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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.... - Ja

https://www.telegraph.co.uk/news/20...virus-began-accident-disease-escaped-chinese/
Exclusive: Coronavirus began 'as an accident' in Chinese lab, says former MI6 boss
Sir Richard Dearlove tells Telegraph's Planet Normal podcast that new scientific report suggests key elements of the virus were 'inserted'
By Bill Gardner 3 June 2020 • 9:17pm

A former head of MI6 has said he believes the coronavirus pandemic "started as an accident" when the virus escaped from a laboratory in China.

In an interview with The Telegraph, Sir Richard Dearlove said he had seen an "important" new scientific report suggesting the virus did not emerge naturally but was man-made by Chinese scientists.

The apparent discovery will raise the prospect of China paying "reparations" for the death and economic catastrophe wreaked upon the world, the former intelligence chief said. It comes as Beijing faces growing pressure to explain precisely how coronavirus first began to spread late last year...
Click to expand...
 
https://www.preprints.org/manuscript/202006.0044/v1
lin, X.; Chen, S. Major Concerns on the Identification of Bat Coronavirus Strain RaTG13 and Quality of Related Nature Paper. Preprints 2020, 2020060044 (doi: 10.20944/preprints202006.0044.v1).
Abstract

A recent manuscript (Zhou, P. et al. “A pneumonia outbreak associated with a new coronavirus of probable bat origin”, Nature 579, 270–273 (2020). https://doi.org/10.1038/s41586-020-2012-7) from Wuhan Institute of Virology claimed the identification of a bat coronavirus, RaTG13, which showed 96.2% genome homology with SARS-CoV-2. In this paper, we raise the puzzling observations surrounding the identification, characterization, unique genome features of this RaTG13 strain, as well as its 100% nucleotide identity in partial RdRp gene with another bat coronavirus strain BtCoV/4991. And the paper presented premature hypothesis of potential bat origin of SARS-CoV-2 while RaTG13 strain was not successfully isolated. We also present the concerns on the methodology, data quality and experiment procedures described in this paper. We call for the authors to provide additional data, to share related samples to be verified and further characterized by other scientists.
Subject Areas

Epidemiology; COVID-19; coronavirus; bat; RaTG13; BtCoV/4991; SARS-CoV-2; Pangolin Coronavirus; next generation sequencing

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Download PDF
Click to expand...

One of the authors of this article is very impressive:
https://ppalm.org/page-18107

Here is the Conclusion for those that don't have a PDF reader. (We can post the whole paper under the license if needed.)
Conclusion:
In summary, as a study that isolated first SARS-CoV-2 strain and identified a bat coronavirus
with high homology to SARS-CoV-2, it is critical that all data relating to viral genomes are of top
quality, since many studies used or might use them as reference sequences. Meanwhile,
although the leadership in Wuhan Institute of Virology might highlight their impressive speed to
complete all related experiments described in the paper16, the accurate patient sample
collection date and sequencing data with better quality needs to be recorded in the scientific
paper.
In addition, there have been no studies on RaTG13’s infectivity in bat/human cells or in animal
models, its interactions with antibodies or antiviral drugs. There is lack of understandings on
RaTG13’s virulence, transmissibility, pathogenicity, immune epitopes, immune evasion
mechanism, etc. This was because WIV did not isolate the RaTG13 virus and does not have any
related viral stocks, if the statement from Dr. Yanyi Wang (the director of WIV) in a recent TV
interview17 was accurate.
Therefore, a careful examination of the related RaTG13 samples and raw data sets of its
genome sequencing are warranted to exclude any possibilities of errors or the potential coinfection
of two different strains of coronavirus. And the authors need to clearly explain the
relationship between RaTG13 and BtCoV/4991, whether they were the same strain or two
closely related strains.
This paper was rushed to make a premature connection between bat coronavirus and SARSCoV-
2, drawing a potential bat origin scenario to support SARS-CoV-2 zoonotic transmission
from bat to human. However, this connection was based on a potential bat coronavirus strain
RaTG13, that may not truly exist, considering its key information missing: such as no related bat
sample description, no sequencing procedure details published, confusion/identity issue with
BtCoV/4991 strain, unusual sequence features, no viral isolation and related characterization,
et al.
In light of these concerns, we call for the retraction of this Nature paper1 to further verify the
sequencing data, patient sample collection date and provide more information regarding the
origin, identification and characterization of this BatCoV RaTG13. Proper verification should
involve Dr. Zhengli Shi sending the RaTG13 and BtCoV/4991-related bat samples to other noncollaborating
laboratories to be analyzed independently. And this Nature paper1 should be
cautious on making the “probable bat origin” hypothesis before RaTG13 existence could be
confirmed.
Click to expand...
 
Last edited:
Fifty-four scientists have lost their jobs as a result of NIH probe into foreign ties

By Jeffrey MervisJun. 12, 2020 , 6:00 PM

Some 54 scientists have resigned or been fired as a result of an ongoing investigation by the National Institutes of Health into the failure of NIH grantees to disclose financial ties to foreign governments. In 93% of those cases, the hidden funding came from a Chinese institution.
...
https://www.sciencemag.org/news/202...lost-their-jobs-result-nih-probe-foreign-ties
 
PC scientists help China dodge probe of how the coronavirus got started

By Betsy McCaugheyJune 18, 2020 | 7:55pm
...
Conquering this virus and devising a vaccine will require unbiased research, no matter where it leads. And the biggest mistake is to limit scientific inquiry...
...
Findings by Cambridge University geneticist Peter Forster indicate three different strains of COVID-19 were circulating in China in the summer of 2019, each later predominating in a different part of the world.

Scientists from the University of British Columbia and the Broad Institute indicate the virus was already capable of spreading to humans when it reached Wuhan.

Harvard scientists, using aerial photographs of crammed hospital parking lots in Wuhan beginning in August 2019, speculate the virus hit that city months before China admits. The Xi Jinping regime calls that suggestion “ridiculous.”

European scientists indicate the disease invaded France, and possibly Italy, by December, though at the time, it was thought to be a regular flu.

Most controversially, a new study by three vaccine researchers published in Cambridge University’s QRB Discovery journal points to a segment in the virus’ genetic code they say may have been engineered in a lab. They argue that the addition is what makes the virus contagious to humans, besides wild animals like bats.

These leads need to be investigated, but instead they’re being denounced as conspiracy theories. Not just by the Chinese, but by scientists from prestigious American universities.
...

https://nypost.com/2020/06/18/pc-sci...virus-started/
 
https://thebulletin.org/2020/06/did...rogram-in-a-chinese-laboratory-very-possibly/
Did the SARS-CoV-2 virus arise from a bat coronavirus research program in a Chinese laboratory? Very possibly.
By Milton Leitenberg, June 4, 2020
Click to expand...

https://thebulletin.org/biography/milton-leitenberg/
Milton Leitenberg is a senior research associate at the Center for International and Security Studies at the University of Maryland (CISSM). His research is concentrated in three disparate areas of study: biological weapons; actual wars and conflicts of the past two decades and the issue of international intervention in these; and the history of nuclear weapons between the United States and Soviet Union and Russia between 1945 and 1995. CISSM published his major monograph, Biological Weapons Arms Control, in 1996. Since 1992, he has published over 30 papers in the area of biological weapons. Several of these papers concern the biowarfare program of the former Soviet Union, and The Soviet Biological Weapons Program: A History was published by Harvard University Press in 2013. Leitenberg published two other recent books on the subject of biological weapons: The Problem of Biological Weapons (National Defense College, Stockholm, 2004) and Assessing the Biological Weapons and Bioterrorism Threat (US Army War College, December 2005).
Click to expand...
 
https://news.cgtn.com/news/2020-07-...n-of-COVID-19-Wuhan-lab-RNvYLcdA1W/index.html
16:32, 02-Jul-2020
France says no link between origin of COVID-19, Wuhan lab
CGTN
France has recently announced that it does not have information to corroborate a possible link between the origin of the novel coronavirus and the Wuhan Institute of Virology...
Click to expand...

But since France was pushed aside once the Wuhan lab no longer needed help, France just has an absence of evidence.

https://www.express.co.uk/news/worl...rance-ties-wuhan-lab-coronavirus-pandemic-spt
Macron fury: France's 'strong ties' to Wuhan lab revealed amid coronavirus pandemic

EMMANUEL MACRON's France is one of many countries to be affected severely by the coronavirus pandemic - and one of the country's labs has strong ties with the Wuhan Institute of Virology which has been at the centre of false conspiracy theories.

By Charlie Bradley
PUBLISHED: 12:45, Thu, Jun 25, 2020 | UPDATED: 15:32, Thu, Jun 25, 2020

....The research centre is based in Lyon, France, and was a source of support for the developers of the Wuhan Institute of Virology.

A BSL-4 laboratory at the Wuhan Institute of Virology received significant and substantial support of the conceptual, engineering and logistical varieties from the International Center for Research in Infectious Diseases.
...
The Wuhan Institute of Virology's origin story has another link to France.

In 2004, the EU's chief Brexit negotiator Michel Barnier – then French Foreign Minister – signed a decree that led to the Wuhan lab's creation.

French firms got only minor roles in the building of the laboratory, and by the time it opened in 2017 cooperation had collapsed.

One group that has come under fire for its role in the pandemic is the Chinese Communist Party...
Click to expand...
 
The most logical explanation is that it comes from a laboratory
The well-known Norwegian virologist Birger S?rensen and his colleagues have examined the corona virus. They believe it has certain properties which would not evolve naturally. These conclusions are politically controversial, but in this interview he shares the findings behind the headlines.

Read more: https://www.minervanett.no/corona/t...ion-is-that-it-comes-from-a-laboratory/361860
 
He says the burden of proof should be on those who say it is not lab created, why? He is the one making an accusation it is for him to make a convincing case and this article is not. I hope he does get published so I can see his evidence but this article gives next to nothing as it is all vague generalisation.
 
it will be resolved with new sequences from nature (or lack thereof ?)
I haven't yet seen evidence, that labs create so many mutations. Well, maybe with some old flu viruses from the 1920s that were
preserved by passaging. But now they freeze those. And I remember papers by Wimmer et.al. creating vaccine-strains by adding
synonymour mutations for the purpose of attenuation.
The lab-origin-people really should explain the many mutations first. I haven't seen it.
And then we can see whether these mutations happened in nature too ...
Looking for an old likely Corona-consensus/index/ancester from which SARS1,SARS2,RaTG13,ZC45 originate (in non-recombined parts).
We probably need more Coronaviruses from Europe,Africa for that.
 
Out of the bat cave: China’s deadly maze
...

By GEORGE ARBUTHNOTT, JONATHAN CALVERT, PHILIP SHERWELL

From The TimesJuly 6, 2020
12 MINUTE READ COMMENTS

In the monsoon season of August 2012 a small team of scientists travelled to southwest China to investigate a new and mysteriously lethal illness.
...
Weeks earlier, six men who had entered the mine had been struck down by an illness that caused an uncontrollable pneumonia. Three of them died.
...
The virus was a huge discovery. It was a “new strain” of a SARS-type coronavirus that, surprisingly, received only a passing mention in an academic paper. The six sick men were not referred to at all.

What happened to the virus in the years between its discovery and the eruption of COVID-19? Why was its existence tucked away in obscure records, and its link to three deaths not mentioned?
...
RaTG13 is almost certainly the coronavirus discovered in the abandoned mine in 2013, which had been named RaBtCoV/4991 in the institute’s earlier scientific paper. For some reason, Shi and her team appear to have renamed it.
...
Nikolai Petrovsky, professor of medicine at Flinders University in Adelaide, said it was “simply not credible” that the WIV would have failed to carry out any further analysis on RaBtCoV/4991, especially as it had been linked to the deaths of three miners. “If you really thought you had a novel virus that had caused an outbreak that killed humans, there is nothing you wouldn’t do — given that was their whole reason for being [there] — to get to the bottom of that, even if that meant exhausting the sample and then going back to get more,” he said.
...
https://www.theaustralian.com.au/wor...910f2cd54a2376
 
This is quite wrong. Any one who is taking this seriously should listen to this explanation by Peter Daszak. In brief the estimated number of spillovers into humans of beta CoVs in S. China is over a million infections annually (based on a small serology study of rural workers). Most of the sequences are derived from bat guano and RaBtCoV/4991 was a short sequence (about a 75th of the genome, form memory, covering the RdRp protein) of no particular interest (among a thousand others) and was an outlier, genetically. It only became interesting when SARS-CoV-2 came along and it was not an outlier to this branch of the tree. RaTG13 is a consensus sequence i.e. not draw from one infection in one bat but the most common sequences from pooled samples. It does however expand the RaBtCoV/4991 to whole genome so we can see what probably was around the short 4991 partial strand. 'The whole reason for being there' was not to investigate anyone's death it was to find the origin of SARS-1 and to find out how close other SL betaCoVs were to causing a new epidemic, hence the serology tests.
https://youtu.be/Et3CHcteWNw if you are only interested in the renaming it is discussed starting at about 51:10 but I would recommend listening to the whole thing as it gives a fuller understanding of how this work is done and why.
 
JJackson: what in The Sunday Times is written is not wrong at all. Probably you do not have experience with publishing, because otherwise you would know that in science you can’t change the name of a sample to avoid losing the sampling location and possible analyses made in other articles.

BtCoV4991 was first described in this article:

"Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft"
Virologica Sinica volume 31, pages31–40(2016)

https://link.springer.com/article/10.1007/s12250-016-3713-9

and it was renamed RaTG13 in this article:

"A pneumonia outbreak associated with a new coronavirus of probable bat origin"
Nature volume 579, pages270–273(2020)

https://www.nature.com/articles/s41586-020-2012-7

where they wrote: “We then found that a short region of RNA-dependent RNA polymerase (RdRp) from a bat coronavirus (BatCoV RaTG13)”. The information that the name of the RdRp sample is BtCoV4991 is missing. The interesting part is that BtCoV4991 was the only SARS-CoV isolated from that mine. A mine where three miners died from a viral pneumonia. You can find more information about it in this article:


https://www.researchgate.net/public...V-2_a_conspiracy_theory_that_must_be_censored

So, was really BtCoV4991 so uninteresting to leave it for 7 years in a freezer?
 
I can see absolutely nothing new in those links. The first paper says exactly what I did that 4991 was a short section of one of the non structural proteins RdRp which we also discussed in the virology discussion. The second paper say RaTG13 is a full sequence genome and they show it as such in the graph, which I also posted in the Virology Discussion thread. Yes the sequence data came from the same mine as some people died after entering but it housed a colony of bats and we happened to get one sequence and no live virus from, that does not imply this sequence caused their illness as I pointed out the bats are estimated to cause a million infections in people near caves annually and that some may die. There are thousands of SARS like strains in these bat populations and we have sampled a fraction of one percent of them.
 
JJackson, do you not *need* at least a whole live virus in order to extract a *full* sequence? Even if just momentarily? I.e. take sample (with live virus), freeze sample (has intact virus), sequence sample (have full sequence). Use a sample in infection studies and tests (now have living and replicating virus)...
 
JJackson: RaTG13 binds to the receptor hACE2 and can potentially infect people

https://www.nature.com/articles/s41586-020-2179-y

“First, we found that bat RaTG13 uses human ACE2 as its receptor suggesting that RaTG13 may infect humans.”

The WIV was called to investigate the miner’s death. See the translation of the two theses linked to this paper:

https://www.researchgate.net/public...spiracy_theory_that_must_be_censored/comments

https://www.researchgate.net/publication/342424323_Li_2013_-_MSc_Dissertation_-_WIP_Englishdocx

https://www.researchgate.net/publication/342424092_Huang_2016_-_PhD_Dissertation_-_WIP_Englishdocx

And you can read more about the miner's story in this paper from an Indian group:

“Understanding the Origin of ‘BatCoVRaTG13’, a Virus Closest to SARS-CoV-2”

https://www.preprints.org/manuscript/202005.0322/v2

You should also give a look to this paper:

https://www.nature.com/articles/s41586-020-2294-9

“Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform”

You just need a sequence to create a functional virus.
 
5-FU seems to be researched a lot as an anti-viral. I think that could be dangerous.

https://www.biorxiv.org/content/10.1101/2020.02.27.969006v1.full
Comparative genomic analysis revealed specific mutation pattern between human coronavirus SARS-CoV-2 and Bat-SARSr-CoV RaTG13
Longxian Lv, Gaolei Li, Jinhui Chen, Xinle Liang, Yudong Li
bioRxiv 2020.02.27.969006; doi: https://doi.org/10.1101/2020.02.27.969006 This article is a preprint and has not been certified by peer review [what does this mean?].
Conclusions
Through comprehensive comparative analysis between SARS-CoV-2 and other coronaviruses, we found the synonymous mutations is dramatically elevated between SARS-CoV-2 and RaTG13 than that of other coronavirus strains, and the nucleotide mutations were enriched in T:C transition. The specific mutation pattern may caused by the loss function of RNA 3’-to-5’ exoribonuclease (ExoN). Moreover, as the SARS-CoV-2 was supposed to be originated from Bat-SARSr-CoV RaTG13, the increased synonymous substitution between SARS-CoV-2 and RaTG13 strain suggested the SARS-CoV-2 genome was under stronger negative (purifying) selection. We also detected some sites in spike protein was experiencing positive selection. These observations suggest that adaptive evolution might contribute to its host shifts. However, as the RNA mutagen (e.g. 5-FU) could induce the same mutation pattern, the mechanism of the mutation pattern observed between SARS-CoV-2 and RaTG13 should be further investigated in future work."
 
https://flutrackers.com/forum/forum...dna-manipulations-cloning?p=875807#post875807
RaTG13 is a consensus sequence i.e. not draw from one infection in one bat but the most common sequences from pooled samples.
Click to expand...

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.
 
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