Claim:HIV Protein Sequences in Covid-19 (report withdrawn by authors) & other "man made" claims

Dan Wilson

Senior Member.
Moderator deirdre
Readers: this thread is for claims that Covid-19 is engineered or man-made.

Claims regarding a natural source of Covid-19 breaking out of the Wuhan lab should be posted in this thread:
https://www.metabunk.org/threads/natural-covid-19-broke-out-of-wuhan-lab-not-man-made.11212/




Hold onto your hats everyone, we have may have a slew of conspiracy theories coming our way. A pre-print on the bioRxiv server (a server where pre-prints of papers can be viewed before they are peer-reviewed) today claimed the following: https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1 (full PDF attached below)

The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV- 1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature.
Content from External Source

MotifsVirus GlycoproteinMotif AlignmentHIV protein and Variable regionHIV Genome Source Country/ subtypeNumber of Polar ResiduesTotal Char gepI Valu e
Insert 12019- nCoV (GP) HIV1(GP120)71 76
TNGTKR
TNGTKR
404 409
gp120- V4Thailand */ CRF01_ AE5 52 211 11
Insert 22019- nCoV (GP) HIV1(GP120)145 150
HKNNKS
HKNNKS
462 467
gp120- V5Kenya*/ G6 62 210 10
Insert 32019- nCoV (GP) HIV1(GP120)245 256
RSYL- - - -TPGDSSSG RTYLFNETRGNSSSG
136 150
gp120- V1India*/C8 102 110.84 8.75
Insert 42019- nCoV (Poly P) HIV1(gag)676 684
QTNS-----------------------PRRA QTNSSILMQRSNFKGPRRA
366 384
GagIndia*/C6 122 412.00 12.30
Content from External Source
The summary in other words is that the researchers found four short portions of the coronavirus genome that highly resemble pieces of two different proteins from HIV and aren't present in other coronaviruses. They comment that these insertions are unlikely to be fortuitous (happen by chance), implying that this virus could have been designed artificially. This is pretty crazy for even a pre-print to suggest, but we have to keep in mind that this has not yet been peer-reviewed.

For what it's worth, my interpretation is that these Coronavirus motifs that are similar to pieces of HIV proteins aren't super striking. It is never really surprising to find that parts of two different proteins resemble each other. However, it does seem unusual that the specific parts that aren't found in other coronaviruses match with pieces of HIV proteins. I can see this fueling conspiracy theories so keep an eye out for this paper and what peer-reviewers will have to say about it.
 

Attachments

  • 2019-nCoV spike protein.pdf
    6.1 MB · Views: 935
Last edited by a moderator:

deirdre

Senior Member.
For what it's worth, my interpretation is that these Coronavirus motifs that are similar to pieces of HIV proteins aren't super striking. It is never really surprising to find that parts of two different proteins resemble each other. However, it does seem unusual that the specific parts that aren't found in other coronaviruses match with pieces of HIV proteins.
there are a few threads on reddit where it sounds like people in related fields are commenting. (if you want to look at it, i'm too much of a laymen to make heads or tails of any of it
ex:



[–]BurrShotFirst1804 47 points an hour ago



Gag sequence:
MGARASVLSG GELDRWEKIR LRPGGKKKYK LKHIVWASRE LERFAVNPGL LETSEGCRQI LGQLQPSLQT GSEELRSLYN TVATLYCVHQ RIEIKDTKEA LDKIEEEQNK SKKKAQQAAA DTGHSNQVSQ NYPIVQNIQG QMVHQAISPR TLNAWVKVVE EKAFSPEVIP MFSALSEGAT PQDLNTMLNT VGGHQAAMQM LKETINEEAA EWDRVHPVHA GPIAPGQMRE PRGSDIAGTT STLQEQIGWM TNNPPIPVGE IYKRWIILGL NKIVRMYSPT SILDIRQGPK EPFRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPA ATLEEMMTAC QGVGGPGHKA RVLAEAMSQV TNSATIMMQR GNFRNQRKIV KCFNCGKEGH TARNCRAPRK KGCWKCGKEG HQMKDCTERQ ANFLGKIWPS YKGRPGNFLQ SRPEPTAPPE ESFRSGVETT TPPQKQEPID KELYPLTSLR SLFGNDPSSQ
Alleged "gag" match: QTNS--------PRRA
Actual gag sequence: QTNSSILMQRSNFKGPRRA
To begin with this is such a tiny random part of gag. Like 1%. It's also not a 100% match. They just ignore the middle part and call it a match anyway.
Except this isn't your standard HIV sequence for gag. It's a unique isotype labs found in India. This sequence is NOT found in actual standard gag. Which is super confusing in general. Also the other matches are from 3 other strains of HIV. So it's not even 4 of the same subtype which just makes this even more ridiculously terrible of a paper.
Content from External Source
Source: https://www.reddit.com/r/China_Flu/comments/ewuotw/discussion_biorxiv_preprint_on_2019ncov_spike/fg4jjrq/


??
 

Arugula

Member
*Edit: It looks like the early peer review process is not going well:



Source: https://twitter.com/trvrb/status/1223387421120684032


Here's another source, thinking the pre-print paper was just a faulty analysis by people not very experienced using BLAST: https://massivesci.com/notes/wuhan-...ar&utm_medium=social&utm_source=meetedgar.com


The stories for the other two sequences are the same. These sequences appear in benign viruses like Peach-associated luteovirus (a plant virus), Bovine papillomavirus type 9 (the cow version of HPV), and Leptopilina boulardi Toti-like virus (a virus that infects wasps).

So the facts are that Wuhan coronavirus may have some new additions to it, but they’re common bits and pieces found in tons of viruses—not just HIV—and there’s no proof that they even have anything to do with how the Wuhan coronavirus behaves.

And there’s definitely no proof that they were put there on purpose.

Content from External Source
 
Last edited by a moderator:

Dan Wilson

Senior Member.
thinking the pre-print paper was just a faulty analysis by people not very experienced using BLAST:
Yep, if you BLAST those short sequences against all known proteins you get 100% matches to a lot of different proteins in a lot of different organisms. Like I said, the length of the matches makes this not very striking. Their conclusions were very overstated, but I think it will be enough spawn conspiracy theories. Prominent anti-vaxxer Del Bigtree has already had guests on his show, The Highwire, talking about how they can tell that the virus was engineered by looking at its genome.
 

Trailspotter

Senior Member.
Hold onto your hats everyone, we have may have a slew of conspiracy theories coming our way. A pre-print on the bioRxiv server (a server where pre-prints of papers can be viewed before they are peer-reviewed) today claimed the following: https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf
The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV- 1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature.
Content from External Source
The summary in other words is that the researchers found four short portions of the coronavirus genome that highly resemble pieces of two different proteins from HIV and aren't present in other coronaviruses. They comment that these insertions are unlikely to be fortuitous (happen by chance), implying that this virus could have been designed artificially. This is pretty crazy for even a pre-print to suggest, but we have to keep in mind that this has not yet been peer-reviewed.

For what it's worth, my interpretation is that these Coronavirus motifs that are similar to pieces of HIV proteins aren't super striking. It is never really surprising to find that parts of two different proteins resemble each other. However, it does seem unusual that the specific parts that aren't found in other coronaviruses match with pieces of HIV proteins. I can see this fueling conspiracy theories so keep an eye out for this paper and what peer-reviewers will have to say about it.
I'm surprised that this manuscript passed initial screening:
https://www.biorxiv.org/about-biorxiv
Articles are not peer-reviewed, edited, or typeset before being posted online. However, all articles undergo a basic screening process for offensive and/or non-scientific content and for material that might pose a health or biosecurity risk and are checked for plagiarism. No endorsement of an article’s methods, assumptions, conclusions, or scientific quality by Cold Spring Harbor Laboratory is implied by its appearance in bioRxiv. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been accepted for publication by a journal.
Content from External Source
The immediate reaction to the paper from the scientific community (currently 10 comments) tears apart the authors' conclusions (see at the bottom of the page https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1)
I think that this paper is ignorant and amateurish pseudoscience. No. Absolutely not. This is not some escaped bioweapon.
Brian Hanley
Content from External Source
Update

The publisher added the following note at the top of the article page:
bioRxiv is receiving many new papers on coronavirus 2019-nCoV. A reminder: these are preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide clinical practice/health-related behavior, or be reported in news media as established information.
Content from External Source
 
Last edited:

Trailspotter

Senior Member.
The first author has made the following comment in the discussion of the preprint (emphasis mine):

Prashant Pradhan5 hours ago
This is a preliminary study. Considering the grave situation, it was shared in BioRxiv as soon as possible to have creative discussion on the fast evolution of SARS-like corona viruses. It was not our intention to feed into the conspiracy theories and no such claims are made here. While we appreciate the criticisms and comments provided by scientific colleagues at BioRxiv forum and elsewhere, the story has been differently interpreted and shared by social media and news platforms. We have positively received all criticisms and comments. To avoid further misinterpretation and confusions world-over, we have decided to withdraw the current version of the preprint and will get back with a revised version after reanalysis, addressing the comments and concerns. Thank you to all who contributed in this open-review process.
: Authors of the Manuscript
Content from External Source
http://archive.ph/tZgVI
 
Last edited by a moderator:

Trailspotter

Senior Member.
Update

This article has been withdrawn. Click here for details

Abstract
This paper has been withdrawn by its authors. They intend to revise it in response to comments received from the research community on their technical approach and their interpretation of the results. If you have any questions, please contact the corresponding author.
Content from External Source
 

Dingo

Member
Not much more to say. Absolute garbage. This is akin to finding two words the same in the Bible and the NIST 9/11 report and then claiming that god did it.
 

Agent K

Senior Member
The "uncanny similarity" here is to the KGB's Operation Infektion disinformation campaign that accused the U.S. of inventing HIV/AIDS as a biological weapon. The accusations were initially published by an Indian newspaper that was set up by the KGB. This was discussed in the Lawfare article, "Is the Threat of ‘Fake Science’ Real?" although it talked about scientific fraud in China, not India.
https://www.lawfareblog.com/threat-fake-science-real
China tops the list of source countries of scientific misconduct in absolute terms, and one estimate attributes roughly half of all retractions due to faked peer review to Chinese sources.
Content from External Source
 

Dan Wilson

Senior Member.
Here is another aspect that may still fuel some conspiracy theorists who have caught onto this story. Chinese scientists started to see that anti-HIV drugs are effective against the coronavirus. However, this is not surprising given that both HIV and the coronavirus are RNA viruses and the drugs target a generic viral protein. I should add that this protein is not the "spike (S)" protein that the focus of the now retracted paper in question in this thread. https://www.sciencemag.org/news/202...r-other-existing-drugs-outwit-new-coronavirus
The Jin Yintan Hospital in Wuhan, China, where the first 41 known patients were treated, has already launched a randomized, controlled trial of the anti-HIV drug combination of lopinavir and ritonavir, according to a 24 January report by a group of Chinese scientists in The Lancet. The combination targets protease, an enzyme used by both HIV and coronaviruses to cut up proteins when they make new copies of themselves.
Content from External Source
Also, this same drug cocktail was effective against SARS, which was also caused by a coronavirus.
There is some evidence that the treatment might work, the authors of The Lancet paper write: A study published in 2004 showed that the combination showed “substantial clinical benefit” when given to patients who had severe acute respiratory syndrome(SARS), which is caused by a coronavirus similar to 2019-nCoV.
Content from External Source
Although the SARS studies were limited and the new coronavirus studies are not complete, it HIV-drugs having an effect is not evidence that the virus was lab-made.
 

deirdre

Senior Member.
Would someone please explain why we are using letters like Q,L,K, etc when there are only ATGC and sometimes U?!
2019-nCoV is a RNA virus.

but I think you are asking about the protein sequencing?
from the study paper (PDF linked in Opening Post above)

x.png

Proteins are composed of the 20 “letters” of amino acids,
Content from External Source
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503725/


Protein sequences consist of
20 commonly occurring amino acids; therefore, it can be said that the
protein alphabet consists of 20 letters
(Figure 1). Each amino acid is defined by a three-nucleotide sequence
called the triplet codon
Content from External Source
https://courses.lumenlearning.com/suny-biology1/chapter/the-genetic-code/


not sure if this answers your question. ?
 

Dan Wilson

Senior Member.
Would someone please explain why we are using letters like Q,L,K, etc when there are only ATGC and sometimes U?!
Just to add to the previous post, DNA is read by machinery in the cell and transcribed into RNA (RNA is what has U instead of T). Then the RNA is read by different machinery and translated into proteins, which you can consider to be the functional units of genes. When the RNA is read, three letters of the AUGC sequence correspond to one amino acid in the protein. Proteins can be made up of hundreds of amino acids, which are abbreviated to letters like R, K, P, and E. There are 20 amino acids in all. Here is a great video illustrating this process. Skip ahead to 3:40 Source: https://www.youtube.com/watch?v=2BwWavExcFI
 

Agent K

Senior Member
From today: https://www.sciencemag.org/news/202...-conspiracy-theories-about-origin-coronavirus
“We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin,” says The Lancet statement, which praises the work of Chinese health professionals as “remarkable” and encourages others to sign on as well.
...
The authors of The Lancet statement note that scientists from several countries who have studied SARS-CoV-2 “overwhelmingly conclude that this coronavirus originated in wildlife,” just like many other viruses that have recently emerged in humans. “Conspiracy theories do nothing but create fear, rumours, and prejudice that jeopardise our global collaboration in the fight against this virus,” the statement says.
Content from External Source

Should we make a new thread about the origin of SARS-CoV-2? This article from 2015 has been making the rounds, forcing the editor to add an Editor's note in March.
https://www.nature.com/news/engineered-bat-virus-stirs-debate-over-risky-research-1.18787
Engineered bat virus stirs debate over risky research
Lab-made coronavirus related to SARS can infect human cells.
Editors’ note, March 2020: We are aware that this story is being used as the basis for unverified theories that the novel coronavirus causing COVID-19 was engineered. There is no evidence that this is true; scientists believe that an animal is the most likely source of the coronavirus.

An experiment that created a hybrid version of a bat coronavirus — one related to the virus that causes SARS (severe acute respiratory syndrome) — has triggered renewed debate over whether engineering lab variants of viruses with possible pandemic potential is worth the risks.
In an article published in Nature Medicine on 9 November, scientists investigated a virus called SHC014, which is found in horseshoe bats in China. The researchers created a chimaeric virus, made up of a surface protein of SHC014 and the backbone of a SARS virus that had been adapted to grow in mice and to mimic human disease. The chimaera infected human airway cells — proving that the surface protein of SHC014 has the necessary structure to bind to a key receptor on the cells and to infect them. It also caused disease in mice, but did not kill them.
...
The findings reinforce suspicions that bat coronaviruses capable of directly infecting humans (rather than first needing to evolve in an intermediate animal host) may be more common than previously thought, the researchers say.
But other virologists question whether the information gleaned from the experiment justifies the potential risk. Although the extent of any risk is difficult to assess, Simon Wain-Hobson, a virologist at the Pasteur Institute in Paris, points out that the researchers have created a novel virus that “grows remarkably well” in human cells. “If the virus escaped, nobody could predict the trajectory,” he says.
Content from External Source
 

Agent K

Senior Member
New study debunking conspiracy theories
"The proximal origin of SARS-CoV-2"
https://www.nature.com/articles/s41591-020-0820-9
SARS-CoV-2 is the seventh coronavirus known to infect humans; SARS-CoV, MERS-CoV and SARS-CoV-2 can cause severe disease, whereas HKU1, NL63, OC43 and 229E are associated with mild symptoms. Here we review what can be deduced about the origin of SARS-CoV-2 from comparative analysis of genomic data. We offer a perspective on the notable features of the SARS-CoV-2 genome and discuss scenarios by which they could have arisen. Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.
Content from External Source
 

Trailspotter

Senior Member.
A new study on probable origin of SARS-CoV-2 published this week in Nature:
Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins
The ongoing outbreak of viral pneumonia in China and beyond is associated with a novel coronavirus, SARS-CoV-21. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection2. Although bats are likely reservoir hosts for SARS-CoV-2, the identity of any intermediate host that might have facilitated transfer to humans is unknown. Here, we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity to SARS-CoV-2 in the receptor-binding domain. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of novel coronaviruses and should be removed from wet markets to prevent zoonotic transmission.
Content from External Source
 

Dan Wilson

Senior Member.
I briefly reviewed and listed some papers describing the evolution and origins of SARS-CoV-2 in a video a couple of weeks ago, right before that Nature paper was published. Source: https://www.youtube.com/watch?v=yh3apmFrP4Y&t=5s
One of the less talked about points that invalidates this conspiracy theory is that two coronaviruses that most closely resemble SARS-CoV-2 were isolated from bats in 2015 and 2017.
https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa112/5721420
Based on our phylogenomic analysis of the recently released genomic data of 2019-nCoV, we showed that the 2019- nCoV is most closely related to 2 severe acute respiratory syndrome (SARS)-like CoV sequences that were isolated in bats during 2015 to 2017 [2], suggesting that the bats’ CoV and the human 2019- nCoV share a recent common ancestor (Figure 1A). Therefore, the 2019-nCoV can be considered as a SARS-like virus and named SARS-CoV-2. The 2 bat vir- uses were collected in Zhoushan, Zhejiang Province, China, from 2015 to 2017 [2].
Content from External Source
https://www.ncbi.nlm.nih.gov/pubmed/32007145
The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%).
Content from External Source
By Occam's razor, this alone allows us to discredit the idea that this virus was somehow engineered. This family of coronaviruses has been spreading, mixing, and evolving within bat populations for a very long time. It was only a matter of time until a strain that can efficiently infect humans appeared and was able to make the jump from animal(s) to human. And it is only a matter of time before it happens again, either with a coronavirus or a different virus.
 

vooke

Active Member
Once dismissed as wild conspiracy theory,it seems evidence is mounting that Wuhan Institute of Virology may have played a role in the outbreak.

The laboratory at the centre of scrutiny over the pandemic has been carrying out research on bats from the cave which scientists believe is the original source of the devastating outbreak.

Documents obtained by The Mail on Sunday show the Wuhan Institute of Virology undertook coronavirus experiments on mammals captured more than 1,000 miles away in Yunnan – funded by a $3.7 million grant from the US government.

Sequencing of the Covid-19 genome has traced it to bats found in Yunnan's caves.


It comes after this newspaper revealed last week that Ministers here now fear that the pandemic could have been caused by a virus leaking from the institute.

Senior Government sources said that while 'the balance of scientific advice' was still that the deadly virus was first transmitted to humans from a live animal market in Wuhan, an accident at the laboratory in the Chinese city was 'no longer being discounted'.

According to one unverified claim, scientists at the institute could have become infected after being sprayed with blood containing the virus, and then passed it on to the local community.
https://www.dailymail.co.uk/news/ar...rming-experiments-bats-coronavirus-caves.html

The sentence on sequencing could be referring to this 2017 paper from which I quote part of the Abstract:
We hypothesize that the direct progenitor of SARS-CoV may have originated after sequential recombination events between the precursors of these SARSr-CoVs. Cell entry studies demonstrated that three newly identified SARSr-CoVs with different S protein sequences are all able to use human ACE2 as the receptor, further exhibiting the close relationship between strains in this cave and SARS-CoV.
https://www.researchgate.net/public..._insights_into_the_origin_of_SARS_coronavirus
 

deirdre

Senior Member.
The sentence on sequencing could be referring to this 2017
SARS -Cov is not Covid-19.

and in this article "more closely related" means it is not an exact match to the cave bats in Yennan Cave. So the "evidence" isn't mounting, there could still be a cave samples haven't been taken from...or newer samples from Yennan that haven't been taken yet ? that would show a closer match to Covid-19. ie. a natural source.

The role of pangolins in the spread of Sars-CoV-2, the virus that causes Covid-19, remains unclear. A closer look at more of the Sars-CoV-2 genome, published last week by Maciej Boni at Penn State University and David Robertson at Glasgow University, together with Chinese and European colleagues, finds that
human versions of the virus are more closely related to the RaTG13 horseshoe bat sample from the cave than they are to the known pangolin versions. It is not yet possible to tell whether the virus went from bat to pangolin to people, or from bat to pangolin and bat to people in parallel.

Content from External Source
https://www.nationalreview.com/corn...to-the-one-in-bats-than-the-one-in-pangolins/
 

Mendel

Senior Member.
SARS -Cov is not Covid-19.

and in this article "more closely related" means it is not an exact match to the cave bats in Yennan Cave. So the "evidence" isn't mounting, there could still be a cave samples haven't been taken from...or newer samples from Yennan that haven't been taken yet ? that would show a closer match to Covid-19. ie. a natural source.

The role of pangolins in the spread of Sars-CoV-2, the virus that causes Covid-19, remains unclear. A closer look at more of the Sars-CoV-2 genome, published last week by Maciej Boni at Penn State University and David Robertson at Glasgow University, together with Chinese and European colleagues, finds that
human versions of the virus are more closely related to the RaTG13 horseshoe bat sample from the cave than they are to the known pangolin versions. It is not yet possible to tell whether the virus went from bat to pangolin to people, or from bat to pangolin and bat to people in parallel.

Content from External Source
https://www.nationalreview.com/corn...to-the-one-in-bats-than-the-one-in-pangolins/
The National Review quotes the Wallstreet Journal:
Significantly, the same analysis shows that the most recent common ancestor of the human virus and the RaTG13 virus lived at least 40 years ago. So it is unlikely that the cave in Yunnan (a thousand miles from Wuhan) is where the first infection happened or that the culprit bat was taken from that cave to Wuhan to be eaten or experimented on.

Rather, it is probable that somewhere much closer to Wuhan, there is another colony of bats carrying the same kind of virus. Unless other evidence emerges, it thus looks like a horrible coincidence that China’s Institute of Virology, a high-security laboratory where human cells were being experimentally infected with bat viruses, happens to be in Wuhan, the origin of today’s pandemic.
Content from External Source
Basically, we know how fast these viruses mutate, so we can tell when their common ancestor lived (approximately).

I'd also say that is clear evidence that the virus did not originate from that laboratory: if that is the closest virus they have, then they don't have SARS-CoV-2. If they don't have it, it can't escape.

(The lab also said that the staff member who was exposed to batshit was quarantined for 14 days.)

The WSJ is unequivocal: there is no evidence, they don't have the right virus
The National Review: somehow it could still have happened
Argh!

The key fact is that virologists sequence the viruses. They know the genome. That is like the DNA on a crime scene: if the DNA does not match, it wasn't the guy!
So when the virologists thought, "maybe it's one of ours", all they had to do is look in their database, and then there's either evidence or there isn't, and the absence of evidence clears them.
 

vooke

Active Member
So @Mendel , @deirdre , the closest virus to SARS-CoV-2 is RaTG13 from Yunnan cave bats such as that collected by the lab in 2013, but these two good back’ forty years,right? That’s my understanding.

The researchers‘ goal is to get a closer match than RaTG13 or exact match in wild animals and with that their source.

I think I can see why the article is sensationalism
 

Mendel

Senior Member.
So @Mendel , @deirdre , the closest virus to SARS-CoV-2 is RaTG13 from Yunnan cave bats such as that collected by the lab in 2013, but these two good back’ forty years,right? That’s my understanding.

The researchers‘ goal is to get a closer match than RaTG13 or exact match in wild animals and with that their source.
Yes, if we could find a closer match in some animal population, that would be interesting to virologists, and help prevent reinfection from the same reservoir. As it is, they did detect what looks like pangolin genes in SARS-CoV-2: there is a virus in pangolins that is pretty close to SARS-CoV-2 and codes some key proteins also found in "our" virus, but not in RaTG13. The idea is that the bat virus infected some pangolins and mutated there, and then transferred to humans. If confirmed, that is another piece of evidence that it's unlikely to have "escaped" from a bat laboratory.
Title: Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak
Authors: Tao Zhang1†, Qunfu Wu1†, Zhigang Zhang1,2*

Summary:
An outbreak of coronavirus disease 2019 (COVID-19) caused by the 2019 novel coronavirus (SARS-CoV-2) began in the city of Wuhan in China and has widely spread worldwide. Currently, it is vital to explore potential intermediate hosts of SARS-CoV-2 to control COVID-19 spread. Therefore, we reinvestigated published data from pangolin lung samples from which SARS-CoV-like CoVs were detected by Liu et al.[1]. We found genomic and evolutionary evidence of the occurrence of a SARS-CoV-2-like CoV (named Pangolin-CoV) in dead Malayan pangolins. Pangolin-CoV is 91.02% and 90.55% identical to SARS-CoV-2 and BatCoV RaTG13, respectively, at the whole genome level. Aside from RaTG13, Pangolin-CoV is the most closely related CoV to SARS-CoV-2. The S1 protein of Pangolin-CoV is much more closely related to SARS-CoV-2 than to RaTG13.

Five key amino acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and SARS-CoV-2, but four amino acid mutations are present in RaTG13. Both Pangolin-CoV and RaTG13 lost the putative furin recognition sequence motif at S1/S2 cleavage site that can be observed in the SARS-CoV-2.

Conclusively, this study suggests that pangolin species are a natural reservoir of SARS-CoV-2-like CoVs.
Content from External Source
https://www.cell.com/pb-assets/jour...BIO_CURRENT-BIOLOGY-D-20-00299-compressed.pdf
 

deirdre

Senior Member.
and the absence of evidence clears them.
no. that is like skepticism 101. The absence of evidence is not evidence of absence.

TO be fair, im hoping it escaped from the lab because then we can eradicate it. But unfortunately I agree with the science i'm reading that it is unlikely they would have engineered covid-19 that way. :(
 

Mendel

Senior Member.
no. that is like skepticism 101. The absence of evidence is not evidence of absence.
In this case, it is, though.
Compare: if the police think a suspect has been shot with a gun stolen from my gun locker, and there is no evidence that any of the guns were stolen, that disproves it. If none of my guns fired the shot, that's it.
If you have the genetic fingerprint of the virus and genetic fingerprints of the viruses in the lab, then the absence of a match clears the lab.
 

Agent K

Senior Member
David Ignatius speculated about the origin of SARS-CoV-2
"How did covid-19 begin? Its initial origin story is shaky."
https://www.washingtonpost.com/opin...75d488-7521-11ea-87da-77a8136c1a6d_story.html
...The Lancet noted in a January study that the first covid-19 case in Wuhan had no connection to the seafood market.
There’s a competing theory — of an accidental lab release of bat coronavirus — that scientists have been puzzling about for weeks. Less than 300 yards from the seafood market is the Wuhan branch of the Chinese Center for Disease Control and Prevention. Researchers from that facility and the nearby Wuhan Institute of Virology have posted articles about collecting bat coronaviruses from around China, for study to prevent future illness. Did one of those samples leak, or was hazardous waste deposited in a place where it could spread?
Richard Ebright, a Rutgers microbiologist and biosafety expert, told me in an email that “the first human infection could have occurred as a natural accident,” with the virus passing from bat to human, possibly through another animal. But Ebright cautioned that it “also could have occurred as a laboratory accident, with, for example, an accidental infection of a laboratory worker.” He noted that bat coronaviruses were studied in Wuhan at Biosafety Level 2, “which provides only minimal protection,” compared with the top BSL-4. Ebright described a December video from the Wuhan CDC that shows staffers “collecting bat coronaviruses with inadequate [personal protective equipment] and unsafe operational practices.” Separately, I reviewed two Chinese articles, from 2017 and 2019, describing the heroics of Wuhan CDC researcher Tian Junhua, who while capturing bats in a cave “forgot to take protective measures” so that “bat urine dripped from the top of his head like raindrops.”
And then there’s the Chinese study that was curiously withdrawn. In February, a site called ResearchGate published a brief article by Botao Xiao and Lei Xiao from Guangzhou’s South China University of Technology. “In addition to origins of natural recombination and intermediate host, the killer coronavirus probably originated from a laboratory in Wuhan. Safety level may need to be reinforced in high risk biohazardous laboratories,” the article concluded. Botao Xiao told the Wall Street Journal in February that he had withdrawn the paper because it “was not supported by direct proofs.”
Content from External Source
 

Mendel

Senior Member.
The Lancet noted in a January study that the first covid-19 case in Wuhan had no connection to the seafood market.
Yep. In that study, the first patient fell ill on December 1st. We know now that that was not patient zero.
27 (66%) patients had direct exposure to Huanan seafood market (figure 1B). Market exposure was similar between the patients with ICU care (nine [69%]) and those with non-ICU care (18 [64%]). The symptom onset date of the first patient identified was Dec 1, 2019. None of his family members developed fever or any respiratory symptoms. No epidemiological link was found between the first patient and later cases.
Content from External Source
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30183-5/fulltext

From the start, the Huanan Seafood Wholesale Market in Wuhan—which sold mammals as well as fish—was considered a likely source of the outbreak because most of the early patients had visited it. On 27 January, Xinhua reported that researchers have found evidence of the new coronavirus in 33 of 585 environmental samples taken at the market on 1 January—the day it was closed—and on 12 January. They all came from the western end, which had a concentration of booths selling wildlife.
Content from External Source
https://science.sciencemag.org/content/367/6477/492

I can't access https://www.scmp.com/news/china/soc...nas-first-confirmed-covid-19-case-traced-back right now, alledgedly it has a more complete narrative of the early cases?
 

vooke

Active Member
On 27 January, Xinhua reported that researchers have found evidence of the new coronavirus in 33 of 585 environmental samples taken at the market on 1 January—the day it was closed—and on 12 January. They all came from the western end, which had a concentration of booths selling wildlife.

i think with the market closed we may never know if indeed SARS-CoV-2 came from there.

A quick one,
how did they figure out SARS-CoV-2 and RaTG13 go back 40 years using two samples? My guess is they measure the rate of mutation of SARS-Cov-2 and divided that by the differences between it and RaTG13 to arrive at how long all the cumulative mutations took. I submit I may be wrong. My question is, is this 40 years a certainty?
 

Mendel

Senior Member.
It could've come from a sexton cleaning out a church steeple full of bat shit, who knows? If they ever narrow down the animal population that has the virus, we might learn more.
A quick one,
how did they figure out SARS-CoV-2 and RaTG13 go back 40 years using two samples? My guess is they measure the rate of mutation of SARS-Cov-2 and divided that by the differences between it and RaTG13 to arrive at how long all the cumulative mutations took. I submit I may be wrong. My question is, is this 40 years a certainty?
Actually, they did look at the mutation rates for SARS-CoV-1 and MERS and HCoV-OC43 and then estimated off that. For context, this is a statistical method,, much like radiocarbon dating, it depends on events happening at a fixed random rate and averaging out over time. Since we're looking at relatively fewer events than carbon decay over centuries, the uncertainties are larger. For example, if you throw a coin 100 times, you're probably going to be closer to 50% heads than if you only throw it 6 times.
This estimate also depends on having identified the pieces that recombined correctly, and the proportions in which they occur in the population. (As an aside, these researchers think that the pangolin virus genes might have jumped from the pangolins to the bats, and that a bat migt have transferred it to us.)
Evolutionary origins of the SARS‐CoV‐2 sarbecovirus lineage responsible for the COVID-19 pandemic

Abstract
There are outstanding evolutionary questions on the recent emergence of coronavirus SARS-CoV-2/hCoV-19 in Hubei province that caused the COVID-19 pandemic, including (1) the relationship of the new virus to the SARS-related coronaviruses, (2) the role of bats as a reservoir species, (3) the potential role of other mammals in the emergence event, and (4) the role of recombination in viral emergence. Here, we address these questions and find that the sarbecoviruses – the viral subgenus responsible for the emergence of SARS-CoV and SARS- CoV-2 – exhibit frequent recombination, but the SARS-CoV-2 lineage itself is not a recombinant of any viruses detected to date. In order to employ phylogenetic methods to date the divergence events between SARS-CoV-2 and the bat sarbecovirus reservoir, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were consistent for all three recombination-free alignments and robust to two different prior specifications based on HCoV-OC43 and MERS-CoV evolutionary rates. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% HPD: 1879-1999), 1969 (95% HPD: 1930-2000), and 1982 (95% HPD: 1948-2009). Despite intensified characterization of sarbecoviruses since SARS, the lineage giving rise to SARS-CoV-2 has been circulating unnoticed for decades in bats and been transmitted to other hosts such as pangolins. The occurrence of a third significant coronavirus emergence in 17 years together with the high prevalence and virus diversity in bats implies that these viruses are likely to cross species boundaries again.
Content from External Source
https://www.biorxiv.org/content/10.1101/2020.03.30.015008v1
(This is a preprint that has not been peer-reviewed, but the authors are a large group from different institutes and countries, so it looks pretty good.)

Note the error margins in the bolded section: the lineages might have split a mere 20 years ago. So, 40 years isn't precise: we could say the lineages split between 20 and 70 years ago and be more confident of being correct.
 
Last edited:

RayLopez

New Member
Hi my first and possibly last post here, but I don't want to invest a lot of time and find my posts deleted due to an over-aggressive moderator, as has happened with other sites. I will see if this post sticks then possibly post more later. Nice site btw, I perused your UFO forum. I'll try and keep this short but with my legal background that's going to be tough...

My background: couple of science degrees, I've done work in patent litigation, now retired, and I firmly subscribe to the Third Law of Litigation ("for every expert there's an equal and opposite expert"). In several decades of experience I have never seen a single litigation in technology, where enough money was at stake, for this law to be violated. E.g. if you are trying to prove the earth is stationary and the sun goes round the earth, which is of course absurd, in litigation you would find a highly distinguished astronomer expert witness, just a distinguished as the opposing counsel's expert witness, to say that indeed the earth is stationary, carefully worded, and possibly not run afoul of the US Fed rules of civil procedure on expert testimony, by saying that for simple navigation you can assume a Ptolemaic model (I believe in fact some maps and/or software still used for simple navigation make this assumption, or indeed after Copernicus, navigators continued to make this assumption since it was convenient to do so). And of course in a US jury trial hope an ignorant jury are not paying attention and/or opposing counsel botches their cross-examination, which happens roughly around 10% of the time regardless of the strengths or weaknesses of one's case (one reason people constantly litigate in the USA). Thus in my opinion in life there's no "Truth" but it's all a function of your priors.

Now on the claims that Covid-19 virus (SARS-CoV-2) is a man made chimeric virus (note that's not redundant, since you can have a natural chimeric organism, see here: https://www.sciencedirect.com/science/article/pii/S0012160616300902 - 'bizarria' plant chimera from over 400 years ago; but for casual conversation 'chimeric' equals 'man-made' through recombinant DNA technology rather than artificial or natural selective breeding or other non-recombinant DNA lab methods)

[1] Source: https://medium.com/@yurideigin/lab-made-cov2-genealogy-through-the-lens-of-gain-of-function-research-f96dd7413748
- hereinafter the Medium article, this is a the 'go-to' article on chimeric viruses and Covid-19. One purpose for posting today was to cite this article.

The hypothesis and stipulations advanced, in no particular order, from the Medium article, unless otherwise noted, are:

(1)(A) SARS-CoV-2 (the Covid-19 virus) is a Dr. Shi Zhengli (Wuhan Institute of Virology (WIV) director until early this year, when she was replaced by a Chinese military biotech officer, and a gag order on all talk about the origins of Covid-19 was ordered by the Chinese government) chimeric virus comprising of DNA from three sources: (i) the 2015 chimeric virus Dr. Shi et al created at the Univ of NC (Chapel Hill) with NIH funding, called the SARS-CoV virus (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797993/), (ii) the RaTG13 bat coronavirus, very similar to the chimeric coronavirus of (i), which Dr. Shi allegedly discovered in the wild in either 2013, but curiously did not disclose until 2020, or in 2016, with the RaTG13 virus possibly being the same as the 2016 published putative natural bat coronavirus RaBtCoV/4991 (https://www.ncbi.nlm.nih.gov/pubmed/26920708), and (iii) a known naturally occurring pangolin coronavirus. See the Medium article on furin cleavage sites, spike proteins, and similarity in amino acid and genome nucleotide positions that shows the SARS-CoV-2 virus can be made from these three viruses with 100% certainty and/or match.

(1)(B) It's stipulated that it is impossible to determine with 100% certainty whether a gene sequence and thus an organism is natural or artificial. Recombinant DNA has been made joining plant DNA with animal DNA for example, which would clearly be deemed artificial, but analogous to the discovery of the platypus, a skilled designer can easily make an artificial DNA organism look natural (more on this later with the March 2020 Nature Medicine article by Kristian Andersen et al allegedly proving the Covid-19 virus was natural and not chimeric).

(2)(A) Dr. Shi and Dr. Ralph Baric, co-authors and co-inventors of the 2015 chimeric virus SARS-CoV, were engaged in a friendly or otherwise competition to design chimeric viruses. Dr. Baric is known as the father of chimeric viruses, and Dr. Shi is also a chimeric virus superstar, known affectionately as "Batwoman".

(2)(B) The WIV had in the fall of 2019 placed an advert for a position for a researcher in bat coronaviruses, as reported in ZeroHedge and elsewhere. This is not unusual since bat coronaviruses are the Drosophila or guinea pig for virus research. In fact, Google Patents lists over 200 hits with keywords "Wuhan", "coronavirus"( https://patents.google.com/?q=coronavirus+Wuhan&oq=coronavirus+Wuhan )

(2)(C) Shi's lab may have raced to beat a December self-imposed deadline, and a chimeric virus escaped the lab, "haste makes waste". Source: https://www.youtube.com/watch?v=G0VJLYRhPHg
From the comments: "Gen Li @Sebastian K Have you read the genetic analysis in the NEJM? I have. The report makes this theory have a great deal of credence. The ACE2 receptor coronavirus matches the pre-pub announcements of the Wuhan lab [in the fall of 2019]. They were rushing research for a big conference [in December 2019]"

(3) (A) China has been the source of leaks from their biotech labs in the past. Specifically, twice with SARS-CoV in 2004 (Beijing). Other countries labs have also leaked the SARS virus (Singapore, Taiwan), and in the US the biotech / bioweapons lab of Ft. Detrick, MD has been sanctioned last year for having a potentially leaky lab (https://www.independent.co.uk/news/...ak-ebola-anthrax-smallpox-ricin-a9042641.html) (Note nearly all countries subscribe to the 1969 convention against bioweapons but nevertheless advance such bioweapons under the cover of 'defensive' medicine to create a vaccine, the WIV undoubtedly being no exception). This stipulated fact is to show that a bioweapons-grade or otherwise chimeric virus could indeed escape the WIV, a BSL-4 lab, as is the Ft. Detrick, MD lab.

(3) (B) China in 1977 accidentally released a strain of H1N1 virus that infected Russians at their border; the virus was lab created (selected or attenuated in strength) and was, as is common with lab viruses, temperature sensitive. The Covid-19 virus is also temperature sensitive.

(4)(A) a widely published scientific paper allegedly rebutting that the Covid-19 virus is man-made is the Andersen et al. March 2020 Nature Medicine article, key passage here: https://www.nature.com/articles/s41591-020-0820-9#ref-CR20 (March 17, 2020) "The proximal origin of SARS-CoV-2" by Kristian G. Andersen et al - "While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal7 and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding7,11. Thus, the high-affinity binding of the SARS-CoV-2 spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise. This is strong evidence that SARS-CoV-2 is not the product of purposeful manipulation."

This article is astonishingly weak yet widely cited. Essentially it is saying that the Covid-19 virus (SARS-CoV-2) is not as optimal at infecting humans as the chimeric virus SARS-CoV that Dr. Shi, Dr. Baric and others invented in 2015 in the Univ of NC (Chapel Hill), hence, being sub-optimal in infecting humans, it cannot be the design of a competent gene jockey. But a moment's reflection should indicate, even to somebody unversed in science, that a competent bioweapons lab creating an infectious chimeric virus would not want to create exactly the same virus as before, the SARS-CoV virus of 2015, for fear of the virus being found to be clearly man made. In particular since this 2015 chimeric virus was so controversial that the US NIH, a sponsor, sanctioned the authors, and extended a ban on such "gain of function" (i.e. radical jumps in genetic structure not usually occurring in nature) chimeric viruses for a full two years afterwards, until 2017. Understandably after such sanctions by the NIH, chimeric virus scientists are naturally reluctant to promote any theory that the Covid-19 virus is chimeric, for fear of future sanctions. IMO this is clearly driving the debate from the experts point of view. It's analogous to asking lawyers to reform the legal profession to make it so you don't need lawyers. To put it mildly, it's not going to happen easily. Further, the SARS-CoV-2 virus has in fact been highly successful at infecting humans, even if it is indeed sub-optimal at infecting humans compared to its predecessor virus, the chimeric SARS-CoV virus of 2015 invented by Shi et al.

(4)(B) - appeals to authority are common when dealing with technical issues, as I can personally attest from years of litigation. Again, the Third Law of Litigation. Mental shortcuts are common with most people outside their area of expertise. So read the below passage criticizing the Andersen et al Nature Medicine article, keeping in mind the scientist criticizing is of the opinion that the Covid-19 virus is not man made. Nevertheless, the scientist indicates the Andersen et al authors made numerous assumptions that, in a litigation setting, would not go as unchallenged as they have in the popular press:

"Professor Richard Ebright of Rutgers University’s Waksman Institute of Microbiology, a biosecurity expert who has been speaking out on lab safety since the early 2000s, does agree with the Nature Medicine authors’ argument that the new coronavirus wasn’t purposefully manipulated by humans, calling their arguments on this score strong"

"Ebright points out that scientists in Wuhan have collected and publicized a bat coronavirus called RaTG13, one that is 96 percent genetically similar to SARS-CoV-2. The Nature Medicine authors are arguing “against the hypothesis that the published, lab-collected, lab-stored bat coronavirus RaTG13 [RaTG13 is similar to SARS-CoV, within 3-4% of SARS-CoV-2 - RL] could be a proximal progenitor of the outbreak virus.” But, Ebright says, the authors relied on assumptions about when the viral ancestor of SARS-CoV-2 jumped to humans; how fast it evolved before that; how fast it evolved as it adapted to humans; and the possibility that that the virus may have mutated in cell cultures or experimental animals inside a lab. "

Note Ebright is saying the Andersen et al authors made assumptions, assumptions that can be easily challenged. In fact, the Covid-19 virus has a "gain of function" of four, usual for a natural virus (but not impossible to achieve) and a genetic drift that indicates it would take 25 to 50 years for the Covid-19 virus to occur naturally (numerous cites online). So 18 years after SARS broke out, and only 5 years after SARS-CoV was artificially created, we are to believe that the Covid-19 virus occurred naturally? Possibly, but, it leads to the next and final point.

(5) no intermediate host or prior to a human host has been found for the Covid-19 virus. No animal save man is known to have the Covid-19 virus; not bats, not pangolins. This is not true of other deadly viruses, like H1N1 (pigs are the host), Ebola virus (bats are the host), MERS-CoV virus (camels are the host) or SARS (civet cats are the host). In fact, in all the prior virus outbreaks, the animal host prior to human infection was quickly found. Such is not the case with the Covid-19 virus. Quite possibly, it's because no such animal exists. Covid-19 is a man made virus.

(6) https://project-evidence.github.io/ is concerned with a natural release of the Covid-19 virus, so it belongs to the other thread in this forum, but the passage below supports the assertion that WIV could have created a "lab virus" simply by selective breeding of bats, allowing the coronaviruses to mutate inside the bats rather than using a test tube and recombinant DNA technology. As per stipulation (1)(B) above, that's about the same thing, functionally.

From the paper on the site: "While the phrase "laboratory-based scenario" is abstract, given prior context, we will assume this again refers to the "Manipulated Virus" theory. It remains plausible for a lab animal to have been infected with SARS-CoV-2, either prior to arriving at the lab or as part of a spillover event occuring in the lab, afterwards spreading the virus to human Patient Zero. From the layman’s explanation of Paper 1 we remember that: Multiple coronaviruses can infect the same bat (coinfection) Coronaviruses like to mix their genes together (recombinate) If two coronaviruses infect the same bat and recombinate, they can potentially result in a novel (never before recognized) coronavirus It only takes a few changes ("exchange of a relatively small sequence segment") between two coronaviruses to result in a third coronavirus that can infect other animals ("host-switching")
The odds of this happening are pretty good! Indeed, wouldn’t it be far more likely for such a recombination event to occur in a laboratory housing many bats in close quarters, such as the WHCDC, rather than anywhere else in Wuhan?"

Final thoughts:

I could include facts about the destruction of the Wuhan wet market (destruction of evidence that, if it was done in a US litigation after commencement of a lawsuit, would result in a default judgement in favor of the party not destroying evidence, here, the China skeptics); about the alleged patient zero (either a senile old man at the wet market or an employee at WIV who allegedly has disappeared); about the alleged adjunct biotech laboratory not many kilometers form the Wuhan wet market, as is the WIV, but a mere couple of hundred meters away which allegedly was removed from Google Maps and has also been closed; how neither bats nor pangolins were sold at the Wuhan wet market, which in any event are found many thousands of kilometers away from the Wuhan wet market, the directive by CHN president Xi Jinping in early January that tightened safety protocols of biotech laboratories in China, which long-time China observers say is a clear signal a breach of safety occurred (Source: https://www.youtube.com/watch?v=G0VJLYRhPHg
), the stories (https://www.washingtontimes.com/news/2020/apr/28/wuhan-laboratory-most-likely-coronavirus-source-us/) that WIV was very lax with their bio-safety protocols, even allegedly selling experimental animals after experiments and even, astonishingly, cooking and eating eggs that were used in experiments (heat inactivates viruses but that's one egg I would not want to crack), the rumors that Dr. Shi in January was upset on social media that her lab may have been responsible for the outbreak, or that she was removed as director of WIV after the outbreak--if that's not a demotion then what is it?--and replaced by a military general and a gag order against Covid-19 origin talk. Further, not just US president Trump is calling for an investigation but also the more neutral EU, reference [*] below.

In US law, the numerous circumstantial evidence surrounding the outbreak of Covid-19 points to a coverup, and of a lab created virus. Without question it would be sufficient to get a grand jury indictment in a criminal case. Whether it would be enough for a conviction is debatable (from a competent jury, I'm not referring to the well-known to US litigators 10% rule that I reference above). Personally, if I was offered 100:1 odds that the Covid-19 virus was chimeric, or even 10:1 odds, I would bet serious money that it is.

The above is not copyright, feel free to cut and paste anywhere without attribution.
--RL

[*] Ursula von der Leyen said the international community should investigate how the coronavirus pandemic started |
The Commission chief says studying the outbreak’s origins is necessary to set up an ‘early warning system.’
By LAURENS CERULUS 5/1/20, 12:00 PM CET Updated 5/1/20, 12:19 PM CET
European Commission President Ursula von der Leyen said the international community should investigate how the coronavirus pandemic started in order to be better prepared for future outbreaks. In an interview with U.S. news channel CNBC published Friday, von der Leyen suggested the international community needed to study the coronavirus outbreak in order to set up an "early warning system." "You never know where the next virus is starting so we all want that, for the next time, we have learned our lesson and we have established a system of early warning that really functions," she said, adding "the whole world has to contribute to that." Von der Leyen's suggestion comes after the Swedish health minister called for an "international, independent investigation" into the origins and the spread of the virus. It also follows a statement by U.S. President Donald Trump, who suggested he had seen evidence that the virus originated in a Chinese scientific lab
 

Mendel

Senior Member.
Taiwannews is not an unbiased source when it comes to China. They cite David A. Relman, and you can read his opinon in the PNAS journal:
Article:
Some have argued that a deliberate engineering scenario is unlikely because one would not have had the insight a priori to design the current pandemic virus (3). This argument fails to acknowledge the possibility that two or more as yet undisclosed ancestors (i.e., more proximal ancestors than RaTG13 and RmYN02) had already been discovered and were being studied in a laboratory [..]

Even though strong opinions abound, none of these scenarios can be confidently ruled in or ruled out with currently available facts. Just because there are no public reports of more immediate, proximal ancestors in natural hosts, doesn’t mean that these ancestors don’t exist in natural hosts or that COVID-19 didn’t began as a spillover event. Nor does it mean that they have not been recovered and studied, or deliberately recombined in a laboratory.

The problem with that is that the first paragraph is a conspiracy theory with no evidence to support it. The lab knows its viruses and knows they didn't come from there; it's in contact with bat virus researchers in other countries who also know which virusus this lab has, there is no secret research going on in this field with that lab.

The main thrust of Relman's article (if you read it in full) is to get going to finally make progress on investigating the animal origin of this virus.
I've slept on this, and I now have an opinion on the subtext of this opinion piece in PNAS.

Fairly early on in the pandemic, most virus experts working in the field came to the consensus that the genetic makeup of this virus showed evidence it wasn't engineered. They called for an investigation into the chain of events that led the virus to "travel" from the bats into the human population, with the leading theory being that it transferred onto pangolins, where it acquired the mutation making it dangerous for humans, and then from pangolins to humans via the Wuhan seafood market. (People in China don't usually eat bats.)

These investigations have started. Relman knows this:
Article:
Conflicts of interest by researchers, administrators, and policymakers on all sides must be revealed and addressed, and all relevant global constituencies must be included. Both the World Health Organization and The Lancet COVID-19 Commission (6) have hinted that they have taken some first steps, but their efforts so far have been cloaked in secrecy (7, 8).
[..]

  1. J. D. Sachs et al.; The Lancet COVID-19 Commission. Lancet 396, 454–455 (2020).
  2. World Health Organization, WHO experts to travel to China. https://www.who.int/news-room/detail/07-07-2020-who-experts-to-travel-to-china/. Accessed 20 September 2020.
  3. P. Nuki, S. Newey, Scientists to examine possibility Covid leaked from lab as part of investigation into virus origins. The Telegraph, 15 September 2020. https://www.telegraph.co.uk/global-...sibility-covid-leaked-lab-part-investigation/. Accessed 27 September 2020.

What he wants is for these investigations to be more transparent. He probably realizes that China has seen pressure from the US over this, and its politicians have been trying to spin the narrative that maybe the virus didn't originate in China. The article pushes for these investigations to be transparent, with a veiled threat of "if you don't do this, we'll start saying it originated in a lab again". The opinion was first published on November 3rd, and I don't think it's coincidence that date marks the end of the US election campaign season.

In support of this, read what Relman is calling for, and what he isn't: "The bottom line is simple: We need to identify the immediate parent(s) of SARS-CoV-2, and they’re missing." That's what his article is supporting. He doesn't talk about how the virus might have been created in the lab, and how to best investigate that; he talks about the need to investigate the origins of the virus, and that is in line with being convinced that there was an animal origin, in line with also being convinced that this process needs to be more transparent.

A Google search for "china investigation bat origins sars-ncov-2" turns up plenty of news that these investigations are ongoing.

December 2nd, article in one of the top science papers in the world, portraying the WHO investigation team:
Article:
The investigation aims to find out how and when SARS-CoV-2 first infected people. Strong evidence suggests that the coronavirus originated in bats, but its journey to people remains a mystery. Scientists say the team is highly qualified, but its task will be challenging.

“This is an excellent team with a lot of experience,” says Martin Beer, a virologist at the Federal Research Institute for Animal Health in Greifswald, Germany.

The group will be working with researchers in China and professionals from several other international agencies, and will start the search in Wuhan — the Chinese city where the new coronavirus SARS-CoV-2 was first identified — and expand across China and beyond.


An Al Jazeera article clarifies the political situation that makes this investigation difficult: China really doesn't want to be the "culprit".
Article:
“WHO has put together a team to go to China and to work with colleagues in China to investigate the origins question but that is of course going to require a lot of cooperation with the Chinese government and scientists in China,” said Angela Rasmussen, a virologist at the Columbia University School of Public Health. “It’s going to be a very complicated political situation and political context in which to do a rigorous scientific investigation.”

[..]

But as scientists prepare to head to China, with signs still pointing to Wuhan as the first chief virus cluster, Chinese state media continues to construct an alternative narrative, often cherry-picking data from global studies that appear to support their case.

On November 16, state news agency Xinhua picked up a study published by the Tumori Journal, the publication of the Milan’s National Cancer Institute, that pointed to an Italian screening of lung cancer patients that found coronavirus antibodies in late 2019.

Another article from the Global Times, a state-run tabloid, on December 2 suggested the possible presence of the coronavirus in the United States before it emerged in Wuhan, while further confusion has been made from studies like an analysis of wastewater in Spain that suggested COVID-19 may have been present as early as March 2019.
[..]

Such studies, however, have done little to challenge the mainstream scientific community’s views, points out Claire Standley, an assistant research professor at Georgetown University’s Center for Global Health Science and Security.

The reason, she says, is that many of the studies are based on serological testing, which looks for virus antibodies. These kinds of tests can cross-react with other coronavirus antibodies, such as those from the common cold, which makes them less reliable than DNA-based testing.


Investigation results take a long time to become public.
Article:
The government is handing out hundreds of thousands of dollars in grants to scientists researching the virus’ origins in southern China and affiliated with the military, the AP has found. But it is monitoring their findings and mandating that the publication of any data or research must be approved by a new task force managed by China’s cabinet, under direct orders from President Xi Jinping, according to internal documents obtained by the AP. A rare leak from within the government, the dozens of pages of unpublished documents confirm what many have long suspected: The clampdown comes from the top.

As a result, very little has been made public. Authorities are severely limiting information and impeding cooperation with international scientists.

[..]

Some state-backed scientists say research is proceeding as usual. Famed virologist Zhang, who received a 1.5 million RMB ($230,000) grant to search for the virus’ origins, said partnering scientists are sending him samples from all over, including from bats in Guizhou in southern China and rats in Henan hundreds of miles north.

“Bats, mice, are there any new coronaviruses in them? Do they have this particular coronavirus?” Zhang said. “We’ve been doing this work for over a decade. It’s not like we just started today.”

[..]

Coronavirus expert Peter Daszak, a member of the WHO team, said identifying the pandemic’s source should not be used to assign guilt.

“We’re all part of this together,” he said. “And until we realize that, we’re never going to get rid of this problem.”


National Geographic, November 6th, debunks the notion that the Chinese destroyed evidence at the seafood market.
Article:
Raina MacIntyre, an infectious diseases expert and professor at the University of New South Wales in Australia, says Chinese scientists have already done significant research on the potential animal origins of the SARS-CoV-2 virus. China and other countries have contributed genetic sequences of the coronavirus collected from humans to a database for tracking the germ’s evolution. By comparing entries, multiple research groups have reached the conclusion that the novel coronavirus “has probably come from bats, perhaps through an intermediary animal host,” MacIntyre says.

The multitude of SARS-esque viruses that horseshoe bats retain make them a prime suspect in the current pandemic’s origins. And those nocturnal cave dwellers are not only found in China but in the bordering countries of Myanmar, Laos, and Vietnam. “We need a WHO-sponsored international collaborative network, like the one we had in 2003, and we need to seriously consider investigations beyond China,” Wang says.

[..]

But disease detective Daniel Lucey says there are indications China has already completed considerable legwork.

“Of course they would have done that,” says Lucey, who works at Georgetown University, because “it’s in China’s national interest to do an investigation as quickly as possible, for the sake of public health.”

Lucey points to China’s tracking of the first confirmed pandemic patient to November 17, 2019. Then there was a January investigation conducted by 29 Chinese researchers across a medley of institutions that examined how many early COVID-19 patients could be linked to the Wuhan wet market. Their results indicated that 14 of 41 early cases weren’t exposed there.

Still, some mystery remains around the initial surveys at ground zero. The Chinese Center for Disease Control and Prevention said in late January that it had collected nearly 600 samples at the market, and Wuhan Institute of Virology virologist Shi Zhengli made public statements this past summer about testing samples from the ground, sewage, and door handles at the market.

But new details from the WHO mission plan say nearly 1,200 specimens were collected from the Wuhan market, which had 653 sellers peddling items ranging from seafood and chipmunks to giant salamanders and sika deer. Yet, of the 336 animals sampled at the market, none tested positive for SARS-CoV-2. By contrast, 8 percent of the environmental swabs—many involving drains and sewage—carried the virus.


The BBC published an article on opposition to reporting on this research by Chinese autorities, but they debunk the "lab theory".
Article:
The Chinese government, the WIV, and Prof Shi have all angrily dismissed the allegation of a virus leak from the Wuhan lab.

But with scientists appointed by the World Health Organization (WHO) scheduled to visit Wuhan in January for an inquiry into the origin of the pandemic, Prof Shi - who has given few interviews since the pandemic began - answered a number of BBC questions by email.

"I have communicated with the WHO experts twice," she wrote, when asked if an investigation might help rule out a lab leak and end the speculation. "I have personally and clearly expressed that I would welcome them to visit the WIV," she said.

To a follow-up question about whether that would include a formal investigation with access to the WIV's experimental data and laboratory records, Prof Shi said: "I would personally welcome any form of visit based on an open, transparent, trusting, reliable and reasonable dialogue. But the specific plan is not decided by me."

The BBC subsequently received a call from the WIV's press office, saying that Prof Shi was speaking in a personal capacity and her answers had not been approved by the WIV.

[..]

Peter Daszak, a British zoologist, has been chosen as part of the team because of his leading role in a multimillion dollar, international project to sample wild viruses.

It has involved close collaboration with Prof Shi Zhengli in her mass sampling of bats in China, and Dr Daszak previously called the lab-leak theory a "conspiracy theory" and "pure baloney".

"I've yet to see any evidence at all of a lab leak or a lab involvement in this outbreak," he said. "I have seen substantial evidence that these are naturally occurring phenomena driven by human encroachment into wildlife habitat, which is clearly on display across south-east Asia."

[..]

In what has become the definitive paper ruling out the possibility of a lab leak, RaTG13 has a starring role.
Published in March in the magazine Nature Medicine, it suggests that if there had been a leak, Prof Shi Zhengli would have found a much closer match in her database than RaTG13.

While RaTG13 is the closest known relative - at 96.2% similarity - it is still too distant to have been manipulated and changed into Sars-Cov-2.

Sars-Cov-2, the authors concluded, was likely to have gained its unique efficiency through a long, undetected period of circulation in humans or animals of a natural and milder precursor virus that eventually evolved into the potent, deadly form first detected in Wuhan in 2019.


And there you have it. The idea that the pandemic was man-made has been debunked in March; there hasn't been any new evidence since then to question that; but it's necessary to investigate the origins of the virus, but the researchers need funding for this kind of work.

And that's a possible second motivation for David A. Relman: if he's applying for reasearch grants himself (or friends of his are), it makes sense to put a paragraph in to convince right-wing politicians deciding on these grants that maybe China is to blame after all, in order to make it easier for them to support the grant and get the money flowing.

It's still scientific consensus that this came from animals, and was not created in a laboratory.
 

A.G.

Senior Member.
Li'l help?

I encountered someone citing the study mentioned above, which has apparently found new life and is being spread via The Daily Mail:

https://www.dailymail.co.uk/news/ar...Jzwqb3pEA5VCrd39yqarJXC_UK03CmWjnl5uzIZknlN5A

The person posting this went several steps further than the Daily Mail article itself (certainly ignoring the skeptical virologist and microbiologist quoted in the article), and claimed that "GP120 hasn't been found anywhere else, neither in bacteria, humans or animals and certainly not in any other viruses". I replied with the Massive Science link mentioned above in this thread, pointing out that there are matches with several viruses if the BLAST search is done right.

My opponent's reply was to link to this Twitter thread, emphasizing "not sufficient homology"
Source: https://twitter.com/Daoyu15/status/1353522381210312704


...and this is where I don't get any further since frankly I don't know where to start in trying to understand what that Twitter thread means. All I can say is that I don't see any mention of rebutting the gp120 being found in viruses - apart from that, I feel I'm going to have to learn a whole lot more about all that "recombination" and "landing pads" and stuff.

Maybe it's sufficient to point out that the thread doesn't address matches with viruses? I suspect that my opponent doesn't really know either. Anyone here who has a better understanding?
 
Top