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Messages - Sam

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1
Consequences / Re: COVID-19
« on: April 18, 2020, 01:05:20 AM »
And now we have entered that phase of the catastrophe where Grief plays an ever larger role. It mangles the responses. It distorts actions. And chaos ensues if there isn't intelligent compassionate wise leadership. We have none of those at the moment.

The data will become messy. The responses will be messier yet, with people and areas running in opposing directions.
  • Some people remain caught in shock and cannot comprehend or accept that this is real.
  • Some are deep in denial wanting the reality to be what it was and refusing to accept the reality as it is.
  • Some have moved on to anger aimed in a thousand directions.
  • Others have moved past anger to bargaining; trying to find a way back to what was, or to escape the ravages of what is.
  • Some have moved on to resignation, and depression.
  • A few have moved to acceptance.
  • And in limited locations (China, Taiwan, New Zealand, Iceland among them) people have begun to move to Testing; feeling out what the new world is like on the other side of the pandemic.
The next several months will no doubt be rugged. In those countries (the US being a prime example) where a large portion of the population remains in a cocoon of denial, anger, betrayal, shock, and worse, the course will be particularly rocky.

This will delay finally resolving the problems. It will make the outcomes vastly worse.

A part of me grieves for that. Another part wishes them well on their journey into disaster and is fine with them committing suicide in their regions, though wishing they wouldn't take innocents along for the ride. Another rages against their stupidity. No one ever said the school of hard knocks was easy, cheap, or in any way safe.

But those too are aspects of grief. And so for my own benefit and healing it is time for me to bow out. I know what I need to do to protect myself, and to aid my friends and family in protecting themselves. I cannot significantly affect or influence the course of events beyond them. All I can do at this point is cause myself injury by engaging. And as a result - I now disengage to focus on healing my own grief.

Be safe everyone, as best you can. The ride from here is going to get very bumpy. Keep your seat belts fastened and your helmets on. Keep your hands inside the car at all times until the ride has come to a complete stop.

Sam

2
Consequences / Re: COVID-19
« on: April 17, 2020, 09:48:38 AM »
Wuhan Death Toll Rises 50%
https://www.theguardian.com/world/2020/apr/17/china-economy-shrinks-record-wuhan-covid-19-death-toll-rises-50-percent

The Chinese city of Wuhan has raised its number of coronavirus fatalities by 1,290 to 3,869, most of China’s total. That brings the total fatalities in China to at least 4,642. It also revised up its number of confirmed cases by 325 to 50,333, the official Xinhua News Agency said.

Wuhan’s prevention and control taskforce have revised the death toll in Wuhan upwards by 50%, from 2,579 to 3,869. The updated figure comes after weeks of scepticism about the reported death toll, as other countries have seen fatalities reach more than 10,000.

The agency said reasons for the change included adding the number of patients unable to reach hospitals, late, mistaken or double reporting, as well as difficulty linking information reported from private hospitals, temporary hospitals and other medical institutions that handled patients.

https://www.thepaper.cn/newsDetail_forward_7014798

The overall accuracy of China's coronavirus data has been questioned both abroad and by the country’s own citizens.

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

Guatemala: 44 Deportees from US Positive for Coronavirus
https://www.aljazeera.com/news/2020/04/coronavirus-deaths-35000-live-updates-200416234342434.html

US flights deporting migrants from Guatemala have been temporarily suspended after a recent flight carried migrants who tested positive for the coronavirus. Out of the 76 people on the Monday flight, 44 were reported to have tested positive

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

Close to two-thirds of Americans think that President Trump's actions to deal with the threat of coronavirus were too slow, according to a new poll conducted by the Pew Research Center. The survey was conducted between April 7 and April 12, using a sample of 4,917 American adults.

While 65% felt that the initial response was too slow, 52% felt that his comments on the pandemic are aimed at making it look better than it really is. Close to 40% felt that his representation of the crisis is accurate and 8% said that Trump is making the situation seem worse than it is.



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

Protests Erupt Along Mexican Border After Deaths at Honeywell, Lear
https://mobile.reuters.com/article/amp/idUSKBN21Y35X

CIUDAD JUAREZ, Mexico (Reuters) - A spate of suspected coronavirus deaths among workers for U.S. companies operating along the border in Mexico has triggered multiple protests in recent days, highlighting friction over which factories should remain open in the pandemic.

On Thursday, dozens of protesters demanded a Honeywell assembly plant in Ciudad Juarez be closed to prevent the spread of the virus after a colleague died.

The company told Reuters one of the plant's workers died this month after being sent to self-quarantine and receive medical attention.

Car seat maker Lear confirmed "several" of its workers had died in the city this month of respiratory illnesses, while technology company Poly, also known as Plantronics, told Reuters two workers in Tijuana died this week of unknown causes. Protesting workers in Tijuana said the deaths were related to the coronavirus.

Similar protests calling for safe conditions or shutdowns with full pay took place outside factories in border cities Mexicali, Matamoros and Reynosa in recent days after the Mexican government ordered non-essential industries to suspend operations.

"We want them to respect the quarantine," said Mario Cesar Gonzalez outside the Honeywell factory, which he said makes smoke alarms. "The manager said that we are essential workers. I don't think an alarm is essential."

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

Hundreds of garment workers in Bangladesh took to the streets to demand unpaid wages after factories suspended operations over coronavirus-related lockdowns across the world. Protests were staged in parts of Dhaka while workers also blocked a highway outside the Bangladeshi capital.

Many protesters blame international brands like Wal-Mart, H&M and Marks & Spencer for canceling orders worth $3.2 billion, which directly affect the 2.26 million workers in the industry.

Notably, the textile industry accounts for close to 85% of Bangladesh’s $40 billion in annual exports.

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

That makes the CFR for SARS-CoV-2/COVID-19 in China a terrifying 9.22% in line with Italy.

It also means that SARS-CoV-2 is indistinguishable in lethality from SARS-CoV-1, which had a global CFR of 9.6%.

The symptomology of the two viruses is nearly identical. The transmission mode is nearly identical as well, though SARS-2 is more infective than SARS-1.

Early on several virologists and epidemiologists kept repeating the mantra that this isn’t SARS. They were right, though not in the way the meant or intended. This is worse.

We have to hope that a single vaccine will be effective for both of these viruses and their cousins.

The world had its first warning in 2002 with SARS-1. The world then had a terrifying second, third and fourth warning with MERS in 2012, 2014 and 2015 with its even more terrifying 39% CFR.

Then the final warning came in late 2019 when SARS-2 was analyzed. The Chinese paid attention. Not many others did. The US and EU decidedly did not. Worse, politicians leading nations all over the world, most especially in the US showed just how incompetent incompetent can be. They - he - made it all vastly worse.

Society as we have known it must now change in dramatic ways. Yet many among us still want to hope and believe that somehow we can end this quickly. We cannot. Ending this will be difficult, painful and costly.

One of those costs is a world and societies forever changed. We cannot go back any longer. The world is now a different place.

My estimates on ultimate fatality rates are now in line with the data. It just took time for the data to catch up. This is not surprising.

As a terrible added note: With the immense loss of sulfate aerosols and fine particulate, we now get to test the climate models. Based on their projections about magnitudes of impacts, this should be a banner year for melting the Arctic ice. By years end we will have the massive Australian fires, COVID-19, the massive melting of the arctic, the impeachment and multiple failures of Donald Trump, and the world financial collapse into the second Great Depression all competing fir story of the year. 2020 has been one hell of a year.

In all of my years of dealing with emergencies and catastrophes, denial was one of the first things to rise to the fore. In those years I learned several phrases that served me well. I did not like it. It served none the less.  “Wait for it .......!”    .... “there it is.” .... “Ok, now“ ....

That also went hand in hand with a life lesson my father taught me in such events ... when to step behind the proverbial nearest largest solid structural column, hold on to my head, ears & ass, close my eyes, and wait ...  for the remnants of the exploding building to pass by on either side - in the relative safety of the shadow of the column. .... “this is going to leave a mark.”

And the last one... “Are you ok?“ ... “Well, I’m not dead yet.”

Sam

3
Consequences / Re: COVID-19
« on: April 17, 2020, 12:57:38 AM »
We cannot afford not to extend lockdown longer. It is fatal to business as well as to individuals to restart soon. Doing that causes the disease to come back and spread. That then either extends the lockdown (bad), or increases the deaths (worse) AND extends the lockdown (much worse). We must focus on the primary problem - the virus and its spread - not the secondary, tertiary and subsidiary problems. Those are important. But they are ONLY solved if we solve the first problem first.

I personally don't believe there is any type of lockdown that can be enforced that will eradicate the virus. Maybe in a place like China, but not on a global scale. After weeks of lockdown, there is now some talk here and there of herd immunity in the single digit percentages (well below 5%). So, all lockdown does, is buy time.

But when you buy something, there is obviously a cost, and at some point the cost becomes larger than what you're getting. In other words, besides lockdowns most likely not being able to eradicate the virus, they also have a breaking point. They simply cannot last too long, because 1) they may cause more damage than the virus will and 2) cascading effects could cause civilisational collapse.

So far, the desired perception has been based on fear, desired by the media for ratings, and desired by governments to make sure people comply. But if lockdowns don't solve the problem, and you cannot risk those cascading effects to civilisational collapse either, you have to move away from fear.

Because the psychological effect of that fear, is that it breeds insecurity and paralysis,which only increases the risk of cascading effects, whether there are lockdowns or not! For the simple reason that people will not buy the goods and services that make the system work (more or less).

I'm very unhappy with the system, I hate consumerism and want it to stop, I'm as radical as they come in this respect, but I prefer to see a gradual transition, rather than a house of cards going up in flames. Because, just as Gandul, I fear for loved ones.

If it needs to happen, so be it, but rather not because everybody is shitting their pants because of the perfect 'invisible enemy'.

Quote
But failure means ultimately infecting about 90% of the population. And that means killing circa 3-9+% of the population in the first wave. And if this virus only provides two year immunity as it appears to, it means killing something like 2-6% in a second wave, and 1-5% in a third wave etc...  Each wave depletes the society of older and vulnerable people, presumably lessening the impact of each wave. But over a decade, this likely sums to 12-15% of the population dying, unless massive controls are put in place, or successful treatments or vaccines are developed. That then might limit the dying to 4% over the decade.

So far, I didn't want to say too much because it's a delicate subject, and there wasn't enough data to say anything really substantive, but I think enough is known now to state that these numbers aren't realistic. I don't believe this virus can cause civilisational collapse just through the amount of people it will kill. But the fear of this 'invisible enemy' might. I could be wrong.

Neven,

I sincerely hope you are right.

Sam

4
Consequences / Re: COVID-19
« on: April 16, 2020, 11:52:29 PM »
The psychological effect of this disease is much more dangerous than the disease itself.

Neven,

This is a basic and common error. Our society is conditioned to think in terms that put commerce as primary. It isn’t. It is essential. It is not primary.

I think you are missing Nevens point.

Following is my reading but if you read what he wrote on Lessons form Covid-19 it is not about commerce being important. See post 182 there.

I don't think so. In #182 of Lessons Learned Never argues about the concentration of wealth and commerce. I agree with all of that. Where I have difficulty is with two points from the post #5554 in this thread.

A long ride will probably mean civilisational collapse, as fear and insecurity, incessantly pumped up by the media, will prevent people from being the consumers they were conditioned to be. Consumerism is a central pillar of our current global system. It could transition to something more resilient (if the lessons of this crisis are heeded), but it will take years, if not decades. It will collapse if everyone's eyes are glued to statistics (with no context), and fear and panic are used for ratings and to make sure people obey the installed measures.

The angle of the narrative will have to change, something along the lines of: 'Yes, this is a terrible new disease, but there are many of those. People are dying, but they are mostly very old and have comorbidities. And besides, 150 thousand people die every day. Death is a part of life. It's true that people die before their time, but on average perhaps a few months, not years, and certainly not 10 years. The only thing that really matters in all this, is that we prevent a collapse of our health care systems, and so we need to do as much as we can, but we must not be afraid, because we cannot afford to be in lockdown much longer.'

The psychological effect of this disease is much more dangerous than the disease itself.

My discussion and post go to the two comments in bold above.

Point 1. ..."we cannot afford lockdown much longer."

We cannot afford not to extend lockdown longer. It is fatal to business as well as to individuals to restart soon. Doing that causes the disease to come back and spread. That then either extends the lockdown (bad), or increases the deaths (worse) AND extends the lockdown (much worse). We must focus on the primary problem - the virus and its spread - not the secondary, tertiary and subsidiary problems. Those are important. But they are ONLY solved if we solve the first problem first.

I agree that we must make the time in lockdown as short as we can. I am firmly of the belief this has to be by making it more effective and enforced, not by lifting it. That ultimately only extends it.

Addenda: In the US the Congress did a bare minimum job of trying to help small businesses and workers. That is more notable in its failing than its success. Government/societal support for workers and small businesses is vital to their welfare and survival. That also means full healthcare without worries, something we entirely lack in the US. No one should be caught as Neven has been, needing to care for his business(es) and his workers, and having that compete with caring for himself, family, society at large, and all the rest. This is another aspect that most governments are woefully failing at.

Point 2. "The psychological effect of this disease is much more dangerous than the disease itself."

This is hugely destructive. We and our leaders can do many things to ameliorate that. Ending the quarantine prematurely isn't one of them. See point 1.

Addenda 2: What we desperately need is intelligent compassionate leaders who can and will reach out to the public to explain, as Franklin Roosevelt did with his fireside chats, precisely what is happening, what the government is doing to help, what people can do for themselves and others, and that calls on the better nature’s of everyone to work together to solve this - not just as a nation, states, communities and individuals, but also as a world- United. Instead we in the US have a conman, thief, liar, narcissist, bully who gathers everyone around to watch him beat up his perceived enemies.

Neven,

My apologies for speaking about you in the third person. I agree with the vast majority of what you have said here. It is these two points that cause me great heartburn.

Sam

5
Consequences / Re: COVID-19
« on: April 16, 2020, 09:48:43 PM »
Sam, this may be too philosophical a question for this thread, but given your view of the threat this virus poses, how are you viewing the rest of your time on this planet? How have you integrated your assessment into your goals, dreams, aspirations, hopes for your kids (if you have any), etc.?

Because if you are right, I am at a loss for how to do that.  Feel free to PM me or perhaps there's a more appropriate thread for this discussion.

For a number of reasons I elected not to have kids when I was 17. That was primarily because of a genetic linked issue that made me vulnerable to a severe form of arthritis. That caused me horrible problems for 30 years until contrary to medical wisdom I cured it. Secondarily, all the way back then in the early 1970s I saw the general outline of this coming. Not this specific virus, but climate change, pollution, wars, famine, pestilence, mass migration. That was also when the Club of Rome report came out.

So dnem, your question about how it impacts my goals and my life are in no way theoretical. They have governed my life from about age 10 onward. Everything in my life has been changed by understanding what was happening, why it was happening, where we were and are headed, and all the myriad factors that could change that.

I spent much of my life trying to change that course to no avail. I spent another large part of my life working on systems and designs. And I spent a lot of time doing emergency response and preparedness. In the course of that I identified and drove resolution of several Chernobyl scale disasters before they could become catastrophes. My name will never be associated with those. My name will never be broadly known. Solving those issues required (yes, required) working quietly behind the scenes. It was the only way to avoid the resistance and blowback that would prevent resolving the issues. Recognition is not and never has been a driver for me, nor for many of those I worked with through those years. We built things. We fixed things. We made things work well. We protected people. We were guardians and shepherds. The results are and were our reward.

I struggle with how to even suggest a solution for you to consider. I made my choices half a century ago. I lived them. Now I mourn the consequences of the things I/we could not fix.

But too I realize just as the father of the green revolution did - that all we did was to buy time for others to actually fix the structural problems. But “they” either never came along, or were not interested in solving the problems. So by buying time, we allowed the conditions to get worse before the inevitable collapse(s) arrived. We collectively made the system more able to support more people for longer, thereby making the descent into collapse harsher and faster.

Had the green revolution not occurred, population collapse and limitations would have happened decades ago. That may well have spread out the rate of change over timeframes that would have allowed civilization to come to grips with its own impacts and changed our behavior in ways that prevented catastrophic climate change. That is doubtful. The path appears to have been inevitable. The rate of changes would have been less. The hardships would have come sooner.

For me personally, I am at peace. I know my place in the universe and the grand scheme. I have the confidence of my own experiences and beliefs (knowing that that is what they are, and testing them constantly). I have lived a long and wonderful life with glorious friends and loves. All will be well.

I do not believe this marks the end even for man, though it may if we are stupid.  And a lot of mankind is truly stupid. Recent events have made that clear. It is going to be a very rough transition for the next several centuries to several millennia.

I joked with my father once when I was about 10. We were talking about these same questions, yes - all the way back in the 1960s. And he asked as you did. I replied flippantly that hey, I wasn’t around for the beginning, it might be nice to be around for the end. That off hand reply has haunted me my whole life. I am only glad that he did not live to see this.

For myself, I have a nice home. I planted a mini orchard a decade ago. It produces more fruit than I can deal with. I can garden and raise enough food for myself and friends. My health is good. So long as all that holds true, I mostly have sanctuary from this storm. In many ways this has not directly touched me. Indirectly it is devastating, as younger friends, children of friends and others suffer. I saw this coming and prepared. Most people did not. Most of them did not. They made other choices, choices that left them vulnerable, despite my protestations and cautions. Being safe while others aren’t when I spent a lifetime protecting others is wane comfort.

But then too, this forces people to face the harsh realities of life and the world. I do not mean the world as they perceived it or desired it to be, but the actual world as it really is. This is the world of scary childhood Fairy tales, where wolves and bears eat children who stray into the woods, and where goblins and monsters reside.

Truly coming face to face with reality and mortality is I think a very good thing. It is a hard and harsh thing. It is often an unwelcome thing. But it is ultimately good. Many will not survive that encounter. Many more will be grievously injured by it. Society though will be made the better for it.

I don’t know that I answered your question. But then I am still not sure I actually have an answer, even for myself. I am still searching. And I will still be searching until the day I die.

Sam



6
Consequences / Re: COVID-19
« on: April 16, 2020, 08:37:27 PM »
More and more credible sources pointing to the origin of the Wuhan coronavirus/Wuhan pneumonia/Chinese virus to the Wuhan Laboratory:

https://www.dailymail.co.uk/news/article-8223779/Coronavirus-originated-bungled-experiments-Wuhan-lab-bombshell-report-claims.html

I've been pointing out this virus came from a lab for weeks, and now we're getting closer and closer to getting that info confirmed.

This is just one more instance of the right wing nuts wanting someone to blame, preferably the Chinese, preferably communism.

There is no truth to it. There never was. This is a natural variation of a virus from nature jumping to humans from animals in a high contact zone, hybridizing with a human virus to gain capability. This happens frequently. This happens more often the higher the population density and the higher the contact rate with the wild.

This is not in any way surprising. It is and was entirely expected. It was so expected that the Chinese focused two large research groups on this very virus family AND began construction of a bio lab to study these viruses - the very lab the right wing nuts want to blame for creating it.

This is not (99+% likelihood) in any way associated with human meddling with this virus. This is nature at work weeding the herd.

Sam

7
Consequences / Re: COVID-19
« on: April 16, 2020, 08:30:09 PM »
It doesn't really matter if the Dutch blood donor data is 100% or only 85% accurate. 3% infected population is very far from herd immunity meaning countermeasures and additional epidemic waves will keep us company for some time. This is gonna be a long ride.

A long ride will probably mean civilisational collapse, as fear and insecurity, incessantly pumped up by the media, will prevent people from being the consumers they were conditioned to be. Consumerism is a central pillar of our current global system. It could transition to something more resilient (if the lessons of this crisis are heeded), but it will take years, if not decades. It will collapse if everyone's eyes are glued to statistics (with no context), and fear and panic are used for ratings and to make sure people obey the installed measures.

The angle of the narrative will have to change, something along the lines of: 'Yes, this is a terrible new disease, but there are many of those. People are dying, but they are mostly very old and have comorbidities. And besides, 150 thousand people die every day. Death is a part of life. It's true that people die before their time, but on average perhaps a few months, not years, and certainly not 10 years. The only thing that really matters in all this, is that we prevent a collapse of our health care systems, and so we need to do as much as we can, but we must not be afraid, because we cannot afford to be in lockdown much longer.'

The psychological effect of this disease is much more dangerous than the disease itself.

I hope that Sweden will be (relatively) successful, that warmer temperatures do turn out to reduce the spread of the virus, and that ending lockdowns doesn't lead to new exponential rises (with everyone becoming paralysed, staring at stats). This will buy time to build out extra hospital capacity and train personnel, to deal with the next waves, as with influenza. And then I hope that some of the lessons this crisis is teaching us, will come through.

Neven,

I agree on collapse; and this virus has the potentially to result in a large-scale collapse.

This virus is oddly the only thing that has managed to reduce greenhouse gas emissions. While it's comforting to know that for a short while, we lowered CO2 output, the long term impacts are dangerous.

Overpopulation, and positive-feedback loops, combined with a paranoid and disillusioned populace will not bode well.

Positive feedback loops alone would have collapsed society, now there's an added element of chaos.

The ignorant masses may not cope very well with a virus they don't have the education to understand - and politicians constantly pouring mixed messages into their fragile mindsets.

And one only need go back to the “Club of Rome” World model for climate change to see this predicted in general terms.

One of the end results of not controlling human growth and behavior resulting in massive climate change is the setting of conditions that lead ultimately and inevitably to pandemic diseases, wars, famine, pestilence, mass migration, and collapse. They were right again.

If you look at the standard run of the original model, and specifically at the downturn of industrial output per capital, we are right on schedule. 

https://logiclogiclogic.files.wordpress.com/2016/06/img_4953-2020.jpg

Sam

8
Consequences / Re: COVID-19
« on: April 16, 2020, 08:25:27 PM »
The psychological effect of this disease is much more dangerous than the disease itself.

Neven,

This is a basic and common error. Our society is conditioned to think in terms that put commerce as primary. It isn’t. It is essential. It is not primary.

The psychological effects of this disease are terrible. The impacts of those on commerce are great. More impactful is the disease itself.  It is not in any way the messaging or narrative that is the problem. That places commerce as the priority to resolve the crisis.

To resolve the crisis requires first understanding that the disease spread is itself primary. It leads. It governs all that happens. The impacts of the disease on psychology are secondary AND important.

The impacts on commerce are tertiary. And their impacts on employment, income, work, social life ... are feedbacks from that. They are all vitally important. But they are tertiary.

Focusing on those focuses on the wrong problem.

The narrative in media is quaternary, not even tertiary. But it is for most people the first thing they see. And between the primacy of that flow of information and the vital importance of economics to day to day survival, it is not in the least surprising to find people believing that to be most important and hence primary. It still isn’t. It also easily lends itself to memes, and to political campaigns focused on those aspects. That still does not make it primary.

The disease and its progression are and remain primary. They drive everything else.

Solving the crisis requires solving the disease spread. Solving the crisis requires focusing on that primary problem.

And there two major aspects. First is the disease itself. Treatments, drugs, herbs, vaccines and such are the primary weapons there. Second is the spread of the disease. That is dominated by human behavior. There is as yet no suggestion even of an animal or insect vector playing any role. Stopping human to human spread is the major control. That then goes to isolation through many means, blocking transmission with masks, sanitizers, hand washing, and behavioral interventions are the major tools.

This virus is as contagious as chicken pox. That is hugely contagious. Controlling it requires actions commensurate with that. And that means lockdown.

If - and this is a huge if - we could simultaneously stop everyone from moving around for five to six weeks, we would likely end the virus. Five to six weeks in very small groups would cause the disease to run its course and die out. Even a few somewhat larger groups, or limited movement of essential people provide pathways for the virus to continue.

And even a single contagion chain is enough that when that isolation is lifted - the virus resumes its rampage. The vast majority of people don’t have five to six weeks of food and essential supplies on hand. Medical and other emergencies still happen.

So, five to six weeks isn’t enough. It requires longer - a lot longer.

That then endangers the existence of small companies. It depletes individual resources or strains them to the breaking point. Accordingly, massive societal sharing (financial bailouts being one such) become essential.

But these are not one time things. They have to last as long as the contagion persists - requiring isolation and shutdown.

And how long that lasts is decided by how tightly we are willing to lock ourselves down (all of us), and by how effective we are at it.

If we do this badly, or even moderately well. The period required is extended indefinitely. And that then drives people bonkers psychologically which causes controls to fail.

But failure means ultimately infecting about 90% of the population. And that means killing circa 3-9+% of the population in the first wave. And if this virus only provides two year immunity as it appears to, it means killing something like 2-6% in a second wave, and 1-5% in a third wave etc...  Each wave depletes the society of older and vulnerable people, presumably lessening the impact of each wave. But over a decade, this likely sums to 12-15% of the population dying, unless massive controls are put in place, or successful treatments or vaccines are developed. That then might limit the dying to 4% over the decade.

However, even a single adverse mutation in all those quadrillions of quadrillion+ copies of the virus throws all of this analysis out. Now we deal with a more lethal disease that spreads faster, and kills more and different people. It perhaps then targets the young, or young adults, or those in middle age.

In time, that too dies out. Extremely lethal viruses are self limiting. They destroy the population in the process.

Focusing on putting business recovery as primary assures that the disease spreads farther and faster and that it kills more people. That raises the decades death toll substantially. AND it destroys more businesses. Focusing on saving business and commerce as primary kills business and commerce.

The problem is not the narrative about the virus. The problem is and remains the virus.

Sam


9
Consequences / Re: COVID-19
« on: April 16, 2020, 06:32:12 AM »
Isn't COVID-19 stressful to the heart, as it needs to work harder when the lungs are less efficient? That would make (hydroxy)chloroquine even more risky and disqualifies it in severe cases.

Yes. Extremely. Though Herr Twittler assures us otherwise.

Sam

10
Consequences / Re: COVID-19
« on: April 16, 2020, 02:47:58 AM »
If it were possible to have extended “lockdowns” for people over 60-65 and by age groups restart the economy for everyone else maybe we could get the economy to reboot. There are plenty of us older than 60-65 still working in critical infrastructure jobs so arbitrary age based lockdowns still need to allow critical infrastructure jobs to continue.
 Schools and schoolchildren probably need to remain in lockdown because schools are not the problem crashing the economy. Colleges could probably restart earlier.
 There needs to be a way to get age groups over 60-65 to live as isolated as possible from other groups getting released from quarantine. Restarting the economy with large households that include grandparents is problematic so perhaps any household that includes members over 60-65 should be required to remain in lockdown . There should be financial incentives to allow seniors the opportunity
to rent an apartment or small house if money problems are keeping them in larger households. 
 I picked 60-65 as an arbitrary number . Deciding on the age of this cohort should be determined by how that age limit affects hospital Covid rates .
 Hospitalization rates should be the determining factor as opposed to trying to get r o below 1.  Keeping r below 1 may require many months or even years of lockdowns. Managing Sars2 is probably a decades long problem and those sorts of timeframes are where some planning exercises need to be headed. If there is a working vaccine for 8 billion people in 12-18 months we can always speed up social reintegration but I fear that integration will tilt to countries that can afford vaccinating their populations. The fact that money can buy you a Covid test when they generally are still not available in the US argues that money will also buy the vaccine .
 

The key isn't precisely age. It is whether the thymus gland is no longer effectively functioning. When it is functioning, barring other factors, the vast majority of people recover through primary immune function actions.

For those of us above 50-60 years of age, whose thymus gland is all but non functional, we rely instead on our innate immune systems to defeat new bugs. And it is the innate immune system through cytokine storms (Il-6 and IL-17a primarily) that it kills us.

Now it may be possible for us to go through a prolonged therapy with HGH, DHEA and metformin to reverse that, to regrow the thymus and add 30 years to our lives. That is currently in clinical trial. But that is going to be a year before we will see it fielded - about the same timeframe as any successful vaccine.

And we do now know that tolicizumab (an IL-6 inhibitor) {and presumably Andrographis paniculata (an herbal IL-6 inhibitor)} does result in near miraculous recoveries by suppressing the cytokine storm.

Likewise, we now have early evidence that Quercitin (especially with added vitamin C & D, and Zinc) is also effective. The supercomputer models suggested this to be true. And there are now successful cases resolved this way.

The nice thing is that Andrographis and Quercitin are readily available over the counter. Quercitin has a very short biological half life of ~2 hours and accordingly requires frequent dosing.

But, it is also likely that many flavanoids and flavonoids are also beneficial including those from a wide variety of vegetables and herbs. They are structurally similar to quercitin and should bind (according to the supercomputers) to the same parts of the spike proteins.

Sam

11
Consequences / Re: COVID-19
« on: April 16, 2020, 02:44:24 AM »
I guess the big questions are 1) can we keep the measures in place long enough for all these <1.0 Rt's to drive the absolute cases number very low?, and 2) how fast will the Rt's rise back above 1.0 after measures are relaxed?


As for 1) I am afraid not, although the Chinese did it so theoretically would be possible
As for 2) If we relax the measure without very strong testing and contact-tracing then sure as hell, numbers will blow up quickly...and unfortunately I do not see the right exit plan anywhere

Exactomundo!

The new page talking about the Rt is immensely useful. It is one of the very few times I have seen Bayesian analysis used well, rather than in service of some set of desires or beliefs. Great work.

But just as you suggest, if we do not drive this to zero, as soon as the pressure is let off the Rt climbs above 1 and we are off to the races. The only question then is how long it takes for the decision makers to "get it" and to then reimpose quarantine.

After one, two or three cycles, they -might- figure out that - hey, we have to get rid of this thing or we can -never- come out of quarantine until there is a good vaccine. AND that then the economy is trashed until then. For many of the leaders that is the one thing they care about. And until they finally "get it" that they cannot restart the economy until they squash the virus, they will continue to focus on the wrong problem.

As it stands now, there are only a few States that are showing a less than unity Rt. And those few are not strongly less than 1. That means it will take a lot of time for the virus to die out on its own (>3-9 months). But until it is fully gone, releasing controls just sets the stage for it to bounce back - vicious as ever.

Also, because the United State is a federation based on open borders, any one State choosing to not "get it" means that we all "do not get it". We are in this together to the bitter end. Until ALL of the States squash the virus, none have truly succeeded. Well, unless of course they leave the Union. And we all know how well that worked out the last time it was tried.

Sam

12
Consequences / Re: COVID-19
« on: April 14, 2020, 11:42:04 PM »
<snipped>
122 new death lower then 234 last week but this includes the easter effect.
<snipped>
Getting accurate fatality counts on easter weekend has proven difficult for milenia. ::)
Terry

The same holds true for all ‘major’ holidays.
<snip>
I think you missed the point Sam. Easter is the celebration of Jesus Christ being alive three days after his execution. This is not the forum to discuss who  believes that or doesn't. The comment struck me as light hearted and made me smile despite the seriousness of the subjects.

Which is precisely why I skipped it - until John The Elder decided to make a point of it - and now you. It is not I who decided to bring this here. It is several of you who elected to bring religion to a science forum followed by a mild insult. If you truly want it dropped, then simply drop it.

Sam

13
Consequences / Re: COVID-19
« on: April 14, 2020, 10:00:12 PM »
<snipped>
122 new death lower then 234 last week but this includes the easter effect.
<snipped>
Getting accurate fatality counts on easter weekend has proven difficult for milenia. ::)
Terry
Terry I appreciated your "joke" but I think it went over the heads of all the scientific people here ;)

I got it - and ignored it, for the very much more important issue of temporal data analysis in the face of human behaviors; rather than pointing out the original myth involved and the underlying story of the "death of the sun", and it's rebirth, heralding the winter's solstice .... etc....

Sam

14
Consequences / Re: COVID-19
« on: April 14, 2020, 08:03:43 PM »
<snipped>
122 new death lower then 234 last week but this includes the easter effect.
<snipped>
Getting accurate fatality counts on easter weekend has proven difficult for milenia. ::)
Terry

The same holds true for all ‘major’ holidays.

In just the few data sets I have examined closely, what seems to help tremendously is to use a centered seven day moving average of the data. There is a lot of noise in the data that results from human variation in reporting based on the day of the week and weekend effects. Holidays and special events compound this. But they too mostly go away in a seven day average. Centering the average helps to put the impacts on the correct dates.

Also, time lagging or shifting the data by 10-11 days also makes things somewhat clearer.

The average time from infection to symptoms seems to be stable at 5-7 days, though the distribution has a broad right tailed distribution with symptoms showing in as little as 2 days and as many as 28 (or longer).

The time to seek treatment seems to average about 2 days. And the time for testing confirmation seems to be about 2-3 days.

The sum of those is 10-11 days.

The serial generation time seems to be less known. Various analyses have placed that at 4.7, 5.9, 7.2 and 7.5 days with fairly tight distributions. These are in conflict with one another due to the tightness of the assessed variations.

The R0 as a result is also variable. Add to that the population density impacts on the R0, and the result is variation from 1.5 to >20 on the R0. Even small variations in the R0 have large impacts on the models.

During the early free growing phase in the first 28 days or so, the cumulative count of cases is most informative. After that it is important to shift to the new case count. In the first fortnight, the exponential growth dominates, and there are few or no recovered cases in the population to muddy the Dara. Also, the total count rate is low making the daily counts less reliable.

After the first fortnight, and especially after social reactions (self quarantine ...) begin, the exponential changes causing muddying of the data; and the relative importance of the recovered cases (who are non infective) grows in the data set. As this happens, the new case per day data becomes more representative. Also, by that point, the rate of new cases per day is larger which also reduces the noise in that data.

What seems to be much more useful is to ignore the serial time, and R0, and to instead use the observed growth rate in daily new cases (using a seven day moving average of the data). This creates other artifacts and introduces other errors, and those must be kept in mind. Still, the daily-growth-rate-changes, in my opinion, better & more smoothly assess the impacts of all of the factors involved in the transmission with a single parameter that is more easily assessed from the data by looking at the slope of the log curves of the smoothed daily data.

Sam

15
Consequences / Re: COVID-19
« on: April 14, 2020, 07:43:21 PM »
Sam, how do you see the large spatial heterogeneity in social distancing compliance and the concomitant impact on the reproductive number playing out here in the US? I don't think projections based on the nationwide reduction mean much as the geographic picture is so varied.

That is, in my opinion, a hugely important set of questions. It also isn’t easy to assess or answer. The data we have is strongly impacted by all sorts of factors, and by choices made by people based on their beliefs. The beliefs are not uniformly distributed, and as a result create large scale variable differences. The end result of which is a comparison of often fairly to quite different things when looking at the raw numbers.

For example: in areas where the beliefs of the leaders guided by experts has led to wider testing, a greater proportion of presymptomatic people, and presumably some significant portion of asymptomatic people, increases the apparent rate of disease to closer to the true rate of disease. In areas where leaders based on political or philosophical beliefs refuse to test, or test less, the converse is true, and the testing evaluated rates of disease are more divorced from reality. These differences have huge impacts on the actions taken and the course of the pandemic.

However, in general the beliefs and testing dichotomy go hand in hand with population density, with testing and response being greater in urban than rural areas.

At the same time, the contact rate (R0) is inherently dramatically different between the two. Urban areas allow for and cause a much higher contact rate and a vastly higher disease growth rate. That seems to be on the order of 1.25 - 1.36 x/day in dense urban areas and 1.06 - 1.20 x/day in rural areas. Those are very crude observations and first order estimates of my own. They are biased by all sorts of factors, including the testing rates, which no doubt makes them wrong. So, they should not be relied upon. We might have a better assessment of that a decade from now in retrospective analyses. But due to the phenomenological issues in the data, that too seems likely to be fraught with problems and to likely lead to far more perceived certainty than is warranted.

One impact of the differences in these two broad groups is that the urban areas are hit first and hardest. They also have the greater contact with outsiders that seeded the disease into the population. The rural areas are not immune or even different really. They are instead only slightly insulated from this first contact and growth rate. Inevitably, the disease will hit them as well.

The responses though will also cause differing impacts. The urban areas will and have seen massive growth rates, immediate impacts and consequences. They responded as expected by going to self isolation and distancing first. Their beliefs incline them to follow the advice of experts. And the impacts are relatively obvious.

The rural areas seeing less impact from growth of viral infection, and being philosophically inclined to distrust authority and “experts”, will and have resisted self quarantine and distancing. Until they see the ravages of the disease first hand they are likely to continue in the same way. Even when they see the impacts personally, they will be inclined to disbelieve them. And since the growth rate is slower, they will likely conclude that they are somehow different, better, and more special. This will reinforce their own beliefs with devastating consequences.

It is quite likely they will be among the first to break quarantine. The disease spread is only slower in these communities. It is still relatively rapid compared to a lot of diseases. And the consequences will be as severe as in urban areas. The rural areas have less resources to be able to respond though, so the impacts will likely be worse. And this will be compounded by the lesser levels of testing, thereby delaying when the leaders “see” the impacts.

Sam

16
Consequences / Re: COVID-19
« on: April 14, 2020, 07:21:31 PM »
Friend is worrying about the forest fire near Tjernobyl.

Well, there was also a bit of a panic in Sweden in the spring of 1986. After that, a few thousand children in the Ukraine got thyroid cancer. Usually treatable.

Now we will be run over by the coronavirus, Tens of thousands will get pneumonia, for which there is no real treatment, which is often fatal.

And the country is not panicking.

Maybe this is due to the mass media being very reassuring etc.

The world is upside down. The Zone may be the safest place on Earth.

Safety is a relative thing. Radiation, except at extremely high levels, takes time to kill. That dissociates the cause and effect in peoples thinking, making it even harder to relate to.

The “red forest” area and others are intensely contaminated. Mankind mostly left the zone. That allowed nature to return. And quite quickly nature has begun recovery. Looked at without considering the devastating impact of human presence, this looks naively like the hazards from radiation must therefor be small. That is flatly wrong.

The plants can tolerate higher doses than animals. They are impacted, but to a lesser degree. The animals are hugely impacted with shortened life spans, increased rates of deformity and disease. But these are nothing compared to the impacts of human presence, and so they are -relatively- flourishing.

The cesium and strontium isotopes are moving slowly deeper into the soil column, and radioactively decaying.  The mobile nuclides like technetium have mostly washed away. The long lived actinides are a larger problem.

The fire did indeed remobilize many of these and send them off on the wind to contaminate other areas - and yes, people. That is indeed a problem.

But just as with the animals, these impacts compete with other impacts. And the delayed effects make them less apparent. Induction of and dying from cancer takes time. The effect though important is relatively small at ~1 in 650 from all causes (cancers plus cardiovascular plus stroke plus gastrointestinal plus neurological deaths) per Sievert of exposure. These are common causes of deaths, and as a result, the radiation causation gets buried in the data with the other causation, except at quite high doses. Even then, the many year to decades long delay between cause and effect makes “seeing” it hard for people. It is non-obvious.

Contracting a virus, suffering its consequences, and possibly dying (~1 in 25), is very fast and relatively certain, and plainly obvious as to cause and effect.

Even then, peoples beliefs and desires often strongly interfere with their ability to believe and therefor to “see” these immediate impacts.

Sam

17
Consequences / Re: COVID-19
« on: April 14, 2020, 07:01:09 PM »
Another bit of good news....

The one part of their solutions that all of these four share is testing, tracing and isolation...

I agree 100%. And I just can't understand why other countries do not copy them as fast as possible. Why doesn't every country (at least those able) perform mass testing and tracing???
In my country, the person responsible for the pandemic said "no testing is able to stop the virus", so they do test only for the very sick. Seriously. Unbelievable. It's like saying "no radar can stop enemy airplanes".

El CID,

That is the single best analogy I have seen or read about testing.  Thank you!

Sam

18
Consequences / Re: COVID-19
« on: April 14, 2020, 10:57:34 AM »
Another bit of good news.

Early reports are that Taiwan may again have returned to zero or near zero new cases, even as mainland China is fighting an influx of cases from outside the country.

South Korea also appears to be nearing zero as well. It looked iffy there for a bit. But they seem to have pulled it off. 

That makes four countries with decidedly excellent results. New Zealand is the fourth that I am aware of. There also appear to be a few more. I am less certain of them.

What I find most promising is that each of these managed it using different approaches.

And though COVID-19 is clearly transmissible via droplets and surfaces, these appear to be mostly manageable.

The one part of their solutions that all of these four share is testing, tracing and isolation.

On the question of the poll, how ever many people end up being infected and however many end up dying in this first wave, this is only the first wave. Through the rest of this years there will likely be at least one and possibly several more waves. Through the 2020s there will be more yet.

A vaccine might be key. Several vaccines may be needed. And these need to be shared globally. No one is safe until everyone is safe. That especially means out of the way places, and poor regions, migrants and displaced peoples, and all of the forgotten everywhere in the world.

Africa and India seem likely to be especially hard hit. Parts of South America may be equally impacted.

And lest we forget, SARS1 and MERS are still around. Vaccines are urgently needed for them as well.

Sam

19
Consequences / Re: COVID-19
« on: April 14, 2020, 10:23:00 AM »
Sometimes those things we can least influence scare us the most.

Exactly.

It is a comforting thought to blame humans for creating this. The real scary part is that infections like this can emerge anywhere at any time.

Freakier is that they have been recurring like clockwork once a century in world spanning outbreaks.

I doubt that speaks about the viruses. I suspect it says something about humanity.

The Indian variant may be and likely is -less- virulent, based on where the mutation affected.

However it points out a grave danger. The longer this thing is extant in the world, the more copies exist in more bodies. Each reproduction is a chance for a new variation. Each variation is a chance for an even scarier disease. And with more people infected comes more co-infections and the opportunity for cross over, and the creation of some new monster.

With variation also comes the potential that the variants require distinct vaccines. And the potential for difficulties, such as occurs with the five variants of Dengue and its vaccine.

On a different note.

It appears that self isolation as done in the US is resulting in something like a -1.5% “growth” rate. I.e. a 0.985 x/day change day to day in the number of new cases. This is excellent news. However, it is - slow. At that rate, and without massive testing, contact tracing, and isolation of those infected, it means that provided this holds across much of the US (unknown) that the new case rate about May 1 will be something like 75% of the new case rate today.

And what that means is that if self isolation / quarantine is lifted on May 1 as threatened by Donald the Dumb, and people actually return to their normal lives that the case rate will begin rising at between 1.18 x/day in mostly rural areas and ~1.355 x/day in urban metro areas.

It will take 10-11 days to see that begin to show impacts on numbers.  It will take about a week of increase to persuade decision makers that they have erred. And in that time the new case rate will have grown to between 35 and 235 times the rate the day the decision was implemented. If that is 75% of the case rate now, then the case rate will have bloomed to between 25 and 175 times the new case rate today.

And in many areas, with the peak in rates being about now, now is when many areas hospitals are at or near saturation. At 25 to 175 times today’s rates, pretty much everywhere will be in saturation. But those rates will continue to rise for another 10-11 days to 130 to 5,000 times today’s rates, before the restored quarantine begins to show effects. Should that happen a whole lot of folks will die who would not have died at lesser rates. That would take the nominal 4.5% CFR for hospitalized cases much much higher.

All of this is of course guesswork, with all sorts of questionable assumptions. People are likely to be gun shy to go back to their normal lives. Many, if not most, Governors are likely to show Herr Dumkopf their middle fingers. So the reality is likely to be much less severe than these numbers might suggest.

Then again, the stacked Federal Courts courtesy of Minnie me McConnell might well trash the Constitution and the tenth amendment and decide that the Commerce Clause supersedes everything.

Still, the impact will be bad. We can only hope that he isn’t as much of an imbecile as he appears, and that he doesn’t try to “restart” the economy on May 1, or anytime in the two months after that, without dramatically changed policies that drive the infection rates to near zero before trying to gently and tentatively restart the economy.

That is of course a vain and ridiculous hope. Our dear loser of a leader has demonstrated at every turn that he is a thin-skinned, self aggrandizing, malignant narcissist, sociopathic liar, conman, bully, idiot, fool, moron, imbecile, racist, zealot, misogynist, and utterly failed business man. Everything he touches turns into a heaping fetid pile of stinking shit the likes of which no one has seen before. There is no reason to hope or believe any decision he is involved in regarding this pandemic will be any different.

And whatever happens he will of course claim to have done the most perfectest and smartetest thing any President has ever even dreamed of doing - never mind the reality. And his troglodyte troll followers will genuflect obscenely and obsequiesly to French kiss his ass as he does it, while simultaneously blaming everything on the commies and their fantasy “deep State”. All the while, our neighbors will be dying for the economy.

Sam

20
Consequences / Re: COVID-19
« on: April 14, 2020, 05:54:50 AM »
Continuing on from #1993 and #2020, covid-19 viral activation and invasion of lung pneumatocytes has unusual and undesirable features that reflect rapid recent evolution of its genome.

The research action centers on the spike protein because it seems to have acquired aggressive new properties from a specific upstream 12-base insertion (creating a 4 amino acid furin-like cleavage site motif) that greatly facilitates adhesion to the ACE2 receptor which facilitates fusion (mediated by a downstream spike domain) with the host cytoplasmic membrane, the entry point of viral RNA into the cell interior where it reproduces.

There are 182 complete covid-19 genomes as of today being studied with both wet lab and dry lab (bioinformatic) approaches. NextStrain collects all these and presents them as a branching phylogenetic tree that grows every day and sometimes gets rearranged.

This tree clusters closely related covid-19 genomes the same way that your desktop organizes related files into a nested folder hierarchy but using advanced statistical methods such as maximal likelihood models that have been under intense algorithmic development for half a century. However these trees can be made under many different assumptions and parameter sets. A tree that aligns amino acids (rather than nucleotides), eg those from the upstream half of the spike protein, might give a rather different topology from a whole genome nucleotide tree.

On the data side, the 182 genomes are mostly not the ones we want: the early ones. Many are just chains of descendants: A in Wuhan gave it to B in Milan and C in Vatican City, B gave it to D in Austria and E in Spain, C gave it to F, G and H in Dubai with 0-2 mutations at each step along the way. The real information lies in more covid-19 genomes from Wuhan but not descended from A.

This is useful early on in a pandemic for the tracebacks and self-quarantining that buy some (mostly squandered) preparedness time but as Sam documents above, that train left the station a month ago.

Molecular biologists want the genomes from the very earliest stages of viral spread in late Nov 2019 for five principal reasons:

-1- to work out the ancestral genome that first crossed the species barrier.
-2- to determine the carrier species because it may harbor many other coronavirus strains.
-3- to determine what adaptive changes took place that caused covid-19 to spread so virulently.
-4- to better understand mutational processes in covid-19 and future properties may evolve.
-4- to resolve whether mutational gain/loss of nucleotides represents an insertion or deletion.

However the epicenter of spread, which is not necessarily the epicenter of origin, has been bulldozed to the ground, its entire stock of wildlife incinerated and its infected denizens cremated without any genetic sampling. Under the circumstances, the focus was eradication; public health mandarins would hardly be bowing to requests for viral agent preservation from scientists.

Prior to the outbreak, Wuhan had two institutes (not one) collecting coronavirus genomes from wild bat populations and requesting isolates from other virology labs around the world, for example the Manitoba, Canada BSL-4 facility.

Assembling such a resource makes research sense in a country like China with strong science and a costly history of viral outbreaks in both livestock and humans. For its part, the US maintained a massive collection of anthrax strains until the FBI autoclaved the entire set after a rogue worker mailed a weaponized one around.

In summary, only a few of the 182 genomes originated early on in Wuhan but because of privacy considerations neither preprints, GenBank annotations or GISAID metadata make clear if any of the people were affiliated with the two corona virus laboratories.There is very little specific clinical information about the eight original ICU patients that triggered the ophthalmologist's alert. We don't know if any of the covid-19 genomes represents the transmitting patient with acute angle glaucoma.

Regardless, the genomes at NextStrain fall into two early-diverging clades (strains) that split early on and never later hybridized (through RNA recombination). These were noticed back in February and denoted L and S clades (for distinguishing mutations that affected leucine and serine codons). The topology of that branch of the tree has been stable ever since.

The original authors were careful to say of the two strains, the L type “MIGHT be more aggressive and spread more quickly”. However nobody since has honored that cautionary statement. Because of transmission chains, subsequent internal mutational divergences in both clades, and lack of healthy human volunteers, this idea is very difficult to pursue. Note that every node on the tree defines, through its descendants, its own clade or strain.

The NextStrain tree is unrooted, meaning that deep ancestry is not indicated by outgroups (closely related corona and other viruses). This is so bizarre that other researchers immediately added a variety of outgroups and recomputed the tree to see which of L and S is closer in genomic sequence to the first covid-19 to escape its initial animal host. And that the 'more ancestral' sequence is said to be the smaller clade, S. That needs to be revisited now that the data set is so much larger.

The phylogenetic tree unambiguously resolves the upstream spike protein mutation as an insertion. This was correctly inferred in the ‘uncanny’ preprint where it is called the 4th ‘HIV’ region. That’s not entirely off the mark but it’s better called the putative gain-of-function furin-like cleavage site resulting from the new four basic amino acid motif.

This preprint was withdrawn by author request; it was not retracted (shame on you FAS) and could conceivably resurface after massive revisions. It never mentions weaponization. The pdf is still offered at biorxiv; there’s a good discussion of its myriad problems too by others in the field:

https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf
https://www.tandfonline.com/doi/full/10.1080/22221751.2020.1727299

To date, there’s still no good explanation for how the furin-friendly insertion arose in the spike protein. Some of the better spike protein analysis is provided in the links and images below.

https://tinyurl.com/th8zpq3 21 Jan 2020 discovery of furin site (in Chinese)
https://www.biorxiv.org/content/10.1101/2020.02.19.956581v1 images and structural analysis AC Walls et al
https://www.sciencedirect.com/science/article/pii/S0166354220300528?via%3Dihub French paper on furin site
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281273/ real furin motifs are longer
http://virological.org/t/evolutionary-epidemiological-analysis-of-93-genomes/405 GISAIS metadata for 93 genomes
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324781/ RNA recombination
https://tinyurl.com/r9fm3zw remdesivir
https://tinyurl.com/uopplv2 L and S clades
https://www.sciencedirect.com/science/article/pii/S193131282030072X?via%3Dihub early paper

This caught my attention when A-Team posted it.
 “The phylogenetic tree unambiguously resolves the upstream spike protein mutation as an insertion. This was correctly inferred in the ‘uncanny’ preprint where it is called the 4th ‘HIV’ region. That’s not entirely off the mark but it’s better called the putative gain-of-function furin-like cleavage site resulting from the new four basic amino acid motif.”
 So if this coronavirus has an ability to infect T-cells is it possible the insertion mentioned by A-team may be the change in Coronavirus that allows the attack ?

This is not at all new.it has been thoroughly studied and reviewed. It was inevitable that something like this would happen. The SARS virus family is large, and mutation events as well as crossover events are common. The danger arises when a crossover happens that allows a zoonotic conversion into a highly infective human virus firm.

I commented on this almost two months ago on February 19, 2020 at 08:15:45 AM.

The small insertion in SARS2’s spike protein is a very common moiety used by a lot of viruses to access the human ACE2 receptor. As it happens, HIV is one of those. That does not then mean that this cane from HIV, though it may well have. It further does not mean that this was bioengineered.

Each species has somewhat different ACE2 receptors. And these sorts of changes resulting in virus moving between species though not extremely common in time, are common enough to be a major factor in virus spread between species.

By far the most likely explanation is something that happens a lot - that some creature (most likely a pangolin, second most likely a bat), or a human (the most likely scenario of all) contracted both the predecessor SARS-COV-2 progenitor AND a human virus containing the spike protein variant that allows insertion via ACE2, and these crossed in that creature or person. The result was SARS-COV-2 and the first human infection.

Bioengineering tools tend to be messy. Though they are intended to target a very defined piece of RNA or DNA, they also can and do match to other segments. The result is ancillary changes unrelated to the intended changes. No such changes have been shown for this virus.

Most of the tools also change larger segments than this. Changing such small segments is a relatively new capability.

As I commented in February, both Occam’s razor and a variation of Hanlon’s razor apply here. The simplest explanation is likely the right one & Don’t attribute to malice that which can be explained by simple stupidity. Occam applies to the technical part of the analysis. Hanlon applies to the folks who see Chinese Communist plots behind every bush, and who immediately attribute to malice all sorts of things more easily and more likely attributed to natural action. In their case, they see malice where there is none. That is the stupidity on their part, rather than malice.

Sam


21
Consequences / Re: COVID-19
« on: April 10, 2020, 04:33:20 AM »
...
Now - of course - humanity may fail to extirpate this virus. In that case, we will lose 4-12% of the population over the next year or two, ...
Sam

Sam, I'd appreciate if you could please tell us how you came to that very high figure, and range!

In Nothern Italy, the highest lethality is 1% of population, and that is in municipalities that have a very old population on average (around 45 years iirc), and with many lifestyle diseases. I would say that 1% lethality is proven under such circumstances of old people and many comorbidities, but cannot see what can contribute to an even higher figure than that?

So why should we expect even higher lethality on a global scale?

Sam will give a better explanation but here is my take on why 10% is possible.

1 - it isn't going anywhere. There are too many carriers without symptoms, it is global and it spreads easily. Even lockdown don't truly stop it. As soon as a lockdown is removed it reappears.

2 - there is a growing body of work that is beginning to suggest that immunity either doesn't happen or disappears quickly.

3 - Without decent medical treatment, a lot more people die. It appears that about 1% of people die when treated well but it leaps up quickly when hospitals are overwhelmed. And soon, it will hit countries with inadequate medical services to begin with.

4 - give the above, the virus can potentially do the rounds over and over again in the same people until they die.

5 - with a mutation rate similar to flu, there is a chance that it will mutate every two years. If that happens, it becomes a flip of the coin as to what it does next.

To me, it is not unreasonable to see a significant ongoing event that will cause many problems for a long time.
I am not saying this will happen..... but it isn't out of the realms of possibility. And if it does happen, 10% will be on the low end of victims.

Precisely.

Round and round and round she goes, until no one susceptible dies anymore.

Meanwhile, the virus is morphing into new forms.

Sam

22
Consequences / Re: COVID-19
« on: April 10, 2020, 01:40:57 AM »
A press release from Cambridge University reveals that:

Quote
Researchers from Cambridge, UK, and Germany have reconstructed the early “evolutionary paths” of COVID-19 in humans – as infection spread from Wuhan out to Europe and North America – using genetic network techniques.

By analysing the first 160 complete virus genomes to be sequenced from human patients, the scientists have mapped some of the original spread of the new coronavirus through its mutations, which creates different viral lineages.

“There are too many rapid mutations to neatly trace a COVID-19 family tree. We used a mathematical network algorithm to visualise all the plausible trees simultaneously,” said geneticist Dr Peter Forster, lead author from the University of Cambridge. 

“These techniques are mostly known for mapping the movements of prehistoric human populations through DNA. We think this is one of the first times they have been used to trace the infection routes of a coronavirus like COVID-19.”

The team used data from virus genomes sampled from across the world between 24 December 2019 and 4 March 2020. The research revealed three distinct “variants” of COVID-19, consisting of clusters of closely related lineages, which they label ‘A’, ‘B’ and ‘C’.

Forster and colleagues found that the closest type of COVID-19 to the one discovered in bats – type ‘A’, the “original human virus genome” – was present in Wuhan, but surprisingly was not the city’s predominant virus type.

Mutated versions of ‘A’ were seen in Americans reported to have lived in Wuhan, and a large number of A-type viruses were found in patients from the US and Australia.

Wuhan’s major virus type, ‘B’, was prevalent in patients from across East Asia. However, the variant didn’t travel much beyond the region without further mutations – implying a "founder event" in Wuhan, or “resistance” against this type of COVID-19 outside East Asia, say researchers.

The ‘C’ variant is the major European type, found in early patients from France, Italy, Sweden and England. It is absent from the study’s Chinese mainland sample, but seen in Singapore, Hong Kong and South Korea.

The new analysis also suggests that one of the earliest introductions of the virus into Italy came via the first documented German infection on January 27, and that another early Italian infection route was related to a “Singapore cluster”.

Here's the associated paper:

"Phylogenetic network analysis of SARS-CoV-2 genomes"

3,160 strains analyzed in a near real-time phylogenetic tree, by country, by clade, ...
https://nextstrain.org/ncov/global?l=unrooted

Sam

23
Consequences / Re: COVID-19
« on: April 10, 2020, 01:38:57 AM »
In case anyone's interested. I'm registered and there are some interesting datasets and participants. Starts tomorrow.

https://albertainnovates.ca/impact/newsroom/covid-19-hackathon/
Quote
COVID-19 Hackathon April 10-May 18
Win prizes, help flatten the curve and assist in economic recovery using COVID-19 datasets

Knowledge is power! COVID-19 is a global pandemic, and “flattening the curve” is a critical approach for slowing the spread of the disease so as to not overwhelm healthcare systems. We can use open data to create analyses and visuals to help “flatten the curve”, as well as map the economic recovery from COVID-19.

Together with our partners Cybera and the Pacific Institute for Mathematical Sciences, we invite you to participate in a virtual open data science hackathon from April 10 to May 18 to building data-driven perspectives derived from COVID-19 datasets.

Goal
The goal of the hackathon will be to collect and curate worldwide open data and to refine, transform, and link that data to provide a visualization regarding the impact of COVID-19.

We will look at two themes:
  • overall understanding of the efforts to flatten the curve
  • economic recovery especially for Alberta and Canada
This is about providing a better understanding of the story, through data.

I am still of the opinion that they have completely missed the obvious.

1) this virus is extremely communicable.
2) the moment containment is let up, absent severe controls, the virus will once again explode in the population.
3) flattening the curve is essential to prevent hospitals going into saturation and exploding the death rate.
4) flattening the curve is a short term strategy ONLY. It is tactics, not strategy. It is NOT a solution.
5) the economy cannot recover until the virus is extirpated
6) flattening the curve does NOT extirpate the virus
7) an explosion of new cases will require immediate reimposition of quarantine controls which requires business restriction. Business restriction will result in bankruptcies and failure with increasing rates until the virus is confirmed to be extirpated.
8 ) hence - failure to do the things necessary to extirpate the virus prior to relaxing controls results not in economic relief and recovery - but precisely the reverse, to horrible economic failure. Focusing on the economy as the primary concern assures failure, failure assures destruction of the economy. Until leaders and decision makers get this, they will continue to focus on solving the wrong problem, and as a result in destroying the very thing they care most about - the economy and profit.
9) add to that, failure to extirpate the virus means ultimately killing the maximum number of people (shy of the added deaths that occur when the hospitals go into saturation)

The answer has to be to focus on the primary problem which is to extirpate the virus. That includes many of the aspects of the solutions used in China, New Zealand, South Korea, and Japan.

If there is some as yet unidentified magic in Germany that is actually reducing the death rate, not just reducing the reported death rate, that too might play a role. There is however NO evidence so far that the Germans are actually reducing the lethality of the virus, or that the strain(s) in Germany is any different from anywhere else. The highest probability is that all of the strains of the virus are roughly equal in lethality everywhere on Earth, with the obvious dependencies on age, and on availability of adequate care.

Treatment interventions (drugs, herbs, ...) may play a large role. They will not substantially change the problem - extirpation of the virus and controlling its spread. This will take time to develop and assess. It will not likely be a strictly positive story.

Vaccines have a greater chance, but they will take time - lots of time. And they may not succeed at all. If they do succeed, the immunity conferred may be seriously limited.

Plasma or other interventions may play a huge role - or not. It will take time for those to be assessed. There will be negative aspects. Those likely won’t be large. However, this might not be an actual treatment solution. It is nine the less hopeful.

Inbound border control with 14-28 day quarantine, testing, isolation and ongoing follow up will be required. For countries that fail to control the virus and extirpate it, travel and trade may be all but impossible for years - or longer. Restrictions on ship crews in the same way will be mandatory. I.e. - no shore leave - for at least years. This includes major countries and groups like the US and the EU. Failing to extirpate the virus can be nationally fatal to trade.

Widespread rapid testing, tracing, follow up and isolation are essential to any solution.

Population tracking will create huge social impacts. These are essential for success. Yet, they are likely to fail due to societal objection and resistance - violent resistance.

And lastly, delay favors the virus. The longer it is around, the greater the chances are that it either mutates in ways that make it uncontrollable, more lethal, more infective, less obvious (silent transmission in some people), or that it moves into some animal reservoir that serves to make it impossible to extirpate.

Now - of course - humanity may fail to extirpate this virus. In that case, we will lose 4-12% of the population over the next year or two, and it will become an ongoing predator, culling the old and infirm, the unhealthy, and the weak. In time, those who are genetically less vulnerable will prevail and have children, lessening the impact of the virus; and conversely - suppressing those genetic lines that are less able to withstand its ravages.

Sam

24
Consequences / Re: COVID-19
« on: April 09, 2020, 10:33:52 PM »
Researchers Identify Six Drug Candidates That May Help Treat COVID-19
https://medicalxpress.com/news/2020-04-covid-drug-treatments.html

An international team of researchers has tested more than 10,000 compounds to identify six drug candidates that may help treat COVID-19.

The research, involving University of Queensland scientist Professor Luke Guddat, tested the efficacy of approved drugs, drug candidates in clinical trials and other compounds.

Professor Guddat said the project targeted the main COVID-19 virus enzyme, known as the main protease or Mpro, which plays a pivotal role in mediating viral replication.

"This makes it an attractive drug target for this virus, and as people don't naturally have this enzyme, compounds that target it are likely to have low toxicity.

Inhibitors (drug candidates):

ebselen
cinanserin
disulfiram
carmofur
shikonin
tideglusib
PX-12
TDZD-8

Open Access: Zhenming Jin et al, Structure of Mpro from COVID-19 virus and discovery of its inhibitors, Nature (2020)
https://www.nature.com/articles/s41586-020-2223-y

Shikonin is a major component of zicao (purple gromwell, the dried root of Lithospermum erythrorhizon), a Chinese herbal medicine with various biological activities, including inhibition of human immunodeficiency virus (HIV) type 1 (HIV-1). G protein-coupled chemokine receptors are used by HIV-1 as coreceptors to enter the host cells.

Ebselen (also called PZ 51, DR3305, and SPI-1005), is a synthetic organoselenium drug molecule with anti-inflammatory, anti-oxidant and cytoprotective activity.

Cinanserin (INN) is a 5-HT2A and 5-HT2C receptor antagonist which was discovered in the 1960s. The molecule is an inhibitor of the 3C-like protease of SARS-coronavirus

Disulfiram (sold under the trade names Antabuse) is a drug used to support the treatment of chronic alcoholism by producing an acute sensitivity to ethanol (drinking alcohol).

Carmofur (INN) or HCFU (1-hexylcarbamoyl-5-fluorouracil) is a pyrimidine analogue used as an antineoplastic agent. It is a derivative of fluorouracil, being a lypophilic-masked analog of 5-FU that can be administered orally.

Tideglusib (NP-12, NP031112) is a potent, selective and irreversible[1] small molecule non-ATP-competitive glycogen synthase kinase 3 (GSK-3) inhibitor.
https://www.alzforum.org/therapeutics/tideglusib

Excellent finds. And interesting target candidates. Hopefully one or more of these or related compounds can become a low-toxicity highly-effective treatment.

Sam

25
Consequences / Re: COVID-19
« on: April 09, 2020, 08:15:19 AM »
I have seen this sort of worthless data posted on line to many times already thanks.
 
Quote
NOTE: Number of deaths reported in this table are the total number of deaths received and coded as of the date of analysis and do not represent all deaths that occurred in that period.

*Data during this period are incomplete because of the lag in time between when the death occurred and when the death certificate is completed, submitted to NCHS and processed for reporting purposes. This delay can range from 1 week to 8 weeks or more, depending on the jurisdiction, age, and cause of death.

The bureaucratic delay inherent in such sources makes reference to them meaningless for a month or two yet.

Nice visualization see here >>

From here >> https://www.reddit.com/r/dataisbeautiful/comments/fxau85/the_recent_drop_in_us_pneumonia_deaths_is/

That is by far one of the best visualizations I have seen portraying the delayed reporting of data - which posts into the correct time period in the past.

It is awfully easy during an event (of many major different types), or even in industrial production, to grab data and trend it believing it is meaningful; even though it actually isn't - precisely because of this sort of information lag.

During the early months of the HIV pandemic in the 1980s I was following the data at first on a daily basis, then weekly, then monthly as CDC shifted their reporting. It was pretty easy to see that the data behaved in a mostly predictable way, with data coming in late and being posted into the correct time era in the past in a mostly repeatable manner.

The data in the graph shows similar behavior. Back in the 80's I developed a predictive algorithm in Lotus 1-2-3 to 'adjust' the reported data to estimate the likely actual data. The same appears to be possible here.

However, in the case of flu, the data is uniform enough that you can almost use the prior years as the guide to the error in the current data. By directly trending how the data changes over time, and then adjusting it based on that algorithm independent of prior years specific data, it is possible to get an early warning that things may be trending away from the prior year norms.

In the HIV case, the data always showed a rising trend (damped exponential) that turned downward at the end in the most recent reporting periods.

Perpetually the news reported that it looked like maybe we were at or near the peak. They never then went back to report that they had erred, and that no such thing had happened, and that instead that they and those who advised them had been deceived by this temporal reporting problem.

I saw this so often in my career that it is one of the first things that I look for. This especially happens when there are human reporting systems involved.

I do not believe that is what we are seeing now with COVID. It is likely that plays a role though.

It appears to me that the sheltering in place and distancing has made a serious dent in the transmission rates. This does not however mean that it will trend to zero as the models suggest. That is an artifact of errors in the assumptions in the models.

At the same time, there are clearly both unreported cases (both asymptomatic AND presymptomatic), and deaths whose causes are misassigned for any of several reasons. In some strongly rule based cultures, this is an artifact of the rules. It isn't YYY until you prove it is YYY. But absent the necessary capacity for testing, testing corpses is a low priority, so the data is corrupted; deaths assignments are recorded and reported wrongly. In those cultures, the error 'may' show up by looking at excess death rates. However, the dramatic change in human behavior from sheltering also changes the underlying statistics, so that too is not reliable.

At the same time, unattended deaths may be arbitrarily assigned any number of causes from heart disease, to pulmonary failure, uncontrolled diabetes, flu, COVID, or others based on a best assessment by a physician, or the coroner. In the US, many corners are only charitably called that. This isn't all that different from months, years, decades and centuries gone by. We just like to pretend we are better at it now than we often are. A century ago, many people died of "heart failure" who actually died of other causes. What was apparent was that the persons heart stopped beating. Absent any other cause --- heart failure.

All of that impacts the data. And as the count of cases rises, it becomes a larger and larger problem. In some ways it is akin to the "fog of war".

I don't say any of this to be critical. The reality on the ground is often different, sometimes greatly different, than we imagine or wish it to be. As a result, the data is often flawed in important and potentially deceiving ways. It is important to recognize that this is or may be happening, and not to take the data too seriously without ground truthing.

Back in the 1970s-1990s there were huge efforts at using statistical quality control, statistical process control and the like. In industrial processes, these helped. But even more than providing more and better data for controlling processes, they actually had as their purpose taking the freaking managers hands off the controls. Managers love to think they understand (when they don't) and to "prove" their worth by "fixing" things. The statistical tools forced them to take their hands off. When they finally understood that was what the tools did, they subverted the tools. This too is often a problem. Donald Trump is a prime example of that sort of stupidity, and an exemplar of how severely it can distort the data and the response; and from that the success or failure of the response.

Humans are silly creatures. We tend to believe what we want to believe, no matter the reality. The old saying "Seeing is Believing" is actually quite often precisely backward. Quite often what is seen is ONLY what is believed, and the proper saying is "Believing is Seeing", meaning that those involved not only ONLY see what they want to see and what they want to believe to be truth, but more over - they simply cannot see anything that runs contrary to their beliefs and desires. They will not even entertain the possibility that the reality is other than what they believe it to be. They can and do change the data to match their beliefs. This happens in dozens of unique ways.

It is in my experience quite rare to find people who see what is, and adjust their beliefs to match the reality, while all the while challenging whether that is the real reality, or whether the tools and systems have embedded within them preconceptions, presumptions, unstated assumptions, beliefs and biases, misunderstandings, and other failings that cause the data to portray one thing, while the reality may not be anything like that at all. And more than that - who watch for the people involved to be willfully mucking things up, even while they think they are "fixing" things.

And this doesn't even get to the willful modification of data and information to conceal things that are viewed as being contrary to the career interests of the manager(s) involved.

Sam

26
Consequences / Re: COVID-19
« on: April 09, 2020, 02:24:41 AM »
If the plasma is proven effective, as I hope it will, it is very likely worth the risks.

The risks:

Quote
Of 4857 transfusion episodes investigated, 1.1% were associated with a serious reaction. Transfusion associated circulatory overload (TACO) was the most frequent serious reaction noted, being identified in 1% of transfusion episodes. Despite clinical notes describing a potential transfusion association in 59% of these cases, only 5.1% were reported to the transfusion service. Suspected transfusion related acute lung injury (TRALI/possible TRALI), anaphylactic, and hypotensive reactions were noted in 0.08%, 0.02%, and 0.02% of transfusion episodes. Minor reactions, including febrile non-hemolytic and allergic, were noted in 0.62% and 0.29% of transfusion episodes, with 30–50% reported to the transfusion service.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5559198/

I really don't mean to be rude, but I don't think you understand this article.  The article is discussing "blood transfusions."  A plasma transfusion is *very* different.  No red blood cells, nor white blood cells, are transfused.  A plasma infusion is far, far safer.

Now, if you can find an article showing the hazards of fresh-frozen plasma, that would be relevant.

It isn’t just red cells and their proteins, or white cells and theirs that are at issue. Those are potentially very important for transfusion reaction. For the vast majority of people these do not come into play at all in terms of risks. For a small fraction of us, that is not so clear cut.

Plasma is also sterilized for pathogens. That does not assure that viruses are excluded or entirely inactivated. Neither does it always assure the all fungi and certain other organisms are eliminated. And neither does it or even can it prevent prion transmission.

These are not huge risks in the calculus for people with life threatening need for these products. And those involved have done a reasonable amount of diligence. However, that does not then translate to widespread giving it to healthy people.

Also, doing so would require a hugely expanded infrastructure to handle the added blood products. Lacking that, people who critically need these products would be denied them. More over we do not yet have very high confidence about the degree of immune protection provided. This is as yet untested.

More than this, we know that the elderly who have been exposed to more things in their lives are dying not from the virus directly, but from their own immune systems reaction to the virus as a cytokine storm damages the hearts and floods their lungs. It is not yet clear that boosting their immune response is at all the right thing to do.

Sam

27
Consequences / Re: COVID-19
« on: April 09, 2020, 01:16:41 AM »
I think governments should be implementing plasma transfusions programs really hard. This is not a revolutionary treatment but it is most likely a viable treatment.  Plasma transfusions is old medicine fraught with dangers, but antibodies are antibodies. C19 antibodies will lower the viral load in many patients.

 The problem is that the rest of the antibodies a person has will be included with the plasma, and they will also react with the recipient. A good crossmatch should avoid most adverse reactions but there are a lot of dangers inherent to blood transfusion.

Be careful what you wish for. That is how the Hep C pandemic came about - the largest single catastrophe of allopathic disease transmission known.

An explosion of Hep C, Hep B, and a dozen other diseases could result. Most of those can be detected via screening. And standard sterilization techniques should eliminate them. “Should” being the operative word. However, a lot of other infections cannot be easily detected. A lot aren’t even identified.  Neither are a whole host of immune factors. The explosion of autoimmune diseases a year or ten later will be startling, and devastating.

Caution is warranted.

Sam

All of this is seriously overblown.  Fresh-frozen plasma (FFP) is very commonly administered for a range of conditions, including the many causes of hemorrhage.  Serious reactions are rare, transmission of pathogens is very rare, and I've never heard of a late autoimmune reaction.  Risks from such therapy is minuscule compared to the risk of Covid infection in high-risk individuals.

Plasma is as carefully screened for pathogens as are whole blood transfusions.  Transmission of pathogens is very rare.

As for A/B/O blood type incompatibility, this concern is also overblown.  First, it's easy to test before infusion.  Second, reactions from such incompatibility are usually mild.

"Because plasma contains ABO antibodies, ideally, fresh-frozen plasma should be of the same ABO type as the recipient. If ABO type-specific plasma is not available, plasma of a different ABO group may be used as long as it does not have high titers of anti-A or anti-B."
https://www.sciencedirect.com/topics/medicine-and-dentistry/fresh-frozen-plasma

Unfortunately - not overblown - in my case. I have an underlying autoimmune disease that has left me with a hyperactive immune system. I am doubly weak D, and weak e through a very unusual antigen, as well as Co(a+b+). For whole blood transfusion, fatal transfusion reaction is a distinct likelihood. I seem to also have an unusual HNA. It is not something I am willing to gamble with given any alternative.

Broad use of plasma (IF IT ACTUALLY WORKS TO TRIGGER AN IMMUNE RESPONSE) makes possible sense in patients with COVID. Doing so willy nilly in those without the virus risks unnecessary injuries.

In the case of Hep C, the physicians thought they knew what they were doing. They didn't. The result was millions of cases of Hep C that then propagated world wide, through IV drug use, sexual contact and for 30% of cases - no known mechanism of transfer.

In the 1950s and 1960s, millions of people were inoculated with Polio vaccine that unknown to those who developed it was contaminated with Simian Virus 40. I lost friends to that. They died of brain cancers in their 40s. I am in that cohort. And I may well have received the tainted vaccine. I likely did. If I did, I was lucky. I survived it.

Blood is complex. There are myriad factors involved that we do know. And there are myriad factors that we do not know. Blood transfusions are routine, as are plasma, platelets and other factors. These have been tremendous in their saving of lives. They have also cost lives in the process because of things we did not know.

There are many unknowns involved. Jumping to answers can be quite dangerous. Caution is in order.

That said, for those with serious illness from COVID the calculus is quite different. The risk is worth taking. For the general population, NO.

Sam

28
Consequences / Re: COVID-19
« on: April 08, 2020, 09:55:37 PM »
I think governments should be implementing plasma transfusions programs really hard. This is not a revolutionary treatment but it is most likely a viable treatment.  Plasma transfusions is old medicine fraught with dangers, but antibodies are antibodies. C19 antibodies will lower the viral load in many patients.

 The problem is that the rest of the antibodies a person has will be included with the plasma, and they will also react with the recipient. A good crossmatch should avoid most adverse reactions but there are a lot of dangers inherent to blood transfusion.

Be careful what you wish for. That is how the Hep C pandemic came about - the largest single catastrophe of allopathic disease transmission known.

An explosion of Hep C, Hep B, and a dozen other diseases could result. Most of those can be detected via screening. And standard sterilization techniques should eliminate them. “Should” being the operative word. However, a lot of other infections cannot be easily detected. A lot aren’t even identified.  Neither are a whole host of immune factors. The explosion of autoimmune diseases a year or ten later will be startling, and devastating.

Caution is warranted.

Sam


29
Consequences / Re: COVID-19
« on: April 08, 2020, 08:45:03 PM »

Convalescent serum is shaping up to be a highly effective treatment (unsurprisingly):

Effectiveness of convalescent plasma therapy in severe COVID-19 patients
https://www.pnas.org/content/early/2020/04/02/2004168117

This treatment (or any effective treatment) is a game-changer for the global trajectory of this pandemic.

Especially since rapid testing results are being rolled out, a treatment approach can be used to dramatically reduce severity and mortality of infections.  That is, when a person with serious symptoms or high risk for a bad outcome is found, that person can promptly be given an infusion.   We can anticipate a dramatically reduced severity and duration of illness, dramatically reduced deaths, and dramatically reduced demand for ICU beds and ventilators.

Supply of convalescent serum will be an initial constraint.  However, a unit of plasma can be divided among 4 recipients,  and donors can give plasma weekly.  (the red blood cells are returned to the donor, so time between donations can be much shorter than for whole blood donations, and volume donated is also larger).

The technology used is pretty low-tech.   This treatment approach has been used for a century.  Even extremely poor nations can do do donations, centrifugation, and infusions.

This treatment (or any effective treatment) can transform this pandemic from a disaster to something not much worse than a bad influenza season.

We just all need to stay alive for the next month or so for this to be widely available.

There are a number of caveats.

1) There need to be enough donors
2) It needs to be shown to be effective (as yet unproven)
3) There needs to be sufficient testing capability (a severe and very serious limitation)
4) The donors and recipients must be matched for plasma type.

Plasma donation and receipt work differently (backward from) whole blood.

Type AB is a universal donor for plasma. Type O is a universal receiver.

The normal cross reactivity issues with blood should not apply. E.g. for me - I can only receive whole blood from about 1 person in 7,600. I have an extremely rare blood type. For plasma, I should be able to receive from almost anyone.

People with other blood types have other issues. Someone with type AB+ blood can receive whole blood from almost anyone (there are rare exceptions), but plasma only from people who are type AB.


30
Consequences / Re: COVID-19
« on: April 08, 2020, 07:33:51 AM »
There are 4 ways out, in order of preference:

1. Vaccines.
2. "a scalable treatment tolerated by a large segment of the population thats easy to give to people"
3. Virtual extinction through quarantine followed by universal masking and intensive testing/tracing/isolating
4. Herd immunity. Let it burn. Maximum fatalities occur and long term consequences are unimaginable.

4 may be out of the question if 1/3 of immunes become susceptible.

Agreed.

A vaccine doesn’t yet exist. At least six different (and possibly as many as twelve) vaccine candidates are in the works. They will take time, likely at least 12 months and more likely 18-24 to develop. There is no guarantee that any of them will result in a successful and safe vaccine.

Treatment has some hope. However, so far there is no magic bullet for treatment.  A few things help now to varying degrees - azithromycin (and possibly cefazolin) [antibiotics that also bind the spike protein and act as antivirals], tocilizumab and related IL-6 inhibitors, remdesivir (and related antivirals), then to a lesser degree hydroxychloroquine {note: 4/10 - it is now clear that Hydroxychloroquine presents an unacceptable cardiac risk; and Chloroquine is even more dangerous}, quercitin, rutin and other flavanoids and flavonoids (each of which binds the spike protein or other parts of the virus thereby inhibiting its function). Ciclesonide may be important for asthmatics. Honeysuckle, Forsythia & Scute, possibly with other herbs like Bupleurum may be useful as well.  It seems likely that a multipronged approach will be needed combining compounds that bind the spike protein, compounds that inhibit IL-6 and possibly other immune system factors, compounds that bind the ACE2 receptor reducing viral access, and targeted short lived locally acting steroids, plus support for cardiac and kidney function and protection.

A better approach might appear. With extensive modeling and targeted design, it is conceivable that a targeted compound might be developed that either binds to the virus rendering it inert without causing harm, or a targeted enzyme might be developed that cleaves the virus into nonfunctional parts. These are as yet not even theoretical. They will also require testing if they are developed. And that too will take time.

Plasma treatment from recovered patients might prove to be a viable treatment as well. Early tests are in progress now.

In a year and a half from now, or longer, option 1 and 2 may play a major role. For now option 2 plays a limited role in treatment.

That leaves options 3 and 4. Option 4 is clearly unacceptable in its several variations. Yet that seems to be the chosen plan in most nations on Earth.

Option 3 has several variants as well. The Japanese approach was valiant. It’s not succeeding. The South Korean approach has also been valiant. But it too is mostly a guard action. The Taiwanese approach worked initially and is now in trouble.

The Chinese approach has worked, though it is a model most nations seem entirely unwilling to follow.

That brings us to New Zealand. So far their approach is working. Can they maintain it?  Will it go the way of Japan and South Korea?  Time will tell.

Both the Chinese and New Zealand approaches are clearly superior to the failed approaches in most countries.

The sub option of option 4 of of putting a malignant narcissist imbecile in charge and letting him randomly decide based on what he thinks makes him look good, or what profits him or his friends is clearly failing. That is a bad model for any country to follow.

It is also important that any option(s) taken must complete in less than two years. The duration of natural immunity from recovery from this virus is as yet unknown. For SARS1 the immunity most often seemed to last about two years with a weakened resistance in the third year. Some individuals appear not to build lasting resistance. Any option(s) requiring more than two years to complete will not be able to eradicate the virus.

It is also vitally important that whatever option is taken that it allows for support of individuals and small businesses throughout the control and eradication period, and that allows a resumption of near normal business activity in a period less than 4-6 months long. Most cases of option 4 fail that test. The option to allow the disease to immediately infect the entire population would meet this criteria, but at the horrible and unacceptable cost of killing more than 10% of the population.

This brings us back to some extremely aggressive version of option 3 combined with aspects of option 2, as we await development of option 1.  And that again brings us to China and New Zealand.

Sam

31
Consequences / Re: COVID-19
« on: April 08, 2020, 02:24:40 AM »
Here is why Jacinda Ardern is one of my heroes.

New Zealand isn’t just flattening the curve. It’s squashing it.

https://www.msn.com/en-us/news/world/new-zealand-isnt-just-flattening-the-curve-its-squashing-it/ar-BB12gstI?li=BBnbfcL

It is possible to beat this virus. Doing so requires wisdom and diligence. New Zealand is now one of the few success cases.

The US due to the actions of many though not all the States has greatly reduced the growth rates. New York and Washington in particular have made great strides. These are as yet far from success. But they are better. That shows up as the current confirmed infection count now being five days behind my projection based on the rates two weeks ago. Those rates will likely slow more.

However, this is only a slowing. This is in no way success. Once the people tire enough of the restrictions and begin to venture out more, the viral transmission will again rise. This will cause the infections to continue for the long term, requiring ongoing shelter in place for month after month after month, destroying the economy in the process. And the longer this goes on, the greater the chance that the virus mutates into an even more virulent and/or an even more lethal form.

If this problem is to be solved, either solutions like those used in China, New Zealand, or possibly South Korea (though that is less successful), OR herd immunity will be required. Achieving herd immunity while not overwhelming the hospitals means that we stay under the current restrictions for at least another year, and possibly as long as two years. That means economic suicide for businesses large and small, for individuals, and for the nation.

Worse though, achieving herd immunity means that a tremendous number of our neighbors will sicken and die.

Just how long will it take our moron in chief to understand this? That’s a rhetorical question. He is entirely incapable of ever understanding or accepting that. Neither is he able or likely willing to understand the necessity of following the path Jacinda has lain out. Moreover, there is no way in hell that he will follow a woman’s lead. So we are stuck here until he is out of office. And that means an ongoing large death toll month after month until then.

Sam

.... and it begins.

A ‘Liberty’ Rebellion in Idaho Threatens to Undermine Coronavirus Orders

https://www.msn.com/en-us/news/us/a-liberty-rebellion-in-idaho-threatens-to-undermine-coronavirus-orders/ar-BB12gfO9

Stupid is as stupid does.     This is why we can’t have nice things.

But then on the success side of the ledger...

China lifts 76-day lockdown on Wuhan as city reemerges from coronavirus crisis

https://www.cnn.com/2020/04/07/asia/coronavirus-wuhan-lockdown-lifted-intl-hnk/index.html

Eleven weeks of lockdown - then recovery.

Addenda: This is not going to resolve as Dr. Fauci thinks or wants to optimistically believe. He is being foolish or self-deluded. This bug is as contagious as Chicken Pox. If we fail to eradicate it or totally contain it, it will immediately come roaring back. This is an extremely dangerous biosafety level 3 agent.

Under current strategies. Schools will not reopen in the fall. Neither will businesses.

The models are wrong in showing a peak then a decline to zero. They only go to zero, because the modelers included on-going highly effective controls in their models. You only get a decline to zero if you achieve herd immunity, or you maintain conditions that prevent transmission sufficiently to accomplish the same AND you do extensive contact tracing and isolation BEFORE releasing controls. Do anything less and it comes right back.

Worse, we do not yet know how long immunity to this bug lasts. The history from SARS1 suggests two years on average with a weak immunity in year three. But, some people exhibit a weaker immune response and can contract it again almost immediately.

This thing is not going to just “be around” as Dr. Fauci suggests, it is a violent virulent predator waiting for us to let our guard down in the least to devour people and ravage the nation - again.

32
Consequences / Re: COVID-19
« on: April 01, 2020, 09:53:19 AM »
Yes.
This is a horrible pandemic.
We must look back to the 1918 influenza to grasp its severity. 


For some perspective, there were about 50 million dead from that flu in 1918, and the global population was about 1.7 billion people.
So a death rate of close to 3%.

The C19 will kill a few million people out of a global population of about 7.7 billion people. A death rate of maybe 0.3%.
C19 is roughly about 1/10 as deadly.
And it will not even dent the incredible population growth going on at the same time as this pandemia: "The current average population increase is estimated at 81 million people per year."
https://www.worldometers.info/world-population/#growthrate

Please stop trying to minimize the danger of this virus. It is vastly more lethal than you want to believe. And a whole lot of people are going to get sick over the next two months with an immense number dying. Cut it out.

We get that you do not want to believe the facts in front of you. That is just plain stupid.

Sam

33
Consequences / Re: COVID-19
« on: April 01, 2020, 09:51:37 AM »
China may not be done yet. They are just now past 10 weeks of quarantine. But ...

From the Guardian.

https://www.theguardian.com/world/live/2020/apr/01/coronavirus-live-news-us-deaths-could-reach-240000

"Authorities reported 130 new asymptomatic cases on Wednesday, bringing the total number of such cases under observation to 1,367."

Sam

34
Consequences / Re: COVID-19
« on: April 01, 2020, 05:49:25 AM »
Another Clusterfuck In the Making: Defense Secretary Won't Yet Evacuate Virus-Hit  Aircraft Carrier
https://www.axios.com/pentagon-wont-evacuate-coronavirus-hit-carrier-f5c6ff7e-1122-4dd7-ab59-54c23883261f.html

Defense Secretary Mark Esper told CBS' "Evening News" Tuesday he doesn't think "we're at that point" of evacuating a nuclear aircraft carrier docked in Guam with more than 100 crew members infected with the novel coronavirus.

The big picture: The captain of the U.S.S. Theodore Roosevelt has asked the U.S. Navy for more resources. Esper said he'd yet to read the letter in detail, but they're trying to contain the virus aboard the ship. "We're providing additional medical personnel as they need it," he said. Acting Navy Secretary Thomas Modly told CNN earlier Tuesday they were working to remove most of the 4,000 people on board the vessel

https://mobile.twitter.com/CBSEveningNews/status/1245122122042785793

... “The Diamond Princess was able to more effectively isolate people onboard than TR, due to a much higher percentage of individualized and compartmentalized accommodations onboard for paying customers. Their measures still allowed hundreds of people to become infected," Capt. Crozier wrote.

“Keeping over 4,000 young men and women on board the TR is an unnecessary risk and breaks faith with those Sailors entrusted to our care," Crozier wrote.

The captain asked for “compliant quarantine rooms” onshore in Guam for his entire crew “as soon as possible.”

On Friday, there were reports of at least two dozen positive cases. But by Monday, a senior officer aboard the massive aircraft carrier told the Chronicle between 150 and 200 sailors had tested positive.

... "We have been working actually the last seven days to move those sailors off the ship and get them into accommodations in Guam. The problem is that Guam doesn’t have enough beds right now." - Acting Navy Secretary Thomas Modly

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

Update: US Navy Evacuating Aircraft Carrier Infected by Coronavirus
https://www.defenseone.com/threats/2020/03/us-navy-evacuating-aircraft-carrier-infected-coronavirus/164254/

The U.S. Navy says it will remove the majority of USS Theodore Roosevelt’s crew so the aircraft carrier can be disinfected, one day after its commanding officer sent an urgent message asking for help controlling a COVID-19 outbreak.

A skeleton crew will man critical stations while Theodore Roosevelt is disinfected pierside in Guam, Acting Secretary Modly said.

“The spread of the disease is ongoing and accelerating,” Crozier wrote in the March 30 letter, which was obtained by the San Francisco Chronicle. “Decisive action is required.”

... Modly said that testing aboard the Roosevelt was initially limited to about 200 sailors per day. He said that will soon be increased by sending tests elsewhere for processing.

A tougher environment to disinfect can scarcely be imagined. A Nimitz-class carrier has more than 3,000 spaces — “rooms,” to non-sailors — that hold all manner of complicated and dangerous machinery, up to and including nuclear reactors.

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

At 5 a.m., the total number of known DoD cases — currently infected, deaths, and recoveries — was 1,295, up 19% from yesterday.

As well, cases being treated at Veterans Affairs hospitals and facilities more than doubled over the weekend, to 1,166

Oh my. Trying to sterilize the engineering spaces while keeping the reactors operating. Oh my. Oh my. Best bet. Tie up to shore power, go to minimum ops. Station security in full mop. And shut down the reactors. Sterilize everything. Then bring in the {gold|blue} crew - whichever wasn’t on board - after verifying that none of them are infected. They might have to go to a blended crew.

Sam

Addenda: added point. Trump’s stupidity has now affected the readiness of the fleet at sea and our national defense in the process. Well done bozo. Flailing and failing on every front - Health, Commerce, Defense, State, Veterans, Interior, the Environment, Treasury, Justice, Ag, Labor, HUD, Energy and Homeland Security, FBI, Customs - you name it. He has messed it up. All that King dipshit touches turns to crap.

35
Consequences / Re: COVID-19
« on: April 01, 2020, 01:32:26 AM »
Vox,

I won’t upstage you by posting the links to the breaking news stories. Actually I am steaming just a little too much to do it. ....

The chief turd after two months of delay and denial, deflection, insults and harangues, and a near endless stream of self serving lies now finally tells the US today to prepare for a terrible two weeks, and potentially 100k-240k deaths.

As you all here know I have been projecting far worse than that for quite literally months now. This wasn’t a surprise. This wasn’t unexpected. This wasn’t unavoidable. This is a Trumpian induced catastrophe. It took Trumpian levels of gross incompetence to kill this many Americans. Other nations have their own equivalents.

I am disgusted in the extreme. I said before that the data and numbers would ultimately tell the tale. Well, we are nearly there. And even now, finally saying the catastrophe will be enormous, they are still grossly downplaying the reality, the horror, of what is about to happen.

Worse, they are gaslighting everyone by showing their pretty (but entirely wrong) Gaussian projections of 1.5 - 2.2 million deaths (that they never shared before) flattening out to 100k-240k with the implication that they did great things to reduce the death toll. But they cannot even keep their story straight. Dr. Birx stands in front of that chart. And separately another chart with a fat right tail from the actual (but still horribly wrong) models. Those wrongly show the case counts going to zero sometime in June or early July.

What is it? Two weeks? No. 30 days? No. Two months? No. Two and a half? Still No!  They cannot even keep their gaslighting story straight.

Fuck you Donald Trump. You did no such thing. Any reduction came from the States acting on their own independently of you and your stooges, with daily and even hourly opposition, stonewalling, deflection, and impedements from you personally and from your administration, fighting you every fucking step of the way. 

And yes, even now, at this very last moment they could save millions of lives if they would just face the truth honestly and act swiftly. They cannot do it. They cannot bring themselves to do it. All they know how to do is double down on PR and lies. Burn in hell bastards.

Be safe everyone. Keep your loved ones and friends safe, safe as you can. Duck. Duck now. The shit is beginning to hit the fan in a big bad way.

For any of you who are first responders or critical staff in any role - THANK YOU! in advance for the risks you are takling for all the rest of us.

Sam

36
Consequences / Re: COVID-19
« on: March 31, 2020, 09:48:45 PM »
If you can not get masks spray the virus away.
Masks and hand sanitizer are unattainable here all stock sold out long ago due to hording.
I use methylated sprints* mixed with a little water and detergent in a spray bottle
Every surface I touch out side of home gets a spray before contact  when possible.
Obviously not possible in shops
In that case I take care to limit contact and spray my hands, car keys ,door handle, steering wheel bank card etc and all goods as soon as I can .
We have good distancing and shops are only allowing limited  persons to enter at a time.

*Methylated spirits Denatured alcohol  is almost pure ethanol here with bittering agent and color added .  water to slow the evaporation rate down, detergent as a surfacent.
It is probably not good for my hands to wash them in almost pure alcohol but who cares if it stops me getting sick or dying. 
 

Add a bit of skin softener (aloe, calendula, ...) and add just a bit of water (~1 part water to four parts alcohol) to get the alcohol down to 70% by volume plus anything you want for fragrance. Peppermint or lavender are excellent, lemon balm, lemon myrtle, ... are also very good. And they add a tough of antiviralness of their own.

70% alcohol is the ideal concentration for denaturing viruses. And it is more gentle on your skin.

If liquor stores are open near you, you can also buy 190 proof grain alcohol. Everclear in the US, other names elsewhere. It will work as well.

Denatured alcohol usually has methanol in the blend as well.

Sam

37
Consequences / Re: COVID-19
« on: March 31, 2020, 08:55:44 PM »
Sam, Good story ! I would rather swim with sharks .
Yesterday I talked with some friends who I have known long enough to watch as their children have grown and had children of their own. Husband wife , grandmother and three children were here taking care of their chicken coop. They came to talk as I was out hoeing weeds in the garden. Everybody knows to keep a distance !  I asked about PPE and explained how to use them . Apparently even gloves are hard to find. Alcohol wipes gone for awhile now. I gave them a dozen pair of gloves and a big new bag of alcohol wipes.
 I keep meeting people who are completely unprepared for what is happening. Or maybe they are just more ready to accept what I am trying to fight. Without adequate PPE for both the medical community and the public, and without good consistent messaging about how to use PPE there remains a huge percentage of the American public walking around naked agains’t this pandemic.
 Like others here I am pessimistic about outcomes and that is a reflection of what I am seeing when      I ( rarely ) venture out. It is a reflection of what I am hearing from friends and neighbors. It is very close now , +twenty in north county SB yesterday. Ten ICU patients in just one hospital. Not seeing evidence of masks or gloves. Wuhan,  NYC, Lombardy , Madrid are just the first big hits. This is going to keep ramping up here in S.Cal unless something like a real quarantine gets implemented. Not just here either, everywhere .
 

That all is concerning. However, information alone can save lives. Knowing how easily the disease spreads, it is easy to minimize contact. Knowing soap and water are excellent at removing and destroying it, combined with knowing that once you touch anything ’out there’ that you need to consider your hand contaminated until you clean it, and to not touch your face - can save lives. It’s the simple stuff that is really important.

But then too, this applies in thinking about how this ends. I looked through one of the models that Dr’s. Fauci, Birx, and others are relying upon. The model is vastly better. They took their hands off the settings and let the data adjust the model. This is good in so far as the data is good. When the data isn’t good, the model goes awry. Still it is better.

And it is good in so far as the model is constructed well. Unfortunately the model is not constructed well. There are presumptions built into it that cause it to fail. These are clear and obvious.

What is most obvious is glaringly obvious, yet has been missed. The model shows a peak in mid-April to mid-May in all locations. It then declines to zero cases by June! That is NOT going to happen. 

They comment on the model that they presume that self-isolation, distancing ... continue through then. That is an assumption, and a critical one. But, that is not sufficient to get to zero cases. What is clear is that the model fails to adequately assess just how infective this disease is. It then falsely and wrongly has it burning out by June.

That simply isn’t going to happen. The pandemic will, even with restrictions in place, continue to burble along.  And the moment the restrictions ease, it will explode again, and again, and again.

What is required to stop it is to 1) Go into hard medical quarantine. This requires that all those critical staff of all types take much enhanced precautions. Even then, they alone will keep the infection chains alive.  2) Massive testing to find the contact chains, to isolate them, and extinguish them. 3) Contact tracing to support 2). And it will take time. The infectivity of this virus is such that in the wild it requires 90+% of the people to have had the virus and to have recovered for it to die out on its own. With self-isolation ... that might be something like 50-60%. But the model doesn’t reflect that.

The model being wrong as it is still projects 100k-200k deaths. That is catastrophic enough. But continuing the infection chains will cause the death toll to be much higher.

Without recognizing these flaws, the experts, and hence the decision makers cannot see that the self-isolation phase will have to continue for something like a year. That is economic suicide.

So what to do. Save the economy by lifting restrictions? That is immoral, unethical, and just plain stupid. It would kill millions and bankrupt the nation. 

The right answer is what it has been since the beginning. Tell the people as plainly and clearly as possible what is required. Seek their help. They will help. Tell them what they can and must do for us to all win. And then and only then impose the strictest quarantines possible. At the same time ramp up production of masks, PPE, ventilators etc...  Push heavily in investigating treatments. Field those early, as early as possible. Push hard on vaccine development, though not crazy hard. Consider other options too.

The right answer will look a lot like China. Get over past animosities, hatreds, and stupidity.  Get over racism, economism, and all the other mental straightjackets. Use what works.

Otherwise, we are caught here in an endless nightmare.

On the flip side, enormous good is, or may, come from this. The environment is improving with our absence. Well that is if we can stop the morons from using this as an opportunity to gut environmental laws. The liars and miscreants are becoming plain. Unfortunately the pain and suffering will have to be very much greater to break their stranglehold on the body politic. And yes I am referring to the dear leader and his supporters, and lackeys. And it may require many of them contracting the virus and dying of it, for real change to happen. But they do not want that change. And they will do everything they can to hold on to power - until their hands are beaten bloody and ripped from the levers of power.

People are having the opportunity to stay home and to be together. They/we are learning what is truly important in our lives. Yes, there is enormous economic hardship. That will lead to massive changes. A lot of people will suffer horribly and unnecessarily. That suffering will no doubt drive demands for different approaches, for change.

Work will likely not return to what it was. Work from home will be vastly more common. The arguments against it have been destroyed.

Etc...

More than this, the modelers seem to have entirely forgotten the lessons of the past, particularly the lessons from the 1918-1920 flu pandemic. This virus, like that virus, is mutating rapidly. The longer it remains in the world, the more likely it is that somewhere a variant will come into existence that will make this version look mild. When (not if) that happens, the second more fearsome wave will start. Then the third. Then the fourth. The model presumes this does not happen - entirely without basis for doing so.

It will be fascinating to see just what changes finally come from this. And it will become a time to mourn.

Sam


38
Consequences / Re: COVID-19
« on: March 31, 2020, 06:52:53 PM »
Harpy,

I know this us useless and I am wasting my breath.

Please stop being a racist.

Sam

39
Consequences / Re: COVID-19
« on: March 31, 2020, 06:51:19 PM »
Covid-19 had similar symptoms to the illness that was caused by vaping.

Vitamin E acetate found to be the reason for vaping deaths

Link >> https://marketrealist.com/2019/12/vaping-deaths-caused-by-vitamin-e-acetate-cdc-says/#adnrb=900000

Not vaping per se is causing these problems, but the wrong use of Vitamin E acetate in vaping liquid.

Kari,

Blumenkraft got it exactly right. Your question is a good one. The symptoms are similar in some ways. This is because both vaping with Vitamin E acetate and the SARS-COV-2 virus cause damage to the same parts of the deep tissue of the lungs and to somewhat the sane degree. They do their damage in different ways.

We have alluded to how SARS-2 does damage, though we haven't directly talked about it. Mostly this is through the immune system itself causing the damage through interleukin 6 (IL-6) and a huge reaction with cytokines (a so-called cytokines storm). The drugs and herbs that work against SARS-2 work in a bunch of very different ways.

Some like azithromycin work by binding to the spike protein of the virus making it hard to mate to the ACE2 receptor. The ACE2 receptor is how it invades the cells.

Others like the inhaled steroid Alvesco work by locally suppressing the immune system (cytokines, interleukins, chemokines, etc...).

Others like many of the herbs and some of the drugs work by either binding to the ACE2 receptor, or by looking like the ACE2 receptor and acting as a sort of decoy for the virus.

Others yet work by interfering in various parts of the immune response (especially IL-6) to slow or stop that and in so doing to slow or stop the damage.

Etc...

For vaping, the problem was different. Vitamin E acetate has two parts. The first part, the vitamin E, is generally good for health. However, vitamin E isn't one substance. It is instead eight substances. These come in two forms tocopherols and tocotrienols. These are slightly different chemical forms that the body can use. Each of these can exist in four different orientations or configurations. Long story there, but it's not important. They are labeled alpha, beta, delta and gamma. One form of each are quite important for health. The tocotrienols are generally good and important for health. The tocopherols generally aren't, and can cause worsening health. The form that is best for each is not usually the form found in supplements.

Ok that was long, but the gist is this. Vitamin E isn't always beneficial. And the form used in vaping fluid very likely wasn't helpful, and may have been somewhat harmful. But that wasn't the key. Focusing on the vitamin E likely caused misdirection away from the real problem.

They key is the other part, the acetate. When the Vitamin E acetate enters the delicate cells deep in the lungs it separates into its two parts - Vitamin E, and acetic acid. That last part is vinegar. But this isn't vinegar like you are used too. This is concentrated. And there in lies the problem. Concentrated vinegar is a powerful corrosive destructive acid.

My personal opinion is this. And it is only my own personal opinion. This is not a medical diagnosis. I am not a doctor. Neither is it backed up by scientific research. It is born from my own personal experience having inhaled both glacial acetic acid vapors and concentrated ammonia. Do not ever do either of these. You -will be- seriously injured! That I escaped injury is equal parts luck and -extreme- experience.

What seems to have happened is that the vapers inhaled enough acetate to chemically burn the deep tissue of their lungs. That burn continues until the acid is neutralized or diluted. The obvious easy treatment that I haven't heard that anyone tried was to inhale very very low concentration ammonia. Ammonia, which is a caustic, causes lung damage as well. Intentionally inhaling that is a really bad idea. However, if you are being eaten alive by inhaled acid, you have to stop that.

Without stopping the acid or diluting it, the acid continues to chemically burn the tissues. The body responds to that by engorging the tissues with fluid (diluting it), and by recruiting every aspect to fight it as if it were a severe infection. This then acts a lot like what happens in SARS-2.

Sam

40
Consequences / Re: COVID-19
« on: March 30, 2020, 10:23:08 PM »
Is it too early to call daily peak globally (at least for this season)? I think so. There has to be at least a couple more days of a downward trend. But at least after weeks of fear, quarantines and horrible news, we are starting to see some good news, or more like a light at the end of the tunnel.

Not even close.

Sam

41
Consequences / Re: COVID-19
« on: March 30, 2020, 09:09:55 PM »
I don't know about Seattle, maybe the infection rate has dropped from 2.7 to 1.4 only, but in Europe, the drop must be so much bigger. Car traffic has fallen by 70%, public transport use by 80-90% in Budapest, no kids go to school, most people work from home, etc.
 
Even if the original R0 was 3, it must be very significantly below 1 by now. Same probably true for most of Europe. Europe is peaking right now (except for idiots who wouldn't do quarantine)

“Must be” doesn’t enter into it. That is an emotional driver. There is what is and what isn’t. That is what matters.

Sam

Addenda: I should also note that in real events conflicting information is frequent. Sorting out what is meaningful and real is critically important. Until that happens, all of it has to be considered potentially credible and acted upon to the degree possible, with caveats.

Many real world disasters and catastrophes were made vastly worse because key decision makers locked up at key points and chose which information they wanted to believe. Chernobyl is one of those. Often the decision makers in those cases decided that the right information “must be” XYZ. 

42
Consequences / Re: COVID-19
« on: March 30, 2020, 09:08:41 PM »
Quite an effort to keep track of sam’s various projections for the US death toll.  25 million, 5 million, 12 million.

We have Dr. Fauci now using a range of 100-200k.  You would expect him to not be the type to exaggerate, so perhaps this is on the low and uncertain side.

Despite some of the generalizations here that the US population is flouting guidance and society is operating BAU, a large number of Americans have been under some degree of physical distancing and/or stay at home orders.  There is some evidence in a few larger metros of case growth slowing.  Too early to draw conclusions, and yes that spreads out the effect over time until there is a vaccine.

I’m in an urban area of Florida, and expect a very bad April and May due to demographics and slow adoption of measures across the state.  Even so, in the absence of data or facts I wouldn’t expect the catastrophic tolls statewide or nationally that some here are pushing.

The future is constantly in motion. As events change, as new data comes in projections (these are neither forecasts nor predictions) do change.

People get hung up on numbers. In catastrophes, projections form a key tool in assessing where things are headed so that experts, decision makers, and all of the emergency managers, planners, responders can prepare and work to CHANGE conditions to reduce the future projected impacts.

Do NOT ever make the mistake of thinking that any of these projections are cast in stone. The only projections that are close to that are the near term projections that account for the lag time between infection and confirmation. Even these have large uncertainties. And don’t think of those as uncertainty bounds. This isn’t statistics, and we have nothing like a representative or full sample assessment. The larger the base of information, the closer the projections are likely to be.

Also, do NOT allow your emotions, wants or desires to enter into this. Doing so if you have any influence at all gets people injured and killed.

Sam

43
Consequences / Re: COVID-19
« on: March 30, 2020, 06:51:41 AM »
Sam, sources don’t seem to back your claim of 35-50 % hospitalization rate. I remember seeing 20% by the WHO and below source states 20.7 - 31.4 % in the US.

https://www.statista.com/statistics/1105402/covid-hospitalization-rates-us-by-age-group/

We need to remember children have extremely low rate of hospitalization.

Possible, but sorting out presymptomatic from asymptomatic is vital along with a temporal follow up. Did the people in the study ultimately go to hospital or not? And what are the statistics for their outcomes. There is nothing simple about answering these questions to get truly meaningful data in the midst of a rapidly expanding pandemic.

Sam

44
Consequences / Re: COVID-19
« on: March 30, 2020, 06:22:45 AM »
Thank you Sam for this and other thoughtful posts, painting the oncoming catastrophe.
I keep trying to think what could make the expected catastrophe go away, and I don't mean actions in this sense, but what major piece of data could turn out to be the crucial factor that makes actual reality less dire than the predictions. IMHO the direr the predictions, the more important this thought exercise becomes.

In other words - where could you be wrong in your predictions?

This is crucial. It is a huge part of figuring out what is real, and what is wrong. It is also crucial for finding vulnerabilities to try change the course of events in beneficial ways, and to avoid horrible paths. I would love to be wrong!

Quote
The only factor I can find so far that could make a large difference is the number of asymptomatic cases. If if turns out that for each diagnosed case there are 10 or 20 undiagnosed mild cases that go nowhere and generate immunity, then the total fatalities and total hospitalizations should be much lower than expected in the dire scenario, and the disease will peak much earlier as it runs out of available hosts. How sure are we of this factor?

This would be wonderful if it were true. And a lot of folks want it to be true. Wanting doesn’t make it so.  We have extremely little data about this so far. The two data points we have suggest a ~65:35 or ~50:50 of non-hospital vs. hospital cases. We will know more in the future. But for now, it is crucial we not bet on such speculation. The downside risk of horrible outcomes makes making any assumption along these lines extremely dangerous. Even taking the 65:35 ratio as a guide is quite dangerous. It may lead decision makers to take less strenuous actions that that and we cannot recover from.

We also have no data on what the disease course or severity is for the non hospitalized portion of the infected population. They may have less disease (mostly due to age and health), or they may be very similar to the hospitalized portion.

We seriously need more data here. Gathering it is difficult.

Also, it is common for some fraction of the population to be relatively invulnerable to various diseases. Often the why of that is not known. In the case of norovirus, people who genetically lack a particular enzyme are wholly unaffected. The virus cannot get into their cells. There might be some portion of the population that is invulnerable or natively immune to this virus. I have seen no data to suggest this is true though.

Quote
Other factors that keep being thrown around:
The climate or weather or seasons - doesn't seem so far to make much of a difference, looking at countries around the world. but bears to keep an eye on.

This is possible, but seems highly doubtful. If it were true, we would expect to see major differences in countries based on their latitude and current weather. Those don’t seem to be at all apparent.

Quote
An effective treatment - from what I've seen so far there is no magic bullet in existence. This will take time and will likely be available only after the main global wave of fatalities is over.

I actually have more hope here. The supercomputer modeling work is very promising. A number of likely existing compounds have been identified. Quercitin, Luteolin, and Yerba Santa, plus several prescription drugs with low toxicities and side effects are promising starts. Azithromycin alone or in combination with Hydroxychloroquine also may play a role.

The prescription IL-6 inhibitor Tocilizumab looks extremely promising for critical patients. Other IL-6 inhibitors may also be hugely important.

Remdesivir and Favipiravir, as well as others, also look promising for early treatment.

Most fascinating is the potential for BCG vaccine to play a major role in decreasing vulnerability.

Quote
An effective and safe vaccine - as above, this will take time and will likely be available only after the main global wave of fatalities is over.

Yes, particularly conventionally developed vaccines. The new constructed vaccines are as yet unproven but have tremendous potential.

Quote
Variations between populations - that the Italians and the Chinese and the Americans are more susceptible due to pollution and malnutrition - doesn't seem to bear out so far. Nearly all countries exhibit the same data trajectory.

I would love to hear your and others' input on this.

This will be interesting in retrospect. It likely won’t play a major role.

Sam

45
Consequences / Re: COVID-19
« on: March 30, 2020, 12:42:05 AM »
Ok, thanks for your honest responses, Sam. I will note that many voices in the media and among what I will called "the recognized experts" are advancing the narrative that getting to that first plateau is "great news" and evidence that there is clear light at the end of the tunnel. The standard narrative is that once the big first flush of cases subsides a bit and the daily multiplier starts dropping from say 1.4x to 1.2x, the "worst is behind us".

In no way saying this is right, only that it is very widely stated.

As in war there are battles and campaigns and fronts in this struggle too. This plateau is a victory in a battle. It doesn’t mark the end of the war. There is a long way to go. As with war, winning a battle can lead to over confidence resulting in losses and setbacks.

Just as in war there are tremendous logistical issues, tactical issues and strategic issues still ahead.

Sam

46
Consequences / Re: COVID-19
« on: March 29, 2020, 11:04:57 PM »
In the meantime, cursing is no reason for me to stay inside. I intend to go to work tomorrow at the university. The canteen will still be open.

So - cursing offends you. But the huge death tolls don't. Man that is quite the set of values and priorities you have.

Sam

47
Consequences / Re: COVID-19
« on: March 29, 2020, 11:03:28 PM »
Before this is done, it now looks like this virus will kill between 1.5% of the populations in countries like South Korea, and 4% of the world generally, except China, as the medical systems are destroyed globally, ERs are overrun, and the ICU treatment fails under the load. Sam

Ok, let me make my query more explicit. Italy has been at about 800 fatalities a day for the last 8 or 9 days. Italy has a population of about 60M. 4% of 60M is 2.4M. It would take 3000 days at 800 fatalities a day to reach 2.4 million.

So, is the current plateau a false one? Will something change to make the daily rate skyrocket in the future? That's what I'm asking.

I suspect it is a little of both. They are working like hell to curb the thing. That is a part of the plateau. No doubt reporting problems are also a part.

But, how long can they keep up this level of control? Is the control tight enough to stop the spread?

If it isn't tight enough (a la China), then the first question is only a matter of timing. When the controls are relaxed even a little the deaths surge. If the controls are held then for the next 12-18 months things stay as they are with the enormous carnage continuing.

Sam

48
Consequences / Re: COVID-19
« on: March 29, 2020, 10:59:55 PM »
There is a very slight glimmer of something, that the US rates appear to be slowing. The timing is right for this to be a reflection of the stay home efforts. This doesn’t fix anything. It only spreads out the damage, lessening the impact on hospitals (still catastrophic) while increasing dramatically the duration of the economic destruction.

Sam

This appears to be the case in several places.  Italy appears to have reached a peak in its new infections and new deaths. They are bouncing around a bit, but not increasing day over day.  Can you explain where you think it might go from here?  The health care system in Lombardia is deeply stressed, but not collapsed. I don't think other areas of Italy are far over capacity.  It seems like the hospitals should be able to now mostly keep up, and perhaps start to get some breathing room if the rates slow a bit more.

Obviously that leaves a long slog to go, but is catastrophe guaranteed?  Can you lay out a time line that you expect to see?

dnem,

I wish I had a clue. Exponentials tend to run away rapidly if you don't aggressively control them. That is equally true in nuclear reactors, chemical reactions leading to deflagrations and explosions, and biologic growth. The details are different for each of these classes, but the principles are the same.

Riding on top of an exponential and trying to control it is delicate and dangerous. You have to have intense negative feedbacks built into the system that work at speeds faster than the exponential driver. Humans aren't nearly fast enough. In nuclear reactors this is accomplished in several ways. Yet every now and then the control conditions are exceeded or people intervene to do stupid stupid things, and in nearly the blink of an eye things go all pear shaped at the very best and catastrophically destructive at the worst.

For chemical reactions it is even dicier though with smaller consequences. Riding the edge of a thermal kinetic reaction is scary - terrifying actually. When they run away the result immediately is a BLEVE (that is a terrifying thing you never ever ever want to experience), detonations (well, you likely won't survive that), or if you are really lucky - deflagrations. You might survive that, maybe, with massive experience and a huge dose of luck. Following the initial event, there may be subsidiary events. Flee! And there are often toxic releases that are vastly more catastrophic than the initial blast.

For biologics, well - you are now living through one of those. They are perhaps the scariest of all and have the largest most catastrophic consequences. They are also the slowest to develop. They too may have secondary and tertiary effects and follow on waves of new infections with similar or different properties that evade most of whatever we learned in the first wave.

Riding on an exponential to try to control it goes as you are seeing it now play out with COVID. If you are really really good, brutal, and fast, as China was, you might just control it - if you are very very good and very very lucky.  Staying in control is like riding a bucking bull bare hand on the deck of a small ship at sea in the midst of 150 foot crashing waves from a hurricane while a team of snipers is shooting at you.  Good luck with that. Catastrophe is all but assured.

And that is where we are now. The catastrophes are playing out in over 100 countries. The experts are behind the curve and applying tools honed for mild seasonal epidemics and ill suited to rapidly spreading pandemics. This thing is moving far faster than anything the vast majority of them were ever trained for. This is a run away.  By that I mean it is running away on its own & your best answer is to run away from it as fast as you possibly can, slamming doors behind you as you go.

When people understand things like this, they act accordingly. I was once involved in an actual activation of a criticality alarm at a US Government site (a detected nuclear run away). It turned out to be a false alarm triggered by a technician working on the alarm system - live. ALL of us ran faster than we have ever run in our lives to flee the area. I saw a coworker quite literally jump over a 12 foot fence on the dead run without ever touching it. Stress can cause you do do amazing things.

For this, we cannot run away. There is no "away" to run to. We have to stand and fight. That fight in this case means sheltering in place until the danger passes. But, this will take long enough to pass that some of us will have to brave it out. These are the heroes. These are the emergency workers of all types and kinds from the obvious from line - the doctors, nurses, EMTs, and their support staff - people like the janitors who are heroes in this battle - to clearly visible people like grocery clerks and staff - to the nearly invisible - the postal workers and delivery people, the long haul truckers, the farm laborers that keep the crops coming in, the restauranteurs and others who keep people paid and working in ways no one planned for, and the emergency operations people who work long hours behind the scene working the logistics to make things happen.

Then there are the people who think they are important and who demand praise - and their front men and women. These are not generally heroes, with exceptions like Governors Cuomo and Inslee. Mostly they are buffoons, cowards, conmen, thieves, and idiots like Trump, Pence and three score dozen (now less) of other Governors in the US. Other nations have their equivalents. (corrected)

As to where this goes and what the time line is?.... well that very much depends on the actions each country, and region choose to take, how well they implement those, and how clearly they think the problem through.

It doesn't matter whether anyone thinks they have the right answer. It will be crucial to watch the data, seek the data, and act on that. By that I absolutely do NOT mean the usual scientific methods. Those are mostly wonderful for proving things, though even there they have terrible failings in dozens of ways. What I do mean is using real time data to make real time decisions and to take real time actions. That involves a good deal of estimation and guess work. It will be at least slightly wrong all of the time. Most of the time it needs to be close. And those "working the problem" must constantly be seeing new insights, new information, new analyses to gauge where they have gone wrong, where they and we are vulnerable - to act - boldly and quickly - all the while knowing that you are going to make mistakes. Some of those will be terrible. And you have to keep moving. You cannot stop or even pause for long.

If all of that goes well, you get the outcome China had. Societally that has huge negative repercussions that will take decades to work through. And it too can go all pear shaped in a whole lot of ways. A political revolt to those limitations during the response can lead to utter collapse and catastrophe. Overly suppressing such feelings can result in equally dire outcomes. The Chinese deserve huge credit for threading the needle in this crisis. Will that ultimately work out well? Who the hell knows? That depends on the leaders involved and on the mass of the populace. If the leaders can avoid the tendency toward authoritarianism - perhaps. If the public can be patient and do their part - perhaps.

The West lacks many of the tools the Chinese had. Can we lead people by example to get them to adhere tightly enough to what is needed to succeed? I sincerely doubt that. One need only look to Donald Trump's followers to see that in spite of direct evidence they believe insane things and act on those beliefs. You can see some of that here.

Desires and core beliefs have to change to succeed. I do not see that happening.

As a consequence, I suspect that most of the world will either let the virus mostly run free with an enormous death toll and financial and economic consequences, OR they will try to ride herd for a time, then ultimately give up (a la Donald Trump deciding to let up before Easter). Depending on how long that takes or how quickly, that too will have even more devastating effects.

Ultimately what is likely to bring it to an end is either of two things.

1) The virus burns itself out having infected 90% of the population. That leaves behind the huge death tolls that are now so obvious.

2) Vaccines are successfully developed and deployed. I do not see that happening in less than a year.

Some nations and places will no doubt try other strategies. And we will ge two see how effective those are and what consequences they bring with them.

One such that seems likely is having everyone over a certain age (55-65) ordered to shelter and stay sheltered for at least six months, likely longer. And then allowing the rest of the nation to intentionally get the disease to try to burn it out of the population through herd immunity. They then also support the older population by bringing things to them while they are isolated.

Would that work? Who the hell knows? But I can envisage some nation trying it.

In the mean time, we can work like hell to try to soften the blow and limit the damage.

Sam

49
Consequences / Re: COVID-19
« on: March 29, 2020, 08:51:38 PM »
Is Sweden now the only country that's going for group immunity ?

Is there any other way? Does any country believe they can hold out until mass vaccination would be available? Or a cure?

I watched https://www3.nhk.or.jp/nhkworld/en/ondemand/video/5001289/
In that Japanese video, the government expert was not confident that they would be able to avoid overshoots of the healthcare capacity.

I am happy not to be locked up. Cycled to a café in the countryside for coffee and cake.

China.

50
Consequences / Re: COVID-19
« on: March 29, 2020, 08:36:54 PM »
Well, I find you quite unfair with Taiwan. +15 is not a lost of control for a country with almost 24 million inhabitants.

If you look at the situation in South Korea or Japan, I think also that it is early to say that they lost the control. Maybe they had a bad day.

Well, if these countries loose control, I guess we'll go all for herd immunity.

Added : maybe confinement is getting difficult to support for some people and this could create some more infections, but if most of the people are careful, this could be just like I said a few bad days.

Perhaps, I am being unfair.  Both countries have a slim chance of regaining control. But it is a very slim chance. The next two to three weeks will be key. If they follow China’s approach, they could regain control. Otherwise, they have lost.

The same holds true around the world. The US has days to make a meaningful difference. But with the current leadership, there is no real chance that anything will be done to meaningfully alter the course. Italy and Spain are likely beyond the point of no return.

Others have a chance, a slim one as well, to make a substantial difference in the outcomes.

The key in all cases is for the leaders and experts to face the brutal truth, and act boldly in accord with what we now know. I won’t hold my breath for that. (That is an American expression that may not translate well. It means - I don’t hold any hope at all.)

There is a very slight glimmer of something, that the US rates appear to be slowing. The timing is right for this to be a reflection of the stay home efforts. This doesn’t fix anything. It only spreads out the damage, lessening the impact on hospitals (still catastrophic) while increasing dramatically the duration of the economic destruction.

Sam

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