Coronavirus

[cherdano]

I have a lot more sympathy, or at least empathy, for vaccine hesitancy.

 

• It's just a strange thing. You feel perfectly fine. You get an injection, and now you feel bad for a day.
  
• Some genuinely have a fear of needles.
  
• You live in the US. You don't have health insurance. When you are sick, you try to get by with house remedies, because who knows what you might get charged. You know people who did go to the doctor or hospital and got a ridiculous bill. Who knows what bill you might get for getting vaccinated.
  
• Pharmaceutical companies and FDA have a revolving door between them. The trial had some remarkable results, everyone was cheering, but then suddenly vaccinated had to wear masks again after all because the vaccines weren't working any more. First they said we need 2 shots, then 3, and now I know plenty who got omicron despite having gotten three vaccine doses.
  

I mean, personally I know exactly what is wrong with the last two, but I don't blame anyone for believing them.

 

Now, the Robert Malones and Alex Berensons and Bret Weinsteins of the world, they should know better, they have caused incredible harm, and if the world were just they would spend the rest of the lives miserable in jail (and that's only because my version of justice is a very lenient one).

[johnu]

[*]You live in the US. You don't have health insurance. When you are sick, you try to get by with house remedies, because who knows what you might get charged. You know people who did go to the doctor or hospital and got a ridiculous bill. Who knows what bill you might get for getting vaccinated.

In the US, Covid vaccinations are free, regardless of immigration or health insurance status so there will not be any "bill".

[cherdano]

In the US, Covid vaccinations are free, regardless of immigration or health insurance status so there will not be any "bill".

I know that. But I don't blame anyone for assuming otherwise, or not fully trusting the claim that it is free.

[pilowsky]

This conversation highlights the problem when the health of the population is an individual problem and not a human right.

Yes, the vaccine is free in America, but what happens if you have a side-effect and need to go to the Doctor?

In America any interaction with the health-"care" system brings with it the risk of incurring a debt.

Wages in the USA are low.

Among the major race and ethnicity groups, median weekly earnings of Blacks ($805) and

Hispanics ($799) working full-time jobs were lower than those of Whites ($1,030) and

Asians ($1,384). By sex, median weekly earnings for Black men were $807, or 71.5 percent

of the median for White men ($1,129). Median earnings for Hispanic men were $845, or 74.8

percent of the median for White men. The difference was less among women, as Black

women's median earnings were $802, or 85.4 percent of those for White women ($939), and

earnings for Hispanic women were $733, or 78.1 percent of those for White women.

Earnings of Asian men ($1,499) and women ($1,165) were higher than those of their White

counterparts.

A visit to the doctor might cost more than 10% of your weekly earnings.

And that's if nothing happens apart from a chat.

Treatment of hypertension is another area where the sufferer is typically symptom free (until they have a heart attack or stroke).

The cost of medication is several hundred dollars/year.

Add on other disorders and all those people living on an income below the median quickly find it hard to weigh up the pro's and cons of paying.

 

Surprisingly, the bulk of the population are not retired (or active) mathematicians that play Bridge.

They find it hard to juggle these costs and risks and keep food on the table.

[akwoo]

In my rural US county, there are several places in the county seat where one can get vaccinated, and one pharmacy in another town that offers vaccines a few days a month. That's it. Some folks would have to drive 50 miles one way partly over dirt roads to get the vaccine.

 

Not surprisingly, the county vaccination rate is at about 50%, despite most of the folks in town (at least by my perception) getting vaccinated.

[y66]

https://www.nytimes.com/2022/01/31/opinion/covid-pandemic-end.html

 

Most histories of the 1918 influenza pandemic that killed at least 50 million people worldwide say it ended in the summer of 1919 when a third wave of the respiratory contagion finally subsided.

 

Yet the virus continued to kill. A variant that emerged in 1920 was lethal enough that it should have counted as a fourth wave. In some cities, among them Detroit, Milwaukee, Minneapolis and Kansas City, Mo., deaths exceeded even those in the second wave, responsible for most of the pandemic’s deaths in the United States. This occurred despite the fact that the U.S. population had plenty of natural immunity from the influenza virus after two years of several waves of infection and after viral lethality in the third wave had already decreased.

 

Nearly all cities in the United States imposed restrictions during the pandemic’s virulent second wave, which peaked in the fall of 1918. That winter, some cities reimposed controls when a third, though less deadly wave struck. But virtually no city responded in 1920. People were weary of influenza, and so were public officials. Newspapers were filled with frightening news about the virus, but no one cared. People at the time ignored this fourth wave; so did historians. The virus mutated into ordinary seasonal influenza in 1921, but the world had moved on well before.

 

We should not repeat that mistake.

 

True, right now we have every reason for optimism. First, Omicron cases are declining in parts of the country. Second, nearly the entire U.S. population will soon have been either infected or vaccinated, strengthening their immune systems against the virus as we know it now. Third, although Omicron is extraordinarily good at infecting the upper respiratory tract, which makes it so transmissible, it seems less able to infect the lungs than earlier variants so it is less virulent. It is entirely possible and perhaps even likely that, spurred by a better immune response, the virus will continue to decrease in lethality; indeed, there is a theory that the 1889-92 influenza pandemic was actually caused by a coronavirus called OC43, which today causes the common cold.

 

All of which makes overconfidence, indifference or weariness, after two years of battling the virus — and one another — a danger now.

 

Signs of weariness — or misguided hope — are everywhere. Although more than 70 percent of the adult population is fully vaccinated, progress has stagnated, and as of Jan. 27, only 44 percent had received boosters, which provide vital protection against severe illness. Although most of us, especially parents, want schools to stay open, parents have gotten only about 20 percent of children ages 5 to 11 fully vaccinated. As in 1920, people are tired of taking precautions.

 

This is ceding control to the virus. The result has been that even though Omicron appears to be less virulent, the seven-day average for daily Covid-19 deaths in the United States has now surpassed the Delta peak in late September.

 

Worse, the virus may not be finished with us. Although there’s a reasonable likelihood that future variants will be less dangerous, mutations are random. The only thing certain is that future variants, if they are to be successful, will elude immune protection. They could become more dangerous.

 

That was the case not only in 1920 with the last gasp of the 1918 virus, but also in the 1957, 1968 and 2009 influenza pandemics. In 1960 in the United States, after much of the population had achieved protection from infection and a vaccine, a variant caused peak mortality to exceed the pandemic levels in 1957 and 1958. In the 1968 outbreak, a variant in Europe caused more deaths the second year, even though, once again, a vaccine was available and many people had been infected.

 

In the 2009 pandemic, variants also emerged that caused breakthrough infections; one study in Britain found “greater burden of severe illness in the year after the pandemic” but “much less public interest in influenza.” Researchers blamed the government’s approach for that. In the first year, the public health response was “highly assertive,” chiefly in providing information; there were no lockdowns. In the second year, they found, “the approach was laissez-faire.” As a result, “a large number of deaths, critical care and hospital admissions occurred, many of these in otherwise healthy people of working age.”

 

Such precedents should make us wary. Vaccines, the new antiviral drug Paxlovid and others could end the pandemic, once billions of doses become widely available globally and if the virus does not develop resistance. But the end is not going to arrive anytime soon. The immediate future still depends on the virus and how we wield our current arsenal: vaccines, masks, ventilation, the antiviral drug remdesivir and steroids and the one monoclonal treatment that still works against Omicron, social distancing and avoiding crowds. As a society, we have largely abandoned the public health measures on that list. As individuals, we can still act.

[y66]

Makes you think

 

Fox News wanted viewers to hear an anti-vax trooper’s story – until he died of COVID.

 

The network has yet to mention Robert LaMay's passing, after turning him into a culture war hero for resigning rather than getting vaccinated. https://mediamatters.org/coronavirus-covid-19/fox-news-wanted-viewers-hear-anti-vax-troopers-story-until-he-died-covid

[thepossum]

A number of stories recently requiring Covid fishing expeditions with between 80-90% of cases either asymptomatic or not feeling sick enough to worry

 

Ignore duplicate

 

In other news I am excited, disappointed and relieved to report that my first RAT was negative. Positive would have been a terrible expensive inconvenience for me and many others. Negative was a relief that I could visit some people

 

Positive would have challenged my ethics and respect for the law. I may have had to carefully sort a few things out and hide by myself for a while

[y66]

 

Two bits of good Covid news today in the UK.

 

First, adding another two weeks of ONS data means Covid’s infection fatality rate has now crossed below the "2x flu" line.

 

Latest IFR is roughly 60% higher than flu and still falling.

 

Second, today’s gold-standard ONS infection survey shows prevalence is flat or falling across all English regions (falling in most), i.e the observed decline in cases is not simply due to people becoming less likely to test.

 

The temporary rise as schools reopened was just a blip

[y66]

Got a Covid Booster? You Probably Won’t Need Another for a Long Time by Apoorva Mandavilli at NYT

[cherdano]

Got a Covid Booster? You Probably Won’t Need Another for a Long Time by Apoorva Mandavilli at NYT

 

I am afraid this article is just completely removed from actual clinical reality. In the UK data, already 10-14 weeks after a Pfizer booster (following Pfizer primary series) we see a waning of efficacy against hospitalisation from close to 90% to around 75% - i.e., more than a doubling of the hospitalisation rate.

 

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1055620/Vaccine_surveillance_report_-_week_7.pdf

 

It's nice that T-cells hold up, but nothing in Mandavilli's article discusses how effective they are at preventing severe outcomes.

 

Over the last 6 months, the NYT unfortunately has consistently and drastically undersold the amazing effectiveness of boosters. I have no doubt that it has contributed to the very low booster uptake in the US, which in turn has contributed to the large omicron death toll.

It's nice to see them turn around and hype the value of boosters now. Though I can't notice this only happens when it can become an argument against a 4th dose...

 

I find it really sad how bad the NYT's coverage of covid data has been. Stacking Leonhardt and Mandavilli at the NYT up against John Burn-Murdoch at the Financial Times or Eric Topol on twitter, and it's such an embarrassing comparison for one of the richest and most influential media companies in the world.

[Cyberyeti]

I am afraid this article is just completely removed from actual clinical reality. In the UK data, already 10-14 weeks after a Pfizer booster (following Pfizer primary series) we see a waning of efficacy against hospitalisation from close to 90% to around 75% - i.e., more than a doubling of the hospitalisation rate.

 

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1055620/Vaccine_surveillance_report_-_week_7.pdf

 

It's nice that T-cells hold up, but nothing in Mandavilli's article discusses how effective they are at preventing severe outcomes.

 

Over the last 6 months, the NYT unfortunately has consistently and drastically undersold the amazing effectiveness of boosters. I have no doubt that it has contributed to the very low booster uptake in the US, which in turn has contributed to the large omicron death toll.

It's nice to see them turn around and hype the value of boosters now. Though I can't notice this only happens when it can become an argument against a 4th dose...

 

I find it really sad how bad the NYT's coverage of covid data has been. Stacking Leonhardt and Mandavilli at the NYT up against John Burn-Murdoch at the Financial Times or Eric Topol on twitter, and it's such an embarrassing comparison for one of the richest and most influential media companies in the world.

 

I had AZ-AZ-Pfizer, I believe there was some data a few months ago suggesting a moderna booster was best, not sure how that is now holding up.

[pilowsky]

I hope it's holding up - it's the same sequence I had.

[pilowsky]

The title of the NYT article is classic click-bait and prima facie likely to be wrong.

The current coronavirus has settled in nicely and is now as endemic as the influenza virus which has been around for >100 years.

We need booster shots for 'flu because every year the H antigen and the N antigen change.

As noted elsewhere the coronavirus spike protein is composed of two parts (akin to H and N in the influenza virus - as in the H1N1 variant).

When there is a significant change to the spike protein the ability to:

1. bind to the receptor on the outside of the cell is affected or

2. The ability to enter the cell after binding is affected.

The changes in binding and entry properties are likely what cause the differences in infectivity and disease severity.

The current variant (omicron) seems to be better at infecting but not as good at causing disease.

I don't know why but one possibility is that the ability to enter cells in the lower part of the respiratory tree is attenuated (that's a guess).

In any event, the virus is now endemic, new variants will appear from time to time and like the 'flu some will be really bad.

There are plenty of other problems viral, parasitic, bacterial and political to worry about in the meantime.

I am so tired of stories in "the media" that start with variations of "The coronavirus is likely to (insert blah here): here's why."

FFS (as eagles123 might remark) how about headlines that tell you what the story is actually about?

[thepossum]

I hope it's holding up - it's the same sequence I had.

Me too

 

I'll be happy if it doesn't kill me or do something scary to my immune system :)

[barmar]

The current coronavirus has settled in nicely and is now as endemic as the influenza virus which has been around for >100 years.

Is it endemic already?

 

From https://www.marketwatch.com/story/moderna-expects-covid-to-become-endemic-in-2023-and-los-angeles-county-is-latest-to-unveil-plan-to-end-face-mask-mandates-indoors-11645716595

Moderna said Thursday it expects COVID-19 to become endemic in 2023, meaning it will be another seasonal disease that can be managed with vaccines and treatments.

...

On a call with analysts, Moderna Chief Medical Officer Dr. Paul Burton said the company “firmly” believes that a fourth dose, or a second booster, will be necessary, likely by fall of 2022.

[pilowsky]

Is it endemic already?

 

From https://www.marketwa...ors-11645716595

 

It is the virus, sars-cov-2, not the disease COVID-19 that is endemic. Diseases don't become endemic - only infectious agents.

The meaning of endemic is that it is endo- like endocrine, endogenous and endometriosis: it simply means "within".

"-emic" as in pandemic, endemic etc is something related to a single group.

[Edit many use epidemic to describe a surge in an existing non-infectious problem. It does get a bit overused though.]

 

This does not mean that it cannot be eradicated eventually but that's another problem.

 

In medicine it also refers to things that are caused by specific physically identifiable particles that have a capacity to reproduce within some kind of host.

In this way tetanus cannot be called an epidemic or even endemic because although Clostridium tetani is found in the ground that you walk on, it isn't transmissible by simple human to human contact.

 

Coronaviruses are here to stay. The subtype sars-cov-2 virus might mutate (for better or for worse) just like influenza, but it now has an animal population that it doesn't harm that we are in contact with all the time where it can mutate and remerge from at any time.

 

In fact, I haven't heard of an animal that it doesn't affect.

I think that this is because the binding receptor 'ACE2' is so old evolutionarily that it is present throughout the animal kingdom and throughout the body.

 

Sars-cov-2 is now endemic. It has a highly mobile collection of hosts - bats, deer, children where it does (relatively) little harm and where it can mutate and occasionally pop-up with new more vicious variant - just like influenza (WHO- "Globally, the World Health Organization (WHO) estimates that the flu kills 290,000 to 650,000 people per year.").

 

In my mind it became endemic when omicron emerged.

At that point it became "tolerable" - unlike smallpox, leprosy and polio which humans would still like to eliminate.

Other agents that cause a massive burden of disease worldwide seem to be of less interest presumably because they tend to cause few problems for wealthy westerners unless they are making nature documentaries.

 

There are other biological mechanisms that infectious agents use to mutate and transmit that are not seen in coronaviruses but these differences do not seem to be an issue for coronaviruses maintaining themselves in human accessible reservoirs.

BTW, coronaviruses were around causing disease in humans for a very long time.

Here's one from 1999.

And in 1973.

 

COVID-19 can also be considered a virus of our time.

It causes most of its unpleasant effects in people that are either older than 65 (something that was much less common in the 1950's - not that long ago).

And in people that have reduced respiratory capacity because of obesity (along with a smaller bunch of other disorders - emphysema, smoking, cystic fibrosis).

This combination of differentially harming people that are overweight/ older than 65/ are smokers is reflected in the populations where it is most damaging.

 

The meaning of endemic is fairly clear it means that something is no longer just passing through the population and will burnout and not be a problem - that would be an epidemic.

 

Our ability to combat any disease is markedly hampered by our (I mean societal) disdain for training people in high-level thinking (PhD and up).

Research funding is now at a very low ebb.

It's much easier to dislike Mexicans, Canadians and New Zealanders than it is to spend two decades of your life training and learning how to solve really difficult problems.

COVID-19 is a disorder that weaves together all the threads in the water cooler: education, climate change, political philosophy and more.

 

Speaking of endemic problems, the current crisis also highlights the epidemic of scam journals and conferences.

I wish some of the cyber-security experts out there like Jim Browning would go after these people - they probably operate from the same call centres as the Amazon scammers.

 

PS

This is also why religion although it is transmissible and "of the population" is not endemic in the USA, or elsewhere - except metaphorically.

[Gerardo]

In my mind it became endemic when omicron emerged.

At that point it became "tolerable"

 

 

Could this be because, while (still) highly transmissible, omicron (reportedly(?))

does not attack the lungs like other variants?

[pilowsky]

Could this be because, while (still) highly transmissible, omicron (reportedly(?))

does not attack the lungs like other variants?

The evidence is very clear that omicron will bind to the ACE2 receptor wherever it is present in the respiratory tract.

It's early days yet and the reason that omicron is less of a problem is unclear.

The cells lining the nose and throat are similar in their expression of ACE2 to the expression in the cells in the lung - it's one continuous layer throughout the airway.

I suspect the largest reason omicron is causing less severe illness and death is because so many people are vaccinated.

In countries where vaccination is patchy omicron is still causing problems.

So-called "natural immunity" and "healthy living" is orders of magnitude less helpful than a three doses of vaccine.

Just to speculate, if the omicron variant changed in such a way that it binds much more avidly to the receptor one could imagine that when you inhale a dose of virus much more of it will be trapped by receptors in the upper airway and this means less gets to the lungs.

This would change the way the disease affects the host.

If you are familiar with chromatography you could imagine that viral particles that bind more strongly would get stuck at the top: the principle is the same.

I'm only suggesting this by analogy to the size-exclusion principle that our airways uses to prevent particulate matter from getting into the lungs.

I have no actual evidence.

 

Another possibility is that something else in the virus particle that determines how easily it latches onto the cellular machinery to make more virus mutated so that if it gets in it is less damaging.

This seems less likely but again, no evidence.

 

Training people and funding research so that when pandemics roll around is vital but not a high priority for government.

The success rate for grant-funding is very low compared to the excellent proposals.

Now we have the additional problem that politicians think they know what should be funded.

They create "priority areas" and funding is not decided solely on the basis of excellence.

How many Hollywood films do we see where a post-doc fights off aliens and saves the world.

 

US movie/video expenditure in 2019 was ~65+ billion. It has been since at least 2007.

The NIH spends about 42 billion annually on medical research.

 

There are other sources of medical research funding but the entertainment industry also includes sport and television.

 

Every hospital bed seems to have a television, but I don't know if it helps as much as a ventilator.

[y66]

I want to flag this thread!

 

https://twitter.com/mattyglesias/status/1499465032547061767

 

Do not entirely agree with the counterarguments offered but it correctly identifies a SIGNIFICANT factual error in my newsletter.

 

@mattyglesias isn’t convinced by the recent preprints (one of which I co-authored) placing the zoonotic origin of SARS-CoV-2 at the Huanan Seafood Market.

 

And after reading https://www.slowboring.com/p/im-not-convinced-by-the-new-lab-leak?s=w it’s clear that he fundamentally misunderstands them.

[barmar]

It is the virus, sars-cov-2, not the disease COVID-19 that is endemic. Diseases don't become endemic - only infectious agents.

The meaning of endemic is that it is endo- like endocrine, endogenous and endometriosis: it simply means "within".

"-emic" as in pandemic, endemic etc is something related to a single group.

That's not what the dictionary says:

(of a disease) regularly occurring within an area or community.

 

Compare with epidemic, pandemic

‘areas where malaria is endemic’

 

But that doesn't seem to be how it's used when saying that the disease/virus will transition from pandemic to endemic. I will presumably still be worldwide, but it will become tolerable like the flu and common cold. As I understand it, modern influenza is a variant of the virus that caused the 1918 pandemic, but regular vaccinations keep it under control.

[pilowsky]

That's not what the dictionary says:

 

 

But that doesn't seem to be how it's used when saying that the disease/virus will transition from pandemic to endemic. I will presumably still be worldwide, but it will become tolerable like the flu and common cold. As I understand it, modern influenza is a variant of the virus that caused the 1918 pandemic, but regular vaccinations keep it under control.

 

It's a fair point - I'll cop to that.

In any event, I think we can say that this diseases caused by coronaviruses are now endemic in the human population and will continue to provide new challenges and mutations in the years to come.

 

Yes, influenza viruses are the same type of virus as the devastating of 1918.

This virus has been around for centuries and occasionally mutates to a more virulent strain.

It doesn't help that there are so many more humans around and that they are much older and insist on travelling around so much when phone calls and zoom/skype are readily available, but I suppose I used to be one of them.

 

Hopefully the RNA vaccine approach will make it more likely that we can have polyvalent vaccines in the future that allow a single shot that targets multiple viruses (as discussed in detail with some nice diagrams here).

[Cyberyeti]

https://www.cam.ac.uk/research/news/cambridge-vaccine-expert-in-42million-partnership-to-develop-future-proofed-coronavirus-vaccines

 

My understanding when this was explained on the radio was they were targeting bits of the virus that were less likely to mutate to try to make a vaccine that would work against future variants.

[pilowsky]

https://www.cam.ac.u...avirus-vaccines

 

My understanding when this was explained on the radio was they were targeting bits of the virus that were less likely to mutate to try to make a vaccine that would work against future variants.

 

I think that's another issue.

Both ideas are possible.

I'm not a virologist but it would obviously be a good thing if they could find an antigen on the virus that was static and could not change without losing virulence.

I do have experience in making antibodies. It's very hard.

There are so many problems here.

1) there might be a protein (called the antigen - antigens can have multiple epitopes which are the individual sites antibodies bind to) that is unique and doesn't change but is not on the outside of the virus.

The protein must be exposed to the host to be an 'epitope' if it isn't it's called a 'cryptotope' (or cryptope) this means that antibodies made against it can't see it in the virus and therefore don't work. This is a really common problem when making antibodies.

2) some proteins are incredibly hard to make antibodies to - some are impossible - don't get me started.

3) even if you find a protein that is a good candidate it has to be really really antigenic to be useful for immunising a whole population because it needs to make >99.99% of subjects immune to be effective. Most of the time when making antibodies in the lab. a 2/3 success rate is acceptable. This will not cut it in immunisation programs.

4) Not all antibodies are the same. You have to have an antigen that provokes a really good response resulting in neutralising antibodies in nearly everyone.

 

I can see why they went for the spike protein. It sits on the outside and looks like the bristles of a brush. Clearly the most likely target.

 

Another approach is to make a drug that blocks the enzyme that the virus uses to turn the cellular machinery into a virus factory - like molnuprivar which blocks the RNA dependent RNA polymerase (RdRp). Of course this is not good as a prophylactic and can't replace vaccination.

[thepossum]

https://www.cam.ac.uk/research/news/cambridge-vaccine-expert-in-42million-partnership-to-develop-future-proofed-coronavirus-vaccines

 

My understanding when this was explained on the radio was they were targeting bits of the virus that were less likely to mutate to try to make a vaccine that would work against future variants.

 

Which to anyone in any discipline would appear eminently sensible. If any Jo Public had to choose to between a general or overly specific vaccine. Not too general etc

 

I realise also I have a tendency to oversimplify. You should see my approach to modeling sometimes. When I found that the RAT could diagnose all forms of SARS with reasonable accuracy I was curious too. Maybe people are concerned about knocking out beneficial variants. Or maybe some other reason that I don't understand. But I know nothing of the practicalities or detailed technical issues involved

 

Can I ask a question of those who do know any of this stuff.

 

From my part-wikipedia level understanding of the immune system doesn't it have a fairly non-specific, complex, allow for error kind-of approach at targetting different parts of invading viruses or other unwanted invaders