Coronavirus

Raven-Knightly · May 8, 2020, 3:15am

(The Atlantic, May 7, 2020):

“The Problem With Stories About Dangerous Coronavirus Mutations -
There’s no clear evidence that the pandemic virus has evolved into significantly different forms -
and there probably won’t be for months.”

“We have evidence for one strain,” says Brian Wasik at Cornell University. “I would say there’s just one,” says Nathan Grubaugh at Yale School of Medicine. “I think the majority of people studying (coronavirus genetics) wouldn’t recognize more than one strain right now,” says Charlotte Houldcroft at the University of Cambridge.

Everyone else might be reasonably puzzled, given that news stories have repeatedly claimed there are two, or three, or even eight strains. This is yet another case of confusion in a crisis that seems riddled with them. Here’s how to make sense of it.

Whenever a virus infects a host, it makes new copies of itself, and it starts by duplicating its genes. But this process is sloppy, and the duplicates end up with errors. These are called mutations - they’re the genetic equivalent of typos. In comic books and other science fiction, mutations are always dramatic and consequential. In the real world, they’re a normal and usually mundane part of virology. Viruses naturally and gradually accumulate mutations as they spread. …

… There’s no clear, fixed threshold for when a lineage suddenly counts as a strain. But the term has the same connotation in virology as it does colloquially - it implies importance. Viruses change all the time; strains arise when they change in meaningful ways. New strains of influenza arise every year. These viruses quickly acquire mutations that change the shape of the proteins on their surface, making them invisible to the same immune cells that would have recognized and attacked their ancestors. These are clearly meaningful changes - and they’re partly why the flu vaccine must be updated every year.

But influenza is notable for mutating quickly. Coronaviruses - which, to be clear, belong to a completely separate family from influenza viruses - change at a tenth of the speed. The new one, SARS-CoV-2, is no exception. “There’s nothing out of the ordinary here,” says Grubaugh. Yes, the virus has picked up several mutations since it first jumped into humans in late 2019, but no more than scientists would have predicted. Yes, its family tree has branched into different lineages, but none seems materially different from the others. “This is still such a young epidemic that, given the slow mutation rate, it would be a surprise if we saw anything this soon,” Houldcroft says. …

… This isn’t to say that the Los Alamos study is bad or wrong - it comes from a respected team and presents interesting data. But the evidence it provides cannot distinguish between two equally plausible explanations - that the G-viruses were more transmissible, or that the G-viruses were just lucky. …

… The bottom line: It will take time to know whether different strains of the new coronavirus even exist, let alone whether any are more or less dangerous than the others. Any claims of that kind should be taken with a grain of salt for the next several months, if not longer. “In the short term, it’s highly unlikely that we’d be able to define new strains,” Wasik says.

Raven-Knightly · May 8, 2020, 3:51am

(CNN, May 7, 2020):

“Rollout of antibody tests met with confusion, little oversight”

… the rollout of millions of antibody tests in the US has created frustration and division among state health departments due to a mix of questionable tests, shifting federal rules and a hodgepodge of different methods for tracking results. While the Centers for Disease Control and Prevention has launched a strategy to use antibody tests for surveys that study the spread of the virus in different locations and populations, the federal government has not coordinated an effort to track the raw data of antibody tests performed in all states. Instead, the Trump administration has instructed states to develop their own testing plans, and now states are split on what to do with antibody tests. …

… out of 41 states that responded to an inquiry from CNN, only 22 states said they are currently tracking or collecting data on antibody testing in some way. Some of those states, including New York, Louisiana and California, now require labs to report results of antibody tests, while others have launched limited surveys to study antibody prevalence. Further complicating matters, some state health departments have expressed concerns about the reliability of available antibody tests, many of which initially came on the market without undergoing review by the Food and Drug Administration. … A CDC spokesperson said the agency does not have estimates on how many antibody tests have been done or information on all of the results of these tests.

Raven-Knightly · May 8, 2020, 7:17pm

(The Guardian, May 2, 2020):

“‘How is this possible?’ Researchers grapple with Covid-19’s mysterious mechanism -
Doctors are still exploring exactly how the coronavirus affects the body,
and what its long-term impacts might be”

… there is no way of knowing which patients will be affected by the most severe symptoms. Clinicians like Darley hope that a disease biomarker - a unique characteristic in the blood, body fluids, or tissues - will eventually be discovered for each stage. … “I don’t think it’s clear yet whether it’s the virus infecting the lungs and the blood vessels, or if it’s the body’s immune system which goes out of control which then causes lung and blood vessel injury,” Darley said. “Or, it could be a combination of both."

“The pathogenesis is not clear yet. We are observing brain inflammation in a subset of patients, and in those we are seeing agitation and a change in behaviour or personality. That’s really interesting, and there are reports coming from elsewhere of some people, including younger patients, suffering stroke. It’s unclear whether the virus is infecting the lining cells of blood vessels in the brain, or whether the patient’s blood is excessively prone to clotting because of all the inflammation, leading to stroke.”

Darley said scans of the lungs of Covid-19 patients are unique, showing “ground glass opacity”, a hazy pattern that does not obscure the underlying lung structure. Lung cancer, for example, would typically show on a scan as a dark, solid lesion, obscuring other structures in the lungs. While other illnesses, for example bacterial infections, can result in ground glass opacity on a scan, there were some unusual features on scans for Covid-19, Darley said. “It has a classic pattern in Covid,” he said. He suspects men are more severely affected than women because the virus is activated by an enzyme controlled by androgens, a group of hormones that play a role in male characteristics.

Raven-Knightly · May 8, 2020, 7:38pm

New IMHE Model Projected Total Released Today for the USA: 182,844 US deaths (by Aug 4, 2020)

Considered over 6 months time (from Feb 4, 2020) that would be almost exactly 1,000 deaths per day.

Update (May 8): Since May 4, estimated number of deaths by August 4 has increased by ~1464 / day.

Source: https://covid19-projections.com/

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(STAT, May 1, 2020):

“Three potential futures for Covid-19: recurring small outbreaks, a monster wave, or a persistent crisis”

What all three scenarios agree on is this: There is virtually no chance Covid-19 will end when the world bids good riddance to a calamitous 2020. The reason is the same as why the disease has taken such a toll its first time through: No one had immunity to the new coronavirus.

SessionDrummer · May 8, 2020, 10:34pm

In DE…

Once they’re here, Delaware will be able to test 80,000 residents per month, the release said. That’s more than quadruple the state’s current testing capacity.

The state will prioritize these tests for certain people:

Anyone with symptoms
Anyone who knows they were exposed
Residents of long-term care facilities, such as nursing homes and assisted living facilities
Elderly residents
Low-income residents
African Americans
Latinos
Certain front-line essential workers. Public health officials are still working on which front-line workers will be prioritized, according to a spokesman for the governor

BoDarc · May 9, 2020, 1:44am

Uhm… and now this

Raven-Knightly · May 9, 2020, 2:09am

I ain’t got no worry about no Kawasaki, as my righteous ride is exclusively on my ginormous Bultaco !

Freddie3 · May 9, 2020, 4:11am

Where do you draw the line? C-19 or Mental Disorder caused by the NEWs and everyone else’s fears and panic.

Mass hysteria" redirects here, - Mass psychogenic illness** ( MPI ), also called mass sociogenic illness , mass psychogenic disorder , epidemic hysteria , or mass hysteria

Raven-Knightly · May 9, 2020, 4:16am

I firmly believe that Boron infusions are the answer, due to many years spent studying Magical Thinking

If a little knowledge is dangerous, where is the man who has so much as to be out of danger?
-Thomas Henry Huxley

Raven-Knightly · May 9, 2020, 4:43am

… because the mind is not an object like the body, it is a mistake to apply the predicate disease to it. … Although medicalization encompasses more than psychiatry, we must be clear about one thing: Psychiatry is medicalization through and through. Whatever aspect of psychiatry psychiatrists claim is not medicalization, is not medicalization only if it deals with proven disease, in which case it belongs to neurology, neuroanatomy, neurophysiology, neurochemistry, neuropharmacology, or neurosurgery, not psychiatry. Psychoanalysis is medicalization squared. It is important, in this connection, not to be fooled by lay analysis, clinical psychology, or social work. These and other nonmedical mental-health and counseling “professions” are medicalization cubed: as if to compensate for their lack of medical knowledge and qualifications, nonmedical mental-health “professionals” are even more deeply committed than psychiatrists to their claim of special expertise in the diagnosis and treatment of mental illnesses. … In short, medicalization is neither medicine nor science; it is a semantic-social strategy that benefits some persons and harms others.

Source: “The Therapeutic State - The Medicalization of Everyday Life”; Thomas Szasz (2007)

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(See Chapter 5, on Page 27):
“Diagnoses Are Not Diseases”,
“The Medicalization of Everyday Life - Selected Essays”;
Thomas Szasz (2007)

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(Nature, May 5, 2020):

In 2018, psychiatrist Oleguer Plana-Ripoll was wrestling with a puzzling fact about mental disorders. He knew that many individuals have multiple conditions - anxiety and depression, say, or schizophrenia and bipolar disorder. He wanted to know how common it was to have more than one diagnosis, so he got his hands on a database containing the medical details of around 5.9 million Danish citizens. He was taken aback by what he found. Every single mental disorder predisposed the patient to every other mental disorder - no matter how distinct the symptoms. … the way clinicians have partitioned mental disorders is wrong. Psychiatrists have tried to solve this by splitting disorders into ever-finer subtypes. … if researchers hoped to demystify psychopathology, they still have a long way to go: the key finding has been just how complex psychopathology really is. … Many now agree that the diagnostic categories are wrong.

Raven-Knightly · May 9, 2020, 3:22pm

(New York Times, May 7, 2020):

“Government Orders Alone Didn’t Close the Economy.
They Probably Can’t Reopen It.
Data shows there was a drop in spending and working
even before any official mandates to stay at home.”

Well before shutdown orders, restaurant reservations were plummeting. Electricity usage, which falls when office buildings and factories empty out, was dropping, too. Public transit in many cities was in free fall. So was the number of air travel passengers passing through T.S.A. checkpoints. Such data, combined with opinion polling today, suggests that Americans who were turning off the economy on their own may not readily reopen it soon - even if officials say it’s OK to. …

… findings in the Nationscape surveys are remarkably consistent across different groups. Residents of states that have already reopened or plan to soon are about as wary of these activities as residents of states that remain locked down, a pattern also found in polling by The Washington Post and the University of Maryland. … Vast majorities … say they would not ride public transit, attend sporting events or go on a flight. Majorities of both say they wouldn’t send their children back to school, a prerequisite to resuming many economic activities. “Here’s this moment where almost everybody in the country agrees on a number of different things,” said Lynn Vavreck, a political scientist at U.C.L.A.

Raven-Knightly · May 9, 2020, 7:20pm

(Nature, May 8, 2020):

“Coronavirus blood-clot mystery intensifies -
Research begins to pick apart the mechanisms behind a deadly COVID-19 complication”

Blood thinners don’t reliably prevent clotting in people with COVID-19, and young people are dying of strokes caused by the blockages in the brain. … Researchers have also observed miniature clots in the body’s smallest vessels. … Why this clotting occurs is still a mystery. One possibility is that SARS-CoV-2 is directly attacking the endothelial cells that line the blood vessels. … The virus’s effects on the immune system could also affect clotting. … there could be other factors at play that aren’t specific to COVID-19. People with the disease who become hospitalized typically have a number of risk factors for clotting. They might be elderly or overweight, and could have high blood pressure or diabetes. They show up with high fevers and, because they’re seriously ill, have probably been immobilized. They might have a genetic predisposition to clotting, or be taking medications that increase the risk.

Raven-Knightly · May 9, 2020, 8:29pm

(MedicalExpress, May 8, 2020):

“Uncovering the potency and evasiveness of the COVID-19 virus”

SARS-CoV-2, the virus that causes COVID-19, is highly infectious. Curiously, in many patients, it triggers poor immune responses, which prolongs illness. This helps the virus spread widely, exacerbating the global pandemic. In a new study published in the “Proceedings of the National Academy of Sciences”, researchers at the University of Minnesota identified the biochemical mechanism that may explain how the virus infects people efficiently while evading their immune responses. …

… Specifically, the team of scientists investigated how the virus “unlocks” human cells using a surface spike protein as the “key.” They made three important findings:

the tip of the viral key binds strongly to human cells;
the tip of the viral key is often hidden; and
when new virus particles are made, the viral key is already pre-activated by a human enzyme.

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The full text of the referenced article (excerpt below): “Cell entry mechanisms of SARS-CoV-2”

SARS-CoV-2 spike binds to its receptor human ACE2 (hACE2) through its receptor-binding domain (RBD) and is proteolytically activated by human proteases. … Here we investigated receptor binding and protease activation of SARS-CoV-2 spike using biochemical and pseudovirus entry assays. Our findings have identified key cell entry mechanisms of SARS-CoV-2. First, SARS-CoV-2 RBD has higher hACE2 binding affinity than SARS-CoV RBD, supporting efficient cell entry. Second, paradoxically, the hACE2 binding affinity of the entire SARS-CoV-2 spike is comparable to or lower than that of SARS-CoV spike, suggesting that SARS-CoV-2 RBD, albeit more potent, is less exposed than SARS-CoV RBD. Third, unlike SARS-CoV, cell entry of SARS-CoV-2 is preactivated by proprotein convertase furin, reducing its dependence on target cell proteases for entry. The high hACE2 binding affinity of the RBD, furin preactivation of the spike, and hidden RBD in the spike potentially allow SARS-CoV-2 to maintain efficient cell entry while evading immune surveillance. These features may contribute to the wide spread of the virus. Intervention strategies must target both the potency of SARS-CoV-2 and its evasiveness.

daath · May 9, 2020, 11:45pm

About a week ago, maybe a bit more, I downgraded my own guesstimate on COVID-19 “true” mortality rate from 0.8% to 0.75%

It looks like a good guess …

Australian scientists compared 13 studies and concluded that 0.75% is a good guess.

That means for every 133 infected, one will die …

Raven-Knightly · May 10, 2020, 12:07am

If I calculate todays (Johns Hopkins) world COVID-19 mortality divided by confirmed cases (6.937%), the ratio of that divided by 0.75% is factor of ~5.25. I may have missed some of your methodology in deriving your ongoing estimates - but (in a simplistic sense), your estimate would seem to imply ~19% of all SARS-CoV-2 infections presently existing on the planet have been diagnosed (thus “confirmed”) ?

One thing that deserves mention is that the short-term (and even potentially permanent) effects upon one’s internal organs and nervous system from contracting the (disease state) “COVID-19” exceeds a simple “binary” dead or alive. The patients (already) most vulnerable (with cardiovascular, kidney, liver, pancreas, as well as lung conditions) can be irreversibly damaged/compromised. As well, people having the above listed chronic conditions and pre-existing disease-states are often immune-compromised, elongating recovery times, as well as likely making lasting and robust immunity to viral re-exposures less likely (actually “true” for all, as far as we presently know). This virus is notably cryptic, adaptive.

There seems to be little doubt that the treatment costs have/will severely strain the US for-profit system.

Reading published accounts of people who have recovered is always humbling and thought-provoking:

(Science Magazine, May 8, 2020):

“‘Finally, a virus got me.’ Scientist who fought Ebola and HIV reflects on facing death from COVID-19”

SessionDrummer · May 10, 2020, 12:21am

Well that seems quite a bit lower than what was being predicted previously.

daath · May 10, 2020, 12:26am

Yes, I believe the “confirmed cases” numbers are useless. We simple haven’t tested enough.
A truly mind boggling number of infections are not recorded at all.

I originally played around with the numbers - South Korea was very useful to play around with. Pretty early on, I noticed that if I set the mortality rate to something high like 5% and calculated the number of infections, that number would be lower than the confirmed cases, which obviously makes no sense. I think initially my guesstimate was 1.5% and has slowly declined since, to 1.2% to 1% to 0.9% then 0.8% and then I settled a bit more than a week ago on 0.75% (also based on stuff I read).

Here is a graph of S. Korea with a mortality rate of 1.95%:

This graph shows that if it was 1.95% they would have tested ALL infected persons in the beginning of March. That of course doesn’t make sense - there has to be unrecorded cases, because they didn’t test everyone.

The dates are 22 days delayed, meaning that when a person died, they were infected 22 days earlier. In the beginning I read that the average time from infection to symptoms was 10 days, and a further 10 days to succumb to the disease. I’ve since adjusted it to 22 days. This number is also uncertain, as I don’t have much data on it - I know that in Denmark the intensive care patients are there very long before they either die or recover - up to 3 weeks.

This is the same graph with a mortality rate of 0.75%:

This looks much more reasonable and reveal that they only “found” about 1/3 of the infected people 22 days ago…

This is the same graph for the whole of the US:

Spain is starting to look better:

As is Italy:

France as well:

UK not so good:

General for the whole world:

Another number that is interesting to look at for predictions, is number of hospitalizations - but those numbers are hard to come by …

daath · May 10, 2020, 12:30am

Depends on where you read, I think. A lot are actually talking about “Case Fatality Rates” which just uses the number of confirmed cases vs. dead - and as I mentioned, I don’t think we can use the confirmed cases number for much, because of how little we test…

Raven-Knightly · May 10, 2020, 5:00am

300 Million years. Several hundred times the age of bozo erectus. We are “just another substrate”.

(Nature, May 4, 2020):

“Profile of a killer: the complex biology powering the coronavirus pandemic -
Scientists are piecing together how SARS-CoV-2 operates,
where it came from and what it might do next -
but pressing questions remain about the source of COVID-19.”

Estimates for the birth of the first coronavirus vary widely, from 10,000 years ago to 300 million years ago. Scientists are now aware of dozens of strains (3), seven of which infect humans. Among the four that cause common colds, two (OC43 and HKU1) came from rodents, and the other two (229E and NL63) from bats. The three that cause severe disease - SARS-CoV (the cause of SARS), Middle East respiratory syndrome MERS-CoV and SARS-CoV-2 - all came from bats. But scientists think there is usually an intermediary - an animal infected by the bats that carries the virus into humans. With SARS, the intermediary is thought to be civet cats, which are sold in live-animal markets in China.

Caped_Conspirathist · May 10, 2020, 6:18am

It might if you’re healthy enough to take it. I hear that stuff can be brutal.