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Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

biorxiv.org

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Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#131

Post by protein_lense »

zozbot234 wrote: post #108
buboard wrote: post #102

The study is probably bunk and sensational. check the comments by this redditor : https://www.reddit.com/r/China_Flu/comments/ewt9ep/scientifi... https://www.reddit.com/r/China_Flu/comments/ewuotw/discussio... The real question is: how far are we from this becoming real ?

Interesting, that user claims to be especially familiar with the 'gag' protein where the paper claims to find a match. User explicitly says that the "matching" portions claimed in the paper are so tiny as to be negligible, and not unique to HIV. They claim that this is easily verifiable with a simple 'blast' search. Could someone comment on these claims?

I BLASTed all 4 2019-nCoV insert sequences and agree with that user. The sequences are short and found in many other proteins. It is appropriate to trim out the gaps (relative to the HIV sequences) in inserts 3 & 4, reducing the length of the query. In other words, we have 4 sequences of lengths: 6, 6, 8, & 12 amino acids, where the alphabet of naturally occurring amino acids is N=20. Amino acid frequency in proteins in non-uniform.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#132

Post by Palptine »

folli wrote: post #126
Palptine wrote: post #123

Earlier quoted context omitted.

What's the chance of hitting all 4 of them though? This is a good step in verification but you are awfully too quick to reject their claim.

Read the paper, they actually only match 2 inserts, the other two inserts are modified by the authors in such a way that they are made to match (Table 1). Both inserts 1 and 2 also match to Streptococcus phage, but a bacteriophage would of course not be such a bold claim as HIV matches are. Also, be aware that because of the scientific interest in HIV, there are hundreds of HIV strains sequenced, a virus known for it…

Large HIV database inflating matches is indeed a big concern. But dismissing one miss matches sounds arbitrary: these segments were not arbitrarily selected, but real insertions on tops of sars.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#133

Post by folli »

45ure wrote: post #130
folli wrote: post #119

Sorry, but it's very easy to verify that these claims are crap by replicating their study, i.e. doing a simple blast search of the insert sequence against the virus database. Here's the result of the first insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS... Although, there are some hits against HIV, there are also equally matching hits against bacteriophages; viruses that only target bacterias, th…

>These guys that published such a paper are either completely clueless or nefarious in trying to stir up conspiracy theories. In your opinion, do you think this kind of subterfuge could have been picked up by Dr. Eric Feigl-Ding or someone with a similar calibre, before broadcasting this preprint for wider consumption? Thanks.

I have not heard from this guy before (I work in microbial genomics, he seems to be in the field of health economics from a quick search), so I can't comment on that.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#134

Post by 45ure »

folli wrote: post #133
45ure wrote: post #130

Earlier quoted context omitted.

>These guys that published such a paper are either completely clueless or nefarious in trying to stir up conspiracy theories. In your opinion, do you think this kind of subterfuge could have been picked up by Dr. Eric Feigl-Ding or someone with a similar calibre, before broadcasting this preprint for wider consumption? Thanks.

I have not heard from this guy before (I work in microbial genomics, he seems to be in the field of health economics from a quick search), so I can't comment on that.

Your reply is much appreciated.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#135

Post by folli »

Palptine wrote: post #132
folli wrote: post #126

Earlier quoted context omitted.

Read the paper, they actually only match 2 inserts, the other two inserts are modified by the authors in such a way that they are made to match (Table 1). Both inserts 1 and 2 also match to Streptococcus phage, but a bacteriophage would of course not be such a bold claim as HIV matches are. Also, be aware that because of the scientific interest in HIV, there are hundreds of HIV strains sequenced, a virus known for it…

Large HIV database inflating matches is indeed a big concern. But dismissing one miss matches sounds arbitrary: these segments were not arbitrarily selected, but real insertions on tops of sars.

Again, take any random six letter amino acid sequence and chances are high that it matches to some HIV protein.

I just did the experiment with my first name that is coincidentally 6 letters long, and lo and behold: a match to HIV env protein!

Has my first name now been designed by a bioweapons facility?

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#137

Post by perseusprime11 »

folli wrote: post #133
45ure wrote: post #130

Earlier quoted context omitted.

>These guys that published such a paper are either completely clueless or nefarious in trying to stir up conspiracy theories. In your opinion, do you think this kind of subterfuge could have been picked up by Dr. Eric Feigl-Ding or someone with a similar calibre, before broadcasting this preprint for wider consumption? Thanks.

I have not heard from this guy before (I work in microbial genomics, he seems to be in the field of health economics from a quick search), so I can't comment on that.

Outside of the assertion that it is related to HIV, does the original argument around deliberate insertions hold any water?

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#138

Post by folli »

perseusprime11 wrote: post #137
folli wrote: post #133

Earlier quoted context omitted.

I have not heard from this guy before (I work in microbial genomics, he seems to be in the field of health economics from a quick search), so I can't comment on that.

Outside of the assertion that it is related to HIV, does the original argument around deliberate insertions hold any water?

Occam's razor says no. The coronavirus spike protein is responsible for receptor binding and entry into the cell. Different strains with different hosts bind to different receptors, so they have differences in their spike protein sequences. Mutations in the spike protein are expected in the evolution of coronavirus.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#139

Post by BogdanPetre »

bawolff wrote: post #68
Andhurati wrote: post #20

Earlier quoted context omitted.

What are the geopolitical ramifications if this is indeed a bioweapon?

Maybe this is naive, but I would assume if it was a bio-weapon it would be a lot more deadly.

Well, it's a Made in China bio Weapon..

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#140

Post by cs702 »

folli wrote: post #122
jszymborski wrote: post #28

I think the important things to know here are: 1. A group of scientist have submitted a manuscript for review with a number of exceptionally (and uncharacteristically) bold claims. 2. A huge amount of scrutiny and additional reproducibility will necessarily need to be conducted before conclusions of this nature can be drawn. 3. This manuscript hasn't even passed the normal muster... a biorxiv post isn't much differen…

#2: replicating their BLAST search is easy: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS... and it shows that the matches of these short inserts are completely by chance and don't constitute any statistically significant relationship.

Thank you for posting this here -- and thank you for taking a quick look at that paper and debunking it.

I just upvoted your comment at https://news.ycombinator.com/item?id=22206393.

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