Conoravirus ...

[Olaf Hart]

The other factor is we are eighteen months down the track and there is still no evidence of an intermediate vector between bats and humans.

[Olaf Hart]

So, this article postulates another theory, that the animal to human transmission occurred some time ago, and the virus evolved through repeated human contacts, where the symptoms were too mild to notice.

Also sounds plausible

https://theconversation.com/the-next-pa ... -it-160429

Doesn’t explain the double CGG thing though,…

[kdh]

OK, my genetic engineering buddies say: "No one knows the answer. If they say they know, they're an idiot looking for public recognition through the press." (To be blunt)

I was also directed to this piece in NATURE: https://www.nature.com/articles/d41586-021-01529-3

After plowing through the Nature article and a number of journal articles, I don't think anyone knows. No one has "proved" anything, all the scenarios I've found are speculation and end with folks saying: "We can't rule this out." in some sort of words. In other words, to be blunt, this is great for selling advertising in media outlets, but quite literally no one has convincing evidence of anything conclusive.

Therefore, I think folk should stop hyperventilating on TV and YouTUBE and wait until the science catches up with all these crazy conspiracy theories.

(BTW, no one has ever found the animal that passed Ebola to humans and it took a long long time to figure out that SARS1 came from a bat, many years.)

Beau, if we're looking for certainty I don't think we'll ever know.

My understanding is that the situation is as you characterized it--"either something really rare happened or someone did it intentionally." Thus, it is highly probable that this was created by humans. In others words, to quote the WSJ opinion piece, "the science suggests a wuhan lab leak," so this should be our leading hypothesis.

Not making a reasonable conclusion because something can't be ruled out for certain is silly in my humble opinion. A snowstorm in June can't be ruled out, but I'm going sailing today anyway, thank you very much.

[Jamie]

After dealing with government institutions in China for 30 years....They sometimes have a very interesting combination of incredible raw talent, hubris and jaw-dropping omission all at the same time. So part of me treats the possibility with skepticism, but I wouldn't rule it out. Even if true, it is equally likely that the central government had no idea what specifically was going on in many of those labs. Despite best efforts, China is still very much a tartan, and not a solid color, though definitely trending towards more solid.

[Olaf Hart]

After dealing with government institutions in China for 30 years....They sometimes have a very interesting combination of incredible raw talent, hubris and jaw-dropping omission all at the same time. So part of me treats the possibility with skepticism, but I wouldn't rule it out. Even if true, it is equally likely that the central government had no idea what specifically was going on in many of those labs. Despite best efforts, China is still very much a tartan, and not a solid color, though definitely trending towards more solid.

Makes sense, another example of chaos trumping conspiracy..

The initial coverup was certainly a local response, and suited the central government at the time. They must be pissed off now, this mess threw a real spanner in the plan for world domination through soft diplomacy.

Shame Oz is still on the receiving end for calling it out early, but who would have thought we now have a mutual support agreement with Japan…

[BeauV]

Keith, as I listened to the scientist talk on the WSJ piece, I had an immediate flashback to Linus Pauling. I've no idea if this guy is as far out of his field of expertise as Pauling was when he proposed the absurd cure for everything thing is to take massive amounts of vitamin C, but it sure felt like that. Media hungry scientists are a serious issue in our society, as they feed the beast of "news" with outlandish statements continuously. The media is replete with supposed experts spouting certainty where there isn't any, especially in the more biased media.

As stated when posting the pieces I've published, the "science" is nowhere near as settled as the "expert" claimed in that piece. I'm not looking for certainty, but I am looking for a rational discussion of the probabilities and not finding it. Having found very very few "experts" who agree with the guy on the WSJ piece, I reserve my own opinion until something credible shows up. Not certainty, just credibility.

[kdh]

Beau, I've done some more reading, and apparently knowledgable peers refute fairly convincingly to me the "CGG arginine is unnatural" claim. I'll refer you to this article.

https://www.forbes.com/sites/startswithabang/2021/06/11/ask-ethan-how-can-you-be-so-sure-that-covid-19-didnt-happen-from-a-lab-leak/

...the zoonotic hypothesis is the only one backed by a solid scientific foundation, while the lab leak idea remains firmly in the realm of conspiracy.

I agree that given the lack of consensus the WSJ article shouldn't have been published. So pathetic that this is a political issue.

[Olaf Hart]

Interesting article, unfortunately by an astrophysicist.

Not too sure he makes a convincing argument about the double CGG, always possible it evolved but the odds must still favour insertion.

No mention of COVID’s propensity for aerosol spread, the most likely way a human could be contaminated in a lab environment. Remember the Wuhan lab was only recently set up by the French, who were excluded from it once it was built, so there was not a lot of infection control expertise onboard in late 2019. It only received full accreditation in 2018.

I realise there is a lot of political static around this issue in the USA, fortunately there is none here in Oz.

Doesn’t make a whole lot of difference in managing the outbreak, but has a lot of implications for the way virologists carry on their business, so there are vested interests at work here apart from the CCCP.

I still think we have to explain how this thing was so exquisitely adapted to infecting humans right from the outset.

[kdh]

Here's the critical passage for me in the Quay/Muller article:



In the case of the gain-of-function supercharge, other sequences could have been spliced into this same site. Instead of a CGG-CGG (known as “double CGG”) that tells the protein factory to make two arginine amino acids in a row, you’ll obtain equal lethality by splicing any one of 35 of the other two-word combinations for double arginine. If the insertion takes place naturally, say through recombination, then one of those 35 other sequences is far more likely to appear; CGG is rarely used in the class of coronaviruses that can recombine with CoV-2.

In fact, in the entire class of coronaviruses that includes CoV-2, the CGG-CGG combination has never been found naturally. That means the common method of viruses picking up new skills, called recombination, cannot operate here. A virus simply cannot pick up a sequence from another virus if that sequence isn’t present in any other virus.

Although the double CGG is suppressed naturally, the opposite is true in laboratory work. The insertion sequence of choice is the double CGG. That’s because it is readily available and convenient, and scientists have a great deal of experience inserting it. An additional advantage of the double CGG sequence compared with the other 35 possible choices: It creates a useful beacon that permits the scientists to track the insertion in the laboratory.

Now the damning fact. It was this exact sequence that appears in CoV-2. Proponents of zoonotic origin must explain why the novel coronavirus, when it mutated or recombined, happened to pick its least favorite combination, the double CGG. Why did it replicate the choice the lab’s gain-of-function researchers would have made?

Yes, it could have happened randomly, through mutations. But do you believe that? At the minimum, this fact—that the coronavirus, with all its random possibilities, took the rare and unnatural combination used by human researchers—implies that the leading theory for the origin of the coronavirus must be laboratory escape.



So just basic probability would say that the double CGG is 35 times less likely to occur naturally than other combinations that have the same effect, and the double CGG is the preferred choice for insertion in a lab. Not certainty, but pretty damning. OH, do you know of anyone refuting this basic conclusion?

[BeauV]

...snip...

I realise there is a lot of political static around this issue in the USA, fortunately there is none here in Oz.

...snip...

OH,

[rant] To be blunt, we had a President who was desperate to blame someone, no ANYONE, other than accept the obvious fact that he failed miserably to lead the country in its response to COVID-19. As a result, the "who done it" part of all this became highly politicized. Recently President Biden asked the various Intelligence Agencies and the CDC to work together to try and figure out what the right answer is, for precisely the reason you said. Big parts of the President's party were furious with him for giving even that much credit to the question. Meanwhile, the recently fired President continues to blather on about all manner of conspiracy including illegal vote counts and quite sadly, this red-herring where he tried so hard to avoid taking the blame for what was obviously his own failure.

To be very blunt, if the recently fired President had shown any competence in managing the COVID-19 pandemic, there's a good chance he'd still be President. But, his deeply flawed character just couldn't let him lead something like this as it required that he admit that there were many others who knew more than himself.

This is what you get when you elect a deeply damaged narcissist.

[/rant]

I'll take this to the political thread next time.

[kdh]

Beau, a lot of us agree with all of that about Trump.

What do you think of the scientific argument that I excerpted above? Have you found anything to refute it? I haven't, but am all ears. Just curious.

If we can know how we came to go through all of this with the pandemic I'd feel better--knowing its origin. I trust everyone's opinion here.

[Olaf Hart]

This Nature article seems to be a reasonable summary of the cases for and against, looks at the double CGG point as well.

https://www.nature.com/articles/d41586-021-01529-3

I am prepared to accept that the “ gain of function” process which optimised the virus could have occurred naturally, it’s possible this could have happened in the community, not the lab.

If the bat virus infected humans in a less virulent fashion originally, the infections are likely to be mild and confused with background virus infections, remember the common cold is a coronavirus.

As time went on, the virus could have evolved to a more virulent state. This could explain the reports of stored blood samples testing positive in Europe in early 2019, as variants were brought there by Chinese tourists and itinerant farm workers.

This natural human laboratory is similar to my experiences researching legionella in the eighties, if cooling towers are shedding all the time, why do we have outbreaks?

Is it because someone thinks to order the right test? In this case, no one thought to check sick people for the virus until it became virulent.

I hope the double CGG question will be answered by Biden’s report, it will be a real test of how far the BS train has been turned around in the US, and good on him for asking for an answer.

[Olaf Hart]

...snip...

I realise there is a lot of political static around this issue in the USA, fortunately there is none here in Oz.

...snip...

OH,

[rant] To be blunt, we had a President who was desperate to blame someone, no ANYONE, other than accept the obvious fact that he failed miserably to lead the country in its response to COVID-19. As a result, the "who done it" part of all this became highly politicized. Recently President Biden asked the various Intelligence Agencies and the CDC to work together to try and figure out what the right answer is, for precisely the reason you said. Big parts of the President's party were furious with him for giving even that much credit to the question. Meanwhile, the recently fired President continues to blather on about all manner of conspiracy including illegal vote counts and quite sadly, this red-herring where he tried so hard to avoid taking the blame for what was obviously his own failure.

To be very blunt, if the recently fired President had shown any competence in managing the COVID-19 pandemic, there's a good chance he'd still be President. But, his deeply flawed character just couldn't let him lead something like this as it required that he admit that there were many others who knew more than himself.

This is what you get when you elect a deeply damaged narcissist.

[/rant]

I'll take this to the political thread next time.

I suspect America needs a mass trauma debrief Beau, may be Biden’s greatest achievement if his middle of the road approach helps people grieve about this whole mess.

You nearly lost the whole game, it’s not over yet, and it has exposed deep flaws in a political and social system that told itself it was the pinnacle of human achievement.

[kdh]

Some more food for thought. Mostly more amplification and detail.

https://thebulletin.org/2021/05/the-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan/

[Olaf Hart]

Great article Keith, loved the reference to the Dutch in 2000 earning the gratitude of rhodents by changing the spike protein to target cats rather than mice…

Summarises all the evidence very well, especially the way the Wuhan lab used level 2 precautions for coronaviruses, they probably didn’t understand their propensity for aerosol spread at that time..

As I said before, this whole story threatens the way virologists do business.

[Jamie]

Still color me a bit skeptical, though there are so many people working with viruses, and nothing can be ruled out. Humanized mouse models, BSL2 labs and spike proteins/lentivirus/nipah viruses can’t be considered evidence of nefarious activity. We have two BSL2s lab in China with all of those things. We use a lentivirus and there is no vaccine for that. We regularly ship viral plasmids internationally the way others send post cards.

Maybe we’re all doing something really stupid. Humans are terrible judges of risk.

* Theoretically BSL2 labs are highly regulated in China requiring a special license to operate; there must be a registered address as well as a “responsible person” - aka a neck to wring if something goes wrong - and the labs are subject to regular inspection. These requirements are new-ish to China so the inspectors have quite a lot to learn. Many types of lab equipment must also be registered with the government. And yet China is a big place with highly variable implementation.

[SemiSalt]

Fairfield County, CT, population approx 1 million, had exactly one new case yesterday.

[BeauV]

Fairfield County, CT, population approx 1 million, had exactly one new case yesterday.

That is wonderful news. Here's hoping the rest of our world can do as well.

[H B]

Fairfield County, CT, population approx 1 million, had exactly one new case yesterday.

That is wonderful news. Here's hoping the rest of our world can do as well.

Well...now you can walk into Wal-Mart where we live and get a vaccine, and I hear local news outlets talking about closing down max vax sites. It seems that those who chose to get the vaccine have gotten it. Too bad we couldn't get to the magical herd immunity number, but I am not walking around with a mask on all summer (again) for the anti-vax crowd.

[Steele]

We have hit 70% vaccination in Seattle, but some not so far away counties are at 30% despite readily available shots. One town had a super spreader event last month. This was followed by an uptick in vaccine utilization that quickly dissapated with a total rate still well less than 50% in that area.

[BeauV]

We have hit 70% vaccination in Seattle, but some not so far away counties are at 30% despite readily available shots. One town had a super spreader event last month. This was followed by an uptick in vaccine utilization that quickly dissapated with a total rate still well less than 50% in that area.

It is similar in the San Francisco Bay area. Within an hour's drive there are places with apx. 30% vaccination rate, while SF over 12 years old is currently at 80% for one shot and 71% for two shots + two weeks.

The difficulty for SF, and our hometown of Santa Cruz, is that a massive number of folks flood the area as tourists. The locals are getting vaccinated, but the tourists generally are from many lower-vax-rate areas. This has resulted in a number of events where there has been a significant spread of the disease and is one of the primary reasons our yacht club in SF is still closed to visitors. This summer is going to be ugly for anyone who can't get vaccinated for a medical reason. They will be masked indefinitely as far as I can tell.

[BeauV]

IMG_1584.jpeg

Then there is THIS sobering graph. This disease is a LONG LONG LONG way from be "over."

[Jamie]

My view is we still have COVID, we're just vaccinated. So it's only kind-of-over for the inoculated in the US. For the moment. With the large pockets of unvaccinated, we're setting up a great petrie dish for the developing the next more virulent version that has a higher probability of overcoming vaccine resistance.

For countries like...say....the Philippines there is no hope in sight and no money to buy anything except gifts from China. Even China is having sporadic outbreaks because their domestic vaccines are weak and why they are striking a deal with BioNTec.

[Tim Ford]

Great articles, thanks Keith. Interesting that prestigious journals are taking an investigative approach to this.

35x is a drop in the probability bucket though, when it comes to CGG mutational likelihood.

[kdh]

Great articles, thanks Keith. Interesting that prestigious journals are taking an investigative approach to this.

35x is a drop in the probability bucket though, when it comes to CGG mutational likelihood.

I'm looking forward to a discussion aboard Restive. (Thanks Rob!)

[kdh]

Another piece about manipulation of a "furin cleavage site" and double-CGG.

Now to me a straightforward probability model is clearly questionable. Also, I didn't know that the Wuhan lab has strongly denied to the scientific community doing any gain-of-function research.

https://www.wsws.org/en/articles/2021/06/22/sci2-j22.html

[BeauV]

Another piece about manipulation of a "furin cleavage site" and double-CGG.

Now to me a straightforward probability model is clearly questionable. Also, I didn't know that the Wuhan lab has strongly denied to the scientific community doing any gain-of-function research.

https://www.wsws.org/en/articles/2021/06/22/sci2-j22.html

Keith - this is great stuff. Thank you!!

[Tim Ford]

Did I read on one of the Scantlings threads that one of us, I think it was someone from the PNW "Oven" area that posted it (but I cannot find it) -- anyway, I think I read that that individual was going in to get jabbed with another vaccine, not the one they got originally.

Reason I ask: I got the J&J one and done. I have heard rumors that it might be a good idea to get the Pfizer or Moderna soon, to be really and truly double secret surely immunized.

But I'm having a difficult time differentiating reality from the hot summer dream state this weather puts me in...so maybe I dreamt it. Who knows? I have a physical in 2 weeks, I'll ask my internist. But I thought I'd throw it out there....THANKS for any opinions.

[H B]

Yeah.. I think tigger is getting one of the mRNA for his 2nd shot after the AZ first shot..

It was in this thread I thought so I did some searching..One page back maybe? This link works, but now it highlights all my search criteria

viewtopic.php?f=5&t=2445&p=110772&hilit=mRNA+AZ+vaccine#p110772

[Tigger]

Tim: yes, it was me. The guidance has changed to follow best practice as identified by research. Due to concerns of a rate but dangerous reaction to AZ for younger folks, it was offered en masse to 55-65, and spoken for within days. Initially, it was going to be two doses of AZ 8 weeks apart. Then, after it was shown that a longer interval was better, it was increased to 12. Following that, the rise of the variants showed that two shots were better than one, and it was decreased back to 8. For #2 of those who got AZ for #1, people were initially offered a choice of AZ or an mRNA. After the publication of studies in Germany and Spain, the official recommendation changed to mRNA for #2. So, I’m a member of team AZ/Moderna. Other than a headache, no reaction to #2. Thankfully, we’ve had 16 months of our Provincial Health Officer (Dr. Bonnie Henry) telling us the truth, so people just went with the flow.