COVID COVID-19 Coronavirus Containment Efforts

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Containment efforts for the COVID-19 Coronavirus are facing significant challenges, with experts suggesting that it may no longer be feasible to prevent its global spread. The virus has a mortality rate of approximately 2-3%, which could lead to a substantial increase in deaths if it becomes as widespread as the flu. Current data indicates around 6,000 cases, with low mortality rates in areas with good healthcare. Vaccine development is underway, but it is unlikely to be ready in time for the current outbreak, highlighting the urgency of the situation. As the outbreak evolves, the healthcare system may face considerable strain, underscoring the need for continued monitoring and response 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.
 
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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
 
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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)
 
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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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  • #4,507
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
 
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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.
 
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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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  • #4,511
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.
 
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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.
Luck? Selection bias? The fact that they were doing well increased the likelihood of doing poorly?
 
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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.
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?
 
  • #4,516
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.
 
  • #4,517
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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There's a whole book of them. I like "Letters in Winning Word of Scripps Spelling Bee" and "Number of People Killed by Venemous Spiders".
 
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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.
 
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In the town I live in it was definitely the summer vacations. We've been exceptionally good in spring and extraordinarily bad since autumn.
 
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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."
 
  • #4,522
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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  • #4,528
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.
 
  • #4,529
Just read that the virus is now on all continents.
 
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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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The mother of a close friend passed away on Friday. She had been in an elder care facility and was receiving immunotherapy for cancer. However, she died from complications of COVID-19.
 
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Astronuc said:
The mother of a close friend passed away on Friday. She had been in an elder care facility and was receiving immunotherapy for cancer. However, she died from complications of COVID-19.
I self-censored the rant against mask deniers I wrote as a reply. It makes me sad to hear such stories. I have a very good friend who also cannot afford to catch any virus, let alone SARS-covid-2, because of immune suppression. So I can imagine how this feels. It is frustrating that there are still people out there, and not only in the US, who actually dare to demand their freedom to - let's say it as it is - infect others.
 
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And Thailand is having outbreaks after months of no cases. The main outbreak last week is at the Central Shrimp Market in Samut Sakhon and the dormitory for the thousands of Burmese migrant workers. Now most ,90% , of the daily appx 100 transmissions are local .Such as 45 infections in a gambling den cluster a few days ago as well as a bikers crowd in Phuket, one member who had visited the Central Shrimp Market at North part of the gulf close to Bangkok.
IMG20201229095757.jpg
 
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A new variant of the novel Coronavirus that was first detected in the United Kingdom is most likely circulating across the United States, . . . .

The new variant of the SARS-CoV-2 virus—dubbed the B.1.1.7 lineage—appears to be more transmissible than the original, although a study from Public Health England found that it does not seem to cause more severe illness.
https://www.msn.com/en-us/health/medical/new-covid-19-strain-almost-certainly-in-multiple-states-biden-advisor-atul-gawande-says/ar-BB1clvvg?li=BBnb7Kz

The new variant has been reported in Colorado. On Tuesday, Colorado Gov. Jared Polis announced that a man in the state had been infected with the new variant—the first case detected in the United States. The individual in question is a male in his 20s and has no history of travel, Colorado health officials said. He is currently recovering in isolation in Elbert County. Prior to that confirmed case, the CDC indicated that the B.1.1.7 lineage has already been circulating in the United States undetected, but "genetic sequencing of the SARS-CoV-2 virus had only been carried out on a small fraction of the roughly 17 million COVID-19 cases in the US." So, did the variant travel from the UK to the US (meaning that it's spreading undetected, perhaps with asymptomatic persons), or the SARS-Cov-2 naturally mutates to this new variant regardless of location?

Meanwhile, in Louisiana, congressman-elect Luke Letlow died Tuesday evening from complications of Covid-19 days before he was set to be sworn into office, his spokesman announced. He was 41, and leaves behind a wife and two children.
https://www.msn.com/en-us/news/politics/congressman-elect-luke-letlow-dies-from-covid-complications-days-before-being-sworn-in/ar-BB1ckGjP

Apparently Letlow had received Remdesivir and steroids, but that was not enough. I don't know if he received the Regeneron monoclonal antibody, but I believe that he did not. It would seem that Remdesivir and steroids alone are insufficient in some (severe?) cases. I wonder if the Remdesivir was started too late.
 
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  • #4,537
Astronuc said:
So, did the variant travel from the UK to the US (meaning that it's spreading undetected, perhaps with asymptomatic persons), or the SARS-Cov-2 naturally mutates to this new variant regardless of location?
It's of course possible that the same set of mutations happens independently elsewhere at around the same time, but it doesn't sound particularly likely. As you wrote, most tests don't sequence the virus. This is in far more places than we know about.
 
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Dec 30 (Reuters) - A 45-year-old nurse in California tested positive for COVID-19 more than a week after receiving Pfizer Inc's Coronavirus vaccine, an ABC News affiliate reported on Tuesday.
https://www.reuters.com/article/hea...ing-pfizer-covid-19-vaccine-abc-idUSL4N2JA181

Matthew W., a nurse at two different local hospitals, posted on social media on December 18 that he had received the Pfizer vaccine, and reporting his arm was sore for a day but that he had suffered no other side-effects. Six days later, on Christmas Eve, he became sick after working a shift in the COVID-19 unit, the report added. He got the chills and later came down with muscle aches and fatigue. He subsequently tested positive for COVID-19 the day after Christmas.

Apparently a single dose of Pfizer's vaccine takes time kickstart the immune system, and it may be insufficient to prevent onset of COVID-19. Time and a second dose are needed.

Meanwhile in NY State, infections and hospitalizations of younger folks are increasing, and the state is approaching 1 million confirmed cases and 30,000 deaths.
 
  • #4,539
AFAIK it takes 2 doses with 3 weeks time in between. But even then, there is no guarantee that it works. IRC they claim around 90% efficiency, which is still above the quote of an ordinary flu vaccine.
 
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fresh_42 said:
...they claim around 90% efficiency, which is still above the quote of an ordinary flu vaccine.
As I recall the 'raw' efficiency of an ordinary flu vaccine is ~ in the same range (but without any seconds, usually).
I mean: against exactly matching strain, within a few months at most, and so on with the constraints...

I wish that that 90% would remain 90% after a year.
 
  • #4,541
Astronuc said:
https://www.reuters.com/article/hea...ing-pfizer-covid-19-vaccine-abc-idUSL4N2JA181

Matthew W., a nurse at two different local hospitals, posted on social media on December 18 that he had received the Pfizer vaccine, and reporting his arm was sore for a day but that he had suffered no other side-effects. Six days later, on Christmas Eve, he became sick after working a shift in the COVID-19 unit, the report added. He got the chills and later came down with muscle aches and fatigue. He subsequently tested positive for COVID-19 the day after Christmas.

Apparently a single dose of Pfizer's vaccine takes time kickstart the immune system, and it may be insufficient to prevent onset of COVID-19. Time and a second dose are needed.

Meanwhile in NY State, infections and hospitalizations of younger folks are increasing, and the state is approaching 1 million confirmed cases and 30,000 deaths.

This is not surprising. The phase 3 clinical trial for the Pfizer vaccine documented 39 people being infected up to three weeks after the first vaccination before getting the second dose (out of a total of 21,669 versus 82/21,686 infections in the placebo over the same time period). As others have mentioned, it takes time for the body's immune system to generate antibodies to the vaccine, and the 95% efficacy figure from the vaccine trial applies only when looking at data starting a week after receiving the second dose of the vaccine (four weeks after the initial dose). Furthermore, because the virus has an incubation period of up to 2 weeks, showing symptoms of the disease 6 days after getting the vaccine is not inconsistent with getting infected before receiving the vaccine.

According to the data from the Pfizer trial, it looks like you have to wait at least two weeks after the first dose before you begin to see signs of protection from the vaccine:
1609433361824.png
 
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6 days (or 9 days if we take the test result) is well within the part where the two curves don't differ, so this is not surprising at all.
It's unclear how much the second dose helps, but expecting to be protected the day after the first one is unreasonable.

Based on this vaccination tracker Israel has already vaccinated 11% of its population. The worldwide average is 0.13%, or 10 million vaccinations.
The phase III vaccine trials used ~15,000 people over ~6 months each for each leading candidate. We get an equal product of people and time every 6 hours now, only rising as the number of vaccinated people goes up. About half of these vaccinations (4.5 million) are in China, however, where the disease is rare anyway. The US is second in absolute numbers, 2.8 million vaccinations. Almost all of them just got the first dose, but the number of people who got it at least 2 weeks ago (should have a good protection now) is rising quickly. Israel and the UK are at 1 million each.
 
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From https://covidtracking.com/data/national/deaths (they mostly agree with the published data from the states and territories)
Oct 01, 2020 199,943 cumulative deaths due to COVID-19
Dec 31, 2020 336,779 cumulative deaths

Difference 136,836 deaths

Difference + Dec 31, 2020, projected by March 31, 2020 - 473,615 cumulative deaths, but it may be more like 480K to 500K, because the downward slope after a peak is not as steep as the ascension. Even though we have a vaccine, it's slowly rolling out, and we currently have a relatively high mortality rate.The mutation of SARS-Cov-2 from southern UK has apparently made it's way to Florida and California after being first identified in Colorado. Health officials believe it came from folks returning from the UK. The two persons in Colorado and Florida who have the new variant do not have a travel history to the UK.

https://www.wfla.com/community/health/coronavirus/new-covid-19-variant-found-in-florida/
https://www.usatoday.com/story/news/health/2021/01/02/new-covid-strain-b-117-explained/4112125001/
CDC (December 29, 2020) - https://www.cdc.gov/coronavirus/2019-ncov/more/scientific-brief-emerging-variant.html - seems to indicate it is not present in US, but other sources indicate otherwise.
 
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  • #4,544
Astronuc said:
because the downward slope after a peak is not as steep as the ascension.
I don't see a downward slope yet. New cases still hover at ~200,000/day, deaths at ~2500/day. Hospitalizations are at an all-time high (120,000).

Vaccines will help protecting the most vulnerable people, its early impact on deaths will probably be larger than its impact on cases, but it needs to be pretty strong to keep the deaths below 500,000 by the end of March.
 
  • #4,545
mfb said:
I don't see a downward slope yet.
No, unfortunately, not yet. New York accumulated over 1 million positive cases on Jan 1. Illinois should exceed 1 million positive cases in about 4 or 5 days. :frown:
 
  • #4,546
The slope is far from downward in the UK. :frown:
 
  • #4,548
The governor of NY State announced that the UK strain B.1.1.7 of SARS-Cov-2 has been found in one individual in Saratoga County, NY. The individual has not history of travel to any area in the US or to the UK, but obviously he was exposed to someone who has, otherwise, the variant spontaneously developed independently from the population in the UK.
Gov. Andrew M. Cuomo on Monday afternoon announced the Wadsworth Lab in Albany had detected the U.K. strain of the virus, known as B.1.1.7, in the 67-year-old Saratoga County man.

The man, who Cuomo did not identify, as well as three other employees of N. Fox Jewelers, at 404 Broadway in Saratoga Springs, all tested positive for coronavirus. However, it is unknown whether the other employees contracted the more transmissible strain; Cuomo said they are waiting on the results of the other employees to answer that question.
Ref: https://www.timesunion.com/news/article/new-covid-strain-detected-saratoga-springs-15845420.php

At least three other persons from the same store have apparently tested positive for COVID-19, but the state is awaiting for a sequence analysis of the strain. The county and state are warning anyone who visited the store between December 18 and December 24 should be tested for COVID-19.

The state attributes the infection to community spread and believes others in the state have been infected with the B.1.1.7 variant, but others have not been analyzed.
The state will be setting up a rapid-testing site at the Saratoga State Park, 99 E. West Rd., Saratoga Springs, on Tuesday from 1 - 6 p.m. The state-run testing site will also be open from 10 a.m. - 6 p.m. on Wednesday, Thursday and Friday. The testing will be focused on individuals who went to the jewelry store between Dec. 18 and 24, state officials said.
 
  • #4,549
https://www.statnews.com/2021/01/04...accines-upping-the-stakes-for-the-rest-of-us/
In an extraordinary time, British health authorities are taking extraordinary measures to beat back Covid-19. But some experts say that, in doing so, they are also taking a serious gamble.

In recent days, the British have said they will stretch out the interval between the administration of the two doses required for Covid-19 vaccines already in use — potentially to as long as three months, instead of the recommended three or four weeks. And they have said they will permit the first dose and second dose for anyone person to be from different vaccine manufacturers, if the matching vaccine is not available.

Paul Bieniasz of Rockefeller University is one of those who is watching the evolving situation in Britain with dread. A retrovirologist who turned from HIV research to work on SARS-2, Bieniasz is studying how the virus acquires mutations that allow it to evade the protective antibodies people develop when they have contracted Covid-19, or when they have been vaccinated against it.

Bieniasz believes Britain is replicating in people the experiments he’s been doing in his lab — and could be fostering vaccine-resistant forms of the virus.
 
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IMG20210105115116.jpg
 

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