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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

Andean immigrants in New York City raise and sell guinea pigs for meat, and some South American restaurants in major cities in the United States serve cuy as a delicacy.[147][33] In the 1990s and 2000s, La Molina University began exporting large breed guinea pigs to Europe, Japan, and the United States in the hope of increasing human consumption outside of countries in northern South America

Andean immigrants in New York City raise and sell guinea pigs for meat, and some South American restaurants in major cities in the United States serve cuy as a delicacy.[147][33] In the 1990s and 2000s, La Molina University began exporting large breed guinea pigs to Europe, Japan, and the United States in the hope of increasing human consumption outside of countries in northern South America
https://en.wikipedia.org/wiki/Guinea_pig

aucun variant imputable au passage en tous ces lieux ?

j'aimerai les r?ponses de g?n?ticiens sv p ...
 
September 14, 2020

Preprint Open Access

Proposed SARS-CoV-2 Spillover During 2019 Review of Samples from a Mineshaft in Mojiang, Yunnan Province, China


This research examines the activity at the Wuhan Institute of Virology in late 2019, when samples from a mineshaft associated with a suspected SARS outbreak were being reviewed. It proposes that spillover occurred during this review of samples including of a virus (BtCoV/4991) only 1% different to SARS-CoV-2 in its RdRp.

https://zenodo.org/record/4029545#.X2OwhxBKg2z
 
Emily it is definitely not my intention to be rude or nasty to anyone here and certainly not you who I have worked with for years and always viewed as friend, the same applies to Sharon. My problem with this thread, and the items in your post, is that they are purporting to be evidence of lab generation of a virus and to someone who does not understand - and I do not include you or Sharon in that because I know better from the the threads we have all contributed to in the past - it looks plausible and authoritative. That is why I have been taking the time to try and explain why they are built on incorrect data or unjustified inferences based on that data, at least as I understand it. My understanding may be wrong and I am happy to change my opinion if there was anything in this thread that made me think I had misunderstood something but nothing presented so far is substantial.
 
"it looks plausible and authoritative"
Hey, I like that! I'll try to put a disclaimer on posts that explore biosafety/ethics rather than offer direct evidence in this particular case since I'll never have access to the only kind of evidence that will work. (And could be thrown out of court by a biased judge, anyway.)
We're good, JJackson.
 
To provide both views here is a recent NatGeo article. My personal experience with this media is that they do not correct inaccuracies in their reporting. Anyway...it is important to always read both views in a controversy.


Why misinformation about COVID-19’s origins keeps going viral

Another piece of coronavirus misinformation is making the rounds. Here’s how to sift through the muck.

September 18, 2020

snip

Finding answers to the precise events that led to a spillover pandemic is a “needle in a haystack proposition,” says Ian Lipkin, an epidemiologist from Columbia University, who co-authored an early research paper in Nature Medicine about the natural origins of SARS-CoV-2. The Yan report claims this Nature Medicine report had a “conflict of interest” due to Lipkin’s work in containing the 2002-2003 SARS epidemic, for which he received an award from the Chinese government. Lipkin says this accusation is “absurd,” and when asked for his view on the role of bioengineering in the origins of SARS-CoV-2, he adds: “There is no data to support this.”

https://www.nationalgeographic.com/s...act-check-cvd/
 
Is it a preprint if someone uploads to Zenodo? I can post there as can you just give them an email address and upload it is probably harder to comment here. I can not see anything on this upload site being accepted by any journal with a peer review process. At least with the bio and medarix some of the papers will eventually be reviewed and published.
 
JJackson said:
Prof. Racaniello felt that Dr. LiMeng Yan's Zenodo post needed examination so the TWiV team (3 Virology Professor and a Professor of Immunology) review it here https://www.youtube.com/watch?v=sBQplOe8-LE
Click to expand...

Thanks for posting. In a search for the truth all the facts must be considered. Interesting.

The group call this paper "pseudoscience" and "an attempt at getting attention".

It is unfortunate is that instead of just sticking to the science at issue they go into the background of the paper and question the motivations of the publishers.

The twiv group has opened themselves up to the same scrutiny about the background (i.e. funding) of their work.

This is going to be a wild ride.
 
It is unfortunate is that instead of just sticking to the science at issue they go into the background of the paper and question the motivations of the publishers.
Click to expand...

I think it is important to look at the motivation of articles that argue against the bulk of scientific opinion, be it petro-chemical companies and climate change or disgruntled Chinese citizens and SARS. It does not necessarily prove they are wrong but it would definitely make me scrutinize their claims and data very closely.
TWiV gets support from the American society for Microbiology and the American society for Virology (ASM/ASV) & and donations from listeners also it has been running for 14 years, about the same as FluTrackers, so its raison d'etre is obvious. The organisation behind that post was founded last year to work on human rights abroad by a Chinese billionaire - which has to raise warning flags when they then start posting highly controversial statements about a topic way outside their remit, especially when it makes accusations against a country their funder has an unrelated beef with.
 
Oh, don't get me wrong about looking at all facets of something. I think everything should be considered, but when you criticize the funding source be prepared for a boomerang. That's all I am saying. I wish the Racaniello group had not opened the door. They had a great discussion on the science.
 
I found this Sharon:

SARS-CoV-2 furin cleavage site revisited

14 MAY 2020
...
An interesting question is the origin of the furin cleavage site it SARS-CoV-2. Its closest relative, the bat isolate RaTG13, does not have this site. Nor do any of the other bat SARS-like CoVs or the pangolin CoVs that have been isolated. However recently a newly isolated bat SARS-like CoV, RmYN02, was shown to contain a poly basic amino acid insertion in the spike glycoprotein. This observation supports the hypothesis that the furin cleavage site in SARS-CoV-2 arose by recombination among bat viruses in nature.
...
--------------------------------------------
Comments section:

RAD
15 May 2020, 10:53 am

Vincent Racaniello said:
> This observation supports the hypothesis that the furin cleavage site in SARS-CoV-2 arose by recombination among bat viruses in nature.

A recombination event is key to this hypothesis. In nature, it requires that a single animal was simultaneously infected by two viruses; a low probability but not implausible event. Recombination in the lab is also plausible but it requires Gain-of-Function type research on the RaTG13 virus. I have no idea how probable this lab scenario is but I’d prefer to see the lab hypothesis falsified rather than dismissed outright.

Bret Weinstein on his Darkhorse podcast thinks the lab hypothesis is much more likely but I think he is overly focused the respiratory infection of cave roosting bats rather than the gastrointestinal infection of bats that spread the disease to other animals through their guano outside of the cave environment.
...
feathers
17 May 2020, 2:18 pm

Vincent – I don’t understand your logic here. You’re basically saying a virus that shares 61% similarity (RmYN02) is a smoking gun to a natural event simply because it also shares the insertion of multiple amino acids at the junction site of the S1 and S2? You realize this virus is something on the order of 11500 bp different from SARS-CoV-2…hardly the precursor virus.
...
Steven Quay, MD, PhD
31 May 2020, 3:32 am

The following statement is false: However recently a newly isolated bat SARS-like CoV, RmYN02, was shown to contain a poly basic amino acid insertion in the spike glycoprotein. This observation supports the hypothesis that the furin cleavage site in SARS-CoV-2 arose by recombination among bat viruses in nature.

SARS-Cov-2 has a furin sequence P-R-R-A. The RmYN02 sequence has NO BASIN AMINO ACIDS!!!

LINK
...
Lilian
13 June 2020, 10:52 am
RmYN02 has not insertions at the S1/S2 junction. The alignment in the paper is wrong.
...
https://www.virology.ws/2020/05/14/...protein of SARS,its disease pattern in humans.
 
Johns Hopkins

In Response: Yan et al Preprint
Examinations of the Origin of SARS-CoV-2 September 21, 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of novel
coronavirus disease 2019 (COVID-19), has caused more than 961,000 known deaths1
since it was reported to the World Health Organization on December 31, 2019. Determining the origin of the
pandemic coronavirus is of great importance, not only to understand the mechanics of how the virus
replicates and spreads but also to anticipate and prevent additional viruses from becoming future
health security crises. If an origin can be found for SARS-CoV-2, steps can then be taken to prevent
a similar pathway for other viruses to lead to a pandemic. For that reason, it is the responsibility of
the scientific community to review and analyze data relating to the origin of SARS-CoV-2.

Several analyses of the potential origin of SARS-CoV-2 have been published in scientific journals
that provide peer review prior to publication.2,3,4,5,6,7,8,9 Peer review is central to the scientific process because
scrutiny by experts allows for meaningful conclusions to be drawn about available data and reduces inappropriate
extrapolation or misinterpretation. It is an imperfect process, often criticized for slowness, but peer review
is a necessary part of building reliability in the scientific record. Complex scientific details are best understood
and critiqued by others who are also experts in a technical field. When the audience for an article is
broadened, even to a technical audience in an adjacent scientific field, data may appear smoother
and less conflicting than it is in reality, leading to a blurring or skewing of its real meaning.

In this document, we have undertaken a scientific review of a recent report, released as a preprint put
forward by the Rule of Law Society, authored by Li-Meng Yan, Shu Kang, Jie Guan, and Shanchang
Hu. The report, Unusual Features of the SARS-CoV-2 Genome Suggesting Sophisticated Laboratory
Modification Rather Than Natural Evolution and Delineation of Its Probable Synthetic Route,
10 presents a theory about the origin of SARS-CoV-2 but offers contradictory and inaccurate information
that does not support their argument. As the report has not been submitted to a scientific peer-reviewed
publication, which would provide the expert scrutiny expected by the scientific community and the
larger public, we aim to provide an objective analysis of details included in the report, as would be
customary in a peer-review process.
...
Page 21 (Conclusion)
1. While the impact of SARS-CoV-2 on global public health is undeniable, the pathogenic
effects of SARS-CoV-2 infection at an individual or cellular level are not unprecedented. Many
viruses are capable of causing high morbidity and mortality,59,60 infecting several organs, and/
or presymptomatic or asymptomatic transmission.61 Additionally, other viral infections (eg,
chikungunya) also induce long-term sequelae.62 Humans have contended with many scourges
and it is a certainty that COVID-19 will not be the last.
...



https://www.centerforhealthsecurity...ive/pubs-pdfs/2020/200921-in-response-yan.pdf
 
Thanks Pathfinder. Very detailed and easier to comprehend than Racaniello's verbal presentation. I also like that unlike the Racaniello group they stuck to the science. Politics deleted.
 
(Disclaimer - no evidence that would hold up in court here.)

From the Hopkins report:

On the capacity to predict function from genotype. Line 28: Yan et al overstate the capabilities
of deducing functional changes from genetic manipulation of coronaviruses, referring to an
“abundant literature indicat[ing] that gain-of-function research has long advanced to the stage
where viral genomes can be precisely engineered and manipulated to enable the creation of novel
coronaviruses possessing unique properties.”10 Technologies like CRISPR have enabled precise,
directed gene editing, and are major advances for the biological sciences. However, the report
overstates current capabilities in designing phenotypes and genetic functions of viruses, which
are not already elucidated, including coronaviruses, and vastly overstates the capabilities of
genetic manipulation of coronaviruses in 2019, before these viruses were the focus of worldwide
interrogation by the scientific community. There were 6 coronaviruses known to infect humans
prior to 2020, but their prevalence and pathology in different age groups is incompletely
understood, which would hamper any potential design of novel coronavirus functions. Prior to
2020, coronaviruses were not as intensely researched as other viruses that cause human disease,
such as HIV, and influenza.
Click to expand...

That is exactly why GOF work is so dangerous.

Now here is what can be done in a lab to make a natural non-human animal virus more dangerous to humans:

https://www.ncbi.nlm.nih.gov/books/NBK535877/
Altered Tropism
Several studies have demonstrated the ability to alter the tropism of viruses. The avian
influenza H7N9 strain has been causing isolated human infections since the initial outbreak in
China in 2013, but sustained human-to-human transition has not been documented. In a recent
publication, de Vries and colleagues (2017) demonstrated that only three mutational changes in
the sequence of the hemagglutinin gene are sufficient to switch the virus’s tropism from avian to
human and support binding to human tracheal epithelial cells. However, the researchers did not
perform follow-up experiments to test whether these mutations were sufficient to make an actual
host range shift in the ferret model. In earlier studies with avian influenza, researchers used sitedirected
mutagenesis to introduce mutations into the hemagglutinin gene to allow wild-type H5N1
virus to bind to human receptors (Herfst et al., 2012). This group went on to show that as few as
five mutations can lead to airborne transmissibility of H5N1 between ferrets (Linster et al., 2014).
Researchers have also used synthetic biology to alter tropism in investigations of the respiratory
syndromes SARS (severe acute respiratory syndrome) and MERS (Middle East respiratory
syndrome). There is considerable evidence indicating that a SARS-like virus in bats was the origin
of the 2003 outbreak of SARS in humans (Li et al., 2005). The bat virus, however, does not grow
in cell culture. To help elucidate the steps that may have occurred to convert bat SARS-CoV into
a virus infecting humans, Becker and colleagues (2008) substituted the human SARS coronavirus
receptor binding domain for the equivalent domain in the bat SARS-CoV virus, making the bat-
SARS virus replication competent in cell culture and mice. Similarly, to develop a small-animal
model of MERS-CoV, researchers modified both the mouse, to express a chimeric receptor, and
the virus (Cockrell et al., 2016).
Click to expand...

And..

Enhanced Transmissibility
Airborne transmission of pathogens occurs through aerosolization and droplets. Airborne transmissibility
determines the distance over which the virus may travel, and the determinants of this property are
complex and dependent on multiple host and viral factors (Herfst et al., 2017). In a follow-up to the H5N1
experiments described under Altered Tropism (above), the mutated virus was sequentially passaged in
ferrets to force natural selection of heterogeneous viral mixtures and, after 10 passages, na?ve recipient
ferrets were exposed to the infected ferrets in an adjacent cage without direct contact. Three of four recipient
ferrets became infected, demonstrating that selection had occurred for airborne transmissibility of the
virus (Herfst et al., 2017). In another study, Imai and colleagues (2012) constructed a reassortant virus
possessing the hemagglutinin from an H5N1 virus and seven gene segments from a 2009 H1N1 virus.
After passaging through ferrets, a mutant of this reassortant was obtained that had four mutations in the
hemagglutinin gene and was capable of respiratory droplet transmission in ferrets. This work demonstrated
that a mammalian transmission phenotype could be conferred to highly pathogenic H5N1 influenza.
Enhanced Stability
The stability of a virus outside the host is influenced by multiple environmental factors including temperature,
ultraviolet radiation, relative humidity, and air movement, as well as the structure of the pathogen
itself. Enveloped viruses are generally less stable outside the host than non-enveloped viruses (Polozov
et al., 2008; Herfst et al., 2017). Although it would be impossible to convert an enveloped virus to a nonenveloped
virus because addition of the envelope is tightly coupled to specific features of the replication
cycle, it may be possible to alter other features of a virus to enhance its stability for weaponization and
mass dispersal.
Click to expand...

Regarding the enhanced stability:
https://www.scmp.com/news/china/sci...antly-surprising-virus-found-be-heat-tolerant
Coronavirus: constantly surprising virus found to be heat tolerant, self-healing and very resilient in lab tests
  • Hungarian team finds virus particle withstands being probed by a nano needle 100 times, possibly making it the most physically elastic virus known
  • French scientists find it can replicate in animal cells after being exposed to temperatures of 60 degrees Celsius for an hour
Stephen Chen in Beijing
Published: 11:00pm, 18 Sep, 2020
Updated: 3:50am, 19 Sep, 2020
Click to expand...

I think this virus is a little more unusual than the Hopkins paper makes it out to be.
 
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