Fear and Loathing, a Rat Flu Odyssey

[bodywhomper]

Apparently, some federal lawmakers are trying to make March 6 Covid Memorial Day.

Despite the fact at present everything is gummed up by politics, I'm somewhat optimistic. The United States spent $340 million prior to the pandemic to develop mRNA vaccine technology and another $32 billion during the first 2 years of the pandemic to accelerate their availability. We spent tens of billions to save trillions. It's a towering scientific public-private achievement that will likely lay the groundwork to usher in a golden age for biomedicine.

Single-dose gene editing for incurable diseases is now showing great promise. Within a few years we will probably have good remedies for most if not all of the following: effective treatments for Covid, for obesity, and vaccines for malaria, for dengue, for RSV, and quite possibly for Lyme disease. The UK is currently undergoing trials for blood tests capable of detecting cancer progenitor cells up to one year before cancer appears.

While weight loss drugs in particular are going to create a new set of problems, and not all of these things are going to work, on balance we're going to be a lot better off as long as governments and antivaxxers don't strangle the biopharma industry.

Thanks for the response. I would like to feel optimistic about it, too. A lot of brains have been dedicated to the response, research, and considering how to mitigate effects from future events.

[XXX-er]

strong 1st post ^^

[PB]

And so on-topic.

[old goat]

After three years of playing Keanu Reeves dodging bullets matrix style, the ‘Rona finally caught me. First day of symptoms sucked, day three today pretty much feels like a cold. I'm 58 and have had my shots.

Haven’t been in the virus threads much lately, is the consensus Pax or no Pax?


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Maybe ask the CDC instead of TGR. (I guess by now you have. It does work very fast in essentially curing symptoms within 24 hours, although that's not the reason to take it. For non-Medicare patients pharmacists can prescribe it for many people. Look up Covid Test to Treat. When I tested positive Kaiser was prescribing Paxlovid based on the home test alone. Unfortunately it took 2 days for me to get the pills--I got impatient and prescribed them for myself at CVS and had them within 30 minutes through the drive thru, for free. I'm still waiting for the rebound.)

You're describing the ultimate in reactive approaches and advocating experience bias. If we have 3 possible ways for something bad to happen we shouldn't only try to prevent the one with the most recent example.

Good point. See: Maginot Line. Although to eliminate all possible routes of transimitting Case 1 they would have to stop searching for, collecting, and studying potential zoonotic diseases. Is that wise? I don't know--how much is learned by studying potential zoonotic disease organisms ahead of any human cases? I have no idea--not my field. Given how quickly genomes can be sequenced and potential vaccines designed (it's the manufacturing and testing that takes time) and given there are a huge number of petential candidates for the next big pandemic maybe it's better to just wait for the next pandemic. Shoudn't have to wait long.

Despite the fact at present everything is gummed up by politics, I'm somewhat optimistic. The United States spent $340 million prior to the pandemic to develop mRNA vaccine technology and another $32 billion during the first 2 years of the pandemic to accelerate their availability. We spent tens of billions to save trillions. It's a towering scientific public-private achievement that will likely lay the groundwork to usher in a golden age for biomedicine.

Single-dose gene editing for incurable diseases is now showing great promise. Within a few years we will probably have good remedies for most if not all of the following: effective treatments for Covid, for obesity, and vaccines for malaria, for dengue, for RSV, and quite possibly for Lyme disease. The UK is currently undergoing trials for blood tests capable of detecting cancer progenitor cells up to one year before cancer appears.

While weight loss drugs in particular are going to create a new set of problems, and not all of these things are going to work, on balance we're going to be a lot better off as long as governments and antivaxxers don't strangle the biopharma industry.

Let us know when there's a pill for stupid, because that will kill you faster than anythng.

[LongShortLong]

So, pandemic response was A-okay everything on target, sorry we don’t have a magic wand?

Patients dying in hallways, healthcare workers traumatized by being overworked, exposure, and attrition. An economy crippled by shelter in place, a populous so polarized we can’t agree on mask mandates. Public statements that the virus is living on fomite surfaces, rescinding that finding, but leaving the sanitation requirements in place. Super spreading, day-to-day businesses not knowing if they can open or what regulations are in place, every major not-for-profit healthcare system in the country on the verge of financial collapse.

Yet we were as prepared as we could be, and we didn’t learn anything that we could do better next time?

I’m not sure we live on the same planet.

I'm trying to make the point that there's many experts in many related fields who both prepared for pandemics, responded to this one, and will adjust their approaches for the next one. Could we prepare "more?" Of course, for someone's definition of more. Keep in mind we live in a society and have many competing goals and competing priorities and limited resources to divide among them. We also have many experts in various fields making the best decisions to allocate the resources available.

As an armchair expert, I could tell you what we should have done this time and what we should do next time. As someone who paid more than casual attention, let me assure you that the experts don't agree on what we should have done, or should do next time. IMO, if the US had responded like China (and a few other countries) the combined efforts and pressure on other countries from the two largest economies likely would have been enough to exterminate Covid in a few months. I also believe you can find experts who say lockdowns suck and we should have "let it rip." And there's many other expert options. Consider also that we have much more knowledge about Covid than was available when many decisions were made.

There is no magic wand we can wave a produce the perfect solution. Humanity doesn't work that way. And it's naive to think it does.

Maybe you'll be comforted to know the experts have expected H5 bird flu to crossover for long enough that we've made a vaccine for it. Or maybe you expect half of Americans to forgo the vaccine and 20% of them to die. Go fund some sociologists to describe options for that problem. Ofc, they ran the flu plan for Covid and you aren't happy with the results. I'm happy I got a great vaccine in about a year - testament to extreme preparation. I'm also happy that China discovered and shared a great deal of information about the disease and its treatment, and also curtailed the Wuhan supercluster that surely bought the rest of us a couple months to get our shit together.

Imagine how this would have gone in 1990. We got a far far better result, thanks to experts' efforts last few decades.

This is the real planet. It's messy here.

[powdrhound]

Physics Girl is severely sick with Long Covid.

https://m.facebook.com/story.php?sto...ibextid=qC1gEa


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[old goat]

The biggest thing we can do to prepare for the next one is to scrap our country-by-county, state-by-state public health system. It may work for tracing STD (or is it STI) contacts but not for controlling a global pandemic. Walensky was pointing out yesterday that the CDC does not have the kind of response authority that FEMA has. It is by law a scientific agency, not a response agency. Once the emergency is delcared over in May it will not even have the authority to require states to report their covid data. It should have authority over the state and county public health agencies during a declared public health emergency--starting with the first case of Covid 24. Fixing this would require Congressional action. IOW we're al gonna die.

[bodywhomper]

I was disappointed in Bennet’s interview of the cdc director yesterday. All soft balls.

[riser4]

We've all seen the movie and it didn't end well for the humans. https://www.cnn.com/2023/03/08/world...scn/index.html

[Danno]

That NYT article that cited a review of studies that concluded that "masks don't work"? Misinterpreted and incorrect: https://www.nytimes.com/2023/03/10/o...smid=url-share

[MultiVerse]

Yeah, saying ‘masks don’t work’ is nonsensical. The Devil is in the details. A person might argue handing out free masks doesn't work or mask mandates don't work due to behavioral issues. However, an effective properly fitted mask when used correctly does work. It mostly comes down to mask adherence when indoors. Folks here in Utah mostly stopped wearing masks when vaccines became available, and I'm more than ok with that, but if a person is at high risk or just doesn't want to catch (or spread) a cold let alone Covid we know masks can block viral particles.

[CarlMega]

That NYT article that cited a review of studies that concluded that "masks don't work"? Misinterpreted and incorrect:

Yeah, but wutabout the mask leak from China doing Sweden? Pureblood, pureblood, I exercise and eat paleo plus my immune system is primed from catching it 3x and strengthened by battling this long covid. My grandma didn't die to just shut down hair studios now!

[jono]

That NYT article that cited a review of studies that concluded that "masks don't work"? Misinterpreted and incorrect: https://www.nytimes.com/2023/03/10/o...smid=url-share

We had some discussion of the problem with claiming mandates=masks in one of these threads last year. But to be fair to the non-maggots at Cochrane, they did mention right in the text:

"Adherence with interventions was low in many studies.

The risk of bias for the RCTs and cluster‐RCTs was mostly high or unclear."

I don't think it was so much their mistake--unless they failed to expect cherry picked quotes on Twitter, I guess.

[Danno]

We had some discussion of the problem with claiming mandates=masks in one of these threads last year. But to be fair to the non-maggots at Cochrane, they did mention right in the text:

"Adherence with interventions was low in many studies.

The risk of bias for the RCTs and cluster‐RCTs was mostly high or unclear."

I don't think it was so much their mistake--unless they failed to expect cherry picked quotes on Twitter, I guess.

I think it was their mistake, because while there were pieces of their report that explained things correctly, they also wrote some things that were easy to misinterpret (including misinterpretation by their own authors). They openly acknowledged this

[The EIC] said that “this wording was open to misinterpretation, for which we apologize,” and that Cochrane would revise the summary.

Soares-Weiser also said, though, that one of the lead authors of the review even more seriously misinterpreted its finding on masks by saying in an interview that it proved “there is just no evidence that they make any difference.” In fact, Soares-Weiser said, “that statement is not an accurate representation of what the review found.”

I don't see how you read that and say they didn't make a mistake.

[bodywhomper]

Fairly interesting synopsis from Topol, plus discussion of a drug that may reduce developing long covid. According to Topol, the small sized drug trial found long covid diagnosed in 14% of unvaxed controls and 7% of vaxed controls.

https://erictopol.substack.com/p/a-b...a-breakthrough

[jono]

I think it was their mistake, because while there were pieces of their report that explained things correctly, they also wrote some things that were easy to misinterpret (including misinterpretation by their own authors). They openly acknowledged this



I don't see how you read that and say they didn't make a mistake.

Fair point. I was thinking of the relative publicity created by those feeding Skidog's echo chamber as the more bad-faith "mistake" but that example is solid.

[CarlMega]

Recent reports that Department of Energy and FBI officials think the COVID-19 pandemic originated with a so-called lab leak appear to have provided all the “evidence” many require. As a scientist who has led or contributed to several peer-reviewed studies that tell a very different story, I’ve looked on with amazement at the growing divide between what the science shows and what much of the public — and a minority of the intelligence community — believe. But I’ve also watched with understanding for those who still suspect a lab leak because I started there myself.

The nucleus of all lab leak conjectures — they are not a single hypothesis but a wide range of sometimes mutually exclusive speculations — was famously captured by the comedian Jon Stewart. “Oh, my God, there’s a novel respiratory coronavirus overtaking Wuhan, China — what do we do?” Stewart said during a June 2021 appearance on “The Late Show With Stephen Colbert.” “Oh, you know who we could ask: the Wuhan Novel Respiratory Coronavirus Lab. The disease is the same name as the lab!”

Stewart didn’t have the name right, but he was referring to the work of the Chinese scientist Shi Zhengli, whose lab at the Wuhan Institute of Virology does indeed study SARS-related coronaviruses from horseshoe bats, the ultimate reservoir of both the original SARS virus and SARS-CoV-2, the virus that causes COVID-19.

The month before Stewart’s tirade, Science published a letter by me and several other scientists arguing that lab leak hypotheses must not be prematurely dismissed. The letter dramatically shifted the debate about where COVID came from; two weeks later, the Biden administration announced a 90-day intelligence community review of the pandemic’s origins.

While the intelligence community did its work, I set about my own. Though I considered a lab leak plausible, I nevertheless thought a zoonotic origin — a jump from animal to human — to be considerably more likely. Around the same time, the likelihood of a natural origin was bolstered by a paper from scientists in China and Britain proving that live specimens of mammal species previously found to harbor SARS viruses had been sold at markets in Wuhan just before the onset of the pandemic.

A scientist’s job is to kick the tires of a hypothesis — to try to falsify it. I tabled all my other research to try to falsify the hypothesis that the pandemic began at one of those markets, the Huanan Seafood Wholesale Market, where many of the earliest known COVID patients worked.

First I investigated the possibility that Shi’s lab had possessed a virus close enough to SARS-CoV-2 to be its progenitor. Shi had collected what was at the time the closest known relative of the pandemic virus, known as RaTG13, from a mine in Yunnan province.

I asked Nature to request that Shi publish several SARS-related coronavirus sequences that had been reported in the journal. Within days, she provided them. The result: no smoking gun; they were all much more distantly related to SARS-CoV-2 than RaTG13.

Next I set out to answer another key question: Were so many of the earliest known COVID cases linked to the Huanan market simply because that was where people were searching for them? It had been suggested that the market was the first place where cases were detected because China was focused on markets with live animal sales such as those where SARS appears to have emerged.

This turned out to be dead wrong. No such surveillance of live animal markets occurred in Wuhan prior to the pandemic. Astute doctors recognized the new viral pneumonia before an epidemiological link to the Huanan market emerged. Before that association was made, more than half the early cases diagnosed had a clear link to the market — a huge share for a workplace with about 1,500 employees in a sprawling city of 11 million. Also, both of the earliest two lineages of SARS-CoV-2, designated A and B, appeared to be geographically linked to the market, as I wrote in Science in November 2021.

But would mapping the residences of the earliest known patients cast doubt on the hypothesis that the market was the epicenter of the pandemic? I found a way to identify most of these locations by overlaying different low-resolution maps from a World Health Organization report. I then teamed up with Kristian Andersen of the Scripps Research Institute, who was leading an independent study of spatial patterns within the Huanan market, and we assembled a large, international team of experts.

We found that the earliest known COVID cases lived much closer to and more centered around the Huanan market than could be explained by chance. Crucially, this was true even of patients who reported that they hadn’t worked at the market, shopped there or knowingly been in contact with anyone who did.

A more scattered distribution of early cases throughout the city would have suggested that the virus was already widespread in December. But the pattern clearly showed that it was only then beginning to bleed into the community surrounding the market and didn’t spread more widely across the city until later.

Our analyses linked the market not only with lineage B, which had already been found there, but also with lineage A, which had not. Just before we first reported these findings in February 2022, George Gao and his colleagues reported that lineage A was indeed present at the Huanan market before it was closed. This shows that the Huanan market wasn’t simply the site of a “superspreader event,” which would have amplified only a single lineage.

Within the market, meanwhile, the surfaces of stalls that sold live mammals or meat were more likely to have tested positive for SARS-CoV-2 just after the site was closed. One stall riddled with positive samples from surfaces associated with animal sales, including a metal cage, had been visited years earlier by my co-author Eddie Holmes of the University of Sydney, who had photographed raccoon dogs there. The same species was among the market animals that tested positive for the SARS virus in 2003.

A highly technical companion study led by UC San Diego’s Jonathan Pekar and Joel Wertheim, along with UCLA’s Marc Suchard, Andersen and me, drew on over 700 of the earliest SARS-CoV-2 genome sequences. The evolutionary trees of these sequences, combined with epidemiological information, shows that the ancestors of lineages A and B almost certainly jumped into the human population separately. We also found that the establishment of these two lineages probably involved about five jumps into individual humans, most of which fizzled out before taking hold. “Molecular clock” analyses indicate that the lineages shared common ancestors that existed around mid-December 2019, corroborating the epidemiological and geographic evidence that the outbreak was largely restricted to the neighborhoods around the Huanan market at that point.

The two studies, which were published in Science following peer review last July, provide overwhelming scientific evidence that the virus that causes COVID emerged at least twice at the Huanan market, likely between mid-November and early December of 2019. And while it may strike some as odd that the virus jumped twice in the same market, research on mink farms and the pet trade shows that when SARS-CoV-2-infected animals are in close contact with humans over a prolonged period, multiple interspecies jumps are inevitable.

And as we showed using cellphone-based mobility data, the Huanan market is an exceedingly unlikely location for the world’s first large cluster of COVID cases unless it was also where the virus emerged. There are hundreds if not thousands of other places where hypothetical lab leak cases could have initiated human-to-human transmission — bars, restaurants, schools, shopping malls — some with a hundred times the traffic of the Huanan market. Even one such event at Huanan is deeply improbable; fold in the strong evidence for two lineages emerging at the market, and the link to the wildlife trade is unavoidable.

Remarkably, some recent reporting suggests that the Energy Department’s new “low confidence” lab leak conclusion may point to an entirely different lab near the Huanan market, the Wuhan Center for Disease Control and Prevention, which would directly contradict all the speculation surrounding the Wuhan Institute of Virology.

There is now a large body of peer-reviewed scientific research consistent with a zoonotic origin of this pandemic. However, there is no credible, peer-reviewed research pointing to a lab leak. Had the evidence gone in the other direction, I’d be reporting that. But it hasn’t.

The “evidence” in favor of a lab leak consists fundamentally of discredited talking points. The lack of a positive sample from an animal sold at the Huanan market, for example, supposedly undercuts the market-origin hypothesis. But not a single relevant live animal was tested there before the market was closed.

Lab leak proponents cling to the contention that the presence of a lab that studies viruses and the emergence of a coronavirus pandemic in the same city can’t possibly be coincidental. But my colleagues and I showed in 2021 that this virus wasn’t going to emerge just anywhere in China: It took a city. Simulations indicate that when a virus with the properties of SARS-CoV-2 jumps into a human in a sparsely populated rural area, it will fail to cause an outbreak 99% of the time. But take that same virus into a huge city like Wuhan, and about a third of animal-to-human transmissions will result in an epidemic.

We should instead be asking: What is the chance that a big Chinese city like Wuhan would have a lab doing the kind of research that has come under suspicion? The answer is, the vast majority of the biggest cities in China have labs involved in such research. If COVID had emerged in, say, Beijing, there would be no fewer than four such labs facing suspicion.

[CarlMega]

^too long so I had to cut:

Opinion piece: https://www.msn.com/en-us/health/med...ut/ar-AA18nI3U

& the closer:

I remain open to any and all evidence supporting a laboratory origin of the pandemic. So far, we have no such evidence.
....
Michael Worobey is a professor and the head of the department of ecology and evolutionary biology at the University of Arizona.

[bodywhomper]

Brief 4-minute interview of long covid researcher Akiko Iwasaki.

https://www.npr.org/2023/03/13/11630...a-lot-to-learn

The HEPA filter in my boot room at the ski hill vanished over the past 2 weeks. Grrrr

[bodywhomper]

Woof?

https://a-z-animals.com/media/raccoon-dog-1.jpg

[twat]

Woof?

https://a-z-animals.com/media/raccoon-dog-1.jpg

Woof it is soooo cute!

[skaredshtles]

Cooties finally descended on our casa earlier this week. Wife and I both tested positive after 3 years of "avoiding" it. Both on the mend now - what I would consider fairly mild experience.

[bodywhomper]

Woof it is soooo cute!

And apparently a wet market treat(!) that may have spread the cooties.

Interesting article on “normalcy bias.”
“Normalcy bias is going to play a defining role in our culture going forward, as the threats we’ve been warned about for decades become daily realities. The mainstream news will keep coming up with cute ways to spin the latest supply chain crisis or epic disaster, right before redirecting our attention to the latest vacation deals. We’re going to see a lot of strange behavior. We’re going to see a lot of people who don’t seem to have any survival instincts at all.”

https://jessicawildfire.substack.com...utm_medium=web

[skaredshtles]

And apparently a wet market treat(!) that may have spread the cooties.

Interesting article on “normalcy bias.”
“Normalcy bias is going to play a defining role in our culture going forward, as the threats we’ve been warned about for decades become daily realities. The mainstream news will keep coming up with cute ways to spin the latest supply chain crisis or epic disaster, right before redirecting our attention to the latest vacation deals. We’re going to see a lot of strange behavior. We’re going to see a lot of people who don’t seem to have any survival instincts at all.”

https://jessicawildfire.substack.com...utm_medium=web

But will tacos still be cheap in Cabo? That's what I want to know...

[Dantheman]

Both on the mend now - what I would consider fairly mild experience.

Glad to hear that. I finally got it last May and despite being fully vaxxed (though about a year out and no booster) my ass was kicked for 2 weeks and I didn't feel 100% for at least 6 weeks.