How?

Survive SARS a couple of decades before you receive the COVID vaccine.

...

[www.nature.com]

Decades-old SARS virus infection triggers potent response to COVID vaccines

People who were infected almost two decades ago with the virus that causes severe acute respiratory syndrome (SARS) generate a powerful antibody response after being vaccinated against COVID-19. Their immune systems can fight off multiple SARS-CoV-2 variants, as well as related coronaviruses found in bats and pangolins.

The Singapore-based authors of a small study published today in The New England Journal of Medicine1 say the results offer hope that vaccines can be developed to protect against all new SARS-CoV-2 variants, as well as other coronaviruses that have the potential to cause future pandemics.

The study is a “proof of concept that a pan-coronavirus vaccine in humans is possible”, says David Martinez, a viral immunologist at the University of North Carolina at Chapel Hill. “It’s a really unique and cool study, with the caveat that it didn’t include many patients.”

...The researchers suggest that such broad protection could arise because the vaccine jogs the immune system’s ‘memory’ of regions of the SARS virus that are also present in SARS-CoV-2, and possibly many other sarbecoviruses

...But the latest study doesn’t identify exactly which sections of the viruses induce the broad immune response, something that would be needed to develop vaccines. That’s the “biggest question”, says Martinez. If it is a region of the virus that is present not just in sarbecoviruses, but in the entire group of coronaviruses, there is potential for creating a vaccine against all of them, he says..

Used the Pfizer mRNA vaccine.

Lots more work to be done before this pays off. If it pays off.

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I keep hoping there was a beneficial reason for Moderna kicking my butt with vigor.

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=wr=

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The study is a “proof of concept that a pan-coronavirus vaccine in humans is possible”, says David Martinez, a viral immunologist at the University of North Carolina at Chapel Hill. “It’s a really unique and cool study, with the caveat that it didn’t include many patients.”

Not too many patients ever caught the original SARS in the 2000s, they were successful in containing it then.

Maybe this would also prevent a substantial fraction of common colds, since some of them are corona virus based.

That's a rough way to get super-immunity !

But... it does raise another interesting point. Suppose you were to make mRNA's from all the gene products made by SARS, and incorporate each of them individually into the vector they're using. Then you do a cocktail mRNA vaccination. While each mRNA will have to be at a lesser dose in the cocktail, you're effectively exposing the vaccine recipient to the SARS virus without actually exposing them to the SARS virus. If that works, and the SARS exposure really covers all the other major coronaviruses, then you've effectively eradicated SARS-CoV-2 and a bunch of the other, more mundane coronaviruses. (Of course, you could do the cocktail mRNA thing with SARS-CoV-2 itself, rather than SARS, but the argument they're making is that SARS is close enough to protect you against all the coronaviruses.)

While this may sound a bit farfetched, anyone who's done work in RNA, and RNAi specifically, can tell you that it's actually not that hard to simultaneously hit multiple targets at once. It actually works quite well, and I like the multitargeted approach, since we already know that this thing mutates its spike protein quite a bit.

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Freya says, 'Hello from NOLA, baby!' (Laissez bon temps rouler!)

Suppose you were to make mRNA's from all the gene products made by SARS

What kind of risk are you taking with this approach when you don't know the function of every gene product? I think it is naive to assume that not one of these gene products could interfere with normal mammalian cell biochemical pathways in unforeseen and detrimental ways, rather than just be expressed and secreted to generate an immune response.

I think it would be more advantageous to identify every protein structure in the viral envelope, make a variety of epitopes from short sequences, and test them as immunogens that can prevent infection of a variety of cell types.

Just my 2 cents.

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neophyte
Suppose you were to make mRNA's from all the gene products made by SARS

What kind of risk are you taking with this approach when you don't know the function of every gene product? I think it is naive to assume that not one of these gene products could interfere with normal mammalian cell biochemical pathways in unforeseen and detrimental ways, rather than just be expressed and secreted to generate an immune response.

I think it would be more advantageous to identify every protein structure in the viral envelope, make a variety of epitopes from short sequences, and test them as immunogens that can prevent infection of a variety of cell types.

Just my 2 cents.

True, though immunizing with all the gene products is more or less the same as giving a vaccine consisting of the inactivated virus ... something we've done for decades now with other vaccines.

Also, it does seem with the mRNA vaccine approaches, the antigen isn't being made or present for very long, maybe 24-48 hours max. That's why people are sometimes feeling sick as a dog right after they get vaccinated.

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Freya says, 'Hello from NOLA, baby!' (Laissez bon temps rouler!)

immunizing with all the gene products is more or less the same as giving a vaccine consisting of the inactivated virus

Respectfully, it is not the same at all, at least not without clarification. You originally stated "Suppose you were to make mRNA's from all the gene products". The presumed intent was to transfect all of these mRNAs into the host's cells, where they would be translated into (perhaps fully functional) proteins, which would be secreted to elicit an immune response. The unknown risk is when these functional proteins are still intracellular. Remember, the viral proteins are evolutionarily adapted to serve 2 main functions: hijack host cell machinery for replication, and assembly and secretion of infectious virus. If you put all the viral genome's mRNAs into a host cell, why wouldn't they make active virus?

Inactivated virus consists of chemical or heat-treatment to denature the proteins and nucleic acids that then serve as immunogens. Denaturing renders them not functional, and in addition they remain extracellular except when engulfed by immune cells for processing.

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neophyte
...Remember, the viral proteins are evolutionarily adapted to serve 2 main functions: hijack host cell machinery for replication, and assembly and secretion of infectious virus. If you put all the viral genome's mRNAs into a host cell, why wouldn't they make active virus?

Because they're not functioning as the genetic code for a virus.

A pile of sand and sodium carbonate doesn't spontaneously form glass.

You're talking about a bunch of stuff in solution together almost randomly distributed, and how your body makes proteins from them will be based on which bit of mRNA nearly randomly finds its way onto which ribosomes. The resulting proteins could cause allergic reactions or trigger an autoimmune response or act as enzymes and damage cells or they could just break down harmlessly so quickly that they don't help to generate an immune response. But they won't snag the mRNA from the vaccine and transform it into a virus. That's not how things work.

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neophyte
immunizing with all the gene products is more or less the same as giving a vaccine consisting of the inactivated virus

Respectfully, it is not the same at all, at least not without clarification. You originally stated "Suppose you were to make mRNA's from all the gene products". The presumed intent was to transfect all of these mRNAs into the host's cells, where they would be translated into (perhaps fully functional) proteins, which would be secreted to elicit an immune response. The unknown risk is when these functional proteins are still intracellular. Remember, the viral proteins are evolutionarily adapted to serve 2 main functions: hijack host cell machinery for replication, and assembly and secretion of infectious virus. If you put all the viral genome's mRNAs into a host cell, why wouldn't they make active virus?

Inactivated virus consists of chemical or heat-treatment to denature the proteins and nucleic acids that then serve as immunogens. Denaturing renders them not functional, and in addition they remain extracellular except when engulfed by immune cells for processing.

1) I think you're assuming that all the proteins will all be functional in the host cell. It's not clear they will be. For example, the spike protein currently being made by the mRNA vaccines is presumably not functional in human cells, but is nonetheless recognized as "foreign" by our bodies, and we make antibody against it.

2) Point taken that you might not want to use ALL the proteins, only a subset ... but remember that vaccination with attenuated virus does produce a useful host response, where the person is indeed being exposed to all the proteins of the virus.

3) Why wouldn't these proteins, when all put together, make active virus? Because the presumption is that a virus cannot simply self-assemble in a non-infectious context. Viral replication isn't just a matter of adding protein A to protein B to protein C and mixing them all together, and voila, you have a virus. (Remember, you also have to have some kind of nucleic acid...)

I think I was more thinking along the lines of attenuated, rather than fully inactivated, virus. That way you don't necessarily have denatured proteins.

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Freya says, 'Hello from NOLA, baby!' (Laissez bon temps rouler!)

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Sarcany

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neophyte
...Remember, the viral proteins are evolutionarily adapted to serve 2 main functions: hijack host cell machinery for replication, and assembly and secretion of infectious virus. If you put all the viral genome's mRNAs into a host cell, why wouldn't they make active virus?

Because they're not functioning as the genetic code for a virus.

A pile of sand and sodium carbonate doesn't spontaneously form glass.

You're talking about a bunch of stuff in solution together almost randomly distributed, and how your body makes proteins from them will be based on which bit of mRNA nearly randomly finds its way onto which ribosomes. The resulting proteins could cause allergic reactions or trigger an autoimmune response or act as enzymes and damage cells or they could just break down harmlessly so quickly that they don't help to generate an immune response. But they won't snag the mRNA from the vaccine and transform it into a virus. That's not how things work.

Mea culpa. I ignored that the fact that PeterB stated all the virus' mRNA, but did not include the long viral RNA that serves as the template for all of these.

However, SARS-CoV-2 does have an RNA-dependent RNA polymerase (which human cells do not), and if this enzyme can work in conjunction with an RNA ligase, longer RNA molecules with multiple coding regions might be formed. Subsequent packaging and export could lead to novel infectious agents. That's not a risk I would take.

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PeterB

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neophyte
immunizing with all the gene products is more or less the same as giving a vaccine consisting of the inactivated virus

Respectfully, it is not the same at all, at least not without clarification. You originally stated "Suppose you were to make mRNA's from all the gene products". The presumed intent was to transfect all of these mRNAs into the host's cells, where they would be translated into (perhaps fully functional) proteins, which would be secreted to elicit an immune response. The unknown risk is when these functional proteins are still intracellular. Remember, the viral proteins are evolutionarily adapted to serve 2 main functions: hijack host cell machinery for replication, and assembly and secretion of infectious virus. If you put all the viral genome's mRNAs into a host cell, why wouldn't they make active virus?

Inactivated virus consists of chemical or heat-treatment to denature the proteins and nucleic acids that then serve as immunogens. Denaturing renders them not functional, and in addition they remain extracellular except when engulfed by immune cells for processing.

1) I think you're assuming that all the proteins will all be functional in the host cell. It's not clear they will be. For example, the spike protein currently being made by the mRNA vaccines is presumably not functional in human cells, but is nonetheless recognized as "foreign" by our bodies, and we make antibody against it.

2) Point taken that you might not want to use ALL the proteins, only a subset ... but remember that vaccination with attenuated virus does produce a useful host response, where the person is indeed being exposed to all the proteins of the virus.

3) Why wouldn't these proteins, when all put together, make active virus? Because the presumption is that a virus cannot simply self-assemble in a non-infectious context. Viral replication isn't just a matter of adding protein A to protein B to protein C and mixing them all together, and voila, you have a virus. (Remember, you also have to have some kind of nucleic acid...)

I think I was more thinking along the lines of attenuated, rather than fully inactivated, virus. That way you don't necessarily have denatured proteins.

1) Spike proteins are not functional because the mRNA vaccines do not encode the entire spike, just a part that computer-generated models suggest is exposed and most likely to be immunogenic. During a COVID infection, the intracellular viral RNA is used as a template to make mRNA molecules that are translated into functional proteins. Why wouldn't introducing those mRNA molecules without the viral genome not make active proteins? We can transfect mammalian cells with mRNA in the lab and get functional proteins.

2) My point was an attenuated virus by definition has denatured (inactive) proteins that are only EXTRACELLULAR, except when engulfed by immune cells which in general have mechanisms that prevent detrimental effects of engulfed proteins (one exception of course is the AIDS virus which infects CD4+ T cells). Being extracellular, the denatured proteins cannot interfere with normal intracellular biochemical pathways.

3) You are correct, I neglected the fact that you stated all the virus mRNA, not its long RNA genome. Still, still see my response to Sarcany above, and my uneasiness with introducing an RNA-dependent RNA polymerase into a milieu with many other viral mRNA sequences. We don't know the entire repertoire of functions these mRNAs are capable of, but they are very good at using mammalian cell machinery to make copies of themselves. I would prefer not to give them an evolutionary boost.

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neophyte
However, SARS-CoV-2 does have an RNA-dependent RNA polymerase (which human cells do not), and if this enzyme can work in conjunction with an RNA ligase, longer RNA molecules with multiple coding regions might be formed. Subsequent packaging and export could lead to novel infectious agents. That's not a risk I would take.

So, in your mind, it's plausible that proteins somewhat randomly distributed in the human body will get together and assemble some 2600 (or so) genetic sequences and stitch them into a living virus?

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neophyte, I never mentioned *anything* about introducing any viral RNA (or DNA), only the mRNAs that encode the viral proteins, which isn't the same thing ... particularly because, as you point out, the mRNAs are often highly modified before they're put into the mRNA vaccine vectors.

My aim in suggesting this was to accomplish pretty much the same as exposing someone to a vaccine containing all the viral proteins (but none of the viral genetic material), which I think we could all agree is probably pretty safe -- assuming someone doesn't have an allergic reaction to the viral proteins. (And this is already in the pipeline anyway, there are a couple of vaccines which are protein-based, like the Novavax.) The likelihood that a viral RNA-dependent RNA polymerase could convert one or more of the viral mRNAs into a functionally replicating viral genome is pretty slim, I'd think.

Edit: oh, and likely that a viral RNA-dep RNA Pol is very likely to be seen by the human immune system as "foreign", just like all the other proteins, and antibodies would be made against it. NOT a bad thing, since I think it's a good thing that we target the other viral proteins and not just the spike.

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Freya says, 'Hello from NOLA, baby!' (Laissez bon temps rouler!)



Edited 2 time(s). Last edit at 08/22/2021 05:19PM by PeterB.

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Sarcany

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neophyte
However, SARS-CoV-2 does have an RNA-dependent RNA polymerase (which human cells do not), and if this enzyme can work in conjunction with an RNA ligase, longer RNA molecules with multiple coding regions might be formed. Subsequent packaging and export could lead to novel infectious agents. That's not a risk I would take.

So, in your mind, it's plausible that proteins somewhat randomly distributed in the human body will get together and assemble some 2600 (or so) genetic sequences and stitch them into a living virus?

Of course not.

I have explicitly stated that these viral proteins are expressed INTRACELLULARLY where they are quite functional as demonstrated by the widespread pandemic. As you know, the IM injection of lipid-encapsulated mRNA molecules encoding segments of spike proteins leads to the fusion of the lipid particles with a host cell (most likely a muscle cell via the IM route), where the mRNA is dumped INTO the cell and is translated into a spike protein segment which is exported (secreted) to an extracellular space where immune cells encounter it and an immunological response is initiated. In PeterB's OP, he speculated about using ALL of the virus' mRNA (encoding ALL of its genome as separate units) to use as an immunogen instead of just the mRNA encoding a segment of spike protein.

Thus WITHIN A SINGLE CELL, all of these genetic sequences, including an RNA-dependent RNA polymerase, will be present, in multiple copies. Although the entire viral RNA genome is not present as a single long strand, its components are present and need only be ligated together and packaged to create a potentially infectious agent. And the RNA-dependent RNA polymerase will ensure many copies are available. Will ligation occur? I don't know, but it seems unwise to rule it out. After all, splicing of nucleic acids occurs in many forms, and ligation is half of that process.

Some mammalian cells already have some viral gene sequences that are expressed (for example, look up intracisternal type A particles (IAPs)). It seems unwise to add an entire, ACTIVE viral genome to a cell simply to try to generate a suitable antigen.

Why should the genetic sequences from the virus assemble in the same order as they do in the virus?

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Why should sequence order matter? Translation of an RNA sequence only requires a binding site for the ribosomal machinery. The long, native viral sequence has many such sites, so many different genes can be expressed at the same time regardless of position along the strand.

I'll grant that if the native viral sequence has overlapping ORFs that make different proteins required for proper viral function, then recreation of these ORFs through simple ligation of mRNA sequences will be rare. But impossible? And how can we be sure that there are no other cellular proteins that are normally expressed that are capable of performing the same function as the missing proteins?

To go back to your analogy: A pile of sand and sodium carbonate doesn't spontaneously form glass.

PeterB's concept is like putting sand and sodium carbonate into a reaction vessel containing some unknown activation energy and assuming that no glass will form.

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PeterB
neophyte, I never mentioned *anything* about introducing any viral RNA (or DNA), only the mRNAs that encode the viral proteins, which isn't the same thing ... particularly because, as you point out, the mRNAs are often highly modified before they're put into the mRNA vaccine vectors.

My aim in suggesting this was to accomplish pretty much the same as exposing someone to a vaccine containing all the viral proteins (but none of the viral genetic material), which I think we could all agree is probably pretty safe -- assuming someone doesn't have an allergic reaction to the viral proteins. (And this is already in the pipeline anyway, there are a couple of vaccines which are protein-based, like the Novavax.) The likelihood that a viral RNA-dependent RNA polymerase could convert one or more of the viral mRNAs into a functionally replicating viral genome is pretty slim, I'd think.

Edit: oh, and likely that a viral RNA-dep RNA Pol is very likely to be seen by the human immune system as "foreign", just like all the other proteins, and antibodies would be made against it. NOT a bad thing, since I think it's a good thing that we target the other viral proteins and not just the spike.

I admitted that I overlooked that the entire viral RNA genome was not in your OP. But you did not state that "modified" mRNAs would be involved, rather you stated

"mRNA's from all the gene products made by SARS, and incorporate each of them individually into the vector they're using. Then you do a cocktail mRNA vaccination."

And you really think ONLY a SINGLE vector will enter a SINGLE cell? More likely, MANY different vectors will enter a SINGLE cell. Surely you have performed transfections of cultured mammalian cells and found that many cells receive no nucleic acids while some receive a high load.

So is this not functionally the same as putting many native viral sequences without overlapping ORFs and untranslated sequences into a single cell? Wouldn't many viral gene products then be expressed within the same host cell?

I agree that a more conventional protein vaccine would be more acceptable, and was indeed hoping the Novamax vaccine would be approved sooner. I wanted to volunteer for the clinical trial for it but the closest test site was more than 200 miles away.

"Edit: oh, and likely that a viral RNA-dep RNA Pol is very likely to be seen by the human immune system as "foreign", just like all the other proteins, and antibodies would be made against it."

The viral RNA-dep RNA Pol is initially made, and functions, within the cell. How would the human immune system see it there and respond to it before the cell lyses? Sure, once lysis occurs you would get an immune response to it, but by then it is too late. And any other cell that contains the viral RNA-dep RNA Pol is similarly not subject to attack by the immune system absent any surface expression of that protein.

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neophyte
Why should sequence order matter? Translation of an RNA sequence only requires a binding site for the ribosomal machinery. The long, native viral sequence has many such sites, so many different genes can be expressed at the same time regardless of position along the strand.

As an example...

The location of surface proteins determine whether a virus can effectively penetrate a cell, hide from the immune system, evade vaccines. Proteins determine the shape of the virus, the utility of the viral envelope, its ability to hijack the host's gene transcription processes.

Create a "virus" with its proteins in the wrong order and arguably you have no virus at all because it will be unable to reproduce.

The genetic sequence of the "virus" will determine which proteins are expressed and where. Mess with that and you don't have a "virus." You might have interesting fragments that will in all likelihood be destroyed rapidly either in the cell's cytoplasm or once out of it.

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Sarcany

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neophyte
Why should sequence order matter? Translation of an RNA sequence only requires a binding site for the ribosomal machinery. The long, native viral sequence has many such sites, so many different genes can be expressed at the same time regardless of position along the strand.

As an example...

The location of surface proteins determine whether a virus can effectively penetrate a cell, hide from the immune system, evade vaccines. Proteins determine the shape of the virus, the utility of the viral envelope, its ability to hijack the host's gene transcription processes.

Create a "virus" with its proteins in the wrong order and arguably you have no virus at all because it will be unable to reproduce.

The genetic sequence of the "virus" will determine which proteins are expressed and where. Mess with that and you don't have a "virus." You might have interesting fragments that will in all likelihood be destroyed rapidly either in the cell's cytoplasm or once out of it.

The location of surface proteins determine whether a virus can effectively penetrate a cell, hide from the immune system, evade vaccines.

True enough, but this relates to overall virus morphology, which is created during viral assembly. And viral assembly is not like erecting a building where you have to build the first floor before you can erect the second floor. All the surface proteins must be present and embedded in the lipid membrane when the virus is released in order to make infectious particles. Where along a single RNA strand a particular gene is located has little consequence, as long as it is translated.

Proteins determine the shape of the virus, the utility of the viral envelope, its ability to hijack the host's gene transcription processes.

True enough, but the proteins responsible for the hijacking are most likely within the viral capsid and not membrane bound because they must act within the host cell, not at the cell surface. Again, they merely have to be present at the viral assembly stage in order to create a virus capable of reproduction and assembly.

The genetic sequence of the "virus" will determine which proteins are expressed and where.

Again, true. But SARS-CoV19 is a single-stranded (sense) RNA virus, so translation signals are all that are required. If you put an AUG start sequence in an RNA strand it will be translated into a protein by the cell's machinery, regardless of whether the resulting protein has any function or not. Again, exact position along the genome is not critical; a single strand can have multiple ribosomes "travelling" along the strand, each translating and making a protein simultaneously with the others.

The SARS-CoV19 genome is only about 30,000 nucleotides, encoding something like 11 (?) genes or so.

It still seems risky to me to potentially put all of those genes into a host cell just to hopefully make an immunogen. We don't fully understand the entire nucleotide "manipulation machinery" within a mammalian cell, and from what I personally understand, it is well within the possibility that such an action could result in the production of an infectious virus. This is my point.

neophyte, my point was that putting all the viral mRNAs into a host cell is not likely to generate any infectious virus, because you're basically just exposing the person's body to a number of foreign proteins ... it's essentially taking the mRNA vaccine tech we're using now, and simply expanding it to proteins other than just the spike. A lot of viral proteins being expressed within the same host cell is fine, it's what you want in fact, because it'll trigger the body to think that there's a viral infection (when there isn't one) and generate antibodies against the proteins. Those cells will then likely get killed, just as they are presumingly getting killed by cells that express the spike protein as an antigen.

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Freya says, 'Hello from NOLA, baby!' (Laissez bon temps rouler!)

...putting all the viral mRNAs into a host cell is not likely to generate any infectious virus, because you're basically just exposing the person's body to a number of foreign proteins

Please define "because you're basically just exposing the person's body to a number of foreign proteins"

Putting multiple viral-derived coding sequences INSIDE a cell so that they can be translated, as well as possibly be manipulated/spliced/altered/recombined by the cell's own nucleic acid manipulating machinery (as well as by the viral encoded proteins) is MUCH MUCH MUCH different than vaccination with a denatured protein delivered EXTRACELLULARLY such that a variety of immune system cells will encounter them, process them, and generate an immune response to them.

You must know that mammalian genome, including our own, is littered with viral sequences, most thought to be inactive (i.e. not expressed) because of mutation. Yet some undoubtedly are, if the Syrian hamster model can be used as a model (see [pubmed.ncbi.nlm.nih.gov], I am a coauthor). I would just as soon not risk the introduction of ALL, or even MOST, of a viral genomes' coding sequences for the sole purpose of hopefully creating an immunogen. The current use of an mRNA encoding a single, truncated sequence has proven to be very effective, and the truncated protein that is expressed is not functional (functional being defined by its inability to mimic the function of its full length version), but serves quite well as an immunogen.

I return again to your phrase "not likely to generate". Respectfully, I would not risk using your approach because I think your "not likely" is actually more likely in unforeseen ways than you have yet to appreciate.

I'd say the issue here is what would be required to generate a viable multi-partite version of SARS-CoV19.

(see "The Strange Lifestyle of Multipartite Viruses"
[www.ncbi.nlm.nih.gov] )

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Janit
I'd say the issue here is what would be required to generate a viable multi-partite version of SARS-CoV19.

(see "The Strange Lifestyle of Multipartite Viruses"
[www.ncbi.nlm.nih.gov] )

Thank you Janit. I have been out of the academic research field for a while now and was unfamiliar with mutipartite viruses.

Unforeseen ways indeed.