Claim:HIV Protein Sequences in Covid-19 (report withdrawn by authors) & other man made claims

Dan Wilson

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 attached below)

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 This is pretty crazy for even a pre-print to suggest, but we have to keep in mind that this has not yet been peer-reviewed.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.
 

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deirdre

Moderator
Staff 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:
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

 
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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 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
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)
Update

The publisher added the following note at the top of the article page:
 
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Trailspotter

Senior Member
The first author has made the following comment in the discussion of the preprint (emphasis mine):
http://archive.ph/tZgVI
 
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Trailspotter

Senior Member
Update

This article has been withdrawn. Click here for details
 

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

Active 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.
 

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
Also, this same drug cocktail was effective against SARS, which was also caused by a coronavirus.
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

Moderator
Staff 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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503725/

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

Active Member
From today: https://www.sciencemag.org/news/202...-conspiracy-theories-about-origin-coronavirus
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
 

Agent K

Active Member
New study debunking conspiracy theories
"The proximal origin of SARS-CoV-2"
https://www.nature.com/articles/s41591-020-0820-9
 

Trailspotter

Senior Member
A new study on probable origin of SARS-CoV-2 published this week in Nature:
 

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
https://www.ncbi.nlm.nih.gov/pubmed/32007145
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.
 
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