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.
  • #3,051
OmCheeto said:
...ended up...
What bothers me the most regarding the/an ongoing pandemic is the usage of 'ended'.
I would reserve that word for later use - it is just not fair and not useful to apply it now.
 
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  • #3,052
mfb said:
Sweden has a population of 10 million. Norway has 5 million, Finland has 6 million, Denmark has has 6 million. I don't know why you brought up total population, but clearly these countries are closer in population than e.g. Germany with 80 million or France with 70 million?
If you think Scandinavian countries are so similar to Western Europe (and no matter where you look, they are not) you would have to explain why they all had death tolls so much lower than most of Western Europe. Well, all except Sweden.

In some ways all these countries have too low a population to be statistically significant. The virus breaks out exponentially in certain areas. A country the size of Denmark can get "lucky" and practically avoid the virus, whereas another small country like Belgium can get "unlucky" and be disproportionately hit. In the larger countries like Italy, Spain and France the data tends to even out. You'll find regions in these countries as badly hit as Belgium and other regions who, like Denmark, have low numbers.

That would be, IMO, a significant part of the reason why Denmark has 95 deaths per million and Belgium 784. If there had been an early major outbreak in Copenhagen rather than Brussels it could have been the other way round.

The virus is not evenly spread across western Europe. There are other countries with low death rates:

Portugal (adjacent to Spain) has 121 per million; Spain has 593.
Austria only 70 per million; whereas Switzerland has 218.

There is a massive spread in numbers, especially across the smaller countries and that points to the randomness of uncontrolled outbreaks.
 
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The Trinity of COVID-19: Immunity, Inflammation and Intervention | Assoc Prof Paul MacAry (Part 2)

Lecture by Paul MacAry, an immunologist at the National University of Singapore. The part from 6:15 to the end gives an introduction to vaccines in general, and an overview of current vaccine efforts. He says it may be possible for a vaccine will become available in early 2021 for emergency use or similar protocols, given the number of ongoing efforts and coordination among governments and the WHO.
 
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  • #3,054
PeroK said:
A country the size of Denmark can get "lucky" and practically avoid the virus, whereas another small country like Belgium can get "unlucky" and be disproportionately hit.

Look at Liechtenstein and the neighboring Swiss canton of Graubunden. Things are an order of magnitude worse in Graubunden. The difference used to be even more evident, but then Liechtenstein got a case.
 
  • #3,055
PeroK said:
In some ways all these countries have too low a population to be statistically significant. The virus breaks out exponentially in certain areas. A country the size of Denmark can get "lucky" and practically avoid the virus, whereas another small country like Belgium can get "unlucky" and be disproportionately hit. In the larger countries like Italy, Spain and France the data tends to even out.
I'd say the first bit slightly differently or even amplify: it's the larger sample sizes that show the smoothest exponential curves. But for "certain areas" the starting point is often one of explosive clusters. At that choir practice in Washington, one person infected a probable 52 others in a single event. If the average reproduction rate is 2.2 and the average time is 5 days, that's 3.5 weeks (5 generations) of growth from a single event. Or put another way, instead of starting with 1 case and 3.5 weeks later having 53, you now have 1,200. That kind of explosive growth early in the pandemic in some places likely had a huge impact on the outcome for smaller areas that happened to be unlucky enough to have them; especially to have them early.
 
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  • #3,057
Coronavirus: Baby develops life-threatening inflammatory condition 'while her twin escapes unscathed'
https://www.yahoo.com/lifestyle/coronavirus-covid1-kawasaki-disease-inflammation-092538403.html

A mother of identical twins has revealed how one suffered a life-threatening illness after overcoming the coronavirus, while the other is thought to have escaped unscathed.

Hannah Godwin, 35, noticed her five-month-old daughter Leia had a rash and fever while lying next to her “healthy and happy” sister Thea.
NHS doctors have been told to look out for signs of “multi-system inflammation” after intensive care units in London saw eight children with unusual symptoms, some of whom tested positive for the coronavirus.

Leia has spent the past three weeks in hospital, . . . . Although Leia is no longer in critical care, doctors have warned she has a long road to recovery.
Even without COVID-19 respiratory distress, the inflammation presents yet another challenge.
 
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  • #3,058
Is it just me or is anyone else alarmed by so called gain-of-function research on dangerous viruses? This is the practice of taking a virus, such as the bird flu and making it more transmittable to humans for the purpose of researching cures and vaccines in the event that virus ever naturally mutates and gets into the human population. I mentioned bird flu because that was debated and defended by prominent scientists a decade ago with references below.

https://osp.od.nih.gov/biotechnology/gain-of-function-research/

https://www.washingtonpost.com/opin...worth-taking/2011/12/30/gIQAM9sNRP_story.html

https://www.bbc.com/news/world-us-canada-16279365

https://www.sciencemag.org/news/201...iments-make-bird-flu-more-risky-poised-resume

Relevant to the current crisis is the fact that NIH funded and NIAID administered gain-of-function research at the Wuhan Institute of Virology and elsewhere using SARS-CoV-2. Basically, we paid them to make it much easier to transmit to humans for research purposes. Here is the NIH funding for EcoHealth Alliance, the organization that funnels NIH money to labs around the world.

https://projectreporter.nih.gov/reporter_SearchResults.cfm?icde=50081038

Notice this statement from the sixth project title down;

Speaking of SARSr-CoVs,;

"We will use S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments and analysis of receptor binding to test the hypothesis that % divergence thresholds in S protein sequences predict spillover potential."

Note that I made no claims that this research was the cause of the pandemic. But representatives of 122 nations just demanded that the actual source of the virus be vigorously investigated.
 
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  • #3,059
bob012345 said:
Note that I made no claims that this research was the cause of the pandemic.
Good, because that claim would be foolish.
bob012345 said:
But representatives of 122 nations just demanded that the actual source of the virus be vigorously investigated.
Why put this completely unrelated point next to the other one?
 
  • #3,060
david2 said:
Moderna Announces Positive Interim Phase 1 Data for its mRNA Vaccine

Interesting. I hadn't been very hopeful for the RNA/DNA vaccines as they need the body to produce the antigen from the RNA, whereas other vaccine contain the antigen. Also, none to date have been approved for any other use in people, although they have veterinary use. However, these are generally thought to be very likely to be safe.
 
  • #3,061
bob012345 said:
Is it just me or is anyone else alarmed by so called gain-of-function research on dangerous viruses? This is the practice of taking a virus, such as the bird flu and making it more transmittable to humans for the purpose of researching cures and vaccines in the event that virus ever naturally mutates and gets into the human population. I mentioned bird flu because that was debated and defended by prominent scientists a decade ago with references below.

https://osp.od.nih.gov/biotechnology/gain-of-function-research/

https://www.washingtonpost.com/opin...worth-taking/2011/12/30/gIQAM9sNRP_story.html

https://www.bbc.com/news/world-us-canada-16279365

https://www.sciencemag.org/news/201...iments-make-bird-flu-more-risky-poised-resume

Relevant to the current crisis is the fact that NIH funded and NIAID administered gain-of-function research at the Wuhan Institute of Virology and elsewhere using SARS-CoV-2. Basically, we paid them to make it much easier to transmit to humans for research purposes. Here is the NIH funding for EcoHealth Alliance, the organization that funnels NIH money to labs around the world.

https://projectreporter.nih.gov/reporter_SearchResults.cfm?icde=50081038

Notice this statement from the sixth project title down;

Speaking of SARSr-CoVs,;

"We will use S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments and analysis of receptor binding to test the hypothesis that % divergence thresholds in S protein sequences predict spillover potential."

Note that I made no claims that this research was the cause of the pandemic. But representatives of 122 nations just demanded that the actual source of the virus be vigorously investigated.

Here is a good video on the topic. Two leading experts give presentations: the first, Marc Lipsitch (Harvard), makes the case against gain of function research, and the second, Derek Smith (Cambridge), makes the case for it.



Regardless if gain of function research at WIV contributed to the outbreak of sars-cov-2, the current pandemic has at least put this topic into public view. I think it's a very important topic that needs to be more widely discussed.

I agree with Marc Lipsitch, that it's not worth the risks. People are not reliable enough to trust with manipulating, creating, and testing dangerous viruses. It seems pretty clear that scientists don't fully understand the risks, but a worst case event/accident can be catastrophic (similar or much worse than what is happening now). Basically, a single screw up at a lab could result in millions of deaths, and bring a new deadly viruse into the world that may never go away. People are constantly screwing everything up.
 
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  • #3,062
What is the medical definition of "Second Wave"?
 
  • #3,063
To truly learn from this pandemic, we must understand why pandemics occur? And how can we prevent a recurrence?
 
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  • #3,064
mfb said:
Good, because that claim would be foolish.Why put this completely unrelated point next to the other one?
While it would be foolish at this point to make such an absolute claim, it would not be foolish to consider that possibility. Let's put this in physics terms. Gain-of-function research farmed out to labs in countries not yet up to level 4 CDC standards is like making nuclear weapons at an insecure facility in Turkey. There is a decent chance a few might go missing. And even in level 4 U.S. labs it's risky. The upside is you might learn something that might be relevant if nature produced a crossover with a sufficiently similar genetic code at some point in the future. The downside is a global pandemic with hundreds of thousands of deaths plunging the world economy into deep depression.

Let's consider the coincidence here. The whole point of doing gain-of-function research is to accelerate nature that might take eons to do the same thing. So, Peter Daszak through EcoHealth Alliance decides to push to do that. Then suddenly, out of the blue, and in a similar timeframe, a pandemic emerges with an incredible ability to be transmittable to humans, even a weird 14 day incubation period where its highly contagious well before symptoms even appear if ever. And yet we are told the possibility of that virus escaping from a lab is impossible and that it must have been a purely natural occurrence. Can you imagine the fallout if it was concluded that the pandemic was caused by the accidental release of a virus after gain-of-function experiments paid for the the NIH? Interestingly, the experts telling us that have a vested interest in not being seen as being in any way responsible for the pandemic. We may be looking at the Chinese version of Chernobyl with the U.S. implicated too.

I included that disclaimer because I can't prove that scenario happened but I'm certainly suspicious that is one possibility and it's entirely related to the demand by the U.N. representatives to find out what really happened.
 
  • #3,065
bob012345 said:
So, Peter Daszak through EcoHealth Alliance decides to push to do that. Then suddenly, out of the blue, and in a similar timeframe, a pandemic emerges with an incredible ability to be transmittable to humans, even a weird 14 day incubation period where its highly contagious well before symptoms even appear if ever. And yet we are told the possibility of that virus escaping from a lab is impossible and that it must have been a purely natural occurrence.

Following your hypothesis that this started in Peter Daszak's lab, why did the outbreak begin in Wuhan?
 
  • #3,066
PeroK said:
Following your hypothesis that this started in Peter Daszak's lab, why did the outbreak begin in Wuhan?

Dr. Peter Daszak heads the EcoHealth Alliance as president which is a organization dedicated to "prevent pandemics" and that includes funding labs studying bat viruses and includes gain-of-function experiments. They received grants from NIH administered through NIAID (Dr. Fauci) and channeled the money to various labs including Wuhan. Daszak doesn't personally do the research in his own lab. He receives grants and funds research. Dr. Fauci is a supporter of gain-of-function research.

https://www.ecohealthalliance.org

Here is the mission statement;

"EcoHealth Alliance is an international nonprofit dedicated to a 'One Health' approach to protecting the health of people, animals and the environment from emerging infectious diseases. The organization formed with the merger of two highly respected organizations, Wildlife Trust and the Consortium for Conservation Medicine. The urgent concern for wildlife conservation and the overall health of our planet has led EcoHealth Alliance to become an environmental science and public health leader working to prevent pandemics in global hotspot regions across the globe and to promote conservation."

It may very well turn out that EcoHealth Alliance are among the heros in all this mess but when people promote potentially risky research with deadly viruses we shouldn't just give them a pass without even being allowed to legitimately ask questions.
 
  • #3,067
bob012345 said:
Dr. Peter Daszak heads the EcoHealth Alliance as president which is a organization dedicated to "prevent pandemics" and that includes funding labs studying bat viruses and includes gain-of-function experiments. They received grants from NIH administered through NIAID (Dr. Fauci) and channeled the money to various labs including Wuhan.

I don't imagine anyone outside the Chinese Communist Party has much influence on what goes on in a lab in Wuhan.
 
  • #3,068
PeroK said:
I don't imagine anyone outside the Chinese Communist Party has much influence on what goes on in a lab in Wuhan.
As I understand it, EcoHealth Alliance gave the Wuhan lab $600k for the purpose of doing experiments on bat viruses including gain-of-function experiments. Free money from the U.S. to do experiments they wanted to do anyway. I find it interesting that the money doesn't come directly from NIH but through an intermediary non-profit. Perhaps that gives the NIH some deniability if outside labs don't follow strict protocols? Obviously, the CCP approved of the work but then when Wuhan scientists started speaking out about the virus breaking out into the human population (whether naturally or by accident), they were silenced.
 
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  • #3,069
bob012345 said:
As I understand it, EcoHealth Alliance gave the Wuhan lab $600k for the purpose of doing experiments on bat viruses including gain-of-function experiments. Free money from the U.S. to do experiments they wanted to do anyway. I find it interesting that the money doesn't come directly from NIH but through an intermediary non-profit. Perhaps that gives the NIH some deniability if outside labs don't follow strict protocols? Obviously, the CCP approved of the work but then when Wuhan scientists started speaking out about the virus breaking out into the human population (whether naturally or by accident), they were silenced.

I found this:

https://www.ft.com/content/255a3524-0459-4724-a92a-58268ab627e2
 
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  • #3,070
FINDINGS FROM INVESTIGATION AND ANALYSIS OF RE-POSITIVE CASES

○ Based on active monitoring, epidemiological investigation, and laboratory testing of re-positive cases and their contacts, no evidence was found that indicated infectivity of re-positive cases.

- Of the 447 re-positive cases as of 15 May, epidemiological investigation was conducted on 285 cases and laboratory analysis on 108 cases. (*473 as of 18 May)

- From monitoring of 790 contacts of the 285 re-positive cases, no case was found that was newly infected solely from contact with re-positive cases during re-positive period.

- Virus isolation in cell culture of respiratory samples of 108 re-positive cases, all result was negative (i.e. virus not isolated).

- Of the 23 re-positive cases from which the first and the second serum samples were obtained, 96% were positive for neutralizing antibodies.
https://www.cdc.go.kr/board/board.es?mid=a30402000000&bid=0030
 
  • #3,071
PeroK said:
It has several denials of the possibility the virus came from the Wuhan lab. Why are they so certain this early? Statements such as this;

"Edward Holmes, an Australian virologist who helped map and share the genetic sequence of the virus, said there was “no evidence” that Sars-Cov-2, the virus that causes Covid-19 in humans, originated in a Wuhan laboratory."

I'm glad the "no evidence" was in quotes because I've seen the logic explained as because the sequence that makes it very effective could not be predicted a priori by computer, it must have been natural. But there are other ways of putting enhancements into the virus without artificial engineering such as using gene editing techniques with naturally occurring sequences. In other words, those claiming "no evidence" may well be parsing subtle distinctions about what is considered natural and what is considered man made that the public wouldn't appreciate.

Also, "no evidence" doesn't mean it didn't happen. It means one doesn't have the evidence at hand to prove it happened. It's far too early to know.

Fauci says he is “very, very strongly leaning toward this could not have been artificially or deliberately manipulated”. He would have to say that or admit he funded research that led to the pandemic.

The article seems to imply the Sars-Cov-2 wasn't even at the Wuhan lab.

This Livescience article also makes that claim but discusses a scenario at the end that researchers may have unknowingly had sars-cov-2 or a precursor virus in the lab samples and even enhanced it by genetic selection as a byproduct of other work. It ends with an appropriate measure of uncertainty.

https://www.livescience.com/coronavirus-wuhan-lab-complicated-origins.html

But then there is this;

WIV was not immune to those concerns. In 2018, after scientist diplomats from the U.S. embassy in Beijing visited the WIV, they were so concerned by the lack of safety and management at the lab that the diplomats sent two official warnings back to the U.S. One of the official cables, obtained by The Washington Post, suggested that the lab's work on bat coronaviruses with the potential for human transmission could risk causing a new SARS-like pandemic, Post columnist Josh Rogin wrote.
 
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  • #3,072
bob012345 said:
Let's consider the coincidence here.
Said the lottery winner to argue that something else must have played a role.
If you look hard enough you'll always find coincidences somewhere. Omit everything that doesn't fit, add some misinformation that was shared online, brew everything together, and you get a completely wrong conclusion.

Can we get back to containment efforts (the topic of this thread)?

One more case in Iceland on Tuesday, a week after the previous case.
 
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  • #3,073
mfb said:
Said the lottery winner to argue that something else must have played a role.
If you look hard enough you'll always find coincidences somewhere. Omit everything that doesn't fit, add some misinformation that was shared online, brew everything together, and you get a completely wrong conclusion.

Can we get back to containment efforts (the topic of this thread)?

One more case in Iceland on Tuesday, a week after the previous case.
Perhaps I should have started a new thread but I wasn't sure if there would be enough interest.

Here's my take on containment. Stop federal funding of dangerous experiments that could possibly lead to catastrophic pandemics and ban outright all gain-of-function experiments. Take a flamethrower to the bat caves and wet markets where this virus came from.
 
  • #3,074
bob012345 said:
Speaking of SARSr-CoVs,;

"We will use S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments and analysis of receptor binding to test the hypothesis that % divergence thresholds in S protein sequences predict spillover potential."

The experiments proposed in this grant would likely not pose the risk of releasing a new pandemic strain of coronavirus. Speaking as someone who has worked in labs that study RNA viruses, there are ways to perform these studies in a safe manner. To study how mutations in the spike protein affect cell entry, scientists create something called a pseudotyped virus. This is essentially taking the spike protein from the coronaviruses that you'd like to study, and putting it on the outside of what is essentially a harmless virus shell. Typically, researchers use lentiviral vectors, which are derived from HIV. These viruses have been extensively modified to prevent them from being able to reproduce, so once the virus enters the cell, it cannot make new copies of itself (see the Addgene link above for more details). This technology is routinely used in many biomedical research labs to introduce foreign genes into cells. These types of experiments using pseudotyped viruses have been done with SARS-CoV-2 spike protein in many published studies (for example, studying which antibodies are able to bind the SARS-CoV-2 spike protein to prevent viral entry). So, this one sentence does not necessarily mean that the researchers were engaged in dangerous gain of function experiments.

Newsweek, however, does report that gain of function studies on bat coronaviruses did occur at the Wuhan Institute of Virology. They write:
The Institute began a program of gain-of-function research into bat coronaviruses in 2015. That involved taking selected strains and seeking to increase the ability of those viruses to transmit from one person to another. The gain-of-function research went hand-in-hand with the surveillance project. As scientists identified new classes of bat viruses that have the ability to infect human cells, that raised the question of what changes would have to arise in nature to make that virus transmissible in humans, which would pose a pandemic threat.

In 2015, the Wuhan lab performed a gain of function experiment using cut-and-paste genetic engineering, in which scientists take a natural virus and directly make substitutions in its RNA coding to make it more transmissible. They took a piece of the original SARS virus and inserted a snippet from a SARS-like bat coronavirus, resulting in a virus that is capable of infecting human cells. A natural virus altered with these methods would be easily flagged in a genetic analysis, like a contemporary addition to an old Victorian house.

The article seems to be referring to this 2015 publication in Nature Medicine. As the Newsweek article notes, genetic analysis of the viral RNA would easily spot a virus generated through such gain of function studies, and the SARS-CoV-2 RNA sequence does not show signs of being manipulated in these ways.

The Newsweek article discusses the possibility that the virus could have evolved through passaging of the virus in laboratory conditions, which could adapt a bat virus to be more transmissible in human cells. Again, genetic analysis of the viral RNA has identified various genetic features of the virus that enable its transmissibility in humans. One feature are a set of mutations in the receptor binding domain of the spike protein that help the spike protein bind to the human ACE2 receptor more strongly. These mutations are similar to mutations found in a Pangolin coronavirus, so these mutations were likely introduced naturally into the progenitor bat Coronavirus through recombination. The other feature is a polybasic furin cleavage site within the spike protein, which is not found in other related coronaviruses. It is certainly possible for such sites to evolve naturally, as many other viruses have evolved furin sites in their extracellular proteins (including the MERS coronavirus), though the exact origins of the SARS-CoV-2 furin site remains unknown. While evolution of furin cleavage sites has been observed in laboratory passage of influenza virus, the SARS-CoV-2 sequence has other features (such as the introduction of a glycosylation site) that would not be expected to be selected for during passage in cultured cells, which would disfavor the laboratory passage hypothesis over a natural origin.

While the exact origins of the virus aren't known (and may never be known), most of the existing evidence supports a natural origin over an accidental release hypothesis. Indeed, we know of many new viruses that have jumped from animals to humans (e.g. HIV, ebola, swine flu, avian flu, Zika virus), including two new coronaviruses that have emerged within the past two decades (the original SARS and MERS). Ultimately, extraordinary claims require extraordinary evidence. While we can't disprove the hypothesis that the virus escaped from a lab, I have not seen any compelling evidence to favor the laboratory escape hypothesis over a natural, zoonotic origin of the virus.
 
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  • #3,075
Ygggdrasil said:
The experiments proposed in this grant would likely not pose the risk of releasing a new pandemic strain of coronavirus. Speaking as someone who has worked in labs that study RNA viruses, there are ways to perform these studies in a safe manner. To study how mutations in the spike protein affect cell entry, scientists create something called a pseudotyped virus. This is essentially taking the spike protein from the coronaviruses that you'd like to study, and putting it on the outside of what is essentially a harmless virus shell. Typically, researchers use lentiviral vectors, which are derived from HIV. These viruses have been extensively modified to prevent them from being able to reproduce, so once the virus enters the cell, it cannot make new copies of itself (see the Addgene link above for more details). This technology is routinely used in many biomedical research labs to introduce foreign genes into cells. These types of experiments using pseudotyped viruses have been done with SARS-CoV-2 spike protein in many published studies (for example, studying which antibodies are able to bind the SARS-CoV-2 spike protein to prevent viral entry). So, this one sentence does not necessarily mean that the researchers were engaged in dangerous gain of function experiments.

Newsweek, however, does report that gain of function studies on bat coronaviruses did occur at the Wuhan Institute of Virology. They write:The article seems to be referring to this 2015 publication in Nature Medicine. As the Newsweek article notes, genetic analysis of the viral RNA would easily spot a virus generated through such gain of function studies, and the SARS-CoV-2 RNA sequence does not show signs of being manipulated in these ways.

The Newsweek article discusses the possibility that the virus could have evolved through passaging of the virus in laboratory conditions, which could adapt a bat virus to be more transmissible in human cells. Again, genetic analysis of the viral RNA has identified various genetic features of the virus that enable its transmissibility in humans. One feature are a set of mutations in the receptor binding domain of the spike protein that help the spike protein bind to the human ACE2 receptor more strongly. These mutations are similar to mutations found in a Pangolin coronavirus, so these mutations were likely introduced naturally into the progenitor bat Coronavirus through recombination. The other feature is a polybasic furin cleavage site within the spike protein, which is not found in other related coronaviruses. It is certainly possible for such sites to evolve naturally, as many other viruses have evolved furin sites in their extracellular proteins (including the MERS coronavirus), though the exact origins of the SARS-CoV-2 furin site remains unknown. While evolution of furin cleavage sites has been observed in laboratory passage of influenza virus, the SARS-CoV-2 sequence has other features (such as the introduction of a glycosylation site) that would not be expected to be selected for during passage in cultured cells, which would disfavor the laboratory passage hypothesis over a natural origin.

While the exact origins of the virus aren't known (and may never be known), most of the existing evidence supports a natural origin over an accidental release hypothesis. Indeed, we know of many new viruses that have jumped from animals to humans (e.g. HIV, ebola, swine flu, avian flu, Zika virus), including two new coronaviruses that have emerged within the past two decades (the original SARS and MERS). Ultimately, extraordinary claims require extraordinary evidence. While we can't disprove the hypothesis that the virus escaped from a lab, I have not seen any compelling evidence to favor the laboratory escape hypothesis over a natural, zoonotic origin of the virus.
The only exception I take is the implication that a laboratory accident and a natural zoonotic origin are necessarily independent.

Is the glycosylation site also evidence against origins that include in-vivo serial passage or knowledge gained through such experiments?

If sars-cov-2 is unlikely to have arisen through gain of function research, would that be evidence that gain of function research on bat coronaviruses is fruitless?
 
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  • #3,076
I just heard about this brand new paper which is bang on topic:

Haushofer, Metcalf, "Which interventions work best in a pandemic?" (Science, 21 May 2020)
http://science.sciencemag.org/content/early/2020/05/20/science.abb6144
A PDF is here.

Abstract:

The only approaches currently available to reduce transmission of the novel Coronavirus severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) are behavioral: handwashing, cough and sneeze etiquette, and above all, social distancing. Policy-makers have a variety of tools to enable these “nonpharmaceutical interventions” (NPIs), ranging from simple encouragement and recommendations to full-on regulation and sanctions. However, these interventions are often used without rigorous empirical evidence: They make sense in theory, and mathematical models can be used to predict their likely impact (1, 2), but with different policies being tried in different places—often in complicated combinations and without systematic, built-in evaluation—we cannot confidently attribute any given reduction in transmission to a specific policy.

Because many of these interventions differ from each other in terms of their economic and psychological cost—ranging from very inexpensive, in the case of interventions based on behavioral economics and psychology, to extremely costly, in the case of school and business closures—it is crucial to identify the interventions that most reduce transmission at the lowest economic and psychological cost. Randomized controlled trials (RCTs) are one of several methods that can be used for this purpose but surprisingly have received little attention in the current pandemic, despite a long history in epidemiology and social science. We describe how RCTs for NPIs can be practically and ethically implemented in a pandemic, how compartmental models from infectious disease epidemiology can be used to minimize measurement requirements, and how to control for spillover effects and harness their benefits.
 
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  • #3,077
I was kind of hoping they'd answer that question rather than pose it.
 
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  • #3,078
Ygggdrasil said:
The experiments proposed in this grant would likely not pose the risk of releasing a new pandemic strain of coronavirus. Speaking as someone who has worked in labs that study RNA viruses, there are ways to perform these studies in a safe manner. To study how mutations in the spike protein affect cell entry, scientists create something called a pseudotyped virus. This is essentially taking the spike protein from the coronaviruses that you'd like to study, and putting it on the outside of what is essentially a harmless virus shell. Typically, researchers use lentiviral vectors, which are derived from HIV. These viruses have been extensively modified to prevent them from being able to reproduce, so once the virus enters the cell, it cannot make new copies of itself (see the Addgene link above for more details). This technology is routinely used in many biomedical research labs to introduce foreign genes into cells. These types of experiments using pseudotyped viruses have been done with SARS-CoV-2 spike protein in many published studies (for example, studying which antibodies are able to bind the SARS-CoV-2 spike protein to prevent viral entry). So, this one sentence does not necessarily mean that the researchers were engaged in dangerous gain of function experiments.

Newsweek, however, does report that gain of function studies on bat coronaviruses did occur at the Wuhan Institute of Virology. They write:The article seems to be referring to this 2015 publication in Nature Medicine. As the Newsweek article notes, genetic analysis of the viral RNA would easily spot a virus generated through such gain of function studies, and the SARS-CoV-2 RNA sequence does not show signs of being manipulated in these ways.

The Newsweek article discusses the possibility that the virus could have evolved through passaging of the virus in laboratory conditions, which could adapt a bat virus to be more transmissible in human cells. Again, genetic analysis of the viral RNA has identified various genetic features of the virus that enable its transmissibility in humans. One feature are a set of mutations in the receptor binding domain of the spike protein that help the spike protein bind to the human ACE2 receptor more strongly. These mutations are similar to mutations found in a Pangolin coronavirus, so these mutations were likely introduced naturally into the progenitor bat Coronavirus through recombination. The other feature is a polybasic furin cleavage site within the spike protein, which is not found in other related coronaviruses. It is certainly possible for such sites to evolve naturally, as many other viruses have evolved furin sites in their extracellular proteins (including the MERS coronavirus), though the exact origins of the SARS-CoV-2 furin site remains unknown. While evolution of furin cleavage sites has been observed in laboratory passage of influenza virus, the SARS-CoV-2 sequence has other features (such as the introduction of a glycosylation site) that would not be expected to be selected for during passage in cultured cells, which would disfavor the laboratory passage hypothesis over a natural origin.

While the exact origins of the virus aren't known (and may never be known), most of the existing evidence supports a natural origin over an accidental release hypothesis. Indeed, we know of many new viruses that have jumped from animals to humans (e.g. HIV, ebola, swine flu, avian flu, Zika virus), including two new coronaviruses that have emerged within the past two decades (the original SARS and MERS). Ultimately, extraordinary claims require extraordinary evidence. While we can't disprove the hypothesis that the virus escaped from a lab, I have not seen any compelling evidence to favor the laboratory escape hypothesis over a natural, zoonotic origin of the virus.
Thanks for the informative answer. If it were just me maybe you would have a case but if it's so 'safe' why were the experts like Fauci and others agonizing over whether to do it or not?

"Ultimately, extraordinary claims require extraordinary evidence. "

I strongly disagree. Escaping from a lab known to have safety issues and known to have done dangerous experiments with deadly viruses is definitely NOT the extraordinary claim here! Asserting near total confidence in a unknown natural pathway in spite of all the issues with WVI and gain-of-function research and the Chinese authorities, THAT is the extraordinary claim.

"genetic analysis of the viral RNA would easily spot a virus generated through such gain of function studies,"

There are assumptions in that. Newsweek pointed out there are possible ways it can be modified without being so obvious or even know by the researchers doing it.

"most of the existing evidence supports a natural origin over an accidental release hypothesis."

Accidental release doesn't have to mean it was modified in any way.

Whenever people are involved, bad things can easily happen regardless of safety protocols. Also, I understand there is a very strong motive to "defend science" and if the accident hypothesis turns out be true, that will set back the field immensely. So, I'm going to be skeptical of the rush to clear WVI and gain-of-function research.
 
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This was on CBC "The Current" today:
MG: Let's talk briefly about timelines. You've been involved with vaccines for decades. How long on average does it take to get one to market?

ROB VAN EXAN: Normal timeline is about 15 years. The range is anywhere from 10 to 30. And I would also point out that there's many diseases for which we've been trying to develop a vaccine for many decades and have been unsuccessful.

MG: When you hear politicians and some manufacturers say we're looking at 12 to 18 months, what goes through your mind?

ROB VAN EXAN: I'm highly sceptical of it for a number of reasons. It's, I mean, there's two things in our favour is that there are a lot of vaccines for this disease in the pipeline. One hundred and some. But you also have to realize that out of all of those vaccines, there's only really eight different platforms or eight different technologies. And all of those vaccines are being developed, pretty much all of them using a single antigen for the COVID-19 virus. The spike protein antigen. And so that the this sort of minimizes all of the benefit of that. The normal probability of a vaccine being successful is about 10 percent. So with all these vaccines, yes, we will get something. But how quickly is a question? The first number might fail. Part of this is due to the fact that we know next to nothing about this virus, it's new.

MG: The other part of it is about the scale and how many we would need. I was reading something last night suggesting that just about everybody on the planet is in some way susceptible to this. So you would need, at the very least, what? Eight billion doses maybe people need a couple of different shots. You need sixteen million doses. How long does something like that take to manufacture?

ROB VAN EXAN: Well, I'm looking I'm looking at the manufacturers themselves and saying, what is your manufacturing capacity? The highest I've seen is about a billion doses a year. So you would be looking I mean, if it's a one dose vaccine and there's only one of them, it's eight years till everybody gets a shot.
 
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Keith_McClary said:
This was on CBC "The Current" today:
I believe it's possible to make 1 billion doses a month globally if they wanted to. They just have to engineer the process and ramp it up to a capacity many times normal. As a simple comparison, 77% of U.S. adults take vitamins so that's on the order of 150 million doses a day. So 8 billion doses is about 50 days production. Of course a vaccine is likely more complicated but maybe it won't be.

I'm old enough to remember getting the polio vaccine as a child. Long lines at the public High School. The vaccine was given in a sugar cube.
 
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ROB VAN EXAN: Well, I'm looking I'm looking at the manufacturers themselves and saying, what is your manufacturing capacity? The highest I've seen is about a billion doses a year. So you would be looking I mean, if it's a one dose vaccine and there's only one of them, it's eight years till everybody gets a shot.
That's a single manufacturer? Now add all up and add something because other companies will join in. We see this with protective equipment and similar things already. Various producers of alcoholic beverages are now producing hand sanitizer, for example.
Even a billion vaccines would help already, however. Let them be 50% effective, that's pretty bad for a virus that doesn't mutate much. That's enough to vaccinate all healthcare workers and some more, 50% of the healthcare workers and 6% overall can't get the virus any more. It gets much easier to control the spread that way.
 
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kadiot said:
What is the medical definition of "Second Wave"?

From Medicinenet:
Second wave: A phenomenon of infections that can develop during a pandemic. The disease infects one group of people first. Infections appear to decrease. And then, infections increase in a different part of the population, resulting in a second wave of infections.

Thanks
Bill
 
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mfb said:
That's a single manufacturer?

Bill Gates has already announced he will start large-scale manufacturing of the 7 most promising, even before testing is complete. Once the best one or two vaccines emerges he will greatly upscale their production with multiple manufacturing plants. He, and his partner in this endeavour, Warren Buffet, have pledged much of their fortunes to eradicate this virus. Add in what individual countries will do and I think we will be in good shape once we get one, which looks more promising each day. Surprising aside - Bill Gates turned down being Trump's Science Advisor, but is Warren Buffet's Science Advisor. Make of it what you will.

Thanks
Bill
 
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bhobba said:
From Medicinenet:
Second wave: A phenomenon of infections that can develop during a pandemic. The disease infects one group of people first. Infections appear to decrease. And then, infections increase in a different part of the population, resulting in a second wave of infections.

Thanks
Bill
Thank you for the definition. I asked the question because the Philippine officials clash on where Philippines is in pandemic. The Secretary of Health claimed on Tuesday, May 19, the Philippines was on a "second wave" of Coronavirus surge and trying to prevent a 3rd. Until that time, most Filipinos thought the country was battling one wave and was preparing for a possible second wave. It seems other top government officials thought the same and were not on the same page as Secretary of Health.
 
  • #3,086
kadiot said:
The Secretary of Health claimed on Tuesday, May 19, the Philippines was on a "second wave" of Coronavirus surge and trying to prevent a 3rd. Until that time, most Filipinos thought the country was battling one wave and was preparing for a possible second wave.

However, what difference is that supposed to make in practice?
 
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Astronuc said:
https://www.latimes.com/world-nation/story/2020-03-29/coronavirus-choir-outbreak
LA Times, March 29, 2020 - In Skagit County, Washington, 60 people went to choir practice on March 10. Members were offered hand sanitizer at the door, and people refrained from handshakes and hugs (but not known if this was 100%). The practice lasted 2.5 hours.

First illnesses appear three days later on March 13. Three of four of two couples began to show symptoms of infection; the fourth first felt ill two days later. In the following days, more choir members became ill, as did some of their contacts.

Three weeks later, 45 choir members have tested positive for COVID-19 or are ill with symptoms (implies some not tested yet?), three are hospitalized and two are dead. According to the LA Times, eight people present at the choir practice maintain that no one was coughing or sneezing, which would imply 'respiratory droplets'. However, it appears that normal singing, or perhaps normal chorale singing with 'voice projection' is enough to release the virus.

This event indicates that the virus is highly transmissible through the air, and it does not require an infected person to be sneezing or coughing.

Edit - this story had me thinking about the attorney in New Rochelle, NY, who commuted from New Rochelle to New York City where he passed through Grand Central Station on the way to his office near GCS. I've done that many times myself for meetings in NY City, and people walk briskly from the train through the station and out to parts of the city, and some head to the subways for further parts. Breathing heavily would push out the virus to those one is passing, who are also rushing and breathing deeply. Many people who are infected apparently don't know they are. This also points to the importance of wearing a mask (preferably N95) in public to avoid expressing the virus and to mitigate inhaling the virus.

Edit/update - On March 26, Mike Baker (NY Times) reported about the Skagit Valley Chorale. Ruth Backlund, a co-president at the Skagit Valley Chorale, said “Nobody was sick. Nobody touched anybody. Nobody shook hands. Nobody hugged everybody like you might do in a group. There was none of that.”
The story would seem to confirm airborne transmission without coughing or sneezing, and whoever brought the infection along did not realize they were infected.
https://www.nytimes.com/live/2020/c...0-people-show-up-for-practice-now-45-are-sick

A report is now available - a symptomatic person attended, and social distancing was not practised. Singing may have augmented transmission. https://www.cdc.gov/mmwr/volumes/69/wr/mm6919e6.htm
 
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Dr.AbeNikIanEdL said:
However, what difference is that supposed to make in practice?
Whether it is the first or second wave doesn't make a difference other than budget justification, I surmise. Unless we get a vaccine, there will almost certainly be another wave, and several more after that. The wave we have to worry about is the next one.
 
  • #3,089
Wittgenstein famously wrote that many of philosophies woes were self-made. Carelessness with language and inattention to its hidden pitfalls were to blame. He recommended his philosophical analysis of language as therapeutic -- getting the fly out of the bottle into which it had flown.

That is the trouble with this wave thing, and whole babel of contending voices it has stirred. We used a metaphor -- and now quarrel over it. How many waves? How does one count waves? In physics, it is not difficult. But when used metaphorically in connection with a pandemic, how do you count waves?

So, let's leave that troublesome metaphor behind and get into the more serious business of asking what the chances are that contaminated persons are not known to health authorities concerned, and that they may have infected others as well. And where it seems that we have held it at bay, let us not hesitate to sound the "all clear" so that lives can return to normal instead of foisting on the public a "new normal" -- which is once more carelessness with language, because it wants us to treat the abnormal as normal.
 
  • #3,090
Brazil becomes the new epeicenter of COVID-19 pandemic as it surpasses Italy, Spain, the United Kingdom, and Germany in number of confirmed cases. Reports say that Brazilian hospitals can reach their breaking points or the inability to admit more patients by end of May, as mass graves fill even in remote Amazonian settelements.
 
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atyy said:
A report is now available - a symptomatic person attended, and social distancing was not practised. Singing may have augmented transmission. https://www.cdc.gov/mmwr/volumes/69/wr/mm6919e6.htm
At the time, some folks who were interviewed mentioned that they were not making contact, but clearly, there was close proximity, and not the social/physical distancing of at least 6 feet (2 m). Those recommendations were being made in Seattle and King County (and may be Snohomish County), but not in the other counties at the time as I recall. My employer implemented social distancing during late February, and we started doing meetings remotely, using hand sanitizer (that actually stated in January) more aggressively, canceled travel and visits from outsiders, but did not implement masks before the stay-at-home orders were issued statewide. Custodians were cleaning heavily trafficked and contacted areas several times a day.

https://www.fredhutch.org/en/news/c...social-distancing--in-seattle-and-beyond.html
https://www.washingtonpost.com/nati...13b3c0-7689-11ea-85cb-8670579b863d_story.html

In May -

A person who was Covid-19 positive attended a church service and exposed 180 people, officials say
https://www.cnn.com/2020/05/17/us/covid-19-mothers-day-church-exposure/index.html

Disagreements over whether religious groups should be allowed to meet amid the pandemic have led to several legal showdowns between religious leaders and public officials, who have expressed concerns that religious services could exacerbate the issue.

In one case in Sacramento County last month, 71 people connected to a single church were later infected with the coronavirus.
 
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  • #3,092
kadiot said:
Thank you for the definition. I asked the question because the Philippine officials clash on where Philippines is in pandemic. The Secretary of Health claimed on Tuesday, May 19, the Philippines was on a "second wave" of Coronavirus surge and trying to prevent a 3rd. Until that time, most Filipinos thought the country was battling one wave and was preparing for a possible second wave. It seems other top government officials thought the same and were not on the same page as Secretary of Health.
Looking at the daily case count data, it doesn't appear to me that the Philippines has had readily identifiable "waves", as a clear peak and clear drop-off in cases is hard to identify. If we speculate that testing limitations artificially decreased the early case counts and caused the data to be chaotic, then perhaps that's a real peak around March 31. But since about a week later, the daily new case rate has more or less been flat at around half that peak.

...But given that it is a nation of islands, it may just be that it simply defies analysis as a single entity and the islands have to be analyzed individually to see their respective peaks and downward trajectories.

https://www.worldometers.info/coronavirus/country/philippines/

Dr.AbeNikIanEdL said:
However, what difference is that supposed to make in practice?
In practice it affects the mitigation policy. If you implement social distancing restrictions and the cases drop, then you lift the restrictions and the cases rise again, that can imply the social distancing restrictions should be put back on.
 
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russ_watters said:
Looking at the daily case count data, it doesn't appear to me that the Philippines has had readily identifiable "waves", as a clear peak and clear drop-off in cases is hard to identify. If we speculate that testing limitations artificially decreased the early case counts and caused the data to be chaotic, then perhaps that's a real peak around March 31. But since about a week later, the daily new case rate has more or less been flat at around half that peak.

...But given that it is a nation of islands, it may just be that it simply defies analysis as a single entity and the islands have to be analyzed individually to see their respective peaks and downward trajectories.

https://www.worldometers.info/coronavirus/country/philippines/In practice it affects the mitigation policy. If you implement social distancing restrictions and the cases drop, then you lift the restrictions and the cases rise again, that can imply the social distancing restrictions should be put back on.
I've heard from an interview with a physician talking to his colleague that its pretty informal. According to him each tiny blip from zero has the capacity to go exponential. So if you squash it with containment, it can still be considered a wave, but a tiny one with epidemic potential. Just to confuse things further since they are both in the medical field, there are 2 definitions of epidemic outbreak: 1. An unusual increase in number of cases of a disease in a short amount of time and 2. Exponential growth. Using case definition #1, even 1 case in a place without any known cases is an outbreak. It is a great academic discussion, but for me and the general public we think they are just splitting hairs.
 
  • #3,094
bhobba said:
Bill Gates has already announced he will start large-scale manufacturing of the 7 most promising, even before testing is complete. Once the best one or two vaccines emerges he will greatly upscale their production with multiple manufacturing plants. He, and his partner in this endeavour, Warren Buffet, have pledged much of their fortunes to eradicate this virus. Add in what individual countries will do and I think we will be in good shape once we get one, which looks more promising each day. Surprising aside - Bill Gates turned down being Trump's Science Advisor, but is Warren Buffet's Science Advisor. Make of it what you will.

Thanks
Bill
After all the shenanigans Gates has done to the public through MicroSoft over the years, that's the very least he could do.
 
  • #3,095
Astronuc said:
At the time, some folks who were interviewed mentioned that they were not making contact, but clearly, there was close proximity, and not the social/physical distancing of at least 6 feet (2 m). Those recommendations were being made in Seattle and King County (and may be Snohomish County), but not in the other counties at the time as I recall. My employer implemented social distancing during late February, and we started doing meetings remotely, using hand sanitizer (that actually stated in January) more aggressively, canceled travel and visits from outsiders, but did not implement masks before the stay-at-home orders were issued statewide. Custodians were cleaning heavily trafficked and contacted areas several times a day.

https://www.fredhutch.org/en/news/c...social-distancing--in-seattle-and-beyond.html
https://www.washingtonpost.com/nati...13b3c0-7689-11ea-85cb-8670579b863d_story.html

In May -

A person who was Covid-19 positive attended a church service and exposed 180 people, officials say
https://www.cnn.com/2020/05/17/us/covid-19-mothers-day-church-exposure/index.html
No doubt some overzealous public officials will attempt to use this crisis to declare church services just to dangerous and should be banned for the foreseeable future...which could be years. But we have a Constitution and the Bill of Rights which thankfully doesn't have a pandemic exclusion clause. If you ban church services you basically have to ban all gatherings since you can't single out religion for special rules.

My church voluntarily remains closed through July as far as in person services go. A few very low key and limited events may be allowed on campus with strict guidelines. In June they will allow small groups to gather in homes for those who feel comfortable but again with guidelines.
 
  • #3,096
kadiot said:
I've heard from an interview with a physician talking to his colleague that its pretty informal. According to him each tiny blip from zero has the capacity to go exponential. So if you squash it with containment, it can still be considered a wave, but a tiny one with epidemic potential.
This is why it would be good to be able to track all the contacts involved and to then effectively test all those potentially infected people to determine if they are in fact infected. Otherwise returning to restrictive social distancing procedures are the best alternative.
 
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bob012345 said:
No doubt some overzealous public officials will attempt to use this crisis to declare church services just to dangerous and should be banned for the foreseeable future...which could be years. But we have a Constitution and the Bill of Rights which thankfully doesn't have a pandemic exclusion clause. If you ban church services you basically have to ban all gatherings since you can't single out religion for special rules.

My church voluntarily remains closed through July as far as in person services go. A few very low key and limited events may be allowed on campus with strict guidelines. In June they will allow small groups to gather in homes for those who feel comfortable but again with guidelines.
Well, in fact, several states phased openings make a huge exception for religious services - while for all other puposes, no gatherings over 10 remains the policy, religious services have no restrictions on gathering size (though they are still supposed to encourage distancing). Since people attending religious services also contact other people, this represents a substantial risk born by others to allow religious services to proceed, while no similar non religious activity is allowed. Thus, instead of being singled out, religious services are hugely privileged in my liberal state.
 
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Any ideas why Japan is doing so well - they have an aged population too:
https://www.bloomberg.com/news/arti...rders-churches-open-virus-update?srnd=premium
Japan’s Success in Managing Outbreak Puzzles Experts (7:20 a.m. HK)
Japan’s state of emergency is nearing its end with new cases of the Coronavirus dwindling to mere dozens. It got there despite largely ignoring the default playbook.

No restrictions were placed on residents’ movements, and businesses from restaurants to hairdressers stayed open. And even as nations were exhorted to “test, test, test,” Japan has tested just 0.2% of its population -- one of the lowest rates among developed countries. Yet the curve has been flattened, with deaths well below 1,000, by far the fewest among the G7 nations. While the possibility of a more severe second wave is ever-present, Japan is set to leave its emergency in just weeks, and likely to exit completely as early as Monday.
 
  • #3,099
Sushi and fish are popular in Japan. They contain lots of vitamin D, which some have speculated could reduce fatalities (not proven yet).
 
  • #3,100
PAllen said:
Well, in fact, several states phased openings make a huge exception for religious services - while for all other puposes, no gatherings over 10 remains the policy, religious services have no restrictions on gathering size (though they are still supposed to encourage distancing). Since people attending religious services also contact other people, this represents a substantial risk born by others to allow religious services to proceed, while no similar non religious activity is allowed. Thus, instead of being singled out, religious services are hugely privileged in my liberal state.
I want to add that despite the above, I am not very worried because almost all churches and temples will voluntarily do the right thing and continue virtual services. The fact is that churches and temples were at the leading edge of safe practices, always one or two steps ahead official policy. The small minority who fully take advantage of their special privilege to congregate are no different than the minority of individuals who ignore safe practices.
 
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