Discussion: Chinese Academy of Sciences (CAS) in Wuhan has been working with bats and coronavirus for many years - DNA manipulations, cloning.... - Ja

[Mary Wilson]

Unclassified
Defense Advanced Research Projects Agency

https://assets.ctfassets.net/syq3snm...R_Redacted.pdf

 

[Mary Wilson]

Tweet


Jeremy Kamil = @macroliter on Spoutible & Mastodon
@macroliter
Total Bullocks. The data were available to all GISAID users. Many of us had been waiting since Feb 2022 when George Gao’s preprint showed lineage A on a glove in stall A20—for China CDC to share FASTQ files. Many others downloaded it before it was removed https://assets.researchsquare.com/files/rs-1370392/v1_covered.pdf?c=1645813311…
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Steve Massey
@stevenemassey
·
19h
Replying to @WashburneAlex
They seem to have gotten priority access to the data, for some reason Very strange
7:57 PM · Mar 16, 2023
·

·
17h
Replying to
@macroliter
Just curious, from what part of GISAID do you download raw sequence datasets ?
Replying to
@stevenemassey
There’s a button next to FASTA download where you can download the FASTQ— if a FASTQ available for the sample in question. We have shared many of our
@LSUHSevtlab
SARS-CoV-2 FASTQ via GISAID.

https://twitter.com/macroliter/status/1636532090832318464?cxt=HHwWgMCzmYLRkLYtAAAA
______________________________
This is a preprint

Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market

https://orcid.org/0000-0002-3869-615X

https://assets.researchsquare.com/files/rs-1370392/v1_covered.pdf?c=1645813311

 

[Pathfinder]

Ministry of Foreign Affairs of the People's Republic of China

Foreign Ministry Spokesperson Wang Wenbin’s Regular Press Conference on March 17, 2023
...
The News York Times: The Atlantic reported that several foreign scientists’ analysis of genetic samples from the Huanan Seafood Market may point to raccoon dogs at the market as a possible intermediary host for COVID. Does the ministry have any response? 

Wang Wenbin: I would refer you to the experts. What I can say is that China always supports and participates in the global cooperation on science-based origins-tracing. We have invited WHO experts to China for cooperation on COVID origins-tracing, and facilitated the sharing of data and research results between competent authorities and experts and the WHO several times, making important contributions to the global origins-tracing. We will continue to do so. Many clues from the international science community are pointing the origins of virus to sources around the world. We also expect that the WHO and relevant countries can share with us the research results of origins-tracing in other parts of the world in a timely manner. 
...

https://www.fmprc.gov.cn/mfa_eng/xwfw_665399/s2510_665401/2511_665403/202303/t20230317_11043921.html

 

[JJackson]

While I would love to get some definitive evidence to clear up the origin question, I am not sure this is of any help. We already know that SARS was present in the market and that many other animals were being sold there, including raccoon dogs, so the presence of both in an environmental swab is not a great surprise.

 

[sharon sanders]

Please see:

WHO found out about these newly released data on March 12, 2023


SAGO statement on newly released SARS-CoV-2 metagenomics data from China CDC on GISAID - 18 March 2023

 

[JJackson]

Sadly, this is unlikely to throw any light on the pandemic's origin. If, and it is unlikely, Lui's finalised paper can reconstitute a complete Sars-CoV-2 genome from the sample, and it is significantly different from either the original A or B strains, then it would be a strong evidence for an intermediate host. The problem is this is a metagenetic analysis from an environmental swab. This approach allows for the identification of viral fragments matching, target host organisms. It found some human DNA, some ribosomal animal DNA and some SARS2 RNA, but even if they get a full RNA sequence, close to the pandemic form, it will not be possible to say which host it came from.

 

[Emily]

'If the glove doesn't fit, you must acquit.'
​

https://www.youtube.com/watch?v=6gEhXiuy2sA

​
Steven Quay, MD, PhD

The Huanan Market Origin of SARS-CoV-2 is Unlikely: The ancestral lineage-containing specimen appears to have arisen from post-collection laboratory contamination. -- Steven Quay is the founder of Seattle-based Atossa Therapeutics Inc. (Nasdaq: ATOS), a clinical-stage biopharmaceutical company developing novel therapeutics and delivery methods for breast cancer and other breast conditions. He received his M.D. and Ph.D. from The University of Michigan, was a postdoctoral fellow at MIT with Nobel Laureate H. Gobind Khorana, a resident at the Harvard-MGH Hospital, and was on the faculty of Stanford University School of Medicine. His contributions to medicine have been cited over 9,600 times. He has founded six startups, invented seven FDA-approved pharmaceuticals, and holds 87 US patents. Over 80 million people have benefited from the medicines he invented. His current passion is the prevention of the two million yearly breast cancer cases worldwide.​

 

[Mary Wilson]

** Download to read**


Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control

March 20, 2023
No citations.
Crits-Christoph, Alex; Gangavarapu, Karthik; Pekar, Jonathan E.; Moshiri, Niema; Singh, Reema; Levy , Joshua I.; Goldstein, Stephen A.; Suchard, Marc A.; Popescu, Saskia; Robertson, David L.; Lemey, Philippe; Wertheim, Joel O.; Garry, Robert F.; Rasmussen, Angela L.; Andersen, Kristian G.; Holmes, Edward C.; Rambaut, Andrew; Worobey, Michael; Débarre, Florence

Report:
Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan:
Analysis and interpretation of data released by the Chinese Center for Disease Control
In an attempt to ensure transparency and engagement towards global partnership, we would like to provide further context regarding the timeline of work and efforts to collaborate on the research presented in the report below.

On 4 March 2023 (dates in UTC), we discovered accessions posted publicly on the GISAID database corresponding to sequences from environmental samples collected at the Huanan Seafood Wholesale Market, Wuhan. On 9 March, we realized that those accessions were associated with raw metagenomic sequence read data files. We further recognised that it was the data underlying the preprint posted on Research Square by Gaoet al. at the Chinese Center for Disease Control and Prevention (CCDC) on 25 February 2022 (DOI: 10.21203/rs.3.rs-1370392). The metadata on GISAID indicated these sequencing data had been uploaded in June 2022, however, they evidently had not been released at that time. We downloaded the public data to search for genetic sequences from non-human animals, which the CCDC did not identify in their February 2022 preprint. The preprint also posited that all SARS-CoV-2-positive samples in the market were the result of human infections, claiming that the market was a site of amplification of an already widespread epidemic. We and others therefore had urgently requested release of the data. The potential for analysis of samples for animal DNA had also been recommended in the mission report of the World Health Organization (WHO)-convened global study of origins of SARS-CoV-2: China Part, released March 20211.

Once the data were identified on GISAID, it became possible to test the veracity of these claims. We found information that was critical to understanding the nature of the origins of the human infections at the Huanan market, as this was the early epicenter of SARS-CoV-2 spread and was likely where spillover occurred and sustained human-to-human transmission was established.

Our analysis of these data found that genetic evidence of multiple animal species was present in locations of the market where SARS-CoV-2 positive environmental samples had been collected. This includes raccoon dogs, which are susceptible to SARS-CoV-2 infection and shed sufficient virus to transmit to other species. However, this also included

1 https://www.who.int/publications/i/...bal-study-of-origins-of-sars-cov-2-china-part


https://zenodo.org/record/7754299#.ZBj5oC2ZORs

 

[Emily]

Unclassified
Defense Advanced Research Projects Agency

https://assets.ctfassets.net/syq3snm...R_Redacted.pdf

Dr. Malone made this easier to read with permission by creating a document without the watermarks:

https://rwmalonemd.substack.com/p/sars-cov-wiv

Then he has a handy list of the supporting documents:

https://rwmalonemd.substack.com/p/sa...-the-documents

And here's a video from one of the early DRASTIC team members. IT goes into a theory he is exploring about the pandemic having been artificially maintained because the pandemic's spread didn't fit either a lab leak or natural origin.

https://www.twitch.tv/videos/1768771940

 

[Shiloh]

Source: https://www.newsweek.com/covid-lab-leak-china-virus-nuclear-war-1787390

'I Suspected a China Lab Leak Early on—but My Research Was Rejected'
Dr Steven Quay
On 3/21/23 at 4:30 AM EDT

I became aware of SARS-CoV-2 in late December of 2019. I happened to hear a news report about a new unknown virus coming out of China and the next day saw an unusual clinical case report about a family in Wuhan Central Hospital.

The mother and father both had this really strange pneumonia. Their son had no symptoms, but his own X-rays showed his lungs had exactly the same lesions.

Their doctor, Ai Fen, knew immediately this was a new form of coronavirus—it clearly passed from human to human and there was clearly an asymptomatic form of the virus—but, she claims, nobody listened to her warnings.

When I initially saw the viral genome, in January 2020, I noticed a pretty esoteric thing. The virus we would later call SARS-CoV-2 has something called a furin cleavage site (FCS).

The FCS, which had never before been seen in a SARS-CoV-2-related coronavirus, is a genetic feature that makes it easier for a virus to infect human cells. So, when I saw this FCS on SARS-CoV-2, I knew it was going to make it easier to infect cells and easier to evade the immune system by tunneling into neighboring cells.

Knowing FCSs were not found in nature in these SARS-related viruses I also knew that for years scientists have been artificially putting new FCSs into viruses to see what they do, and in every case I have seen, in which they published their results, it has increased infectivity, transmissibility, pathogenicity, or a combination of them.

I found that when you looked at this virus, it had none of the properties of natural infection and it still doesn't to this day. I have not found a single shred of actual evidence that supports the idea SARS-CoV-2 is a type of spillover infection that we have ever seen in the past.

To me, it looks much more like what would happen as the result of a lab accident.

In late 2020, I conducted an analysis in which I determined there was a 99 percent probability that SARS-CoV-2 was not a natural zoonosis, but was instead laboratory-derived.

While I believe very few people were focused on theories about where this virus came from at the time, I am one of the many people in my field who received a lot of pushback about this premise.

I did a lot of television and radio interviews at the time but, despite testifying in Congress about my findings, was never invited by any of the left-leaning mainstream media outlets.

Throughout my career, I have written 390 peer-reviewed papers and reports. Normally, the process involves sending in a paper to be reviewed by journal editors and expert scholars. The paper is then reviewed; it is heavily criticized in a back-and-forth process, and in most cases, it is then published. My papers are always better because of this peer review system.

But in 2020, both myself and colleagues who were saying similar things were sending out papers to be peer-reviewed, but getting rejected without any review of the merits of the data and by who knows whom at the journals. In these cases, there were never comments or scientific criticism offered, they just said effectively: "We're busy, we can't be bothered to send it for peer review."

While my papers have since started to get peer-reviewed, at that stage, it felt like they were refusing to engage with this type of research, and then in public were saying: "Well there's no peer-reviewed data that shows SARS-CoV-2 came from a lab."...

 

[Mary Wilson]

Law, Policy, & AI Update: China Requires AI Watermarks, ChatGPT Won’t Make it to U.S. Courtrooms. Feb 6, 2023 | Peter Henderson
... China enacted new regulations on deep-synthesis technology, including deepfakes and other types of generative AI systems in January, issued by the Cyberspace Administration. The rule places significant restrictions on AI-generated media, including the requirement of carrying identifiers, like watermarks. This comes as several new tools (including ones from OpenAI and Stanford, among others) launched to identify AI-generated content, which could be used for cheating on exams, spreading disinformation, and more. ...
https://hai.stanford.edu/news/law-p...watermarks-chatgpt-wont-make-it-us-courtrooms

 

[Emily]

SARS-CoV-2′s claimed natural origin is undermined by issues with genome sequences of its relative strains

Deigin, Y., & Segreto, R. (2021). SARS-CoV-2′s claimed natural origin is undermined by issues with genome sequences of its relative strains. BioEssays, 43:e2100015. https://doi.org/10.1002/bies.202100015

Abstract

RaTG13, MP789, and RmYN02 are the strains closest to SARS-CoV-2, and their existence came to light only after the start of the pandemic. Their genomes have been used to support a natural origin of SARS-CoV-2 but after a close examination all of them exhibit several issues. We specifically address the presence in RmYN02 and closely related RacCSxxx strains of a claimed natural PAA/PVA amino acid insertion at the S1/S2 junction of their spike protein at the same position where the PRRA insertion in SARS-CoV-2 has created a polybasic furin cleavage site. We show that RmYN02/RacCSxxx instead of the claimed insertion carry a 6-nucleotide deletion in the region and that the 12-nucleotide insertion in SARS-CoV-2 remains unique among Sarbecoviruses. Also, our analysis of RaTG13 and RmYN02's metagenomic datasets found unexpected reads which could indicate possible contamination. Because of their importance to inferring SARS-CoV-2′s origin, we call for a careful reevaluation of RaTG13, MP789 and RmYN02 sequencing records and assembly methods.

 

[Shiloh]

Source: https://news.yahoo.com/china-blasts-chief-over-offensive-172435281.html

China blasts WHO chief over ‘offensive’ comments on COVID-19 origin search
Olafimihan Oshin
Sun, April 9, 2023 at 1:24 PM EDT·2 min read

Chinese health officials have called out the World Health Organization’s (WHO) Director-General Tedros Adhanom Ghebreyesus for his “offensive” comments in the ongoing search for the origins of COVID-19.

Speaking at a news conference, the director of China’s Center for Disease Control and Prevention, Shen Hongbing said that Ghebreyesus’ recent remarks were “offensive and disrespectful,” accusing the health agency of “attempting to smear China” and said it should avoid helping others “politicize COVID-19.”

In remarks made last month, Ghebreyesus said that the newly disclosed genetic material gathered in Wuhan, China should’ve been publicly shared three years ago.

The genetic material mentioned by Ghebreyesus was uploaded recently to a global database, being collected three years ago at a Wuhan-based wildlife market where wildlife was sold.

“As a responsible country and as scientists, we have always actively shared research results with scientists from around the world,” Shen said at a news conference...

 

[Mary Wilson]

Adding Genbase sequences to usher #337

aviczhl2 opened this issue Apr 10, 2023

Starting from March 2023, China began to upload most of its sequences not to GISAID but to a self-developed platform called GenBase. Sequences are free to download on NGDC by selecting dataset ”GenBase".

https://github.com/yatisht/usher/issues/337

 

[Pathfinder]

Chinese scientist claims COVID-19 may have originated from humans
...

Emre Aytekin |
10.04.2023 - Update : 11.04.2023

BEIJING
...
China's State Council's Information Office held a press conference in Beijing on Saturday to discuss latest findings in the origins-tracing of the virus.

Scientists claimed that the DNA data shared in Nature, an international scientific journal, showed that strains found in samples from the Huanan seafood market in Wuhan, where the first cases emerged, are more likely to have come from humans.

Researchers analyzed more than 1,300 DNA samples collected from animals and the environment in the market.

There was no coronavirus in any of the 457 animal samples examined, which invalidates the possibility of transmission from animals.

“These findings indicate that in the cases on the market, the virus was transmitted from other people, not from animals sold,” said Tong Yigang of the Beijing University of Chemical Technology.

There was not yet sufficient evidence to back up recent studies that had suggested raccoon dogs were the origin of the coronavirus, he added.
...
https://www.aa.com.tr/en/health/chi...id-19-may-have-originated-from-humans/2868679

 

[Pathfinder]

True origins of Covid may never be revealed, says Chinese doctor there 'at the very beginning'
...

By
Paul Nuki,
GLOBAL HEALTH SECURITY EDITOR, LONDON
14 April 2023 • 8:09pm
...
Dr George Fu Gao, who is thought to know more about the origins of the disease than any other scientist, has told the Telegraph he is “not optimistic” the origin of the virus will ever be known, citing both political and scientific obstacles.

“It’s too sensitive; too politicised,” he said.
...
On the science, Dr Gao added that the theory that there was an intermediate animal species between bats and humans that provided a “reservoir” of the virus might be wrong.

“I too thought there must be an intermediate host - a reservoir - but now I’m not so sure. It’s possible there is no animal reservoir,” he said.
...
Dr Gao, who appeared good humoured and gregarious, has a political tightrope to walk at home and is almost certain to know more about Covid’s origins than he lets on.

No doubt aware that China had officially apologised for its slowness in dealing with the 2002/3 SARS epidemic, he was careful to claim the country had acted promptly on SARS-Cov-2.

China’s CDC had been the first to detect, isolate and share the genetic sequence of the virus, he told the London conference.
...

https://www.telegraph.co.uk/global-...-covid-never-be-revealed-china-george-fu-gao/

 

[Emily]

I hope he wasn't dismissed because he was in the way of using the lab leak theory as war propaganda against China.

https://www.telegraph.co.uk/world-n...tist-covid-lab-leak-theory-sexual-harassment/
WHO scientist who doubted Covid lab leak theory sacked for sexual harassment

Peter Ben Embarek, who contests the accusation of misconduct, led WHO's mission to China to investigate Covid's origins
By Nick Allen Washington 3 May 2023 • 11:04pm
A senior World Health Organisation scientist, who concluded it was "extremely unlikely" Covid-19 leaked from a Chinese laboratory, has been dismissed for sexual misconduct.

The UN agency said Peter Ben Embarek, a Danish scientist, was removed from his post last year.

Dr Embarek said he contested the accusation of harassment and was challenging his dismissal.

He previously led WHO's "One Health" initiative on diseases jumping from animals to humans.

Dr Embarek was the most senior WHO representative on a mission to China in 2021 to investigate where Covid-19 came from.

It determined that a leak from the laboratory in Wuhan was "highly unlikely" despite calls from other scientists to investigate that possibility...

​

 

[sharon sanders]

Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market

View ORCID Profile
Jesse D. Bloom
doi: https://doi.org/10.1101/2023.04.25.538336

This article is a preprint and has not been certified by peer review
80001901146

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ABSTRACT


The role of the Huanan Seafood Market in the early SARS-CoV-2 outbreak remains unclear. Recently the Chinese CDC released data from deep sequencing of environmental samples collected from the market after it was closed on January-1-2020 (Liu et al. 2023a). Prior to this release, Crits-Christoph et al. (2023) analyzed data from a subset of the samples. Both studies concurred that the samples contained genetic material from a variety of species, including some like raccoon dogs that are susceptible to SARS-CoV-2. However, neither study systematically analyzed the relationship between the amount of genetic material from SARS-CoV-2 and different animal species. Here I implement a fully reproducible computational pipeline that jointly analyzes the number of reads mapping to SARS-CoV-2 and the mitochondrial genomes of chordate species across the full set of samples. I validate the presence of genetic material from numerous species, and calculate mammalian mitochondrial compositions similar to those reported by Crits-Christoph et al. (2023). However, the number of SARS-CoV-2 reads is not consistently correlated with reads mapping to non-human susceptible species. For instance, 14 samples have >20% of their chordate mitochondrial material from raccoon dogs, but only one of these samples contains any SARS-CoV-2 reads, and that sample only has 1 of ∼200,000,000 reads mapping to SARS-CoV-2. Instead, SARS-CoV-2 reads are most correlated with reads mapping to various fish, such as catfish and largemouth bass. These results suggest that while metagenomic analysis of the environmental samples is useful for identifying animals or animal products sold at the market, co-mingling of animal and viral genetic material is unlikely to reliably indicate whether any animals were infected by SARS-CoV-2.
​
source: https://www.biorxiv.org/content/10.1101/2023.04.25.538336v2

 

[Shiloh]

Source: https://www.bbc.com/news/world-asia-65708746

Covid: Top Chinese scientist says don’t rule out lab leak
Published 1 day ago

By John Sudworth & Simon Maybin
BBC News

The possibility the Covid virus leaked from a laboratory should not be ruled out, a former top Chinese government scientist has told BBC News.

As head of China's Centre for Disease Control (CDC), Prof George Gao played a key role in the pandemic response and efforts to trace its origins.

China's government dismisses any suggestion the disease may have originated in a Wuhan laboratory.

But Prof Gao is less forthright....​

 

[Pathfinder]

HAZARD ZONE Scientists at Wuhan lab were mixing world’s most deadly coronaviruses to create a new mutant strain, investigators say

Ed SouthgateJames Liveris
Published: 15:31, 11 Jun 2023 Updated: 15:38, 11 Jun 2023

SCIENTISTS were working with the Chinese military to create a mutant virus and pursue bioweapons just as the pandemic started, investigators believe.

They were running secret dangerous experiments combining the most deadly coronaviruses, which reportedly caused a leak from a Wuhan lab.

And it is believed vaccine research was going on there in the autumn before the outbreak, pertinent to the Covid-19 vaccination.

The findings follow a team of US investigators who combed through top-secret intercepted communications and research.

They say there is no published information on the work because it was done with researchers from the Chinese military, which was funding the projects.

Evidence suggested researchers working on the experiments were taken to hospital with Covid-like symptoms in November 2019, just a month before the West became aware of the pandemic.
...
An investigator said: "We were rock-solid confident that this was likely Covid-19."
...
Dr Huff, who worked at EcoHealth Alliance from 2014 to 2016 and served as vice president from 2015, worked on the classified side of the research programme as a US government scientist.
...
He claimed: "China knew from day one that this was a genetically engineered agent.
...
https://www.thesun.co.uk/news/22659...b-deadly-coronaviruses-strain-investigators/​