Nature Medicine corrective to some myths about the origins of Covid-19.

[NNadir]

The paper I'll discuss in this post is this one: The proximal origin of SARS-CoV-2 (Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes & Robert F. Garry, Nature Medicine (2020). https://doi.org/10.1038/s41591-020-0820-9)

The scientific publication community has agreed to make all Covid-19 open sourced so you are encouraged to use the link to read it, as it is a useful corrective to racist conspiracy theorists infesting the White House while the nation experiences a severe shortage of leadership which has led to a severe shortage of toilet paper.

Some excerpts from the paper:

Since the first reports of novel pneumonia (COVID-19) in Wuhan, Hubei province, China1,2, there has been considerable discussion on the origin of the causative virus, SARS-CoV-23 (also referred to as HCoV-19)4. Infections with SARS-CoV-2 are now widespread, and as of 11 March 2020, 121,564 cases have been confirmed in more than 110 countries, with 4,373 deaths5.

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 symptoms6. 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...

...The receptor-binding domain (RBD) in the spike protein is the most variable part of the coronavirus genome1,2. Six RBD amino acids have been shown to be critical for binding to ACE2 receptors and for determining the host range of SARS-CoV-like viruses7. With coordinates based on SARS-CoV, they are Y442, L472, N479, D480, T487 and Y4911, which correspond to L455, F486, Q493, S494, N501 and Y505 in SARS-CoV-27

The letter codes, for example, "Y442," here refer to amino acids in the spike protein which binds to human cells and their position in the amino acid sequnce. For those mentioned as being critical for binding the codes (which you can look up in many places) are Y = tyrosine, L = leucine, N = Asparagine, D = Aspartic Acid, T = Threonine, S = serine.

N, asparagine, is very important in molecular recognition, a feature of metabolism that is exploited by viruses to infect cells, since often on the side chain of this amino acid, which terminates in a structure called an "amide," a carbonyl group bound to an amine, one of the hydrogens in the amine is displaced by a link to a special type of (usually) highly branched sugar polymer called a glycan. Glycans bound to asparagine are called "N-Glycans."

The importance of glycans in molecular recognition has long been known - differences glycans are the origins of blood types - however the molecular complexity of glycans has made them very difficult to understand. Since it has been technically easier to release glycans from asparagine in proteins they are, despite their complexity, somewhat easier to study than the other class of glycans, "O-Glycans." Glycans are usually studied using high resolution mass spectrometry, and special tools and software have been developed for their analysis, as long as they can be released from the proteins for study.

O-glycans are attached to amino acids having a hydroxyl function on their side chain. These are serine, threonine and tyrosine, all of which are found in the important binding in the SARS-CoV viruses including Covid-19 listed above. It has been historically very difficult to release O-glycans from the amino acids to which they are bound. The technology for doing so has only become prominent in the last few years, and it is still "at the cutting edge" and not widely used. (This event should stimulate wider use however.)

All of this is important because of the following text in the paper:

The second notable feature of SARS-CoV-2 is a polybasic cleavage site (RRAR) at the junction of S1 and S2, the two subunits of the spike8 (Fig. 1b). This allows effective cleavage by furin and other proteases and has a role in determining viral infectivity and host range12. In addition, a leading proline is also inserted at this site in SARS-CoV-2; thus, the inserted sequence is PRRA (Fig. 1b). The turn created by the proline is predicted to result in the addition of O-linked glycans to S673, T678 and S686, which flank the cleavage site and are unique to SARS-CoV-2 (Fig. 1b). Polybasic cleavage sites have not been observed in related ‘lineage B’ betacoronaviruses, although other human betacoronaviruses, including HKU1 (lineage A), have those sites and predicted O-linked glycans13. Given the level of genetic variation in the spike, it is likely that SARS-CoV-2-like viruses with partial or full polybasic cleavage sites will be discovered in other species...

...The function of the predicted O-linked glycans is unclear, but they could create a ‘mucin-like domain’ that shields epitopes or key residues on the SARS-CoV-2 spike protein18. Several viruses utilize mucin-like domains as glycan shields involved immunoevasion18.

Some excerpts on origins:

It is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus. As noted above, the RBD of SARS-CoV-2 is optimized for binding to human ACE2 with an efficient solution different from those previously predicted7,11. Furthermore, if genetic manipulation had been performed, one of the several reverse-genetic systems available for betacoronaviruses would probably have been used19. However, the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone20...

...As many early cases of COVID-19 were linked to the Huanan market in Wuhan1,2, it is possible that an animal source was present at this location. Given the similarity of SARS-CoV-2 to bat SARS-CoV-like coronaviruses2, it is likely that bats serve as reservoir hosts for its progenitor...

...Malayan pangolins (Manis javanica) illegally imported into Guangdong province contain coronaviruses similar to SARS-CoV-221. Although the RaTG13 bat virus remains the closest to SARS-CoV-2 across the genome1, some pangolin coronaviruses exhibit strong similarity to SARS-CoV-2 in the RBD, including all six key RBD residues21 (Fig. 1)...

...Neither the bat betacoronaviruses nor the pangolin betacoronaviruses sampled thus far have polybasic cleavage sites. Although no animal coronavirus has been identified that is sufficiently similar to have served as the direct progenitor of SARS-CoV-2, the diversity of coronaviruses in bats and other species is massively undersampled...

...It is possible that a progenitor of SARS-CoV-2 jumped into humans, acquiring the genomic features described above through adaptation during undetected human-to-human transmission. Once acquired, these adaptations would enable the pandemic to take off and produce a sufficiently large cluster of cases to trigger the surveillance system that detected it1,2.

Viruses, in particular RNA viruses, have a spectacular ability to evolve because 1) their replication machinery is primitive and prone to error and 2) they can produce a huge number of generations in a single day, 3) they produce a lot of descendants, including many whose mutations are not fatal but on the contrary are better adapted than the original virus was in its host.

Again, the article is open sourced, and you are invited to open it. This is, of course, a scientific publication, and not some nonsense dripping off the tongue of a racist poorly educated, very unstable and intellectually impaired spoiled child as is in the White House.

However, it is wise to admit to ignorance if one has it - and I am personally ignorant of many things - so that one can eliminate one's ignorance by asking questions of someone who knows more than one does one's self. This process is called "education." Education differs greatly from making stupid assertions involving "alternate facts" since you definitely have to be some kind of idiot to invent that oxymoron.

It is possible, as I spend most of my time reading scientific publications, that I may be able to answer some questions associated with this paper if one has opened this and has them. I will be happy to try to help in that case.

I certainly hope our country will remedy the critical shortage in leadership by putting an experienced, competent and decent leader in the White House once again, former Vice President, Joe Biden.

Figure 1:



The caption:

a, Mutations in contact residues of the SARS-CoV-2 spike protein. The spike protein of SARS-CoV-2 (red bar at top) was aligned against the most closely related SARS-CoV-like coronaviruses and SARS-CoV itself. Key residues in the spike protein that make contact to the ACE2 receptor are marked with blue boxes in both SARS-CoV-2 and related viruses, including SARS-CoV (Urbani strain). b, Acquisition of polybasic cleavage site and O-linked glycans. Both the polybasic cleavage site and the three adjacent predicted O-linked glycans are unique to SARS-CoV-2 and were not previously seen in lineage B betacoronaviruses. Sequences shown are from NCBI GenBank, accession codes MN908947, MN996532, AY278741, KY417146 and MK211376. The pangolin coronavirus sequences are a consensus generated from SRR10168377 and SRR10168378 (NCBI BioProject PRJNA573298)29,30.

Enjoy your Sunday evening.

[in2herbs]

1. I have a question. I have read reports that UV light kills CV-19. If it works at all why can't

some of these patients be put in a tube (like a tanning tube) with UV light for treatment? Have you read anything about this? We need to generate multiple cures, not just a vaccine. BTW, thanks for your articles over the years. Don't always understand them but like to challenge my thinking capacity.

Namaste.

[NNadir]

2. Actually, there have been a number of developments in what is called "phototherapy."

It is sometimes used in cancer treatment.

All gamma radiation treatments are actually a subclass of phototherapy, since gamma radiation is electromagnetic energy, a form of light, as is UV.

In general "phototherapy" as described in the literature however excludes gamma radiation.

To return to your question, the problem is getting the light to site of infection. It is probably true that exposing one's self to UV will kill cells on your body surface albeit at a risk of inducing skin cancer, a well known side effect of UV exposure.

This type of exposure can safely be used to sterilize infected materials as opposed to skin.

There are commercially available safety hoods that do exactly this.

(Since I am well known for advocating for the use rather than dumping products in used nuclear fuel - so called "nuclear waste" - I note that gamma radiation, with its penetrating ability would certainly be useful for sterilizing the huge volume of biohazard waste this pandemic will generate. Unfortunately fear and ignorance associated with radiation has made this option viable at a tiny scale rather than the large scale it might have been useful to have.)

The tissue that is attacked by the corona virus is internal epithelial tissue, lung and airway tissue. Moreover, once a cell is infected, killing it will simply release more copies of the virus. It is simply not possible to get the light to the infected material. However if one has a UV lamp, it is probably the case that it can be utilized to kill the virus, although to my knowledge this has not been proved.

A common tool used in gamma radiation based "phototherapy" is to couple a radioactive atom, technetium-99m is a popular radioactive nuclide for doing this - to a protein that is known to bind to a particular receptor on, in the most common example, that is exclusive to cancer cells. (This is also done with chemical anticancer toxins bound to an antibody; where it is called an "ADC" - for antibody-drug-conjugate.) Designing drugs of this type can take many, many years, and in any case has not be used for infectious agents like viruses.

Thanks for your question; it's a good one.

[in2herbs]

3. Once I asked the ?? I began to think of how the UV light would get inside the body. You explained

this in your response while also bringing up a good point about treating the hazardous waste that is being created. UV light therapy might be effective on this waste -- at least in a home setting??

In addition to reading about CV, my horse has West Nile Virus and so I have been barnstorming my brain for his treatment as there is nothing out there effective against a virus if one stays only within the RX arena. But two days ago, I started him on colloidal silver and lysine which is a great herbal anti-viral. In 24 hours there was a slight improvement in his gait. Because he's a crippled rescue horse he's on pharmaceutical anti-inflammatories every day and I think that has been one reason his WNV is a mild-moderate case, but today I included devil's claw (an herbal pain reliever and AI) and he responded well. I'll keep working on it.

[intrepidity]

4. When you posted this, I wasn't questioningly the virus origin

However, recently I've begun to consider whether it could have been an accidental lab release. So far, I am not convinced, either way.

A hypothetical scenario goes like this: animal specimens are collected and brought into the lab. The typical experiments are performed, such that the various viruses are cultured and isolated and characterized. Careless handling of samples results in transfer to lab personnel. Lab personnel transfers non-lethal version of virus unknowingly to surrounding community, where the virus quickly mutates to the current lethal form.

Unfortunately, this paper relies on, (IMHO), a weak argument here: (bold mine)

Furthermore, a hypothetical generation of SARS-CoV-2 by cell culture or animal passage would have required prior isolation of a progenitor virus with very high genetic similarity, which has not been described. Subsequent generation of a polybasic cleavage site would have then required repeated passage in cell culture or animals with ACE2 receptors similar to those of humans, but such work has also not previously been described.

The scenario above that I proposed doesn't depend upon the publication of characterization of the virus that escapes the lab. I realize that the Nature paper must rely upon the literature to form it's argument, but reality doesn't.

The virus may well have mutated in vitro in the lab, even unnoticed and undetected by the lab, and still managed to escape.

Further, according to job postings that were seen in Nov and Dec 2019 from labs in Wuhan, there was active recruiting to work on characterizing novel bat viruses -- strongly suggesting that there were plenty of uncharacterized viruses in the lab.

Getting back to the knowns: there's a bat virus with high homology to SARS-CoV2, but it's RBD doesn't match. There's a pangolin virus with an RBD that matches, but the rest of the virus doesn't match as well as the bat virus does. Neither of those viruses have the polybasic cleavage site, nor the glycan feature (which presumably mutated within humans).

At this point in the story, it feels like a toss-up.

I think the only conclusion this paper can really make convincingly, is that the virus wasn't deliberately engineered.

But I can still see how it may have come from a lab.

I know zero about zoonotic dynamics, but what is the proposed sequence of events for an assumed wet market transfer? A bat infects a pangolin, which then ends up in a Wuhan market, where it infects humans?

Even if a bat infects a pangolin, the virus still needs to recombine with the pangolin virus to get the correct RBD. Or, do both viruses coexist in the pangolin and both infect the human, where the recombination then occurs? Are bats and pangolins living together naturally, or only in the wet markets?

I can envision all kinds of scenarios, but have no idea how likely or even possible they are.

There's just too much to know, sigh.

[NNadir]

5. In my opinion, you are making a common error that lay people make when reading scientific reports.

The error is to assume that a negative statement, usually a statement of uncertainty, suggests that the positive statement must be or is likely to be true.

The authors of this paper live in the world of molecular biology, with a focus on viruses. They are scientists who have been publishing widely on virology and epidemiology in very prestigious journals. The lead author, Dr. Kristian Anderson, is at Scripps institute, a world class research group. He received his Ph.D. at the University of Cambridge and did post-Docs at the three major research institutions in the Boston area, the Broad Institute, Harvard, and MIT.

Here is the web page of Dr. Anderson: Kristian G. Andersen, PhD

Now, it is possible for a excellent scientist to be wrong about something; the mark of an excellent scientist is often the willingness to express uncertainty, but I don't take this remark in the paper in quite the same way you do.

Here is how I interpret the remarks you put in bold...

Furthermore, a hypothetical generation of SARS-CoV-2 by cell culture or animal passage would have required prior isolation of a progenitor virus with very high genetic similarity, which has not been described. Subsequent generation of a polybasic cleavage site would have then required repeated passage in cell culture or animals with ACE2 receptors similar to those of humans, but such work has also not previously been described.

...I take this remark to mean, "...if someone engineered this virus, we would know about it, because we are experts in this field..."

What I view as your mistake is a common one. I have been known to have made it myself, many times, particularly in the period where I was less educated than I am now. We do need to exercise our critical thinking muscles, and doing so requires looking at both sides of an issue, but I think you are focusing on a "hole" that is not really all that big.

[intrepidity]

6. It's been several months now, but at least one published author shared my view

Do you find these authors to also be mistaken, I wonder?

I have not followed this topic closely recently, but apparently the question continues to remain unsettled and debatable.

https://onlinelibrary.wiley.com/doi/10.1002/bies.202000240

The genetic structure of SARS‐CoV‐2 does not rule out a laboratory origin

SARS‐COV‐2 chimeric structure and furin cleavage site might be the result of genetic manipulation

Rossana Segreto Yuri Deigin

First published: 17 November 2020

https://doi.org/10.1002/bies.202000240

Andersen et al.[2] also state that “subsequent generation of a polybasic cleavage site would have then required repeated passage in cell culture or animals with ACE2 receptors similar to those of humans, but such work has also not previously been described.” It should not be excluded that such experiments could have been aborted due to the SARS‐CoV‐2 outbreak, before a possible publication of the results or that the results were never intended to be published.

[NNadir]

7. You are, again, assuming that "does not rule out" is the same as "is."

There are, right now, literally, millions of papers being written on the origins of Covid. I encounter some from time to time, via email from announcements from scientific publications to which I subscribe.

Some are more convincing that others.

This paper is, in my view, an outlier.

The observed mutations in human populations, being covered all over the world, suggest that viruses mutate without manipulation.