A lot of people have been working really hard for the last year to discover, understand, and know these things. It’s the foundation for how the mRNA vaccines work.
I seems my intuition is well-founded here. According to Sarah Constantin the peptide here are selected in silico and not based on antibodies developed by infected people.
Sarah Constantin is confused, and likely has not spent significant time reviewing the vaccine design. From page 32 of the whitepaper:
“Empirical evidence should dominate selection criteria. Here are some best types of evidence:
Mapping of epitopes in blood and other samples collected from convalescent patients (ideally stratified by severity of illness). This can be accomplished by a few primary means:
3D structural studies and modeling of neutralizing antibody binding to a viral antigen (e.g. Spike protein)
Mapping of linear B-cell epitopes by binding antibodies in convalescent sera to a library of peptides representing viral antigens. A strong signal in a linear epitope mapping study does not guarantee that the epitope peptide in the context of a vaccine will trigger the production of an antibody that binds to this epitope within the context of the virus. However, it is a good indicator that this is at least possible. Peptides can be constrained to approximate native conformation, making it more likely to bind the native epitope.
Mapping of T-cell epitopes by stimulating convalescent T-cells with epitope peptides, and measuring their response (e.g. cytokine secretion; ELISpot)
Epitope peptides from a peptide vaccine that has shown protection against infection
Successful use of epitope peptides in vaccines that elicit antibodies (or serum) effective in virus neutralization assays. B-cell epitopes that allow antibody binding to the virus but don’t block viral function might increase risk of antibody-dependent enhancement.
Mapped epitopes that are effective in virus neutralization assays (e.g. peptides compete with viral sequences in cellular infection assays).
Successful use of epitope peptides in vaccines that elicit T-cell responses, or peptides shown to stimulate T-cells or cytokine production in ELISpot or other T-cell assay in cells from convalescents.”
Speaking about what are the best types of evidence is different from demostrating that this evidence exists for individual sequences.
If we start with the list the first is Spike 802-823cir. They provide no citations to papers for this and changed the structure in a way the believe to be benefitial (likely based on in silico modelling).
Spike 802-823cir: FSQ c LPDPSKPSKRSF c EDLLF ( Cys4, Cys17 disulfide) IN TESTING, vaccine Generations 5, 6, 7, 8. 9 To preserve the loop structure present in the native conformation, we substituted cysteines for amino acids 4 (Ile>Cys) and 17 (Ile>Cys).
They perform the substitution to keep the shape that our immune system is looking for by recreating a disulfide bond that to form a loop with the same sequence the B-cells are targeting in the virus.
While I agree their expression was “potentially beneficial” (or close) it seems clear to me the point was our B-cells are bonding to that loop and if there are not other aspect in the larger peptide that lead the cell to that site for bonding, construction the loop via the disulfide bond they introduce logically should result in triggering an immune response.
I’m not sure why they would need to provide some type of citation for this, much less that they would even have a source for this specific application.
The argument about the substition of the amino acids looks to me like it rests completely on in silicio modeling.
logically should result
That’s theory-based reasoning and not empirical evidence based. Sarah Constantin says that everything is theory-based reasoning (supported by computer modeling) and Dentin argues that they not only do theory-based reasoning but also have empiric evidence for individual peptides.
While it does seem there was a certain amount of shotgun aproach following a few different lines of reasoning, that critism is difficult to square with actually reading the paper. It looks like the peptide selection was largely empirical and cited. The decisions about how to actually package that info into a vacine is largely educated guesswork (as you say theory, supported by computer modeling).
“Mapping of linear B-cell epitopes by binding antibodies in convalescent sera to a library of peptides representing viral antigens. A strong signal in a linear epitope mapping study does not guarantee that the epitope peptide in the context of a vaccine will trigger the production of an antibody that binds to this epitope within the context of the virus. However, it is a good indicator that this is at least possible.”
Or as I understood from elsewhere: present antibodies from recovered people to every possible short peptide sequence and see which ones they actually attacked. Make the inference that people with less severe infection had better antibodies than those with more severe symptoms in the event antibodies differed. Package a selection of promising looking pepties into a vacine; choose enough that there’s likely multiple effective peptides even if 2/3rds of the choices are duds.
I also don’t understand her comments about the peptide ‘not neutralising COVID in cell [culture]’ - why would it? The peptide is just an antigen to get the body to raise an immune response; on its own it doesn’t kill COVID.
I was also confused about that. I’m sure some kind of cell-culture method is useful for testing vaccines, but I don’t know exactly what’s involved. Just culturing immune cells, maybe?
It’s my impression that the peptides in question are the antigens to those particular antibodies.
Yes; sorry I was unclear. Those peptides generate the antibodies we care about, that are known to be effective against the full virus.
It’s unclear to me to what extend we know this and your description looks to me like it asserts that we know things that are very hard to know.
A lot of people have been working really hard for the last year to discover, understand, and know these things. It’s the foundation for how the mRNA vaccines work.
Perhaps take a look through this:
https://www.sciencedirect.com/science/article/pii/S2319417020301530
I seems my intuition is well-founded here. According to Sarah Constantin the peptide here are selected in silico and not based on antibodies developed by infected people.
Sarah Constantin is confused, and likely has not spent significant time reviewing the vaccine design. From page 32 of the whitepaper:
“Empirical evidence should dominate selection criteria. Here are some best types of evidence:
Mapping of epitopes in blood and other samples collected from convalescent patients (ideally stratified by severity of illness). This can be accomplished by a few primary means:
3D structural studies and modeling of neutralizing antibody binding to a viral antigen (e.g. Spike protein)
Mapping of linear B-cell epitopes by binding antibodies in convalescent sera to a library of peptides representing viral antigens. A strong signal in a linear epitope mapping study does not guarantee that the epitope peptide in the context of a vaccine will trigger the production of an antibody that binds to this epitope within the context of the virus. However, it is a good indicator that this is at least possible. Peptides can be constrained to approximate native conformation, making it more likely to bind the native epitope.
Mapping of T-cell epitopes by stimulating convalescent T-cells with epitope peptides, and measuring their response (e.g. cytokine secretion; ELISpot)
Epitope peptides from a peptide vaccine that has shown protection against
infection
Successful use of epitope peptides in vaccines that elicit antibodies (or serum)
effective in virus neutralization assays. B-cell epitopes that allow antibody binding
to the virus but don’t block viral function might increase risk of
antibody-dependent enhancement.
Mapped epitopes that are effective in virus neutralization assays (e.g. peptides
compete with viral sequences in cellular infection assays).
Successful use of epitope peptides in vaccines that elicit T-cell responses, or
peptides shown to stimulate T-cells or cytokine production in ELISpot or other
T-cell assay in cells from convalescents.”
Speaking about what are the best types of evidence is different from demostrating that this evidence exists for individual sequences.
If we start with the list the first is Spike 802-823cir. They provide no citations to papers for this and changed the structure in a way the believe to be benefitial (likely based on in silico modelling).
Doesn’t this speak to your concern:
They perform the substitution to keep the shape that our immune system is looking for by recreating a disulfide bond that to form a loop with the same sequence the B-cells are targeting in the virus.
While I agree their expression was “potentially beneficial” (or close) it seems clear to me the point was our B-cells are bonding to that loop and if there are not other aspect in the larger peptide that lead the cell to that site for bonding, construction the loop via the disulfide bond they introduce logically should result in triggering an immune response.
I’m not sure why they would need to provide some type of citation for this, much less that they would even have a source for this specific application.
The argument about the substition of the amino acids looks to me like it rests completely on in silicio modeling.
That’s theory-based reasoning and not empirical evidence based. Sarah Constantin says that everything is theory-based reasoning (supported by computer modeling) and Dentin argues that they not only do theory-based reasoning but also have empiric evidence for individual peptides.
While it does seem there was a certain amount of shotgun aproach following a few different lines of reasoning, that critism is difficult to square with actually reading the paper. It looks like the peptide selection was largely empirical and cited. The decisions about how to actually package that info into a vacine is largely educated guesswork (as you say theory, supported by computer modeling).
“Mapping of linear B-cell epitopes by binding antibodies in convalescent
sera to a library of peptides representing viral antigens. A strong signal in a
linear epitope mapping study does not guarantee that the epitope peptide
in the context of a vaccine will trigger the production of an antibody that
binds to this epitope within the context of the virus. However, it is a good
indicator that this is at least possible.”
Or as I understood from elsewhere: present antibodies from recovered people to every possible short peptide sequence and see which ones they actually attacked. Make the inference that people with less severe infection had better antibodies than those with more severe symptoms in the event antibodies differed. Package a selection of promising looking pepties into a vacine; choose enough that there’s likely multiple effective peptides even if 2/3rds of the choices are duds.
I also don’t understand her comments about the peptide ‘not neutralising COVID in cell [culture]’ - why would it? The peptide is just an antigen to get the body to raise an immune response; on its own it doesn’t kill COVID.
I interpreted this to mean antibody against the peptide.
I was also confused about that. I’m sure some kind of cell-culture method is useful for testing vaccines, but I don’t know exactly what’s involved. Just culturing immune cells, maybe?
Do you have doubts? It seems plausible to me?