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Coronavirus: How dangerous a threat?

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There is an informative article in the April 6, New Yorker by Elizabeth Kolbert titled "The Spread" summarizing the historical impacts of pandemics. It is enlightening from a social and political standpoint as we are facing conditions that are similar, yet uniquely challenging.
"Opening" the US, or any other economy is going to be an act of interdependence. Rushing to get employees working on a production line when suppliers in other parts of the world are not active is a huge challenge. That also carries the aforementioned social and political characteristics as different groups seek to gain some advantage. I fear that the rush to be the first at something in this case may simply mean you win the race to the next, more extreme round of the pandemic. I've yet to see any cost projections on a premature reopening of businesses that then need to go through the cost of another shut down. Likely nobody wants to admit that sort of miscue would be potentially fatal to the business.
Anyone willing to barter their health or the well being of others to "get working" without precautions may lose both future work stability and health.
 
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Beat me to it. Here's more of a breakdown

New York governor Andrew Cuomo announced that a study of antibody tests from across the state indicates the coronavirus death rate may be lower than some estimates.
Cuomo said that 3,000 antibody tests conducted across New York indicate 13.9% of state residents are positive for antibodies.
But those figures vary dramatically by region. While 21.2% of New York City residents tested positive, only 3.6% of residents from upstate New York have the antibodies.
Cuomo said a 13.9% infection rate would translate to 2.7 million people infected statewide. Considering the more than 15,000 deaths recorded by the state, New York’s coronavirus death rate is approximately 0.5%, which is lower than some estimates had predicted.
But Cuomo acknowledged that statistic could change as the state starts to account for more coronavirus deaths that took place at home, which have so far largely not been included in the official death toll.
 
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That makes more sense. I thought the state numbers represented upstate alone and looked too high. 3.6% for that subset is plausible. I wonder if it is worse in Madrid. I think we are about to enter phase II in this outbreak soon in the hardest hit places where there will start to be evolutionary pressure for mutant viruses to arise to beat the pockets of herd immunity developing. So far, there is not much evidence to show that COVID19 is mutating because there has been no selective pressure. The small differences in sequences seen so far are not expected to functionally change the virus, but provide good tools to map its spread.

Should probably note that this is not really a random sample as my post implied.
 
I wonder to extent that given all the complicating conditions in NYC in terms of a significant number of deaths and hospitalizations: elderly, negatives and comorbidities of structural poverty and enforced working conditions, substandard health/care institutions, delayed time to quarantine etc, no/negligible testing and tracking, if the virus can mutate sufficiently to keep posing a significant threat once identified and contained. That is, a major population threat beyond the overlapping target predispositions.
 
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Unclear what kind of uncertainty this number has, but it does tell us what ballpark we are in. Still a lot of susceptibility in the population even at the hottest hot spot. View: https://twitter.com/brianmrosenthal/status/1253351733163692034
In Ortisei in the Val Gardena they tested over 9% of the inhabitants, (so over 450 people) and 49% of them tested POSITIVE for coronavirus antibodies. In the Alpes the areas with the big ski stations are the biggest hotspots, besides the larger towns.
Source: https://www.dolomitenstadt.at/2020/04/20/in-st-ulrich-im-groedental-bereits-50-prozent-immun/
 
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In Ortisei in the Val Gardena they tested over 9% of the inhabitants, (so over 450 people) and 49% of them tested POSITIVE for coronavirus antibodies. In the Alpes the areas with the big ski stations are the biggest hotspots, besides the larger towns.
Source: https://www.dolomitenstadt.at/2020/04/20/in-st-ulrich-im-groedental-bereits-50-prozent-immun/
Thanks. I stand corrected. One cruise ship that was touring the Antarctic ended up with nearly 60% of the ship infected. I would say that is the minimum we should expect for herd immunity with this virus.

I wonder to extent that given all the complicating conditions in NYC in terms of a significant number of deaths and hospitalizations: elderly, negatives and comorbidities of structural poverty and enforced working conditions, substandard health/care institutions, delayed time to quarantine etc, no/negligible testing and tracking, if the virus can mutate sufficiently to keep posing a significant threat once identified and contained. That is, a major population threat beyond the overlapping target predispositions.
That is a big question. It is unclear what changes to the spike protein will allow the virus to evade the neutralizing antibodies while maintaining pathogenicity. Then again, we don't even know how durable the immunity will be.
 
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I wonder to extent that given all the complicating conditions in NYC in terms of a significant number of deaths and hospitalizations: elderly, negatives and comorbidities of structural poverty and enforced working conditions, substandard health/care institutions, delayed time to quarantine etc, no/negligible testing and tracking, if the virus can mutate sufficiently to keep posing a significant threat once identified and contained. That is, a major population threat beyond the overlapping target predispositions.
So I'm jumping off a cliff here because I've only recently become a virus expert. :rolleyes: and in so doing I've read so much info in the last 30 days that its all smashed together (maybe I know less now because of overload). The mutation to camouflage itself might be irrelevant if the C19 protein can't 'dock' with the host cell correct? Plus, at least so far, C19 mutations are very slow and minimal. There is also a chance that mutations make the virus weaker. So my 'expert' answer to your question is no.

I read an article about two flu A combining to form a third flue A , and HIV does something similar (antigen shift? Is that correct?). I wonder if C19 might also do something similar. Less mutating and more evolving?

Not to your post, but...The common understanding that flu vaccines last about a year is somewhat misleading because while that could be true for some, for others it might barely get them through the worst of the flu season. It completely depends on individual immune memory. This will be part of the C19 vaccine discussion as well. Will a C19 vaccine protect you for 3, 6, 12 months like the flu, or will it protect you for much longer like the mumps?
 
I read an article about two flu A combining to form a third flue A , and HIV does something similar (antigen shift? Is that correct?). I wonder if C19 might also do something similar. Less mutating and more evolving?
Yes! One huge difference between CoV and Flu is that the latter has a segmented RNA genome. So, if two different flu virus particles infect a cell, the RNA segments can be shuffled so that one resulting virus might have 7 RNA segments from one virus and 1 RNA segment from the other, or any combination (8,0.... 0,8). This is almost certainly what happened in 1918 and other flu pandemics when a human influenza recombined with an animal influenza to create a novel virus that was something nobody had much immunity to. These are the real deadly ones.

CoV encodes its genome on a single RNA segment, so antigenic shift is not likely to be a problem. Antigenic drift can occur and it is more like what happens to seasonal flu on a yearly basis. Small mutations change the docking protein enough to evade the antibodies its predecessors (or vaccines) made in previous years. This gives the slightly altered virus a big competitive advantage. But, since this change is less drastic than antigenic shift, people usually have some immunological memory. This is one reason why 30-60m people get infected with influenza in the USA in a year, but most recover without much drama. Everyone has some degree of immunity to influenza based on repeated past encounters.
 
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Thanks for the replies.

To an extent this is where I was going with that question

"Your immune system functions as a reflection of your overall health. And part of that you can’t change, like your age and maybe some genetic predispositions. But part of it you can change.
Your immune system is also shaped on a more granular level over the years by your lifestyle, by sleeping well and eating well and avoiding stress and exercising. These things all have small impacts on those cytokines and how hypersensitive that immune system is, how efficient it is at targeting what it needs to target and not targeting what it doesn’t.

But not everybody can do those things. This disease is killing people of low socioeconomic status and people in traditionally marginalized racial groups in ways that are not genetic. The disease is killing the same people who are more likely to die of any disease. They’re predictable lines that we draw that shape a person’s overall resilience.
If you get sick, and you are just getting over another cold, you are almost certainly going to have a worse experience than if you were top of your game.

We have very good predictors. It’s not just age and chronic disease. Those read to me now as euphemisms. It effectively ages you to not have stable income, to not be able to sleep at night, to not feel safe at home, to not have reliable access to good food."


And then I'm wondering how this will be factored in the US in terms of moving forward to counter future possible instances not just in terms of exclusion of certain groups, but in factoring the poor health of much of the population in general. What does it do to cellular memory and adaptability for example to have it under constant duress from a multitude of material and or psychological factors.


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Thanks for the replies.

To an extent this is where I was going with that question

"Your immune system functions as a reflection of your overall health. And part of that you can’t change, like your age and maybe some genetic predispositions. But part of it you can change.
Your immune system is also shaped on a more granular level over the years by your lifestyle, by sleeping well and eating well and avoiding stress and exercising. These things all have small impacts on those cytokines and how hypersensitive that immune system is, how efficient it is at targeting what it needs to target and not targeting what it doesn’t.

But not everybody can do those things. This disease is killing people of low socioeconomic status and people in traditionally marginalized racial groups in ways that are not genetic. The disease is killing the same people who are more likely to die of any disease. They’re predictable lines that we draw that shape a person’s overall resilience.
If you get sick, and you are just getting over another cold, you are almost certainly going to have a worse experience than if you were top of your game.

We have very good predictors. It’s not just age and chronic disease. Those read to me now as euphemisms. It effectively ages you to not have stable income, to not be able to sleep at night, to not feel safe at home, to not have reliable access to good food."


And then I'm wondering how this will be factored in the US in terms of moving forward to counter future possible instances not just in terms of exclusion of certain groups, but in factoring the poor health of much of the population in general. What does it do to cellular memory and adaptability for example to have it under constant duress from a multitude of material and or psychological factors.


\\


The thing that was put out by WHO on Remdesivir was only on the stopped trial in China. That trial was stopped early and has very little usable data. Also Gilead had no control over it and said when they got the results back that very little if any of those results were useful. We need to wait for next week until Gilead released the trial results from the US which have shown a lot of hope. I wouldn't put much stock at all into what the WHO put up and pulled down on the China trial.



Then there is this report. Where there is a thought that China is worried Remdesivir is too effective and are trying to sabotage it.



There are tests all over the US and some in Europe. We will wait until next week. The likelihood is that the news from Boston and Chicago are closer to reality than a stopped test in China that was for lack of patients.
 
Why should Gilead have any control over the tests?

The Forbes article is a bit all over the place; which happens when you write at speed to try and reestablish solid ground. I’m not going to touch this one other than to note that WHO has made no more mistakes and dubious calls than any other compromised major global body in this ongoing event.
 
Why should Gilead have any control over the tests?

The Forbes article is a bit all over the place; which happens when you write at speed to try and reestablish solid ground. I’m not going to touch this one other than to note that WHO has made no more mistakes and dubious calls than any other compromised major global body in this ongoing event.


Because all pharmaceuticals have control over their clinical trials to ensure they are run so they get accurate results. (The Forbes article is from last week.)
I would dismiss what the WHO put out as it was incomplete. The two groups that actually saw it have said it was incomplete information. Again it was from a stopped trial, thus by definition it was incomplete data with not much useful data. Until next week's full report comes out I would just ignore what was wrongly released by WHO.

We have reports out of both Boston and Chicago saying Remdesivir helps and antidoteal evidence out of Washington (state) that it is helpful. So it's best to wait for the full report with actual results from full testing instead of a incomplete information that was leaked.
 
While 21.2% of New York City residents tested positive, only 3.6% of residents from upstate New York have the antibodies.

The case rate in upstate NY (everything outside of NYC) is about 1.1%, so this would suggest about 2/3 of the infections are asymptomatic (actually a little more, because some in the sample would be recently positive for the virus, but not yet have developed Abs). This is very much consistent with many other studies, mostly of the virus rather than of antbodies, that have been discussed here, which suggest 50-75%.

But also note that the 3.6% figure should be an absolute maximum that the false positive rate could be--even if there were no true positives at all, which obviously wouldn't be the case--so unless the NYC tests were done differently in some way, it would seem that false positives would not have a major effect on the estimate of what proportion of people have Abs in the city. And the case rate for the city is not that much higher than upstate, about 1.6%.

A statistician argues that lockdowns don’t work.

https://www.thepublicdiscourse.com/2020/04/62572/

He defines lockdowns very precisely, as including three types of policies: compelling people to stay at home except for essential purposes; bans of gatherings of small numbers of people; and closing businesses indiscriminately. He isn’t opposed to many restrictive policies, including quarantining sick or exposed people; closing schools; travel restrictions; and outlawing large assemblies. He believes all of these practices clearly reduce spread of the virus.

Some of his main evidence that lockdowns don’t work comes from examining their effect on deaths. He begins by citing studies indicating that on average, most people die from C19 at least twenty or more days after infection. He then looks at the pattern of deaths following lockdowns in several major countries, and concludes that in most cases the number of new deaths peaked and began to fall before this twenty day period. IOW, he believes other, less restrictive measures, that were put in place before the lockdown, must have been the cause of the fall in number of deaths. He then goes on to provide evidence that these other measures work, even estimating their effectiveness (using county data from all over the U.S.) with a statistical model that determines how many days the measure has to be in practice to save one death per 100,000 people.

A well-thought out analysis. However, I think the conclusion lockdowns don’t work is overdoing it. He might argue at best that they don’t add any additional benefit, but to say that stay at home orders, for example, don’t reduce the spread of the virus, and therefore deaths, doesn’t make sense. How could they not?

In fact, his examples, though showing that peaks in deaths begin before this twenty day period ends, don't follow them long enough to see whether they continue to drop. Perhaps a further effect, due to the lockdowns, would be evident.

Also, I don’t know how one interprets the U.S.—granted, a very heterogenous situation—where the number of deaths has been more or less constant for the past two weeks. (By the way, what happened to that projection of 60,000 deaths in the U.S., I think by early August? We're at about 50,000 now, and appear likely to reach 60,000 by the end of the month).

There’s also the example of Michigan, where a stay-at-home order began March 24. The number of new deaths seemed to peak around April 16, 23 days after the order, suggesting that the order did indeed work by the author’s criterion. But after three days of lower numbers, a new high was reached on April 21, and the succeeding two days saw death totals around what had occurred during the peak. There are other factors, of course, that can affect the number of deaths and the author does take into account some of them in his county-by-county model.

By the way--this supports a point Cannavaro was making earlier--some people are touting some of these Ab tests as proof that the mortality rate is very low, only around 0.1%, no worse than the flu. Don't look now, but Belgium is already more than halfway there, with deaths per million of population at 0.056%. So unless half the population or so of Belgium is already infected, the mortality rate for that country almost certainly is greater than 0.1%.




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Has an accurate antibody test been verified yet?
Roche Pharma was claiming reliability while deriding accuracy of most tests on the market.
The current reality is; unless a government wants it mass produced we'll be inundated with the quickest-fix antibody tests to get workers and citizens free to move about. As I understand it the anti-body levels present in blood plasma has much to do with future resistance to subsequent C19 outbreaks. I haven't heard anyone state definitively that a lower level of antibodies clears all risk of reinfection and transmission. It's that great amount of antisymptomatic population that makes the antibody testing additionally tough to rely on until there is a vaccine as well.
 
San Diego is doing many things including renting,leasing and buying hotels and motels for homeless people..w an emphasis on homeless people who have at risk profiles in advanced age or underlying serious conditions.
For my cross from Mexico to the US..I showed my water and sewer bill..showed bank statement..and when I say showed the officer doing the interview with me just looked at the documents from my hand and did not read them. I asked if showing the same on the way back would satisfy residency requirements..he said no problem.
Many grocery stores in East San Diego look like they are calming down..no big cues of people waiting to enter..probably encouraging.
My mountain bike parking spots are overflowing in Mexico and East San Diego,right outside Alpine Ca.
Listened to a radio story about robust business at area bicycle shops. If parks,beaches and fishing all reopen ,my opinion is that politicians will get a little relief..in the U.S. they keep harping about digital divide..Sweetwater High school district here in San Diego has yet to be able to contact @30% of their students..?
In Baja elementary school classes are broadcast on TV channels and YouTube..most grades have class instruction at 6am and 1pm..for people who don't have the flexibility of You Tube.
I was sitting watching a 7th grader go over questions..some about the United States..it was in Spanish..I tried to act like that was the problem..it wasn't..I didn't know the answers..
 
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The case rate in upstate NY (everything outside of NYC) is about 1.1%, so this would suggest about 2/3 of the infections are asymptomatic (actually a little more, because some in the sample would be recently positive for the virus, but not yet have developed Abs). This is very much consistent with many other studies, mostly of the virus rather than of antbodies, that have been discussed here, which suggest 50-75%.

But also note that the 3.6% figure should be an absolute maximum that the false positive rate could be--even if there were no true positives at all, which obviously wouldn't be the case--so unless the NYC tests were done differently in some way, it would seem that false positives would not have a major effect on the estimate of what proportion of people have Abs in the city. And the case rate for the city is not that much higher than upstate, about 1.6%.

A statistician argues that lockdowns don’t work.

https://www.thepublicdiscourse.com/2020/04/62572/I think the conclusion lockdowns don’t work is overdoing it
Just noticed this whilst I take a break working at home during our lockdown. I wonder how this man would explain Australia's case trend? Our lockdown commenced on March 22. Looking at the daily case trend since then I think the evidence is strong that lockdowns absolutely do work. The restrictions in Australia are very similar to what he mentions.
 
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