out the body makes a broad response to #SARSCoV2 and even just the spike protein. “It would be a real challenge for a virus to escape from that.” Measles and polio vaccines still work and are "historical examples suggesting not to freak out.”

Increased transmissibility is still really bad news. It’s not clear how much more transmissible the variant really is. But the numbers that modelers have come up with are worrying. Our job to keep the numbers down until people are vaccinated has likely become a fair bit harder.

How does the increase in transmission come about? We don’t know. There are several hypotheses: the variant might infect children better than previous variants. It might transmit faster. @BillHanage has a great thread on a preprint looking at this.

The South African variant: We know less about 501Y.V2. This variant too seems to be spreading faster and there is anecdotal (meaning very weak) evidence of more severe disease in younger, healthy people. @JeremyFarrar told me he was at least as concerned about this variant. Why?

1. It has 3 mutations in the RBD, an important part of the spike protein. All seem a bit worrying by themselves and we don’t know what the combination means. @JeremyFarrar: "These South African mutations I think are more worrying than the constellation of the British variant"

2. Africa has largely escaped the brunt of this pandemic. Many scientists think younger age and warmer climate together with other factors make #SARSCoV2 spread less efficiently there. Worry is that an increase in transmissibility could get over these factors.

So, lastly, what does it mean that these variants popped up in the first place? There are two important strands to that: How we discovered them and how they arose.

Discovery: The UK has sequenced more #SARSCov2 viruses and done so faster than any other country. The story shows how important and helpful genomic surveillance can be and that we are affording ourselves an awful lot of blindspots in this pandemic.

There are already indications that the last few days have prompted many countries to sequence more, release more data. So if there is a flurry of new variants/mutations announced in the next days and weeks that is partly because we are now looking more closely/sharing more.

Origin: Most likely hypothesis for now is that these variants arose in patients whose immune system was weakened and who were infected over a long period of time. “It’s simply too many mutations to have accumulated under normal evolutionary circumstances”, @stgoldst told me.

There are at least two reports of immunocompromised patients infected for more than 100 days showing that the virus accumulated some of the same mutations seen now in the variants in UK and South Africa. https://t.co/8Da6XuO4Kk

It's possible that virus sequences in these patients are a window into the future, showing us what to expect from #SARSCoV2 evolution. @jbloom_lab has a fascinating paper showing something similar for flu:

There probably needs to be more debate about how best to care for such chronically infected, immunocompromised patients, what treatments make sense and how to make sure they don’t transmit onwards late in the infection. I also hope we get more research on virus evolution in them.

But the biggest take-away from all this is what @mvankerkhove told me: We need to keep number of infections low even as vaccinations start. “The more of this virus circulates, the more opportunity it will have to change,” she said. “We’re playing a very dangerous game here.”

So the two-sentence, sad summary: The UK/SA variants show that we should be doing what we should have been doing all along, keeping the number of infections really, really low. That job has become even more important now - and even harder.

vox_mundi

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Re: COVID-19
« Reply #10389 on: December 24, 2020, 02:20:50 PM »
Africa CDC: New Virus Variant Appears to Emerge In Nigeria
https://apnews.com/article/international-news-public-health-coronavirus-pandemic-africa-south-africa-58c20bb87f1208c932654f03fbfb2b20

NAIROBI, Kenya (AP) — Another new variant of the coronavirus appears to have emerged in Nigeria, Africa’s top public health official said Thursday, but he added that further investigation was needed.

“It’s a separate lineage from the UK and South Africa,” the head of the Africa Centers for Disease Control and Prevention, John Nkengasong, told reporters. He said the Nigeria CDC and the African Center of Excellence for Genomics of Infectious Diseases in that country — Africa’s most populous — will be analyzing more samples. ... “Give us some time ... it’s still very early,” he said.

The alert about the apparent new variant was based on two or three genetic sequences, he said, but that and South Africa’s alert late last week were enough to prompt an emergency meeting of the Africa CDC this week.

The variant was found in two patient samples collected on Aug. 3 and on Oct. 9 in Nigeria’s Osun state, according to a working research paper seen by The Associated Press.

Unlike the variant seen in the UK, “we haven’t observed such rapid rise of the lineage in Nigeria and do not have evidence to indicate that the P681H variant is contributing to increased transmission of the virus in Nigeria. However, the relative difference in scale of genomic surveillance in Nigeria vs the U.K. may imply a reduced power to detect such changes,” the paper says.

... The African continent now has more than 2.5 million confirmed cases, or 3.3% of global cases. Infections across the continent have risen 10.9% over the past four weeks, Nkengasong said, including a 52% increase in Nigeria and 40% increase in South Africa.

-----------------------------------------

Detection of SARS-CoV-2 P681H Spike Protein Variant in Nigeria
https://virological.org/t/detection-of-sars-cov-2-p681h-spike-protein-variant-in-nigeria/567

... Following the release of the UK report, we did a quick analysis of samples recently sequenced at the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Nigeria and we identified two SARS-CoV-2 sequences that share one non-synonymous SNP in the spike protein in common with this lineage, but none of the 22 other unique lineage-defining mutations of B.1.1.7.

These were found in two patient samples collected on the 3rd of August 2020 and 9th of October 2020 from individuals in Osun State, Nigeria.

The non-synonymous SNP, S:P681H, has been observed in global data outside of the B.1.1.7 lineage, and likely represents an independent, homoplasic occurrence of this substitution from the UK.

The P681H spike protein mutation has been previously noted to be directly adjacent to the furin cleavage site, which may have biological significance.

https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563

At the moment, only about 1% of the SARS-CoV-2 genomes from Nigeria share any of the 17 protein-altering variants from the UK lineage of concern (B.1.1.7). However, this might change in the next few weeks when we sequence more samples from the recently reported surge of covid-19 in Nigeria. Other reported mutations such as the N501Y, A570D, and the HV 69 - 70 deletion in the spike protein have not been detected in our genomes yet, this could also be associated with non-increase of the lineage in Nigeria currently. Inasmuch as the full effect of this mutation isn’t known yet and it is still being studied, the importance of a robust genomic surveillance system cannot be overemphasized as we can identify and report changes in the genomes of pathogens such as SARS-CoV-2 that are of public health interest.
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pietkuip

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Re: COVID-19
« Reply #10390 on: December 24, 2020, 04:53:35 PM »
The doubling time is about a week in the parts of England where the new variant has high prevalence.
https://twitter.com/etymologic/status/1342110653377605632

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Re: COVID-19
« Reply #10391 on: December 24, 2020, 05:55:27 PM »
COVID-19 Severity Affected by Proportion of Antibodies Targeting Crucial Viral Protein
https://medicalxpress.com/news/2020-12-covid-severity-affected-proportion-antibodies.html

COVID-19 antibodies preferentially target a different part of the virus in mild cases of COVID-19 than they do in severe cases, and wane significantly within several months of infection, according to a new study by researchers at Stanford Medicine.

The findings identify new links between the course of the disease and a patient's immune response. They also raise concerns about whether people can be re-infected, whether antibody tests to detect prior infection may underestimate the breadth of the pandemic and whether vaccinations may need to be repeated at regular intervals to maintain a protective immune response.

"This is one of the most comprehensive studies to date of the antibody immune response to SARS-CoV-2 in people across the entire spectrum of disease severity, from asymptomatic to fatal," said Scott Boyd, MD, Ph.D., associate professor of pathology. "We assessed multiple time points and sample types, and also analyzed levels of viral RNA in patient nasopharyngeal swabs and blood samples. It's one of the first big-picture looks at this illness."

The study found that people with severe COVID-19 have low proportions of antibodies targeting the spike protein used by the virus to enter human cells compared with the number of antibodies targeting proteins of the virus's inner shell.

Antibodies that recognize and bind to the spike protein block its ability to bind to ACE2, preventing the virus from infecting the cells, whereas antibodies that recognize other viral components are unlikely to prevent viral spread. Current vaccine candidates use portions of the spike protein to stimulate an immune response.

The researchers studied 254 people with asymptomatic, mild or severe COVID-19 who were identified either through routine testing or occupational health screening at Stanford Health Care or who came to a Stanford Health Care clinic with symptoms of COVID-19. Of the people with symptoms, 25 were treated as outpatients, 42 were hospitalized outside the intensive care unit and 37 were treated in the intensive care unit. Twenty-five people in the study died of the disease.

Boyd and his colleagues analyzed the levels of three types of antibodies—IgG, IgM and IgA—and the proportions that targeted the viral spike protein or the virus's inner shell as the disease progressed and patients either recovered or grew sicker. They also measured the levels of viral genetic material in nasopharyngeal samples and blood from the patients. Finally, they assessed the effectiveness of the antibodies in preventing the spike protein from binding to ACE2 in a laboratory dish.

"Although previous studies have assessed the overall antibody response to infection, we compared the viral proteins targeted by these antibodies," Boyd said. "We found that the severity of the illness correlates with the ratio of antibodies recognizing domains of the spike protein compared with other nonprotective viral targets. Those people with mild illness tended to have a higher proportion of anti-spike antibodies, and those who died from their disease had more antibodies that recognized other parts of the virus."

"Antibody responses are not likely to be the sole determinant of someone's outcome," Boyd said. "Among people with severe disease, some die and some recover. Some of these patients mount a vigorous immune response, and others have a more moderate response. So, there are a lot of other things going on. There are also other branches of the immune system involved. It's important to note that our results identify correlations but don't prove causation."

As in other studies, the researchers found that people with asymptomatic and mild illness had lower levels of antibodies overall than did those with severe disease. After recovery, the levels of IgM and IgA decreased steadily to low or undetectable levels in most patients over a period of about one to four months after symptom onset or estimated infection date, and IgG levels dropped significantly.

"This is quite consistent with what has been seen with other coronaviruses that regularly circulate in our communities to cause the common cold," Boyd said. "It's not uncommon for someone to get re-infected within a year or sometimes sooner. It remains to be seen whether the immune response to SARS-CoV-2 vaccination is stronger, or persists longer, than that caused by natural infection. It's quite possible it could be better. But there are a lot of questions that still need to be answered."



Katharina Röltgen et al. Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome, Science Immunology (2020).
https://immunology.sciencemag.org/content/5/54/eabe0240
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gerontocrat

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Re: COVID-19
« Reply #10392 on: December 24, 2020, 07:05:18 PM »
So the two-sentence, sad summary: The UK/SA variants show that we should be doing what we should have been doing all along, keeping the number of infections really, really low. That job has become even more important now - and even harder.

A bit of a problem in the UK

Maybe Italy will succeed
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gerontocrat

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Re: COVID-19
« Reply #10393 on: December 24, 2020, 07:16:35 PM »
https://www.worldometers.info/coronavirus/#countries

As record keeping might be a bit wobbly over the Xmas period here is the state of play as at 23rd December for the world and the US.
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vox_mundi

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Re: COVID-19
« Reply #10394 on: December 24, 2020, 09:58:29 PM »
Could COVID-19 Have Wiped Out the Neanderthals?
https://phys.org/news/2020-12-covid-neandertals.html
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Richard Rathbone

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Re: COVID-19
« Reply #10395 on: December 25, 2020, 12:43:11 AM »
First sign of Tier 4 bending the curve looks like its appearing in the English testing data. It needs another day to confirm, because lag has got worse recently and reporting is going to be inconsistent over the Xmas period, but the curves in the Tier 4 regions (London, South East and East) do seem to have started to bend while the areas with lesser restrictions are still on the way up.

https://twitter.com/RP131/status/1342164475672195074/photo/1


vox_mundi

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Re: COVID-19
« Reply #10396 on: December 25, 2020, 01:58:51 PM »
New Virus Strain’s Transmissibility to Cause More Deaths: Study
https://www.bloombergquint.com/amp/coronavirus-outbreak/new-virus-strain-s-transmissibility-to-cause-more-deaths-study
https://www.npr.org/sections/goatsandsoda/2020/12/24/950144667/how-worried-should-we-be-about-the-new-u-k-coronavirus-variant?ft=nprml&f=

The mutated coronavirus strain that’s been spreading in the U.K. appears to be more contagious and will likely lead to higher levels of hospitalizations and deaths next year, a new study showed.

"Given all the biological and epidemiological evidence that has come together in the past few weeks, I think the picture is getting more and more consistent with something pretty serious," says mathematical modeler Nick Davies, who led the study.

The variant is 56% more transmissible than other strains, according to the study by the Centre for Mathematical Modelling of Infectious Diseases at the London School of Hygiene and Tropical Medicine. There’s no clear evidence that it results in more or less severe disease.

https://cmmid.github.io/topics/covid19/uk-novel-variant.html

... No matter the underlying reason, policymakers should take this new variant very seriously, says epidemiologist Bill Hanage of the Harvard T.H. Chan School of Public Health. If it's indeed 50% more transmissible, it will be difficult to stop its spread.

Given the assumptions in their models, it's really quite hard to avoid a situation very much like what happened last spring, in terms of hospital bed capacity and surges, without a very high rate of vaccination," Hanage says.

Measures like England’s national lockdown in November are unlikely to reduce the reproduction number -- the new infections estimated to stem from a single case -- to less than 1 unless schools and universities are also closed, the report said. It also said vaccine rollouts may need to be accelerated to contain its spread, to a rate of 2 million people a week from the current pace of 200,000.

The variant will likely come to the U.S. — if isn't here already. The study strongly suggests that people should be even more diligent about preventive measures: avoiding large gatherings. wearing masks, physical distancing and washing hands. On top of that, Hanage says, "the vaccine needs to be getting out at a very, very high rate."

-------------------------------------


South Africa variant

-------------------------------------

Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England
https://cmmid.github.io/topics/covid19/uk-novel-variant.html

A novel SARS-CoV-2 variant, VOC 202012/01, emerged in southeast England in November 2020 and appears to be rapidly spreading towards fixation.

We fitted a two-strain mathematical model of SARS-CoV-2 transmission to observed COVID-19 hospital admissions, hospital and ICU bed occupancy, and deaths; SARS-CoV-2 PCR prevalence and seroprevalence; and the relative frequency of VOC 202012/01 in the three most heavily affected NHS England regions (South East, East of England, and London).

We estimate that VOC 202012/01 is 56% more transmissible (95% credible interval across three regions 50-74%) than preexisting variants of SARS-CoV-2. We were unable to find clear evidence that VOC 202012/01 results in greater or lesser severity of disease than preexisting variants. Nevertheless, the increase in transmissibility is likely to lead to a large increase in incidence, with COVID-19 hospitalisations and deaths projected to reach higher levels in 2021 than were observed in 2020, even if regional tiered restrictions implemented before 19 December are maintained.

Our estimates suggest that control measures of a similar stringency to the national lockdown implemented in England in November 2020 are unlikely to reduce the effective reproduction number Rt to less than 1, unless primary schools, secondary schools, and universities are also closed. We project that large resurgences of the virus are likely to occur following easing of control measures. It may be necessary to greatly accelerate vaccine roll-out to have an appreciable impact in suppressing the resulting disease burden.


Full Text: https://cmmid.github.io/topics/covid19/reports/uk-novel-variant/2020_12_23_Transmissibility_and_severity_of_VOC_202012_01_in_England.pdf



Fig. 1. (A) Proportion of VOC 202012/01 in South East, East of England, and London NHS England regions versus the rest of England from 28 September – 1 December 2020 (mean and 95% CI). Grey shaded areas (panels A, C, D) reflect the period of time when England was in a second national lockdown. We cut off the data after 1 December 2020 due to a substantial decrease in representativeness after this time (Fig. S4). (B) Proportion of S gene drop-outs (5 – 11 December) versus mean reproduction number (27 November – 4 December) by local authority in England. The one-week lag accounts for delays from infection to test. (C) Percentage change (95% CI) in Google Mobility indices relative to baseline over time and (D) setting-specific mean contacts (95% CI) from the CoMix study (9) over time and by age for local authorities that went into Tier 4 compared to the rest of England. Educ = education setting. Some local authorities that were within the South East, East of England, and London NHS England regions did not go into Tier 4 and were therefore included in the rest of England for panels C and D. (E) Estimates of R0 (50% and 95% CI) from CoMix social contact survey compared to Rt estimates from REACT-1 SARS-CoV-2 prevalence survey for England. R estimates based on single and aggregated REACT-1 survey rounds are shown.
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vox_mundi

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Re: COVID-19
« Reply #10397 on: December 25, 2020, 02:17:04 PM »
Study Finds Evidence of Immunity After Mild or Asymptomatic COVID-19 Infection
https://medicalxpress.com/news/2020-12-evidence-immunity-mild-asymptomatic-covid-.html

New research involving scientists from Queen Mary University of London has found evidence of protective immunity in people up to four months after mild or asymptomatic COVID-19.

The study, published today in Science Immunology, analyzed antibody and T cell responses in 136 London healthcare workers who had mild or asymptomatic COVID-19 infection dating back to March 2020.

The team, including researchers from Queen Mary, Imperial College London and University College London, found that 89 percent of healthcare workers analyzed carried neutralizing antibodies 16-18 weeks after infection.

The researchers found most also had T cells capable of recognizing multiple different parts of the virus, however the two responses did not always persist in harmony, with some individuals showing T cell immunity but no evidence of antibodies, and vice versa.

... Much of this debate around protective immunity has focussed on the different roles of B cells, which make antibodies, and T cells, white blood cells which work in several different ways to help protect from viruses, including direct killing.

In this study, the researchers show that whilst protective antibody responses were usually complemented by a T cell response, over half of the healthcare workers had mismatched antibody and T cell responses, and did not produce a T cell response specific to proteins found on the outer layer of the SARS-CoV-2 virus.

They also found that T cell responses tended to be higher in those with the classic, defining symptoms of COVID-19, while asymptomatic infection resulted in a weaker T cell immunity than symptomatic infection, but equivalent neutralizing antibody responses.

The new study also provides reassurance for vaccination efforts, suggesting that even following mild infection, individuals carry antibody and T cell immunity to many parts of the virus, known as epitopes. Whilst new variants are appearing, the changes to the virus don't necessarily occur within these epitopes so it is hoped the vast majority of immune recognition can likely continue unperturbed.

Discordant neutralizing antibody and T cell responses in asymptomatic and mild SARS-CoV-2 infection. Science Immunology  23 Dec 2020.
https://immunology.sciencemag.org/content/5/54/eabf3698
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vox_mundi

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Re: COVID-19
« Reply #10398 on: December 25, 2020, 04:50:05 PM »
Workers at UK Lab That Processes Over 50,000 Coronavirus Tests a Day Hit By Their Own COVID-19 Outbreak
https://www.businessinsider.com/uks-biggest-coronavirus-testing-lab-hit-by-covid-19-outbreak-2020-12

The UK's biggest coronavirus test processing facility has been hit by a COVID-19 outbreak of its own. Staff at Milton Keynes Lighthouse Laboratory — which has reportedly been asked to process 70,000 tests per day — have contracted the virus in recent days.

Staff on three of the four scientific teams at the lab, as well as administrative and warehouse staff have been infected

The British government confirmed to Sky News that the outbreak exists, but insisted that the lab has followed all protocols for staying COVID secure in the workplace.

Workers at the laboratory, however, expressed concerns to Sky News that demands to process a higher volume of tests as the UK battles a rapidly-spreading outbreak of a new coronavirus variant have led to corners being cut. The report says that the center is being asked to process 70,000 tests per day, but is currently processing around 50,000.

... It is not known how many people have been affected by the outbreak, but around 20 people in one 70-person lab team are currently isolating, according to a worker at the laboratory who asked to remain anonymous.

... Sky News understands the Lighthouse Lab is supposed to have a bubble system in place in order to keep staff separate, following a recommendation from the Health and Safety Executive, which visited the site recently.

Yet according to the source, the bubble system is not being respected with workers at the short-staffed lab being moved between groups, risking further cross-contamination. The lab worker said there had also been mixing in the building's lobbies and at the canteen.

The lab worker said that new recruits had been sitting in the canteen while they waited for their test results.

According to the lab worker, one new warehouse staff member received a positive test result after they had sat in the canteen during a period when a whole lab team had been in there for a break. "The whole thing's a joke," they said.

Sky News understands the lab administration is still largely run by a team from management consultancy Deloitte.

https://news.sky.com/story/covid-19-major-uk-testing-lab-suffers-coronavirus-outbreak-after-claims-of-safety-breaches-12172290

-----------------------------------------

... voice of experience: never hire bean-counting MBAs to run a laboratory
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Shared Humanity

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Re: COVID-19
« Reply #10399 on: December 25, 2020, 05:30:08 PM »
Thanks again vox_mundi. Highly informative posts and cause for some hope with regard to immunity. We simply need to get the vaccines out.