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Discussion: Chinese Academy of Sciences (CAS) in Wuhan has been working with bats and coronavirus for many years - DNA manipulations, cloning....
Discussion: Chinese Academy of Sciences (CAS) in Wuhan has been working with bats and coronavirus for many years - DNA manipulations, cloning....
RaTG13 is a consensus sequence i.e. not draw from one infection in one bat but the most common sequences from pooled samples.
JJackson, that is news to me. I think quite a few scientists are confused about that, too. In the Nature paper by Zhou and Shi they talk about RaTG13 as if it is an intact virus they found in nature. https://www.nature.com/articles/s41586-020-2012-7
Is Daszak the one saying that RaTG13 is something they cobbled together from a pool of samples? Sometimes he sounds rather muddled to me.
"...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party
(My posts are not intended as advice or professional assessments of any kind.) Never forget Excalibur.
MSCOX - PCR does not need live virus or even a whole strand, if you give it a whole strand it will break it into bits anyway. These short sections are then compared to the probes you have selected to test the sample against (this will be a short sequence, 20NTs typically, of SARS 30,000 NT genome) and then makes a DNA equivalent of any matches. A fluorescent marker is normally added to the nucleotides in the solution and are incorporated into this new DNA. The solution is then thermo-cycled (which basically doubles the DNA) repeatedly until there is enough DNA fluorescing to be detected. If there is any RNA present that matches the probe you will eventually get a glow the question is how many doublings does it take to get to that point. If it comes back positive after 10 to 20 cycles, this would be a strong positive from a clinical sample, if you get to 35 cycles without detection then it is deemed a fail, these numbers are typical but you can pick your sensitivity threshold. The sample you start with could be from a single infected patient or from bat guano (with a mix of viral, bat, bacterial and other RNAs) in either case the PCR is going to look for matches to your probe which is selected from a region you think/hope is unique to the virus you are interested in. The CDC uses 3 probes in its assay all short sections from the N gene.
Emily – In the link I provided Daszak states that it was a consensus sequence. In the whole interview and an earlier one, from Dec. 2019 pre outbreak, he explains clearly how they go about collecting the samples. SL betaCoVs are endemic in the bat population but circulate at fairly low level so only a few percent would be PCR positive at any time and 30% would be seropositive, much like avian flu strains in wild bird populations. Micro-bats are very difficult to sample in volume so PCR of guano is the normal method of finding out what viruses are prevalent in the population. The BSL4 lab in Wuhan has 4 live strains that they are culturing none of them are RaTG13. All this work was done prior to SAR-2 and mainly to look for the origin of SARS-1 and to find other SL sequences that are close to the Zoonotic edge and are therefore ripe to make the species jump to humans.
Kathy – You seem determined to see nefarious actions on the part of Shi et. al. when I would argue that all of what has happened is typical zoonotic behaviour we have seen played out hundreds of times in animal to human spill overs and requires no other mechanism. A Furin cleavage site has been found in other samples and all of reading frames that occur in SARS, 1 or 2, can be found in bats if we look, but then the funding to look has been cut so if you want the truth try and get the funding re-established.
Thanks for clarifying, JJackson. Gathering bat guano is fine. Mist netting is the thing I don't approve of, or collecting live bats and doing lab experiments on them.
Also I agree with Kathy that nobody is accusing Shi of anything nefarious, or even of having made a mistake personally.
JJackson: I never accused Shi. Any lab having the right sequence might have synthetized RaTG13 and manipulated it. The furin cleavage site is not natural in this group of viruses as I wrote it already several times and I won't repeat it. The RmYN02 strain has been claimed to have a kind of insertion but the alignment is false and there is actually no insertion, just mutations with no function in cleavage. This is an example of fabricated evidence for the natural origin for SARS-CoV-2.
I am not aware of the hundreds of natural spill-over as SARS-CoV-2. This time there were no intermediate jumps and adaptation from animals as in the first SARS and in MERS. SARS-CoV-2 was from the beginning perfectly adapted to hACE2:
“SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence?”
I do not know which reason you have to do your best to support the natural origin theory for SARS-CoV-2. Many researchers do it because they have big conflicts of interests, as Daszak and Lipkin.
As respect for more than 500.000 people who already died because of the virus I take the lab hypothesis very seriously. I am concerned that we will have soon one pandemic after the other if these gain of functions studies will not be stopped.
COVID-19: COVID: Eight questions for the WHO team going to China next week to investigate pandemic origins
BY GUEST WRITER ON JUNE 30, 2020.
By Daniel R. Lucey M.D., MPH, FIDSA
...
1. What animals in the Wuhan Huanan Seafood Market were tested, what types of specimens were obtained, and what were all the results?
2. What does a “One Health” (human, animal, environmental) blueprint map of the market show...
3. What exactly were each of the 33 virus-positive environmental samples (e.g., what type of sewage, cutting boards, door handles, garbage truck)?
...
4. What are the detailed results of testing in other markets in Wuhan, outside Wuhan in Hubei province, and outside Hubei province?
...
5. What are the complete data referenced in the March 13, 2020 article in the South China Morning Post (by Josephine Ma) titled: “Coronavirus: China’s first confirmed Covid-19 case traced back to November 17.”
...
6. Given that the origin of the virus has been stated by the China CDC Director not to be the Wuhan Huanan Seafood Market (as quoted in the May 23 SCMP (by Zhuang Pinghui) was quoted in the South China Morning Post May 23 saying: it is important to address questions about any potential laboratory source of the virus, whether in Wuhan or elsewhere e.g. What kind, if any, “Gain-of-Function” experiments were done with coronaviruses...
7. Were any type of laboratory ferret-to-ferret passage of coronaviruses performed whether in Wuhan or elsewhere in China, or in collaboration with foreign laboratories? If so, what viruses were studied and what were the results? Were coronaviruses studied in any ferret-to-ferret studies that came from different animal e.g., bats, pangolins, and/or other animals?
8. Why was the single specific environmental virus isolate from the Wuhan Huanan Seafood Market used chosen, as well as the single specific human isolate of the virus chosen in the experiments to infect ferrets in the “in the biosafety level 4 and animal biosafety level 4 facilities in the Harbin Veterinary Research Institute (HVRI) of the Chinese Academy of Agricultural Sciences (CAAS)”?
...
"Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear." -Nelson Mandela
Structural analysis of COVID-19 spike protein provides insight into its evolution
9-Jul-2020 12:45 PM EDT, by Francis Crick Institute
Newswise — Researchers at the Francis Crick Institute have characterised the structure of the SARS-CoV-2 spike protein as well as its most similar relative in a bat coronavirus. The structures provide clues about how the spike evolved and could help inform vaccine design.
A characterising feature of SARS-CoV-2, the virus that causes COVID-19, is the protein spikes which cover the surface, which the virus uses to bind with and enter human cells.
Analysing the structure of these spikes could provide clues about the virus' evolution. It is not yet known how SARS-CoV-2 evolved to infect humans and whether this happened directly from coronaviruses in bats or via an intermediary species.
In their study, published in Nature Structural & Molecular Biology, the researchers characterised the spike protein in high resolution using a technique called cryo-electron microscopy, which allowed them to achieve a greater level of detail than previously reported structures. They then compared this structure to the spike protein of a bat coronavirus, RaTG13, which has the most similar spike to that of SARS-CoV-2.
While the spikes as a whole were over 97% similar, the researchers found a number of significant differences at the location where SARS-CoV-2 binds with a receptor on human cells, called ACE2, and at the surfaces that keep the subunits of the spike together.
These differences mean the spike of SARS-CoV-2 is more stable and is able to bind around 1,000 times more tightly to a human cell than this bat virus.
Based on their findings, the researchers suggest it is unlikely that a bat virus similar to RaTG13 could infect human cells. This supports the theory that SARS-CoV-2 is the result of different coronaviruses coming together and evolving over time, potentially also through several host species.
Antoni Wrobel, co-lead author and postdoctoral training fellow in the Structural Biology of Disease Processes Laboratory at the Crick, says: "The spike is the entry key that allows SARS-CoV-2 into human cells. Changes in the virus' genome, which affect the spike's structure, therefore have potential to make the virus either more or less able to enter the host's cell."
"At some point in the evolution of this virus, it seems to have picked up changes, like the differences we found, which made it able to infect humans."
Donald Benton, co-lead author and postdoctoral training fellow in the Structural Biology of Disease Processes Laboratory at the Crick, says: "The exact process of how SARS-CoV-2 evolved remains unclear and is something many researchers are trying to piece together. Our work provides a piece of this puzzle, as it suggests that the virus did not come straight from the bat coronaviruses currently known."
Steve Gamblin, group leader of the Structural Biology of Disease Processes Laboratory at the Crick says: "The world was caught off guard by SARS-CoV-2. Examining the structure of this virus, and its likely precursor, helps us understand where it came from, and how it interacts with human cells."
The Crick researchers will continue to study the structure of the virus, with a view to finding further clues as to its evolutionary path.
The spike protein structures are open-access, so other researchers can use these in their work and to aid with drug discovery and vaccine design.
"Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear." -Nelson Mandela
EXCLUSIVE: Chinese virologist accuses Beijing of coronavirus cover-up, flees Hong Kong: 'I know how they treat whistleblowers'
Li-Meng Yan told Fox News that she believes China knew about the coronavirus well before it claimed it did. She says her supervisors also ignored research she was doing that she believes could have saved lives.
snip
She also claims the co-director of a WHO-affiliated lab, Professor Malik Peiris, knew but didn't do anything about it.
Peiris also did not respond to requests for comment. The WHO website lists Peiris as an "adviser" on the WHO International Health Regulations Emergency Committee for Pneumonia due to the Novel Coronavirus 2019-nCoV.
Yan was frustrated, but not surprised.
"I already know that would happen because I know the corruption among this kind of international organization like the WHO to China government, and to China Communist Party," she said. "So basically... I accept it but I don't want this misleading information to spread to the world."
EXCLUSIVE: Chinese virologist accuses Beijing of coronavirus cover-up, flees Hong Kong: 'I know how they treat whistleblowers'
Li-Meng Yan told Fox News that she believes China knew about the coronavirus well before it claimed it did. She says her supervisors also ignored research she was doing that she believes could have saved lives.
snip
She also claims the co-director of a WHO-affiliated lab, Professor Malik Peiris, knew but didn't do anything about it.
Peiris also did not respond to requests for comment. The WHO website lists Peiris as an "adviser" on the WHO International Health Regulations Emergency Committee for Pneumonia due to the Novel Coronavirus 2019-nCoV.
Yan was frustrated, but not surprised.
"I already know that would happen because I know the corruption among this kind of international organization like the WHO to China government, and to China Communist Party," she said. "So basically... I accept it but I don't want this misleading information to spread to the world."
On Friday 3 July, all staff of the HKU-Pasteur Research Pole gathered for a very special happy hour to express their heartfelt and sincere thanks to Professor Malik Peiris, who is stepping down as Co-Director of HKU-Pasteur.
Malik Peiris co-directed the HKU-Pasteur Research Pole for 14 years alongside Professor Roberto Bruzzone, who welcome Malik by briefly remembering how his work has been significant to HKU-Pasteur and to science as a whole.
In the presence of Professor Keiji Fukuda, Director of the School of Public Health (HKU), Alexandre Giorgini, Consul General of France in Hong Kong and Macau, and Diane-Sophie Trevoux, Attach?e for Education, University and Science, the evening went along in a very warm and friendly atmosphere.
Guests thanked him for his groundbreaking scientific work within the lab as well as his remarkable contribution in teaching, and highlighted how his discoveries, notably in the field of coronaviruses, have been decisive for the current response to the pandemic...
See also post #190 on connections of France's lab to Wuhan BSL-4 lab.
The young leader of the group must propose a multidisciplinary, innovative and ambitious international research program in infectious, tropical or neglected diseases in collaboration with the BSL4 laboratory, localized in Wuhan Institute of Virology – Chinese Academy of Science.
The P4 laboratory in the city of Wuhan, where the virus SARS-CoV-2 first appeared, has nothing to do with the Institut Pasteur of Shanghai (IPS)
Yet there is a connection and potential conflict of interest. That does not make anyone guilty of any wrongdoing, but the potential should be disclosed. The French lab discussed in post 190 is the International Center for Research in Infectious Diseases and Pasteur Institute is part of that.
xhttp://ciri.inserm.fr/en/the-ciri/organization/
"...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party
(My posts are not intended as advice or professional assessments of any kind.) Never forget Excalibur.
A search of Dr. Yan on PubMed yields the following papers:
Viral dynamics in mild and severe cases of COVID-19.
Liu Y, Yan LM, Wan L, Xiang TX, Le A, Liu JM, Peiris M, Poon LLM, Zhang W.Lancet Infect Dis. 2020 Jun;20(6):656-657. doi: 10.1016/S1473-3099(20)30232-2. Epub 2020 Mar 19.PMID: 32199493 Free PMC article. No abstract available.
Pathogenesis and transmission of SARS-CoV-2 in golden hamsters.
Sia SF, Yan LM, Chin AWH, Fung K, Choy KT, Wong AYL, Kaewpreedee P, Perera RAPM, Poon LLM, Nicholls JM, Peiris M, Yen HL.Nature. 2020 May 14. doi: 10.1038/s41586-020-2342-5. Online ahead of print.PMID: 32408338
Dr Malik Peiris is listed as an adviser to International Health Regulations (IHR) Emergency Committee for Pneumonia due to the Novel Coronavirus 2019-nCoV for all the meetings:
...
Advisors
...
Dr Malik Peiris
Director, School of Public Health and Chair in Virology, Co-Director, WHO H5 Reference Laborator, The University of Hong Kong, Hong Kong SAR People's Republic of China
...
International Health Regulations (IHR) Emergency Committee for Pneumonia due to the Novel Coronavirus 2019-nCoV
30 April 2020 Emergency committee members and advisers
"Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear." -Nelson Mandela
Chinese state media has offered a rare glimpse of the lab at the heart of coronavirus conspiracy theories, as it seeks to push back against claims the facility was the source of the global pandemic.
China Offers Glimpse Inside Lab Near Wuhan Virus Origin
President Donald Trump and other US figures have repeatedly suggested the virus could have leaked from the Wuhan Institute of Virology, or even been deliberately produced there.
WorldAgence France-Presse Updated: July 09, 2020 04:59 pm IST
...
Footage broadcast by state-run CCTV is believed to be the first from within the institute's P4 lab -- for highly-dangerous Class 4 pathogens -- since its inauguration in 2017.
However, it offered no new information on the lab's workings.
...
Yuan said that while some might view the lab as a "secretive black box", he insisted it was "very open and transparent" and that the facility hopes to become "a platform for international exchanges and to see more foreign scientists come to work in our lab".
"...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party
(My posts are not intended as advice or professional assessments of any kind.) Never forget Excalibur.
EXCLUSIVE: Chinese virologist accuses Beijing of coronavirus cover-up, flees Hong Kong: 'I know how they treat whistleblowers'
Li-Meng Yan told Fox News that she believes China knew about the coronavirus well before it claimed it did. She says her supervisors also ignored research she was doing that she believes could have saved lives.
snip
She also claims the co-director of a WHO-affiliated lab, Professor Malik Peiris, knew but didn't do anything about it.
Peiris also did not respond to requests for comment. The WHO website lists Peiris as an "adviser" on the WHO International Health Regulations Emergency Committee for Pneumonia due to the Novel Coronavirus 2019-nCoV.
Yan was frustrated, but not surprised.
"I already know that would happen because I know the corruption among this kind of international organization like the WHO to China government, and to China Communist Party," she said. "So basically... I accept it but I don't want this misleading information to spread to the world."
HKU responds to the media concerning a former staff member’s TV interview
11 Jul 2020
Dr Yan Limeng was a post-doctoral fellow at HKU. She has left the University.
While HKU respects freedom of expression, Dr Yan’s past or present opinions and views do not represent those of the University.
HKU notes that the content of the said news report does not accord with the key facts as we understand them. Specifically, Dr Yan never conducted any research on human-to-human transmission of the novel coronavirus at HKU during December 2019 and January 2020, her central assertion of the said interview.
We further observe that what she might have emphasised in the reported interview has no scientific basis but resembles hearsay.
HKU does not act on hearsay and we will not further comment on this matter.
"Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear." -Nelson Mandela
I think she did do some research on human-to-human transmission in January 2020 because she is cited as a co-author of this correspondence published in the Lancet "Viral dynamics in mild and severe cases of COVID-19" in which the authors mention the similarity of SARS-CoV-2 to SARS in 2002–03. https://www.thelancet.com/pdfs/journ...20)30232-2.pdf
WHO remains tight-lipped on experts sent to investigate coronavirus in China
...
Simone McCarthy
Published: 11:00pm, 12 Jul, 2020
...
The WHO said last week that two experts – an animal health specialist and an epidemiologist – would start work on Saturday but by Sunday evening there was still no word on the name of the specialists, the schedule of the trip, and their agenda.
...
Yanzhong Huang, a senior fellow in global health governance, also with the Council on Foreign Relations, said a transparent investigation by the WHO could be a chance for the organisation to “rebuild its reputation and show it is an authoritative neutral actor in global health governance”.
But the “composition of the [future international] delegation, where are they going to visit, what is the plan of the investigation, this is all subject to negotiation,” he said, adding that even the WHO’s comments last week that Wuhan would be the starting point for the inquiry “is subject to negotiation or has to be decided by the Chinese side”.
Much depends on how much access the team gets to data and to investigate different scenarios, including the theory that the virus is linked to a Wuhan lab, some observers say.
Daniel Lucey, an infectious disease and outbreak expert at Georgetown University Medical Centre, said the international team would need to “adequately address” this theory.
...
Foreign Ministry Spokesperson Hua Chunying's Regular Press Conference on July 13, 2020
...
Asahi Shimbun: Two WHO experts have arrived at Beijing and talked with the Chinese side. Have the two sides determined when and where to conduct virus tracing work?
Hua Chunying: After consultation between the two sides, the Chinese government has agreed that WHO will send experts to Beijing to exchange ideas with Chinese scientists and medical experts on science-based cooperation to trace the origin of the COVID-19 virus. Two WHO experts have already arrived in China.
A basic consensus between China and WHO is that virus tracing is a scientific issue that should be studied by scientists through international research and cooperation across the globe. It is also the view of WHO that it is an ongoing process probably concerning many countries and localities, and WHO will conduct similar trips to other countries and regions in light of the actual need.
...
Reuters: What has been done by WHO experts since their arrival in China? Where have they been and whom they met? How long will they stay in China?
Hua Chunying: I have no information at hand to share at this moment since these are very specific matters. What I can tell you is that WHO experts are indeed in China now after consultations between the two sides. Considering quarantine rules and regulations still in place, the competent Chinese departments have stayed in close communication with relevant experts and provided all convenience to them. Chinese scientists and medical experts will also maintain communication, cooperation and exchange on such issues including scientific cooperation on source identification of COVID-19. We will release further information once we have it.
...
"Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear." -Nelson Mandela
Hong Kong virologist claiming coronavirus cover-up tells 'Bill Hemmer Reports': 'We don't have much time'
...
By Charles Creitz | Fox News
...
"I am waiting to tell all the things I know, provide all the evidence to the U.S. Government," Yan added. "And I want them to understand, and I also want the U.S. people to understand how terrible this is. It is not what you have seen ... This is something very different. We have to chase the true evidence and get the real evidence because this is a key part to stop this pandemic. We don't have much time."
A Hong Kong virologist who fled to the U.S. earlier this year told "Bill Hemmer Reports" in an exclusive interview Monday that that lives could have been saved if the Chinese government hadn't censored her work.
"Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear." -Nelson Mandela
Mark Kortepeter, a former top figure in the United States’ biodefense programs, argues that the coronavirus most likely started from natural causes rather than escaped from a lab in Wuhan. Click the link above to learn about his arguments.
Carla SimmonsJun 21, 2020 11:23 PM EDT
Speculations have been going around about the coronavirus "escaping" from a lab in Wuhan. Some even say that the virus was genetically manipulated by man and has gotten out of control.
However, Mark Kortepeter, the former deputy director of the United States Army Medical Research Institute of Infectious Diseases, argues that the virus most likely spread through natural channels rather than from a "hot zone" lab.
....
Kortepeter considers two possible scenarios in the lab. He says either someone got exposed to a natural origin such as an animal, or an exposure to a manipulated virus. His theory is that it started from exposure in the natural environment. However, considering being a biodefense and Army official, he says he does not shut out the possibility of someone trying to do things for vicious intents...
"...there’s an obvious contest that’s happening between different sectors of the colonial ruling class in this country. And they would, if they could, lump us into their beef, their struggle." ---- Omali Yeshitela, African People’s Socialist Party
(My posts are not intended as advice or professional assessments of any kind.) Never forget Excalibur.
The virus structure can only tell so much. What fuels suspicion is the sudden crackdown on communications from the labs along with the purging of their files.
Sadly the WHO is quite beholden to the national governments and hence incapable of any forceful investigation. So the clouds will linger.
That said, it is silly to blame China for the global scale of the outbreak. There was plenty of warning, but no clear understanding or leadership in much of the world.
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