Author Topic: Need help from all you science/research people - Wuhan coronavirus paper  (Read 1442 times)

Freedomin5

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My friend and I are having a discussion about a research paper on the Wuhan coronavirus.

Hereís the abstract.

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Abstract:
We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019- nCoV). 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. This work provides yet unknown insights on 2019-nCoV and sheds light on the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.

She thinks this means that the virus was man-made because the 4 inserts are unlikely to be fortuitous in nature. I donít think this is what the paper is claiming but am having a difficult time getting through the terminology.

The paper is written by researchers at a university Iíve never heard of, and published in a journal that Iíve never heard of, and that is not peer-reviewed, so Iím already suspicious of its quality.

Can someone who has a graduate-level background in a biological/medical field explain what the abstract means in laymenís terms?

I donít want to provide the link to a potentially unhelpful paper, but let me know if you think reading the full paper will help.

Thanks!

ixtap

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OtherJen

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #2 on: February 01, 2020, 08:39:56 PM »
I meet your criterion (PhD in immunology) and would like to read the paper to see what was actually done. I'm more than a little skeptical, given the speed at which it appeared in the literature.

OtherJen

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #3 on: February 01, 2020, 08:42:47 PM »
Will this guy do?

Thanks for posting this. I'm going to read it now.

Freedomin5

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #4 on: February 01, 2020, 08:45:18 PM »
I meet your criterion (PhD in immunology) and would like to read the paper to see what was actually done. I'm more than a little skeptical, given the speed at which it appeared in the literature.

Hereís the link: https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf

Would love to hear your insights.

@ixtap That helps as it refers to the same paper Iím talking about. Thanks!
« Last Edit: February 01, 2020, 08:46:59 PM by Freedomin5 »

OtherJen

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #5 on: February 01, 2020, 09:10:55 PM »
I agree with this quote from the blog author:

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In other words, the sequence overlap is not actually uncanny, and there is no big scoop here. The group in India fell prey to some of the pitfalls of bioinformatics research.

The identification of novel gene inserts is actually fascinating from an immunological perspective, as those might create useful epitopes for vaccine design.

But yes, bioinformatics is somewhat limited in that it gives you a shit-ton of information but it is not wise to draw conclusions from it. It's best used as a starting point to identify something genomic of interest on which to base more in-depth work.

I also find the paper to be somewhat irresponsible. I didn't dig too deeply into the background and am nowhere near a virus expert, but I would be surprised to learn that no other matches for those inserts were identified in their analysis. Those are not particularly long sequences. I suspect the most attention-grabbing match was chosen for the headline. Unfortunately, mainstream science reporting tends to be subpar, so the publicity grab will likely work.

The blogger also commented that the inserts are also in hypervariable gene regions and yes, those can mutate rapidly and spontaneously. It happens in nature: your B cells do that when faced with an infection, so that they can produce even more specific antibodies that bind more strongly to pathogens.
« Last Edit: February 02, 2020, 05:56:22 AM by OtherJen »

Freedomin5

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #6 on: February 02, 2020, 01:16:26 AM »
@OtherJen

Thank you! I sent your response to my friend. Hopefully, it will help her to feel better. They are stuck in China and havenít been able to leave, and sheís quite upset and worried by all of this. Hopefully, this can help her focus on what she can actually do to keep her family safe and healthy.

OtherJen

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #7 on: February 02, 2020, 05:58:43 AM »
@OtherJen

Thank you! I sent your response to my friend. Hopefully, it will help her to feel better. They are stuck in China and havenít been able to leave, and sheís quite upset and worried by all of this. Hopefully, this can help her focus on what she can actually do to keep her family safe and healthy.

Oops, had messed up the tagging. Tis a hazard of responding on a phone screen.

That must be so scary for your friend. I imagine that people stuck in the center of this epidemic are looking for some explanation, something to blame. It's human nature.

OtherJen

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #8 on: February 02, 2020, 12:06:49 PM »
Tangentially related -- this article outlines how one of the people involved in disseminating this and other articles related to the coronavirus became a twitter sensation.  He has since dialed back one of his early sensationalist posts, but not before he gained a lot of followers, including many in the conspiracy theory trenches:

https://www.theatlantic.com/technology/archive/2020/01/china-coronavirus-twitter/605644/

Ugh. So irresponsible. I note that none of these sensational claims have been made by experts in virology or infectious disease.

maizeman

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #9 on: February 02, 2020, 12:20:34 PM »
The folks I follow on twitter were getting thrilled to use this as a teaching opportunity for statistics, false discovery rates, and BLAST e-values a couple of days ago.

Completely agree with everything the guy in the link ixtap posted said. It's complete nonsense, several of the sequences posted aren't actually inserts at all but alignment artifacts, and the places where there are insertions they are

1) the sort of small insertions and deletions you always see comparing similar proteins between related species

2) so short that they exist by chance alone in all sorts of proteins from every branch of the tree of life.

The paper is written by researchers at a university Iíve never heard of, and published in a journal that Iíve never heard of, and that is not peer-reviewed, so Iím already suspicious of its quality.

Just in bioRxiv's defense, it is not actually a journal, but a preprint server. It's a place people can post first drafts of papers while they are undergoing peer review. It's actually be really beneficial for the community because we get to read a lot of cool science anyway from six to eighteen months earlier (while it is working its way through the peer review process). You just have to be aware that there will also sometimes be papers posted that clearly would NOT pass peer review, so the reader, as a scientific peer, have to be critically evaluating all the claims, reasoning, and methods, just as they really should be in any paper, peer reviewed or otherwise.

The problem that crops up from time to time, and coronavirus has been a big one, is that the media/general public will sometimes come across these preprints (or bad actors, including sometimes the authors, will disseminate them) and treat them like a validated part of the peer reviewed literature, instead of a glimpse behind the curtain at how the sausage gets made.

There have been a bunch of calls for people to start doing ad hoc peer review of coronavirus preprints right there on bioRviv since so many non-scientists are searching through, and a lot of stuff is being posted, some incredibly timely useful -- the complete sequence of the novel corona virus was posted there about a week ago -- and a lot of it is complete junk. I don't know how effective that will be since posting "reviews" on BioRxiv just looks like random internet comments at the bottom of the page, and people outside the field aren't going to give them much weight.

The warning posted at the top of the website now may help more:

"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."


Freedomin5

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #10 on: February 02, 2020, 05:53:57 PM »
@maizeman I think that's what happened here. My friend was searching for any and all information on the virus, came across this, and unnecessarily freaked out.

Since I know the folks on this forum tend to be more educated than the general population, and I know there are quite a few experienced folks in various STEM fields, I thought it would be good to get some other perspectives. However, not everyone knows how to even begin to verify data -- confirmation bias and all that.

Thanks for clearing this up for me!

fuzzy math

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #11 on: February 04, 2020, 04:10:22 PM »
At the same time, one person at a pharmaceutical company (industry background) providing a refutation does not invalidate the research done by the original authors. It appears the authors are rewriting their paper at this time based off suggestions. This partial refutation was posted on a prepper site.

There is NOT a consensus that this is natural in origin. Other people have weighed in an provided some pretty compelling food for thought.

https://jameslyonsweiler.com/2020/01/30/on-the-origins-of-the-2019-ncov-virus-wuhan-china/?fbclid=IwAR01r9_9vBuvN8WYzPmLvYqrredDxOXOg9T6BB8M6RoWhpQbSTeSXD8GMN4

https://www.theepochtimes.com/scientific-puzzles-surrounding-the-wuhan-novel-coronavirus_3225405.html


maizeman

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #12 on: February 04, 2020, 05:42:47 PM »
Fuzzy math, whoever wrote that article doesn't seem to understand how bootstrap support works. The 76% bootstrap values aren't particularly low to begin with and even if they were, they are looking at the bootstrap value on the branch leading to all the novel human corona virus sequences. If their argument is that there isn't strong evidence supporting the sequence coming from bats, they should look at the branch leading to the most recent common ancestor of the bat and human sequences. That's the one marked with the arrow labelled "clade 2". Which, as you can see, has 100% bootstrap support. So 100% of the time, the bat and human sequences in clade 2 are clustered together to the exclusion of all other sequences in the tree, which is exactly what we'd expect for a virus transmissed from bats to humans.

The branch with 76% boostrap value indicates that it's not always possible to recover a separate clade of only the human isolate corona virus sequences which does not also contain the two bat corona virus sequences. Which again is what one would expect from a virus that has only just jumped from bats to humans where hasn't been enough time for sequence divergence.

fuzzy math

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #13 on: February 04, 2020, 09:13:46 PM »
Please do not take anything published by The Epoch Times too seriously.  It is associated with Falun Gong and has a long history of pretty inflated/biased reporting on anything related to mainland China.

https://en.wikipedia.org/wiki/The_Epoch_Times

Did you even read the article?

rahaparta

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Re: Need help from all you science/research people - Wuhan coronavirus paper
« Reply #14 on: February 16, 2020, 06:29:43 PM »
Read this today ..

https://time.com/5783838/coronavirus-symptoms-wuhan-survivor/

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Doctors put him on an IV drop and administered Kaletra, a combination drug used to treat HIV that has shown some success in combating the virus, bringing his temperature down to 37 degrees by the end of the day.