Coronavirus

[Swerd]

The World Health Organization called for Chinese health authorities to release genetic sequences of SARS-CoV-2 the country recently took down from an international database, after an analysis of the data found it offered new clues that might point towards an animal origin for the COVID-19 pandemic.

Analysis of those samples found "molecular evidence" of animals like raccoon dogs at the market intermingled in swabs from the same spots that turned up the shedding from the virus itself in the market.

These samples were taken in early 2020 around the Huanan animal market in Wuhan, which investigations by US and Chinese authorities had pointed to as a potential early epicenter for the outbreak.

New genetic analysis finds clues to animal origin of COVID outbreak

Analysis presented to the WHO offers clues to whether animals, possibly raccoon dogs, were infected at the Huanan animal market in early 2020.

www.cbsnews.com

 

[mtrycrafts]

The World Health Organization called for Chinese health authorities to release genetic sequences of SARS-CoV-2 the country recently took down from an international database, after an analysis of the data found it offered new clues that might point towards an animal origin for the COVID-19 pandemic.

Analysis of those samples found "molecular evidence" of animals like raccoon dogs at the market intermingled in swabs from the same spots that turned up the shedding from the virus itself in the market.

These samples were taken in early 2020 around the Huanan animal market in Wuhan, which investigations by US and Chinese authorities had pointed to as a potential early epicenter for the outbreak.

New genetic analysis finds clues to animal origin of COVID outbreak

Analysis presented to the WHO offers clues to whether animals, possibly raccoon dogs, were infected at the Huanan animal market in early 2020.

www.cbsnews.com

Confused. Are the codes taken down is what was analyzed or came some other way? Can I assume that the 2020 sequence is what was taken down?
Can any of the sequences be fixed to mimic an animal sequence?

 

[Swerd]

Confused. Are the codes taken down is what was analyzed or came some other way? Can I assume that the 2020 sequence is what was taken down?

I was confused too. That CBS News article was an early report. I've found a more recent report in The Washington Post that explains things better:

The protracted and rancorous debate over the origin of the covid pandemic has added a small but potentially significant data point: A sample taken in a Wuhan market in early 2020 showed genetic traces of both the coronavirus and a raccoon dog, according to scientists who have analyzed newly obtained data from China.

Like so many elements of the mystery, the new data, first reported by The Atlantic, falls short of proving how, where and when people first became infected with the virus. But it boosts the theory that the pandemic started through natural spillover from animals rather than emerging from a laboratory, a theory favored by some researchers.

The new evidence comes via swabs taken in animal stalls at the Huanan Seafood Market in Wuhan. Investigators collected them in early 2020 after the market had been closed and all the animals removed. One swab contained a mixture of genetic material that included a large amount from a raccoon dog along with traces from the coronavirus, said Stephen Goldstein, a virologist at the University of Utah who was part of the team that analyzed the data.

The data come from Chinese scientists who have submitted a paper to a scientific journal that has not yet been published, Goldstein said. The scientists involved in the new analysis, which has not been peer-reviewed or published in a journal, said they plan to post their work online within the next couple of days.

“We can’t definitively prove that there were infected raccoon dogs who were the first source of the virus going into humans,” Goldstein said, “but it is highly suggestive of that.”

Other animals that were probably sold in the market are also capable of being infected with SARS-CoV-2, the virus that causes covid-19. But the new evidence “moves raccoon dogs to the top of the list of animals that started the pandemic,” Robert Garry, a virologist at Tulane University who took part in the new analysis and has long favored the market theory, said Friday in an email.

“It’s just one more brick on this massive wall of evidence that all fits together,” Worobey said. “If it weren’t so politicized, it’s one of the clearest sets of evidence for how a pandemic emerged that we’ve ever had.”

But David A. Relman, a professor of microbiology and immunology at Stanford University who has said both origin scenarios are plausible, called the new data “very inconclusive” in an email. “Frankly, the breathlessness and alacrity with which stories like this one are promoted, in the face of very incomplete and confusing ‘data’, leaves me frustrated and concerned,” he said.

The virus origin debate has become heavily politicized, and this latest data point, coming from scientists who have long argued for a market origin, is unlikely to shift the views of those who favor the lab leak theory.

I've quoted from a longer article:

https://www.washingtonpost.com/science/2023/03/17/covid-origins-raccoon-dog/

Can any of the sequences be fixed to mimic an animal sequence?

Are you asking if the DNA sequences identifying a raccoon dog can be faked, or confused for another species? I'd say that's highly unlikely. The odds are very high that the sequence is genuine racoon dog.

 

[mtrycrafts]

...
Are you asking if the DNA sequences identifying a raccoon dog can be faked, or confused for another species? I'd say that's highly unlikely. The odds are very high that the sequence is genuine racoon dog.

Not quite. What I am trying to figure out if the racoon dog DNA can be faked to have the Covid markers added, so it takes the blame away from the lab itself? King of a forgery, transferring the evidence from the lab to the dog.

Starting to read that article and your clip.
This may be where I have the question:
A sample taken in a Wuhan market in early 2020 showed genetic traces of both the coronavirus and a raccoon dog, according to scientists who have analyzed newly obtained data from China.
This newly obtained data, can this have been created over the years since the early 2020 to shift blame to the dog and be claimed that it is the original sample actually taken in 2020.
Do we have the original 2020 sample with credible provenance?
I am just skeptical why it is newly obtained after all these years as there is plenty of time to so forge the evidence is it can be forged, to make it look like it was the original sample not a great forgery.

 

[Swerd]

Not quite. What I am trying to figure out if the racoon dog DNA can be faked to have the Covid markers added, so it takes the blame away from the lab itself? King of a forgery, transferring the evidence from the lab to the dog.

Data can always be faked. It's up to the paper's authors to convince the journal editors that their data is believably honest. That's what scientific peer review is all about. The reviewers have to be good enough to smell something fishy. I suspect this manuscript will get plenty of scrutiny as it gets reviewed.

(Edit: It takes a scientist experienced in that specific kind of work to fake things convincingly, and it gets exposed as fake sooner or later. Nearly everyone with that kind of experience would be highly unlikely to risk his/her career. Such scientific fraud has happened in the past, but it ends up ruining a career. If fake data is combined with a highly unusual or controversial conclusion, other scientists WILL try to reproduce it. If they can't, they WILL publish that, exposing it as wrong or scientific fraud. Considering the lies & fraud I've seen from right-wing Republican politicians, I've always felt that this is why few right-wing Republicans make scientific research a career choice.)

I should add this. The paper claims that a single swab sample, collected in early January 2020, contained both raccoon dog DNA and SARS-CoV-2 RNA. The authors don't claim that the raccoon dog was infected by the virus, only that they were in the same location around the same time. This may very well be the best evidence available, but it still doesn't prove conclusively that the virus first infected the raccoon dog, and that this was how it spread to humans. But it could be better than any suspicion about the virus leaking from that lab in Wuhan. Right now, we know of no hard evidence for that.

It's like OJ Simpson's DNA. It was found at the crime scene where his ex-wife was murdered, and on the bloody glove found nearby. That doesn't prove he killed Nicole Simpson – only that he was at that location when her blood was spilled.

 

[mtrycrafts]

.... The paper claims that a single swab sample, collected in early January 2020, contained both raccoon dog DNA and SARS-CoV-2 RNA. The authors don't claim that the raccoon dog was infected by the virus, only that they were in the same location around the same time. ...

Thanks. Much better explanation, two separate DNA at the same location and time. Now it becomes interesting where, how and who brought that Sars-CoV-2 there to be spread further.

 

[Swerd]

Thanks. Much better explanation, two separate DNA at the same location and time. Now it becomes interesting where, how and who brought that Sars-CoV-2 there to be spread further.

With what we know now, it could be very difficult to come across or stumble over answers to those questions. It will require a lot of hard work and a large amount of luck … even if China actually cooperated.

From the precious little that we now know, I favor the idea that SARS-CoV-2 spilled over to humans from an infected animal at the Wuhan market. I never bought the idea that it came from a Chinese biological warfare lab, because we have no evidence to support it. It is not impossible that this actually happened. But until there is some credible evidence to support this, it's only a feverish paranoid dream from US right wing politicians.

China's interference over this issue is the biggest obstacle to learning what did happen. Interference from the Congressional GOP seems like a good idea only if you compare it to Chinese interference.

 

[mtrycrafts]

...

China's interference over this issue is the biggest obstacle to learning what did happen. ...

Again, thanks. It is puzzling why China would interfere if it is an animal transfer. Cannot be face saving as a lab accident would really be a bad thing versus an animal transfer in a wet market.

 

[Trell]

Again, thanks. It is puzzling why China would interfere if it is an animal transfer. Cannot be face saving as a lab accident would really be a bad thing versus an animal transfer in a wet market.

This is what dictatorships do.

 

[Swerd]

It is puzzling why China would interfere if it is an animal transfer. Cannot be face saving as a lab accident would really be a bad thing versus an animal transfer in a wet market.

As a westerner I know I have trouble thinking like people from the far east or middle east. Americans in particular have quite different ideas of what face saving is compared to many other parts of the world. We run into this problem often, and almost never get it.

When it comes to why China is hiding what happened with the outbreak of Covid-19, we tend think like westerners – that they are trying to hide a biological weapon meant to be used against us. We tend to think the worst when people act like they have something to hide.

Asians in general, including Chinese, Koreans, Japanese, or others, tend to hide things that embarrass them. (I am painting with a broad brush here, so take it with a large grain of salt.) Chinese like to believe that they are the oldest and most highly evolved civilization. They regard all foreigners as barbarians, especially those from Europe or North America. For a long time, westerners have told China that it's fresh meat & fish markets are a frequent source of animal-borne diseases that can make the jump to humans. I'm only guessing here, but it could be that the Chinese govt. is too proud to admit to those western barbarians that they still haven't cleaned up their markets.

I repeat – this is only a guess. It could be for many other reasons that I haven't thought of.

 

[Trell]

As a westerner I know I have trouble thinking like people from the far east or middle east. Americans in particular have quite different ideas of what face saving is compared to many other parts of the world. We run into this problem often, and almost never get it.

When it comes to why China is hiding what happened with the outbreak of Covid-19, we tend think like westerners – that they are trying to hide a biological weapon meant to be used against us. We tend to think the worst when people act like they have something to hide.

Asians in general, including Chinese, Koreans, Japanese, or others, tend to hide things that embarrass them. (I am painting with a broad brush here, so take it with a large grain of salt.) Chinese like to believe that they are the oldest and most highly evolved civilization. They regard all foreigners as barbarians, especially those from Europe or North America. For a long time, westerners have told China that it's fresh meat & fish markets are a frequent source of animal-borne diseases that can make the jump to humans. I'm only guessing here, but it could be that the Chinese govt. is too proud to admit to those western barbarians that they still haven't cleaned up their markets.

I repeat – this is only a guess. It could be for many other reasons that I haven't thought of.

I doubt that the Japanese or South Koreans would have shown such intransigence and tried hiding a potential source of the virus outbreak that the Chinese did.

 

[Swerd]

I doubt that the Japanese or South Koreans would have shown such intransigence and tried hiding a potential source of the virus outbreak that the Chinese did.

Japanese or South Koreans (who among us know any North Koreans?) are a lot more familiar with westerners than most Chinese are. They know how to hide things better, without raising our suspicions that they're hiding something. They may be very polite on the outside, but can be aggressive & pugnacious on the inside. And most Americans never get that.

I've met Japanese & Korean scientists who were not only highly educated, they were also selected to come to the USA and work for 2-3 years in labs at the National Institutes of Health (NIH). They were the cream of the crop. And they were too embarrassed to admit to western scientists what they did and didn't know.

I got to know one Japanese scientist well enough for both of us to open up and share secrets about our fears & short comings. He told me Japanese bio-medical research was a very small and poorly funded field. The only financial support for research came from private industry. It had to be directly on a subject with practical & profit-making applications. He also told me how that whole field of science was controlled by a few senior scientists at the top, who had connections with various university medical schools & pharmaceutical companies. Young scientists had no option but to win over one of these guys as a mentor. You could not get a job or research funding anywhere in Japan without their direct help. If they called you about an open job position, you had no choice but to accept it. If you didn't, they wouldn't call you again. That whole subject essentially became taboo – something that they didn't dare discuss with anyone who wasn't Japanese. They feared we talked to those senior scientists back in Japan.

As a result, during the 2 or 3 years they were at the NIH, they worked their butts off because it was probably the only time in their whole career when they could afford to be scientifically curious without the big boss looking over their shoulder. They never knew when that phone call might come.

After I learned all that, I finally understood how embarrassed they were to admit that reality to their American colleagues. That was also true in Korea and certain European countries. Science in the USA is certainly political & highly competitive, but nothing like it was in other countries.

My point here is the Asian scientists I knew were hiding what it was like back in their home countries. That's was nothing that I could have imagined on my own. And that's what leads me to believe we don't really know what the Chinese feel the need to hide.

 

[Trell]

Japanese or South Koreans (who among us know any North Koreans?) are a lot more familiar with westerners than most Chinese are. They know how to hide things better, without raising our suspicions that they're hiding something. They may be very polite on the outside, but can be aggressive & pugnacious on the inside. And most Americans never get that.

I've met Japanese & Korean scientists who were not only highly educated, they were also selected to come to the USA and work for 2-3 years in labs at the National Institutes of Health (NIH). They were the cream of the crop. And they were too embarrassed to admit to western scientists what they knew and didn't know.

I got to know one Japanese scientist well enough to open up and share secrets about our fears & short comings. He told me Japanese bio-medical research was a very small and poorly funded field. The only financial support for research came from private industry. It had to be directly on something with practical & profit-making applications. He also told me how that whole field of science was controlled by a few senior scientists at the top, who had connections with various university medical schools & pharmaceutical companies. Young scientists had no option but to have one of these guys as a mentor. You could not get a job or research funding anywhere in Japan without their direct help. If they called you about an open job position, you had no choice but to accept it. If you didn't, they wouldn't call you again. That whole subject essentially became taboo – something that they didn't dare discuss with Americans. They feared we talked to those senior scientists back in Japan.

As a result, during the 2 or 3 years they were at the NIH, they worked their butts off because it was probably the only time in their whole career when they could afford to be scientifically curious without the big boss looking over their shoulder. They never knew when that phone call might come.

After I learned all that, I finally understood how embarrassed they were to admit that reality to their American colleagues. That was also true in Korea and certain European countries. Science in the USA is certainly political & highly competitive, but nothing like it was in other countries.

My point here is the Asian scientists I knew were hiding what it was like back in their home countries. That's was nothing that I could have imagined on my own. And that's what leads me to believe we don't really know what the Chinese feel the need to hide.

In this case I was thinking of government responses.

 

[harley52]

Let’s see. Getting biden to declassify the documents was like pulling teeth. They now go to DNI with orders from biden to redact whatever shows that the American people were lied to. The fbi acknowledges the lab is more likely than not where the virus came from. That’s enough proof right there that the virus didn’t come from an animal. Add that to all of the fentanyl flowing from china to mexico and it’s looking like china will conquer America without ever firing a shot.

 

[Trell]

Why don’t the intelligent Republicans stop stupidity like the following? Have they left the party or just lack courage and moral integrity to stand up?

Missouri House advances bill to limit nonexistent vaccine microchips—just in case

The bill aims to stop COVID vaccine mandates while promoting conspiracy theories.

arstechnica.com

>>>In the latest efforts by Republican lawmakers to enshrine into law Americans' right to freely spread deadly infectious diseases to each other, the Missouri House this week advanced a bill that would bar governments, schools, and employers from mandating certain vaccines—as well as things like vaccine microchips, which do not exist.

The bill, HB 700 (PDF), was sponsored by Rep. Bill Hardwick, a Republican from Waynesville. Hardwick told the St. Louis Post-Dispatch that he believed people "lost their minds" during the COVID-19 pandemic, and that legally barring officials and employers from requiring life-saving vaccination, even among health care workers, feels "like it's the right thing to do." …<<<

 

[TLS Guy]

First the good news.

US mortality from Covid 19 is now the lowest since the pandemic began.

This is to be expected as the infection is now in the endemic phase.

One note of caution is that a variant of concern has cropped up in India XBB.1.5. It is an Omicron variant and similar to what is circulating here.

A VA study with recent data, published today, shows that Covid 19 remains significantly more lethal than seasonal influenza.

30 day Covid 19 mortality 5.97%

30 day seasonal influenza mortality 3.75%

Excess mortality Covid-19 over seasonal influenza 2.23% for a hazard ration of 1.61%

More good news is that the mortality of Covid-19 over seasonal influenza is much reduced from early in the pandemic where it was 17 to 21% higher depending on the studies, so the gap is now down 15 to 19 percentage points over influenza. This is due to a combination of decreased virulence of newer variants and vaccination.

This is following a very similar pattern and time scale to the 1918 Spanish Flu pandemic.

 

[Mr._Clark]

It looks like bacteria can be engineered to express tumor antigens which in turn causes Swerd's favorite immune cells (T cells) to be produced that attack the tumor.

>>>Engineered bacteria as melanoma vaccine
The skin microbiome usually lives in harmony with our tissues without inducing inflammation or mounting an infection. However, certain bacterial colonists, including the skin bacterium Staphylococcus epidermidis, can induce a highly specific adaptive immune response, the function of which is unclear. Chen et al. engineered an S. epidermidis strain to express melanoma tumor antigens and then tested their ability to drive antitumor immune responses (see the Perspective by Sajjath et al.). Engineered S. epidermidis generated tumor-specific T cells that infiltrated and reduced the growth of localized and metastatic melanoma. In combination with immune checkpoint inhibitors, these engineered skin bacteria caused mice to reject established tumors. These findings suggest that immune responses from engineered commensals may have therapeutic potential against other tumor antigens of interest.<<<

https://www.science.org/doi/10.1126/science.abp9563

 

[Mojo Navigator]

It looks like bacteria can be engineered to express tumor antigens which in turn causes Swerd's favorite immune cells (T cells) to be produced that attack the tumor.

>>>Engineered bacteria as melanoma vaccine
The skin microbiome usually lives in harmony with our tissues without inducing inflammation or mounting an infection. However, certain bacterial colonists, including the skin bacterium Staphylococcus epidermidis, can induce a highly specific adaptive immune response, the function of which is unclear. Chen et al. engineered an S. epidermidis strain to express melanoma tumor antigens and then tested their ability to drive antitumor immune responses (see the Perspective by Sajjath et al.). Engineered S. epidermidis generated tumor-specific T cells that infiltrated and reduced the growth of localized and metastatic melanoma. In combination with immune checkpoint inhibitors, these engineered skin bacteria caused mice to reject established tumors. These findings suggest that immune responses from engineered commensals may have therapeutic potential against other tumor antigens of interest.<<<

https://www.science.org/doi/10.1126/science.abp9563

This is the same technology that has been used for years to engineer E. coli to produce insulin and other hormones such as hGH.

 

[Swerd]

This is the same technology that has been used for years to engineer E. coli to produce insulin and other hormones such as hGH.

Close, but not quite the same technology. With insulin or other proteins, the protein product's gene was inserted into bacteria, and grown up in large scale culture. Then it was isolated from the bacteria and purified, before injection into humans.

This new method uses the recombinant Staph. epidermidis bacteria to colonize the skin of mice, not the purified melanoma proteins purified after growing in culture. These engineered skin bacteria, expressing tumor antigens from melanoma, were found to induce a T cell immune response in mice, that was capable of rejecting transplanted melanoma tumor cells in these mice. If something similar happens in humans, it will be a big breakthrough.

This is a new and different technique. It's not said in these abstracts, but purified tumor antigen proteins like this were probably already tested in mice. Injected this way, they could generate an immune response directed against the protein molecules, but was not effective against tumor cells.

https://www.science.org/doi/10.1126/science.abp9563

Abstract
Certain bacterial colonists induce a highly specific T cell response. A hallmark of this encounter is that adaptive immunity develops preemptively, in the absence of an infection. However, the functional properties of colonist-induced T cells are not well defined, limiting our ability to understand anticommensal immunity and harness it therapeutically. We addressed both challenges by engineering the skin bacterium Staphylococcus epidermidis to express tumor antigens anchored to secreted or cell-surface proteins. Upon colonization, engineered S. epidermidis elicits tumor-specific T cells that circulate, infiltrate local and metastatic lesions, and exert cytotoxic activity. Thus, the immune response to a skin colonist can promote cellular immunity at a distal site and can be redirected against a target of therapeutic interest by expressing a target-derived antigen in a commensal.

https://www.science.org/doi/10.1126/science.adh3884

Abstract
Human health relies on carefully tailored communication between the immune system and commensal microbiota, a diverse community of microorganisms that naturally reside in tissues. Several commensal bacteria trigger antigen-specific T cell responses, which help control tissue homeostasis. Could such interactions be harnessed therapeutically, by engineering symbionts to prime immunity against designated targets? On page 203 of this issue, Chen et al. test this hypothesis by customizing the skin commensal Staphylococcus epidermidis to express a foreign antigen borne by melanoma cells. Upon colonization of mouse skin, these bacteria substantially bolstered organism-wide, T cell–driven attack of resulting tumors. The findings highlight the broader potential of microbiota-induced immunity toward host defense and open new doors to customized commensal bacteria therapies against a myriad of human diseases.

 

[Swerd]

It will be very interesting to see how the FDA responds to this. In the past, they were interested in techniques like this, but they were understandably wary of introducing any live organism that had the potential of becoming pathogenic in humans, especially those who might have impaired immune responses due to cancer.

If a pharmaceutical company develops this process as a therapeutic treatment, it will be up to them to come up with data good enough to satisfy the FDA that this method is safe to use in cancer patients. That may very well be tougher than showing this immunization method is effective against melanoma.