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

[Kathy]

From the article of Zhou et al: https://www.nature.com/articles/s41586-020-2012-7

"We then found that a short region of RNA-dependent RNA polymerase (RdRp) from a bat coronavirus (BatCoV RaTG13)—which was previously detected in Rhinolophus affinis from Yunnan province—showed high sequence identity to 2019-nCoV. We carried out full-length sequencing on this RNA sample (GISAID accession number EPI_ISL_402131)"

Where was this sequence stored in the last 7 years if it was so special as we now all see?

I believe RaTG13 means R = Rhinolophus A =affinis TG= Total Genomic 13= 2013 sequence. Was it then already full sequenced in 2013? Why was it never published before 2020? Why the spike protein of BtCoV/4991 was sequenced but never made public? BtCoV/4991 looks also very special, see the phylogenetic trees in the only two works that cite this sequence.

If there is nothing to hide, we should get the complete genomic sequence for BtCoV/4991 and RaTG13 should be sequenced by another group. The number of wobble bases in the S2 region of the spike protein seems to be too high (76, I read) in relationship with other coronaviruses. By contrast, no one aminoacidic change.

It is not so common that different viruses share exactly the same RdRp, otherwise this gene would not be used for phylogenetic analysis, I believe.

[JJackson]

"Why the scientific journal Nature does not want to clarify the relation between the two strains?"
Why would they? RdRp is heavily constrained and conserved across all CoVs and recombination is rife. It is normal to find common sequences. TMPRSS2 is used for cleaving S1/S2 and it is used by flu does this mean a flu sequence has been bio-engineered into SARS-2? Bits of any bat betaCoV will have 100% homology with any other virus derived from the same genetic pool and small sections will have the same AA sequence with other pathogens. 30% of our DNA is of viral origin but I do not think I was a genetically engineered lab escape based on that.

[Kathy]

RaTG13 might not be the backbone of SARS-CoV-2, but what about BtCoV/4991 (KP8765469)? Found in the same year, in the same place, from the same group of scientists as RaTG13, with 100 % identity for RdRp with RaTG13? Why the scientific journal Nature does not want to clarify the relation between the two strains?

https://twitter.com/r_h_ebright/stat...67062956314624

https://ccnationalsecurity.org/is-ba...d-19-cover-up/

[JJackson]

Tackling Rumors of a Suspicious Origin of nCoV2019

Novel 2019 coronavirusnCoV-2019 Evolutionary History


profbillg1901
Feb 7



I have been privately dealing with rumors and inquiries, focused on the RRAR potential furin cleavage site, that nCoV2019 may have a suspicious origin as an engineered, laboratory-generated virus either accidentally or deliberately released in the area of the Wuhan seafood and animal market. The publication of the highly similar RaTG13 sequence about a week ago has fueled this type of speculation.
As I have told people privately, I see no evidence at all to support such a claim. In sharp contrast, I have studied the question in detail, using RaTG13 and Wuhan sequence at the S1/S2 boundary, and find convincing proof of exactly opposite conclusion – that RaTG13 could NOT be a proximal source of the Wuhan virus.
At first glance of an alignment of the S protein sequence of both, it is natural that the issue of an engineered insertion should be considered. On either side of the new furin site, the amino acid sequence is identical in both from aa614 to aa1133 – an apparent insert of PRRA is the only difference in an otherwise 100% conserved 519 amino acid region.
RaTG13 vs Wuhan peptide1419?96 43.7 KB

But that is at first glance.
One has to consider that the PRRA is an unusual sequence to introduce to generate a furin site – others even among coronaviruses like MHV A59 are so much better. Also that the underlying code CCTCGGCGGGCA introduces an unnecessarily G and C rich region where none otherwise exists. Not likely scenarios for something a gene jockey would do.
Then one looks at the actual RNA alignment. The “insert” is actually not in frame, but CTCCTCGGCGGG, or -2 out of frame. Again, who does that?
But the PROOF lies in looking at the 288 alignable nucleotides on either side of the “insert”. While they cover identical protein sequence, the RNA is not at all identical, but 6.6% different – 19 mutations out of 288. All 19 are mutations in the wobble base of their respective codons. There are so many that the frame can be inferred from the 2/1 pattern even without knowing the beginning or the end, or indeed that the encoded protein sequence is identical – those are self-evident by looking at the RNA itself.

We know from influenza H1N1, for which we have serial isolates from 1918 to the present, that wobble base mutagenesis occurs at a rate of 0.95% per decade. This permits an estimation of the TMRCA of the two sequences nCoV2019 and RaTG13 of 69.5 years ago – roughly 1950 +/- 10 years or so.
RaTG13, or anything nearly identical to it at the RNA level, simply could not be a proximal source of nCoV2019. It just LOOKS like it might be…at first glance.
Given that furin cleavage signals are present in other coronaviruses at exactly that point in the S1/S2 boundary region, it only LOOKS unusual, especially against the backdrop of SARS. The preponderance of evidence, coupled with Ockham’s razor (that the simplest explanation is preferred) dictates that the PRRA sequence has been conserved in nCoV2019 from a long ago ancestor virus. It is not of suspicious origin. The closest bat virus sequence is really not close at all.

RNA don’t lie.

Bill Gallaher

http://virological.org/t/tackling-rumors-of-a-suspicious-origin-of-ncov2019/384

[JJackson]

Scientists Are Tired of Explaining Why The COVID-19 Virus Was Not Made in a Lab

https://www.sciencealert.com/here-s-what-scientists-think-of-the-coronavirus-was-made-in-a-lab-rumour

JACINTA BOWLER
20 APRIL 2020





It's a rumour that just won't die. When asked whether the COVID-19 virus was genetically engineered in a lab, scientists have already said "no" rather firmly, but the matter of the new coronavirus' origin is unlikely to be put to rest so easily.

Discussions around this subject have become even more pertinent since US government intelligence officials are reportedly investigating the potential source of the pandemic, focussing on theories that it may have originated in a laboratory, despite all evidence pointing to SARS-CoV-2 not being human-made.
"All evidence so far points to the fact the COVID-19 virus is naturally derived and not man-made," explains immunologist Nigel McMillan from the Menzies Health Institute Queensland.
"If you were going to design it in a lab the sequence changes make no sense as all previous evidence would tell you it would make the virus worse. No system exists in the lab to make some of the changes found."

[JJackson]

The coronavirus was not engineered in a lab. Here's how we know.

https://www.livescience.com/coronavirus-not-human-made-in-lab.html

One persistent myth is that this virus, called SARS-CoV-2, was made by scientists and escaped from a lab in Wuhan, China, where the outbreak began.

A new analysis of SARS-CoV-2 may finally put that latter idea to bed. A group of researchers compared the genome of this novel coronavirus with the seven other coronaviruses known to infect humans: SARS, MERS and SARS-CoV-2, which can cause severe disease; along with HKU1, NL63, OC43 and 229E, which typically cause just mild symptoms, the researchers wrote March 17 in the journal Nature Medicine.

"Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus," they write in the journal article.

[JJackson]

Virus Researchers Cast Doubt On Theory Of Coronavirus Lab Accident
https://www.google.com/url?sa=t&rct=...Qv8mrfHarsyXkI

By Geoff Brumfiel and Emily Kwong

NPR.org, April 23, 2020 ? Virus researchers say there is virtually no chance that the new coronavirus was released as result of a laboratory accident in China or anywhere else.

The assessment, made by more than half-a-dozen scientists familiar with lab accidents and how research on coronaviruses is conducted, casts doubt on recent claims that a mistake may have unleashed the coronavirus on the world.

[JJackson]

Claim That Coronavirus Came from a Lab in China Completely Unfounded, Scientists Say

https://www.newsweek.com/claim-that-coronavirus-came-lab-china-completely-unfounded-scientists-say-1498308

There is no evidence to back claims the coronavirus that has caused the COVID-19 pandemic emerged from a lab in China, scientists have told Newsweek.

Adam Lauring, an associate professor at the University of Michigan Medical School and an expert in the evolution of viruses, told Newsweek: "This claim is a conspiracy theory and it is not supported at all by the available data."

Alexandre Hassanin, a lecturer at France's Sorbonne University National Museum of Natural History department of origins and evolution, similarly highlighted to Newsweek: "Even if it is difficult to prove that a laboratory accident did not take place, you should know that SARS-CoV-2 is not closely related to any previous viruses; it was never sequenced (even partially) in previous studies, and the COVID-19 outbreak began in November/December, as in previous SARS epidemic events (2002 and 2003)."

Hassanin said: "These two points suggest therefore that the current outbreak was not the consequence of a laboratory accident."

[JJackson]

Did COVID-19 escape from a lab?

https://allianceforscience.cornell.edu/blog/2020/04/did-covid-19-escape-from-a-lab/

A frenzy of speculation has arisen around the idea that the novel coronavirus responsible for the global COVID-19 pandemic might originally have escaped from a laboratory in the Chinese city of Wuhan.

While there is so far no evidence being offered to support this suggestion, the fact that the mere possibility is being reported in mainstream media outlets like the Washington Post and Yahoo News might seem to give credence to earlier conspiracy theories about the virus being engineered in a biowarfare laboratory and deliberately released into the human population.

But don’t be fooled. Whether the virus first infected humans at the infamous Wuhan “wet market” or somehow took a more complicated route via a so far unidentified Chinese laboratory, the ultimate source of the novel coronavirus is still the same: wild populations of bats.
The bat connection


None of the current speculation changes the one fact that is established beyond reasonable doubt — SARS-CoV-2 is a zoonotic virus, meaning it came from an animal and jumped into the human population.

It appears that the Wuhan Institute of Virology is currently under suspicion because its scientists were studying bat coronaviruses in order to evaluate the possibility of the emergence of just such a pandemic as is currently underway.

Indeed, it is thanks to their work that we know that SARS-CoV-2 is 96 percent “identical at the whole-genome level to a bat coronavirus” (to quote from a Feb. 3 Nature paper co-authored by the institute’s scientists) and that its most likely original host is the horseshoe bat.

[JJackson]

Coronavirus: False claims by politicians debunked


Stolen face masks, an effective cure and biological weaponry: Reality Check’s Chris Morris takes a look at some of the false coronavirus claims made by leading politicians.

https://www.bbc.co.uk/news/av/52299689/coronavirus-false-claims-by-politicians-debunked

[JJackson]

Coronavirus: US and China trade conspiracy theories

https://www.bbc.co.uk/news/world-52224331

From the early stages of the coronavirus outbreak, conspiracy theories about the origin and scale of the disease were spread on online platforms.

Among these were the false claim that the virus was part of a Chinese "covert biological weapons programme", and a baseless claim that a Canadian-Chinese spy team had sent coronavirus to Wuhan.

The claim that the virus was man-made has been pushed by numerous conspiracy groups on Facebook, obscure Twitter accounts and even found its way on to primetime Russian state TV.

And months into the outbreak, not only have these theories not faded away, but new, unverified claims have been promoted by government officials, senior politicians and media outlets in China and the US.

[bertrand789]

Merci, c'est un honneur d'?tre un lecteur de ce lieu. Je retiens de ce texte, que le probl?me n'est pas chinois, mais mondial. Si la crise coronavirus pose des probl?mes, il peut y en avoir bien d'autres. Mon p?re a fait une m?ningite herp?tique suite ? un mauvais usage, notamment de cortico?des. Les herpes me semble de bons candidats pour faire bien des b?tises.
Que les Chinois actent que la d?marche ONE HEALTH prenne une vraie place est le pr?alable. Je suis totalement contre la suppression de certaines pratiques culturelles alimentaires, si les ?tats ou cela se pratique font ce qui se doit. Mais, l'ensemble des scientifiques, qui travaillent sur les dangers microbiologiques, seraient bien inspir?s de faire leur part du travail... Je doute que l'O.M.S, vu son organisation actuelle, soit le bon lieu pour cela, mais je suis int?ress? de lire toutes les propositions positives pour faire ?merger ce qu'il faut pour maintenir les activit?s scientifiques et respecter la Vie... A ce stade ces solutions ne peuvent qu'?tre mondiale, c'est un sacr? d?fi...

[Kathy]

A very informative site on the topic possible genetic manipolation of SARS-CoV-2:

https://medium.com/@yurideigin/lab-made-cov2-genealogy-through-the-lens-of-gain-of-function-research-f96dd7413748

[bertrand789]

Je ne n'ai jamais fait la moindre critique des scientifiques chinois, je ne dispose pas des faits. Mais je connais les possibles et sans vraie r?ponse ? une question pos?e avec courtoisie, je reste dans le doute...

C'est quand m?me plus simple pour permettre le passage, avec des animaux fait pour cela, que des sauvages. Mais ensuite cela va en bien des lieux, l'exemple du jour :

Coronavirus : des visons d’?levage infect?s aux Pays-Bas, premier cas av?r? au monde

https://www.sudouest.fr/2020/04/26/c...0976-10997.php

[sharon sanders]

We should keep open minds on all issues about SARS-CoV-2. Science will lead us to the truth.