COVID-19 , immunity

[gsgs]

recent remarks by jjackson about reinfection and immunity , Oct.2020
================================================== ==================

I would be shocked if the reason the reinfection was not as mild
was due to either higher initial viral load or a different phenotype.
The viral load generated by in host replication will quickly swamp
what ever viral load there was at infection and there is no record
of any other circulating phenotype.
Obviously the first infection did not provide sterilising immunity
but may well have induced an immune response that kicked in hard
and fast second time around. Without further details of what
happened next in this patient's second infection it is difficult
to attribute a mechanism. Did he quickly clear the virus or did he
go on to get seriously ill? If the former then the fast immune
response releasing lots of inflammatory cytokines fits but if
the later I would be looking for residual damage from the first
infection leaving him more vulnerable to infections generally.

---------------------------------------------------------------

I think initial viral load is very important. (That's why COVID parties
are a bad idea even for young people and why even sub-N95 masks can
reduce severe illnesses in certain high-risk circumstances.)
The research about ultimate viral load and outcomes seems to have
more conflicting research right now. I think that is what you are
thinking about.

------------------------------------------------------------

Emily as the article at
https://www.medpagetoday.com/infecti.../covid19/88692
points out this is one competing hypothesis.
It goes on to show a correlation between high viral loads and disease
outcome but this is not high initial viral load but peak viral titers
which will have much more to do with how well the immune system is
handling the infection. In this disease, for most patients, they have
little or no replicating virus when they are most ill, they are dealing
with the immune dis-regulation and damage caused by it.
PCR readings for patients who are infectious are of the order of
1million RNA matches, to the probe, per ml of swab.
I have difficulty seeing how the tiny quantity of initial innoculum
can have any bearing on this unless everybody's immune response is
identical. Fortunately we are all different.
COVID parties are definitely a bad idea, and will lead to more illness,
but I do not think it will make any difference to the illness severity
spectrum which will match the age and comorbidity profile of the partygoers.
If you have seen any data showing otherwise I would be keen to have a
look if you have links.
The use of the term Variolation in this article is misleading as it is
to do with introducing the virus into a part of the body that does not
have many cells the virus can attach to and infect but does allow
immune cells to interact with it and prime the immune system against
reinfection. https://en.wikipedia.org/wiki/Variolation

--------------------------------------------------------

gs
In answer to your droplet vs aerosol question the short answer
is I do not know.
The long answer goes back to your 'complicated fight' which has far more
moving parts to it than my simplified comment. In the evolutionary arms
race between host and pathogen many measures and countermeasures and
counter-countermeasures have been evolved. For example flu has a -ssRNA
genome and negative sense RNA is not produced by the host so there is a
mechanism to detect -RNA in cytoplasm and destroy it.
CoVs have +RNA which there is plenty of in the cell as it is produced
as mRNA in transcription. mRNA is short, compared with vRNA
(nearly 30,000 bases for CoVs), so that host cells have developed two
trans-membrane proteins such that if the RNA is long enough to stretch
between them it turns on a pathway that leads to the translation of a
protein to chop it up. There are lots of other defense mechanisms and
it will also need to produce a protein to let it breach the nuclear
membrane as the vRNA is too big to use the nuclear pores.
From the cells point of view it will immediately start ramping up
interferon production and releasing it (INF is normally retained
in the producing cell) so neighboring cells can detect it and start
shifting transcription to defensive proteins.
The cell also starts making MHC class 2 proteins and inserting them
in the cell wall (normally cells, apart from some immune cells,
do not have class 2) which display peptides that can be detected
by T cells and mark the cell for destruction by CD8 cells.
From all of this if a cell gets a low viral load it may be longer
before it is detected and the cell's response will be dose related
i.e the more copies detected the faster and more aggressive the response.
A rapid response at a point source may be less of a problem to deal
with than lots of dispersed low level warnings any one of which that
got control of the cell could rapidly produced lots of infectious virions.
There are some interesting advances in microfluidics that allow the
placing of one cell in each of many wells which can then all
be infected and there are vast differences in the rate at which
disease progression occurs between the wells.
Normally in a plaque assay you can not observe this as you only see the
net effect.

Edit. On re reading this I note that I did not explain the relevance
of the microfluidics. The cell placed in each well are the same
(Vero cells or similar) and they all get a similar initial viral load.
New virus produced by any of the wells stay in that well and can not
infect others in the well grid.
When looked at under the microscope most of the single cell wells
develop disease but at wildly different rates.
In vivo, if you get the same behaviour, the same amount of virus
infecting lots of separated cells will elicit some that handle the
infection well and some that get immediately overrun.
With our current technology finding out exactly how each of these
battles played out is still out of reach.

------------------------------------------------------

A science journalist has very kindly been providing TWiV with expanded
bullet points, in English, from Christian's Das- Coronavirus podcasts.

https://www.microbe.tv/das-coronavirus/

The paper being discussed
https://www.medrxiv.org/content/10.1...896v1.full.pdf
looks at the accumulation of relatively broad acting low avidity T-Cell
accumulation with age. The mechanism by which B cells produce
antibodies (and a very similar mechanism in T-cells although they do
not release their antibody equivalent protein but retain it trans-membrane)
is one of the great marvels of evolutionary biology and a fascinating
study in its own right.

[gsgs]

from NDR-Drosten podcast #58
an English summary is also at https://www.microbe.tv/das-coronavirus/

------------------------------------------

(part 2 , pages 10-14 in the German skript)
CROSS IMMUNITY AGAINST SARS-COV-2?

Korinna Hennig
That means there are also losses of effectiveness because of the
Response is so broad. So the reaction can
do not do that much, because like a water
beam from the watering can goes wrong a lot,
figuratively speaking.

Christian Drosten
You could say that, but I wouldn't
interpret so far. You don't even have to say: there
something has been lost. One can simply say:
That's just a fragmentary response. And now
one can also go further. One can go to
Example say: Then let's take away from ourselves
Patients - whether SARS infected or not SARS-
infected by some people - the T cells out,
those against the proteins of the cold coronaviruses
react. Now let's not test against the SARS
2 virus, but we test against cold corona
viruses. And what we see here is interesting. So
when we prepare these cells - I'll say that now
so therefore, this is really high-tech, it is a lot
high analytical art of doing that in the laboratory ...
So what the authors did is: Prepared
T cells that react against this cold coronary
aviruses and they tested them again in yours
Responsiveness. Then, interestingly, you see:
There is a cross-reactivity, each from
one alphacoronavirus to another alphacoronavirus
rus. So the human coronavirus 299E reacts
cross against the human coronavirus NL63. And
This also exists within the beta coronaviruses. So
the human coronavirus OC43 reacts crosswise
against the human coronavirus HKU1, but not
between alpha and beta coronavirus, not between
the genera. That said, these viruses are apparently
so far apart that there is no real one
relevant cross-stimulation or cross-activation
activity And interestingly, there is this cross activity
against the SARS-2 virus at all.

Korinna Hennig
Neither of the two.

Christian Drosten
I agree. This is exactly what I call
Virologist can now judge well, namely how far
these viruses are each distant from each other in their
Degree of relationship. And there is the SARS virus, that
is also a beta coronavirus, but it is very much
far outside. Genetically we would say that is
a basal beta coronavirus from the perspective of these two
Viruses. That is roughly the same distance from everyone
that is equidistant. I explain this to students
always happy with geographic examples. That would
like saying Mainz and Cologne are both
in West Germany and distinguishable from one another
other away, you have to go a long way
drive. And now one would say that Cologne is in northern
Rhine-Westphalia and Mainz it is in Rhineland-Palatinate,
these are two different federal states. But
Bielefeld is also in North Rhine-Westphalia. And now is
but not so necessarily that one would say ...
So it's true, Bielefeld is definitely closer to it
Cologne, but that's pretty far away.
It's almost equidistant from both, even if we are
have to admit, it is closer to Cologne. But
it's both quite a drive. No matter if we
drive to Cologne or Bielefeld. That's a little
this proportionality. So the SARS-2 virus is there
Bielefeld and these beta corona viruses, i.e. OC43 for
Example that would be Cologne and it is an alpha coronavirus
Mainz. So you can imagine it a bit
from the degrees of distance.

Christian Drosten
Yes. There are actually even then superordinate
similarities that cannot be explained geographically,
such as the carnival. But now we will
very entertaining here.

Korinna Hennig
It also has a meaning in the infection process.
hen had. But we're not pursuing that any further now
at the point.

Christian Drosten
I agree. To come back to that
real problem: we can use this
Appreciate a finding very well that it is true
apparently little real cross-reactivity, cross-
protection against the SARS-2 virus. And we can
do another countercheck. We can also
prepare the cells again from SARS-2 patients
and that stimulate again against this human
Viruses, against human cold coronaviruses and
also against control viruses. And what we see is: The
Stimulation is relatively bad anywhere. That is too
about as bad as against ... So if we
SARS-2 has been through is knowledge or who
Activation of these cells, which we then fight against
human coronaviruses are relatively bad.
And it's actually not much better than
against influenza. So that's all in the range of
Noise background. None of that really has anything to do with it
to do with the viruses that we are even examining here.
In other words, it is highly unlikely
that there is something like a real cross protection
gives.

Korinna Hennig
This background immunity that many have hoped for
have.

Christian Drosten
I agree. We can probably tell what one
in these studies is not a cross
immunity, but only one cross-activation, one
Cross-reactivity, whatever you want in words
like to express. So the cells can
Signal, but that is certainly not strong and active
enough to really keep an infection out
the body. So we probably can't
really speak of immunity. And this is
of course now here is an individual finding in this study.
Other studies have to come to that further
interpret. And the authors avoid this too
very good and very careful. All of that means by the way
also not at all that survived by one
Infection with SARS-2 no cellular immunity
stands. We haven't checked that here at all,
it's just about cross-activation.

Korinna Hennig
So I hold on tight: the hope that I
when i went through a lot of colds and there
the common corona viruses were also among them, relatively
I am protected from infection with the coronavirus,
that is, to put it mildly, possibly
unfortunately off the table.

Christian Drosten
So "off the table" is not careful enough to formulate
lates. I would say it more carefully. The
Authors of the study also formulate this more cautiously.
But unfortunately it's just that hope is now
already a bit dwindles to the fact that one is fundamentally
in addition, a population-wide effect in this
Has direction.


DOES A STRONG IMMUNE SYSTEM HELP ?

Korinna Hennig
The other part that you already hinted at is
but now that of the cellular immune response, which is strong
fails and is accompanied by a severe course.
So this untargeted position of the immune
systems, that actually sounds like an advantage, first
once, thought from the common sense. The immune
system reacts, it immediately goes into fighting stance.
Is that actually a disadvantage?
so this unspecific reaction of T-memory
cells?

Christian Drosten
Yes, so what was done here in the study,
after it was noticed that it was too
this incomplete, unclean way of reacting
T cells exist and that they can be measured well here
can with these laboratory tests, one has also
looked at how it is actually with patients who
have had this disease, the SARS-2
Infection, and then either harmless or
had a severe course. You can do that in this one
Divide into two groups. And there you can see
another interesting additional finding.
I can from this whole department of this investigation
only briefly mention individual findings.
For example, what you can see is that the patients
which had a difficult course, actually like that
have an improper response. So also those
when exposed to the protein fragments
from the SARS-2 virus, they don't react so nicely
clean with the signal on these structural proteins,
but they need a relatively large number of fragments, protein
fragments from other pieces of the virus to still
react cleanly to make a good signal
although they are already reacting strongly overall, so
after the infection, these memory cells are already there
available. There are many, there are many cells
measure up. So there is a lot of signal, but that
Pattern of this reaction is not as clean as at
those who had mild courses.
And that can now be done with further laboratory tests
underpin. For example one can look at
like the diversity of T cells in theirs
Transcription pattern is. So this is a character
the general metabolic activity
RNA level. And on this basis you can create patterns
recognize the specific functional units of
T cells that are descended from each other, we speak
of clones, make them identifiable. And there you can
tell the patients with a severe course that
have a relatively colorful one after an infection
Image. So they have, they say a polyclonal one
Situation, i.e. a high degree of diversification of existing
those T cell cloning, while the patients who are mild
had a very severe course after the infection
strong clonality. You can also see CD8 clones very nicely
the real effectors of the cellular immune
systems that attack infected cells, such as
one imagines where one is really very targeted
engages with the T cells while purposefulness here
just not that great with those who are serious
Had gradients.
Now, of course, it's like this: This untargeted reaction
pattern, this is more common in patients who
such characteristics of an aged immune system
to have. Logically, that happens more often
old people, in patients who are older. But
the real determinant is precisely this measure of the
Immune age in the laboratory test, which one actually
correlated. So if you, in other words, very
has a lot of memory T-cells, so if you have a
has a broad T-cell memory and less
naive T cells, then you may not be in that
Able to have new immunoreactivity and new ones too
Build up immune memory compared to someone
the one who still has many naive T cells, a young one
Immune system. It is rather targeted against this
Virus build up a new immune memory while
an older person may fall back on old experiences,
which are not always correct, based on old immune
gen, and then generates a scattered response.

Korinna Hennig
But that fits in with the observation that younger people
People, if they belong to the risk group,
are more at risk. So when I'm younger, but one
Got over cancer or another
If you have chronic illness then the condition could be
my T cells are at risk of severe disease
represent, right?

Christian Drosten
Yes, that's an interesting, good thought in principle.
But I definitely don't want this to be done on any individual
Break down diseases. Because the immune
diseases that fall into this and the other
Direction off. But if you basically have one
pre-aged T-cellular system would have where one
has fewer naive cells, more memory cells in the
Proportion, then that might also be predictive for
a more difficult course, so a not so targeted one
Opportunity to react, a not so good then too
later building up memory.

Korinna Hennig
But as a rule an immunological one goes higher
Age often at least with the biological height
age of the person.

Christian Drosten
Right, that goes hand in hand, of course, that is very clear.
Only here was really the first time in this study
carefully looked at cause and effect. There is
it is so that the real cause is not
is the pure biological age of the patient, rather
a very strong component in the cause of one
severe course in the immune age.


WHAT DO THE FINDINGS MEAN FOR
THE VACCINE DEVELOPMENT?

Korinna Hennig
Can we use this finding about the T cells,
who react differently, derive insights,
possibly, or new questions for the
Development of vaccines and therapeutic
Medication?

Christian Drosten
Yes, sure, you can definitely do that. The
T cells are absolutely essential. And we want exactly
do that with such a vaccination, an immune
trigger memory, create so the immune system
then is prepared for it. That's exactly what we do
want. So we want memory cells there
are both CD8 and CD4 memory cells, and
Of course, memory cells in the B-cell area as well.
And then we want to get antibodies out of that
B-cell area, getting a cellular response out
the CD8 T cell area and then a helping one
Effect from the CD4 memory area. And this is
for example often a groundbreaking effect. So
there are CD4 cells that have an immune memory
and they then tell the CD8 cells: You have to go to them
Lungs, you don't have to be floating around somewhere
whole body, but this virus, you will
see in the lungs. That would of course also be
good if you put a vaccine like that in your lungs
so that this site-specific immune
memory also forms. And put one in the lungs
Vaccine not so easy, but in the nose it is. And
this is not the first vaccination in the future vaccination
generation, they won't do that yet. There is
usually intramuscular injections. But
it is already anticipated that one will go to
Example makes a vaccination so that you can
Putting the vaccine up your nose instead of injecting it. And
that the information can then also be sent there locally
suggests that this virus is found in the respiratory tract
and that there are certain memory lymphocytes
which then direct the immune response towards the airways
conduct. So these are the things that really happen
also in vaccine development.
And with the vaccines that are now coming
men ... I think we need to get into vaccines
keep talking about the next podcast episodes,
because this vaccination issue is also luckily coming
comes. Luckily there will be vaccines soon, hopefully
very soon. But 'very soon' in this case means
just still that it's been a few months.

Korinna Hennig
And not the first vaccine brings the
fracture.

Christian Drosten
Probably not in that sense. So not in
the sense of sterile immunity. So not how
in measles - a vaccination and immune and lifelong
you will never get infected again - it will be that easy
not be that. You will surely be against
the severe symptoms are protected, but not
against a somewhat superficial cold,
which you might get through the virus
can be imagined.
And there are vaccines that are stronger
against the induction of a cellular response
the virus designed. And others are much stronger
designed for a good neutralizing antibody response.
You will have to take another look at how
well then there is one at the level of the CD4 cells
applied immune memory is formed. The
will certainly not be the same with all of these vaccines
be strong.

Korinna Hennig
Finally, Mr Drosten, the question - because we are now
last about immunological age and biological
Alter spoke: How important is it that
elderly people in these vaccine studies
men? And to what extent is that possible? There is a
current study in "JAMA Internal Medicine", which says
they are underrepresented in many studies.

Christian Drosten
Yes, that was probably the case at the beginning, that
is actually quite natural. Vaccines will be
first of all evaluated in such a way that one is under the
Prerequisite works, they might not be able to do that well
that might have side effects.
So it is clear what kind of patient you are going to start with
times includes in the studies: as healthy as possible
young people, of course no children either, but just
Adults who do not have diseases. Only it is
yes, already clear to all vaccine manufacturers who do
that is not completely blind and without thinking about it-
think about who already all know that at the beginning of the
There is not enough vaccine availability at first
Vaccines will be there ... They also know exactly
because it probably isn't that the vaccines
will be absolutely perfect: in the first generation
the vaccines will try to identify groups of indications
preferred to vaccinate. That also includes
the older. That's why it is certainly the same without
that I now know this in detail, I would now
say in most or even all of the major now,
ongoing phase three studies will then gradually and
after including elderly patients.
Otherwise you can't actually do it for this one
older populations.

=============================================

SOURCES
Meta study on infectious mortality:
https://www.medrxiv.org/content/10.1...895v5.full.pdf
JAMA Pedriatrics: Comparative Study on Children and
Adult:

https://pubmed.ncbi.nlm.nih.gov/32975552/

Study on the importance of T cells and the question of
coronavirus cross immunity:
https://www.medrxiv.org/content/10.1...896v1.full.pdf
Study to consider the elderly
Vaccine Studies:
https://jamanetwork.com/journals/jam...rticle/2771091
Validation of the PCR test:
https://www.eurosurveillance.org/con...#html_fulltext
GLOSSARY
You can find explanations of the technical terms here:
ndr.de/coronaglossar
ADDITIONAL INFORMATION
ndr.de/coronaupdate
PODCAST TIP
Synapses: Science in the new podcast
ndr.de/synapsen
eat.READ.sleep. - books for you

https://www.ndr.de/eatreadsleep

Both podcasts are of course available in the ARD audio library.
Coronavirus disease (COVID-19)
Get the latest information

------------------------------------

A science journalist has very kindly been providing TWiV with
expanded bullet points, in English, from Christian's
Das- Coronavirus podcasts. https://www.microbe.tv/das-coronavirus/
The paper being discussed
https://www.medrxiv.org/content/10.1...896v1.full.pdf
looks at the accumulation of relatively broad acting low avidity T-Cell
accumulation with age. The mechanism by which B cells produce
antibodies (and a very similar mechanism in T-cells although they do
not release their antibody equivalent protein but retain it trans-membrane)
is one of the great marvels of evolutionary biology and a fascinating
study in its own right.

[JJackson]

I found the translation a little hard to follow but the first section looks at cross reactivity to the four seasonal flu CoVs.
What they found was a little cross reaction but not enough (see edit) to have any real effect on a SARS infection.
In the second section he is explaining that as you age you produce fewer naive T-cells (these are cells that have not differentiate to be specific for any particular peptide). This leaves the older patient with many targeted cells from past infections which, if they show any reactivity with SARS peptides, may start ramping up production of a badly targeted response and less naive T-cells that are free to develop in to SARS-CoV-2 specific T-cells.

The vaccine section then looks the likely response and he looks at the different levels of T-cell targeting between severe and mild cases. This probably needs a little background to understand this differentiated response. In a mild infection there will not be as much cell damage and death so the dendritic cells, which collect peptides and take them to the thymus, will be presenting more external and structural protein fragments to the B & T cells than in a severe infection. In the more severe case many infected cells undergo apoptosis and release their contents, which will include a lot of non structural protein peptides, causing the naive B and T cells to be primed to these. This is not so useful, particularly in the case of B cells, where you want not just anti-bodies to everything but targeted to epitopes exposed on the outside of the intact virion and preferably to a part of it that when bound blocks cell entry and gives sterilising immunity. The vaccines are unlikely to provide sterilising immunity or very long lasting immunity but should, hopefully, provide a much milder pathology. One problem with this is that on infection the vaccinated may still be shedding virus and capable of infecting others without showing much, or any, symptoms themselves.

I have written more about immunology here and here the second of these was written in 2008 so is looking at H1N1 not SARS-2 but the immunology has not changed.
And found these useful in learning.
T cell differentiation https://www.youtube.com/watch?v=JeV-HuPq7CI (I find the presentation style a bit annoying but it is clear and covers everything well)
Innate immune system ( https://www.youtube.com/watch?v=F9TClYS_Ch0 ) & Adaptive immunity ( https://www.youtube.com/watch?v=28gIJ2rrN7I ) these are targeted at Virology undergraduates so keep it fairly short and virus orientated.
The complement system https://www.youtube.com/watch?v=DPNnZE4OtCM
More specifically on SARS-2 TWiVs with Jonathan Yewdell #597 & #620
also TWiVs #601 & #659 with Christian Drosten and Ralph Baric #591, 626 & 661
The Immune podcasts generally with #34 looking specifically at CoV T-cell cross reactivity.
HLA Basic Terminology and Nomenclature. LOL, don't let the word 'Basic' fool you this is getting heavier but it crams a lot of information into a short time, if you can keep up.


If anyone is looking for anything specific let me know and, if I have looked at anything relevant, I will try and find the link.

[gsgs]

@florian_krammer
Immunological imprinting for SARS-CoV-2 exists. Mostly with betaCoVs HKU1 and OC43
and likely not RBD but S2 driven.

https://www.medrxiv.org/content/10.1101/2020.10.14.20212662v1.full.pdf

[kiwibird]

https://www.liebertpub.com/doi/10.1089/MAB.2020.0029

A Novel Hypothesis for Original Antigenic Sin in the Severe Disease of SARS-CoV-2 Infection

Perhaps not just the fact of previous infections - but the time between them - can also influence severity. Will look for a paper.

[sharon sanders]

bump this

[JJackson]

OAS is basically what Christian Drosten was talking about and I covered in the first part of post #3.

For those trying to get into the nitty-gritty of SARS-2 human immune interaction you may find this paper interesting.

https://www.cell.com/cell/pdf/S0092-8674(20)31067-9.pdf

It starts by looking at postmortem histology of germinal centers which show severe pathology of some particular cell types that are instrumental in germinal center development. Without this maturation the normal class switching involving folicular T helpers cell differentiating B cells is impaired. The functions the B cells would normally be developing in the germinal centers are improved antibody affinity, IgM to IgG switching and plasma cell development but this is not occurring, or at least not to the same extent. As this data is all from fatal cases it is difficult to draw conclusions about how relevant it is for the 99% who do not die so they look at the correlation between bio-markers in the germinal centers and those in non-fatal controls blood and find enough coincidence to think a similar pattern may be occurring in the less severe cases.
This paper was also discussed in more detail in immune #36 https://www.microbe.tv/immune/immune-36/

[gsgs]

https://www.medrxiv.org/content/10.1....06.20227215v1
Our studies indicate that most individuals possessed hCoV-reactive antibodies before
the COVID-19 pandemic. We determined that ~23% of these individuals possessed
non-neutralizing antibodies that cross-reacted with SARS-CoV-2 spike and nucleocapsid proteins.
These antibodies were not associated with protection against SARS-CoV-2 infections
or hospitalizations, but paradoxically these hCoV cross-reactive antibodies were boosted
upon SARS-CoV-2 infection.

[JJackson]

I do not see why they think that it is paradoxical that these antibodies were boosted by a SARS-2 infection. This is something I would expect to happen as it implies sufficient commonality between antigenic sites between viruses of the same family so both viruses should generate these antibodies. Unfortunately none of these antibodies show any evidence of a measurable effect on disease severity.

[Emily]

MIS kids are very low in antibodies for common coronaviruses.

https://ars.els-cdn.com/content/image/1-s2.0-S0092867420311570-gr6_lrg.jpg

Here's the study:

https://www.sciencedirect.com/science/article/pii/S0092867420311570

[JJackson]

In this post I aim to look in a little more detail at the role of the spike protein and SARS-CoV-2 viral fusion from a structural virology perspective and how that may impact antibody efficiency in some of the circulating variants.

The problem the virus faces is the need to penetrate the animal cell wall which is a phospholipid bi-layer in a stable energy state. To puncture this layer it needs energy which it cannot generate as it is inert. Nature's solution is to provide this energy by ‘spring loading’ the S protein at assembly so it is in a stable state but has lower energy states available if it can overcome an energy hump (like a loaded mouse trap it is happy where it is but a small nudge and it releases lots of energy and adopts a lower energy very stable form). This occurs in a number of steps.

The virus is a Class 1 enveloped virus (along with Influenza, HIV, Ebola and many others). All of these have use a ‘spring loaded’ homotrimeric trans-membrane proteins with a RBD and use the stored energy to force an opening in the cell wall.

The cutaway image below shows the viral structure. In the centre there is the nucleocapsid (+ssRNA in a nuclear protein (N) coat). Around which is the capsid protein (M) and the viral lipid membrane that was acquired from the cell wall of the cell that made the virion as it was shed. This is the membrane that needs to be fused with new cell’s membrane (bottom of frame) and embedded in which is the Spike (S) trimer.


The next image shows a single S protein with the Receptor binding domain (RBD) in purple and the N terminal domain (NTD) in turquoise with the C terminal domain, which is anchored in the viral membrane, right at the bottom. Three of these make the Spike homo-trimer but it is easier to see the key domains in a single protein.


The next image shows a trimer with one of it three S1/S2 furin cleavage sites marked.



Having identified some of the key sites in fusion we can look at the sequence of events.

The first is usually cleavage at the S1/S2 furin site. This is not found in most SARS like bat viruses and is not needed for infection but if it is not cleaved it makes a later step, which I will return to, more difficult. This can occur at any time after the viral capsid is made including before it leaves the cell that made it.

The second step is the binding of the RBD to the ACE2 which causes a conformational change and allows the release of the S1 section of the Spike which can float away, if cleaved at step one, or if not it will float about tethered by the S1/S2 join and impede access of the host protease needed for step 3 cleavage.

I have not shown a diagram for the step 3 cleavage site (S2') because it is buried deep inside the Spikes stalk to protect it from premature cleavage. This cleavage has to happen for infection but it is not until after the changes caused by step two that it becomes exposed. Once cleaved the protein undergoes a major conformational change that brings the NTD down to the cell membrane where it anchors itself. With the N terminal embedded in the host membrane and the C terminal in the virus the conformational change brings the two membranes together to cause a pore and cell entry.

So to recap
Step1 – Cleavage at S1/S2 – useful but not essential leading to minor conformational change effecting RBD.
Step 2 – S RBD to ACE2 Binding – essential leading to conformational change releasing S1 cap and exposing the fusion peptide.
Step 3 – S2 prime cleavage of the fusion peptide – essential as it allows anchoring of the NTD in the cell membrane so the attendant conformational change can first pull the virus and cell together and then surmount the energy barrier to fuse the host and viral lipid membranes.

With an understanding of the process I hope this animation will make sense. I would watch it straight through and then again at one quarter speed to watch the concertinaing of the strands by the formation of alpha helixes from less structured strands. (I do not know how many Spike trimers are need to pull in concert to achieve this process but in flu it seems 3 HA trimmers are normally involved in fusion)
https://youtu.be/e2Qi-hAXdJo

Armed with the process the virus needs to happen we can look at the changes in the various circulating viruses and what effects they may have on the immune response or vaccines.

Two more graphics, one showing the RBD to ACE2 interface with some of the key sites labelled the bottom figures shows the electrostatic surface charge in the bound and unbound forms and a table showing various monoclonal antibodies tested against engineered viruses expressing some of the main amino acid changes of interest.





The Class 1 & 2 mAbs bind to various areas within the RBD while Class 3 are neutralising but outside the RBD (at a guess most would be NTD as this is external in the pre-cleavage form but critical for attachment.) The circulating variants AA changes form the columns with the numbers in the boxes IC50 values in ng/ml so low numbers mean high binding affinity.

I do not know what was used as the wild type (column 1 wt) but it does not seem to include S D614G (last column) although this is now dominant at that position (and AFAIK present in the vaccines), interestingly it is more susceptible to these mAbs than the wt in most cases as is R683G (column 2) but when R683G is combined E484K it is dramatically worse across much of the RBD. Unfortunately they have not included E484K alone for comparison. One other point to consider is the fact all of the main vaccine candidates, except Astrazeneca, have made a change to the sequence near the Step 3 cleavage site adding some Prolines which stiffens the joint but does not stop cleavage. The reason for the change relates to Step1 if that S1/S2 furin cleavage site is cleaved it alters the shape of the RBD, so antibodies may be made to both forms, but for the vaccine we want to maintain the pre-cleavage form so the immune system makes antibodies to that configuration which will give improved binding in a subsequent natural infection. The N-K changes at 439 & 440 both interfere with neutralising binding but outside the RBD. Each of these changes is being tested individually and, as can be seen with the R683G/E484K dual change, just knowing how they work alone does not necessarily predict how they behave in the more complex combinations found in nature.

All of the above only covers the first step in viral infection, getting in the door, and needs to be performed again to get the nucleocapsid out of the endosome and into the cytoplasm. The exterior of the virion is covered in spike trimers and only a few will have been facing the cell surface which leaves plenty to repeat the process in getting through the endosome's lipid bi-layer. Up to this point Corona and Influenza virus both follow a very similar process but at this point the flu virus remains in the endosome which the cell acidifies as it turns into a lysosome flu uses its M2 ion pump to acidify its interior and destabalise the bonds that bind the M1 proteins which form its capsid.

N.B. This is just my interpretation of my reading and may not be accurate in all aspects. If you think I am wrong on any particulars please post so I can research further and make corrections.
As always I hope it helps.

[mscox]

JJackson, it both helps and is very much appreciated. Thanks

I found these summaries extremely useful and approachable as guides into the more detailed references.

[senegal1]

Even for those of us who are not scientists this was understandable and interesting. Thank you.

[JJackson]

Thanks to you both but just to be clear I am not a scientist just an interested layman.

I wish I had listened to TWiV 714 & 715 before writing the above post as they cover exactly this topic and I have learnt a lot of new information which has generated new questions.
Firstly it appears in addition to the pathway I described above there is another which is similar to that used by HIV. From the first post you may recall that HIV also employs Class 1 fusion but instead of the whole virion entering in an endosome, which it has to get out of as an additional step, the capsid releases its payload directly through the pore into the cytosol - SARS-2 can perform the same trick but SARS-1 couldn't or at least to the same degree. This finding comes out of research into why Hydroxychloroquine worked well in cell culture but not in a clinical settings. The answer lies in the transmembrane host protease TMPRSS2 which is a major cleaver of the furin S1/S2 site in SARS-2 but SARS-1 did not have a furin accessible site at this point. SARS-1 was susceptible to HCQ as were the vero cells used in cell culture which had the human ACE2 receptor but very few TMPRESS2. If you re-engineer the vero cells to display plenty of TMPRSS2 then the HCQ stops working. This and a raft of confirmatory experiments showed TMPRESS2 cleavage of the furin site at S1/S2 prior to S2' cleavage enables direct entry into the cytoplasm by bypassing the endosome. The graphic below shows both routes of entry are available.



In the first post I had said the S1/S2 cleavage was optional but helped, which is true as far as getting into the endosome, but it is obligatory at some point. For SARS-1 this happens in the endosome by another protease cathepsin-L. SARS-2 can use either route. Yet more experiments show HCQ is acting on the endosomal pathway and did not work with SARS-2 because it largely bypassed it.

The next image relates more to the first post but shows the positioning of the all the areas I discussed along the S chain although their proximity in the tertiary protein structure has little to do with how close they are here.



Edit:
I forgot the links.
714 is a conversation with Jason McLellan relating to the action of the Spike trimer and its cleavage sites.

https://www.microbe.tv/twiv/twiv-714/

715 covers the HCQ inactivation and links it to an additional entry pathway avoiding HCQ's antiviral activity.

https://www.microbe.tv/twiv/twiv-715/

The paper being discussed can be found here.
https://journals.plos.org/plospathog...l.ppat.1009212

[JJackson]

In the previous two post I looked at the S protein and some of the RBD antigenic sites and variant changes and how they affect binding.

This time I aim to think a little bit about these sites and the immune system.

If you look at the antibodies in sera from different individuals, post natural infection, you will find a lot of different antibodies and significant differences in their relative abundance between individuals. There are however a number of points along the RBD, and spike more generally, that are over represented generally both in quantity in one serum and frequency across all the sera. They are concentrated in more neutralising antibodies and surprise, surprise they closely correlate with those areas targeted by the MAbs which showed the most reductions in neutralisation in the table in post #9 e.g. S 417, 484 & 501.

What I am building up to is the hypothesis that these are occurring now because they are immune escape changes that effect a change at key antibody binding sites. If this is the case then the change would need to have a functional effect and it should become more prevalent as the number of potential hosts with pre-existing antibodies increases. What data is there and does it support this hypothesis?

If we take the E484K change, found both in South Africa and South America, the side chain changes its charge from – to +. If we look at how it has changed over time The graphics below show firstly how K has grown over time and then the full tree – green being E484 and yellow K484 - and finally recorded case of SARS-CoV-2 globally.






I have attempted to line up the dates on the X axis so they correspond.

The first will be hard to read but it should be possible to see some yellow by October but a closer examination shows it reached 1% by the first week in July and is now 14% (There were about 4.5m active cases in July so 1% would give 45,000 active infections carrying K484).
The tree in image 2 will not be readable but the things to note are the yellow clump near the top (S America) and the one nearer the bottom (S Africa) the smaller intermediate clump is mainly Nigeria. Also note they are all independent emergences in different clades and have been happening for a while but have only taken off since October. A closer examination of the top branch shows the first case in Brazil on the 9th of October but that the calculated date for the route of that branch is late July. On the S African branch the route is dated as early July with the first sequenced case on the 28^th of October.
Moving to the bottom graph Mid July shows about 15 to 20 million cases which climbs to nearer 40 million by the first sequenced cases and then on to over a hundred million.

Brazil and South Africa have the most cases on their respective continents so will have a relatively high sero-prevalence rate. In Brazil they have about 5% of the population as PCR confirmed cases with that actual number probably 3 times that. In SA the percentage is 2.5% but its undercount is probably even greater. These numbers will be beginning to challenge the virus at any critical points that are no longer doing what the virus needs them to due to antibody interference. Any change at these points that does not carry too big a fitness penalty will now begin to establish itself as it now has a selective advantage at least in the previously infected. As the percentage of the population that have antibodies to E484 increases the K484 variant’s advantage will grow.
I will not go through all the others in detail but N501Y makes it more hydrophobic, there are 3 main unrelated branches with no sequences until late Oct. but routed back in the spring.

The sera from vaccinated individuals is much the same across the Spike protein but lacks all the other antibodies generated against the rest of genome. While these are not likely to induce many neutralising antibodies they will react to a subsequent challenge activating the their B and T cells which can release cytokines and, in the case of CD8+ cells, kill infected cells displaying the peptides they can recognise. This may not be as effective as stopping cell fusion but will stimulate the immune response generally. Only recognising antigenic sites on S means they can target the antibody response to the most effective sites but on the down side that is the least conserved part of the least conserved protein. Any change in these site will impact it disproportionally, compared to a natural infection, as it does not have any other antibodies to fall back on.

Single AA changes at any one point will only effect one or two of the most important 15 antibodies so without a radical change across many of these (which would probably render the RBD non-fuctional) it should give most of the protection against a variant you would have got to the strain the vaccine was based on. This protection should contain the virus to non-severe infection giving your immune system time to generates new antibodies to the changed antigens and boost all of the ones that had not changed. Under the scenario I have outlined the variants we have encountered to date are not a major concern even if they show reduced protection as long as they buy the patient time to redress the balance. I view the decline as much the same as the decline you are going to get anyway as time elapses from your last infection or vaccination.

[gsgs]

> the most important 15 antibodies

is there a list ? I'd like to have the sequences

------------------------------
-----------------------------------------------------
Evolution of antibody immunity to SARS-CoV-2
received Nov3 , published Jan18 , Nature , 30 pages .pdf
they test 122 ("monoclonal"?) antibodies
they assign Cxxx numbers to them, e.g. C144

V367F,S477N,N439K,V483A,N440K,RBD ,R346S,A475V,E484K,Q493R

figure 3a) 122 selected monoclonal antibodies
figure 3b) 52 antibodies
figure 3e) 26 antibody clonal pairs
C098,C099 ; C202,C542 ; C032,C080 ; C132,C512 ; C108,C573
C564,C546 ; C151,C062 ; C148,C060 ; C091,C092 ; C044,C045
C548,C549 ; C114,C571 ; C005,C043 ; C143,C055 ; C164,C055
C089,C090 ; C058,C059 ; C058,C057 ; C085,C086 ; C144,C051
C021,C097 ; C554,C555 ; C002,C095 ; C144,C052 ; C144,C050
C144,C053

=============================================

comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding
domain that affect recognition py polyclonal human serum antibodies
Jesse D.Bloom et.al. , Jan04, BioRxiv , 35 pages .pdf
most important is E484
figure 6B)
S477N,N439K,N501Y,Y453F
E484K,K417N,S494P,L452R,G446V,F490S,L452M,L455F,E4 84Q,F486L,G485R
zero hits for 144 or monoclonal (mAb)

=============================================
definitions :

a monoclonal antibody (mAb or moAb) is an antibody made by cloning a
unique white parent blood cell
----------
polyclonal antibodies (pAbs) are antibodies that are secreted by
different B cell lineages within the body. They are a collection of
immunoglobulin molecules that rreact against a specific antigen,
each identifying a different epitope.
-----------
an antibody (Ab) also known as an immunoglobulin (Ig) is a
large Y-shaped protein used by the immune system to identify and
neutralize foreign objects such as pathogenic bacteria and viruses.
The antibody recognizes a unique molecule of the pathogen called an antigen.
-----------------
an antigen (Ag) is a molecule or molecular structure such as may be
present on the outside of a pathogen (spike?), that can be bound by an
antigen-specific antibody or B-cell antigen receptor.
(# I assume the antibody binds to one of the spikes and the whole virus
together with its other 20-100 spikes hangs at it)

[JJackson]

gs I do not think there is a list of the type you want but the antigenic sites and the mAbs that react with them in the table in post #9 were selected because these are the serum antibodies that are most common. There are 12 in the table which would be a good start to your list. The IgG is about 150kDa where as the Spike is nearer 800kDa and, as it is a glycoprotein, you would need to add the weight of the glycans (just to get a sense of scale). I do not know if it will form clumps with SARS-CoV-2, as you would see in a agglutination assay, where the two branches of the IgG bind to spikes on two virions which then clump with others using more IgG bridges until you get a raft in which none of the virions able to infect a cell. The exposed Fc portion of the antibody will also bind other immune cell receptors which can then induce clumping by a similar bridging mechanism. This is not an uncommon mechanism.

[JJackson]

Having looked a little at the Spike?s antigenic sites and the antibody interactions with it this post is going to look at the B cells that produce these antibodies.
Again I will start with some graphics which will help with the discussion.



In the diagram above we can see the 8 step process that takes a stem cell in the bone marrow through to the mature B cell in the Lymph nodes. This is not the main focus of this post but I will run through it briefly. The first 6 steps occur in the bone marrow and the last two in the Lymph nodes. From left to right the stromal cell binds to a receptor on the B cell causing it to produce a second receptor type which also binds causing IL7 release from the stromal cell initiating the production of the membrane bound antibody in the pre cell. This is further refined in the Immature cell which then travels to the secondary lymph nodes to complete the process.

Before we get to the antigen dependent part of the process it is worth looking a little at these last two steps in which the Ig light and heavy chains are added. Complex multicellular organisms, like us, can?t evolve on the same time scale as viruses so need a mechanism to quickly react to novel pathogens with which they have no prior experience ? like SARS-2. Nature?s solution is to make antibodies which have a fairly common fc portion, which is the trunk of the ?Y? shaped receptor in the diagram, and a variable short light and heavy chains. It achieves this by having thousands of these short gene sequences in our DNA for both the light and heavy chains the combinations of which can produce millions of different antibodies. Each B cell produces one of these millions most of which will die without ever having encountered a matched antigenic site. In an individual who has not suffered any recent antigenic challenge they still have about 80% of the number of these random B cells as someone fighting an infection. All these are just circulating waiting for their chance to interact with their matched antigen. In the unlikely event that this happens they then mature and start to rapidly divide and produce and release the antibodies which have the same heavy & light chain combination they presented on their surface. The first dose in a prime boost vaccine initiates this process and the second dose is timed to repeat it. The second dose instead of only having one in a million chance of interacting with a matched antibody the rapid multiplication of the original matched B cell has produced thousands more matched cells. All of these are ready to be activated and start the production of vast quantities of matched antibodies and yet more B cells to produce them.
The rest of this post is going to look at how that original light chain / heavy chain combination, which is close enough to the antigenic site to bind but probably not very strongly, is refined to give a better and better match. Again some graphics depicting some important players and sites.



The dendritic cells are a key player but only the green half of the image is relevant to our discussion. They are the body?s garbage collectors and are attracted to any sites of infection. Their octopus like shape allows them to squirm between tissues and on their surface they have MHC 1 & 2 receptors. They collect any bits of protein or nucleic acid they encounter and display them on their MHC cells. The Dendritic cells will then return to the lymph nodes and present the collected fragments to B and T cells. If their surface antibodies are a match for the presented antigens they will start to divide. T cells have a very similar heavy and light chain to the B cells and fall into two main groups, depending on their surface receptors, those with CD8 receptors target and kill infected cells presenting peptides that match their antibodies. The CD4 presenting cells are more relevant to the processes being discussed as they can become follicular helpers cells (Tfh). Most cells do have MHC1 receptors on their surface, which present very short pathogen peptides, due to their length they are not particularly specific and the matched CD8+ cytotoxic T cell?s will bind to them and kill the cells but upon infection they will also start making MHC2 receptors which present a slightly longer and more specific peptide presenting a higher bar to recognition. It is these that the CD4+ T cells recognise and dendritic cells always have MHC2, as well as MHC class 1, this allows them to become follicular helper cells which can then regulate the process of somatic hypermutation in the lymph node germinal centres. While the body may not care too much about CD8+ T cells killing a few cells that did not have exactly the right peptide on their MHC1?s it is fussier about making miss-targeted Tfh?s as it does not want to ramp up production of miss-matched antibodies ? hence the slightly higher bar set by the longer peptides presented by MHC2 cells.

The next two graphics show the lymphatic system and the germinal centres which are found within them.




The germinal centres have two zones, the light and the dark, in the light zone the follicular dendritic cell (FDC) can be seen with the red dots representing the MHC sites and the collected peptides with a B cell?s light and heavy chains bound to them. To the right of the B cell is a Tfh CD4+ cell which must also have the correct activation site. If both conditions are met the B cell can enter the dark zone where an enzyme is added that causes rapid mutation (hyper-mutation) of the light and heavy chains sequences which are then re-tested against the Tfh. Any with a low binding affinity die but those which have improved their bind go on to be reproduced. This process is repeated again and again against whatever peptides the dendritic cells have found and presented.

If we consider how this relates to a natural SARS-CoV-2 infection a cell is infected and presents viral peptides on the cell?s MHC1 surface protein. Millions of B and T cells interact with it until that one in a million match finds it and binds and becomes activated. The cell also begins MHC2 production which can bind and start the CD4 T cell activation turning it into a Tfh. The B cells will start antibody production but of relatively poorly matched IgM antibodies. The B cells then refine the antibody in the germinal centres and switch to a better targeted IgG antibody which is then fine-tuned in the dark zone until an even better binding strength is achieved. At this point the B cell can take two paths either it turns in to a very long lived Memory B cell or it turns into an effector cell, or plasma cell. The effector cells produce antibodies during the acute phase of the disease and then die off. The plasma cell becomes much larger and is packed with rough endoplasmic reticulum which produces vast quantities of protein for export from the cell. These proteins are the matched IgG antibodies and they have so much rough ER they can churn out 2000 IgG per second. As long as there is some viral fragments left somewhere in the body the dendritic cells will find them and present it in the lymph nodes to help the B and Tfh cell refine the IgG affinity.

If we now consider what would happen if you had been vaccinated, or had a natural infection, to one strain of the virus but then get challenged at a later date by a variant of that virus. This is only likely to have a few changes some of which reduce the binding affinity as we saw in the earlier post looking at weakened Mab to RBD binding. This time most of the antibodies work fine but some may not be as good as they were. The unaffected ones will give you a good level of protection while the process of somatic hyper mutation and Tfh matching for high affinity fits will start to produce new better fits to the changed antigenic sites. You are likely not to be symptomatic while this is occurring as the unchanged antigenic site / antibody interaction across all the unaffected sites give adequate protection while the germinal centres go about refining the one or two sites that had become less well paired.

Finally I will get much more speculative and give some thoughts on what I think is going to happen next in the battle between SARS-2 and us. With the Northern hemisphere winter we have seen clear evidence that this respiratory virus has a strong seasonality. As we head out of this season cases should drop which will be further strengthened by the increasing level of herd immunity induced by the combination of already infected plus those vaccinated. Sadly this will highlight the discrepancy between rich and poor nations as only the former will initially have much of a vaccine component. Over the past year there has been a continuous process of single nucleotide mutation (SNPs) most of which have had little impact on spread and either died out or continued to circulate at low levels. As more people have some level of immunity changes that were neutral, and at low levels, now convey a selective advantage if they weaken the neutralising effect of important antibodies. This is going to cause these changes to suddenly begin to take off and become dominant. This has nothing to do with increased virulence or transmissibility ? although if any of those changes do change either then it may impact them either up or down ? but that is a secondary effect.

The hypermutation can cope with gradual change but not massive jumps that cause many of the key antibodies to stop working effectively. In the 2009 flu pandemic, although many of us had antibodies to seasonal H1N1 (H & N being the two spikes which carry the antigenic sites to which the neutralising antibodies bind), the new strain had entirely new H1 & N1?s from another species which were sufficiently different for our immune system to view it as a new virus. This is likely to also happen for SARS. Although corona viruses only have one RNA strand and cannot therefore achieve this by recombination there is a reservoir in bats which is likely to cause a SARS 3 & 4 at some stage. The fact that SARS-2 has been transported all over the world by humans allowing it to interact with many new species like mink, dogs, cats etc. it is quite likely it will also set up shop in a novel species where it can adapt to that host for a while attaining enough changes to be viewed as new if it jumps back into us. This is the bigger risk in my opinion as these prospective host species have more interactions with humans and are physiologically closer to us than bats so a host optimised mink strain is likely to be better intermediate host as it started from a human optimised form and would probably retain a respiratory infection path rather than oral/fecal.

This was long but is a simplified explanation and only covers a small part of the whole immune response but it is important in understanding why the variants are not the doomsday scenario the MSM has been depicting.
Again if you see errors please point them out so I can make corrections.

[Emily]

You have a wealth of information about the immune system organized here. Even though I don't grasp this as well as you, my sense is that you are right about the variant threat - there isn't a biological basis for fear at this point.
I don't fear a threat from other species as intermediates. I would think that if a human origin virus adapts to another species, it would lose its ability to spread easily among humans. That seems to be the usual pattern with farmers getting swine flu's. It is a risk we take to benefit financially or socially from relationships with other animal species.
Chinese scientists are doing some cruel experiments with dogs and flu, justifying this by claiming dogs might be mixing vessels.

[Vibrant62]

Thank you for your interesting post. In terms of the final paragraph above, the study linked below provides some interesting (and concerning) insights. If this study is correct, it is not just mink and cats we need to be concerned about, but pigs. See https://www.nature.com/articles/s414...04MUUzWa2XuZRM. The linkage to C. Dromedar is also concerning, in view of MERS

[JJackson]

The one I am probably most concerned about are deer mice in the US. They are very common and frequently live around humans so are a perfect intermediate host if it gets established in this susceptible population.

[bertrand789]

il y a ceci :

https://fr.wikipedia.org/wiki/Immunit%C3%A9_gr%C3%A9gaire

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

https://zh.wikipedia.org/wiki/%E7%BE%A4%E4%BD%93%E5%85%8D%E7%96%AB

et puis cela

https://de.wikipedia.org/wiki/Herdenimmunit%C3%A4t

avec

https://de.wikipedia.org/wiki/Herdenimmunit%C3%A4t#Effizienzfaktor_E

ce serait bien pour paraphraser Sharon de bosser cela , non ?

[Vibrant62]

Interestingly, a few new papers that expand on the potential risks here. I would suggest a MERS vaccination for camels asap would be prudent. Cats would seem to be less of a problem for us than we are to them.

1.https://www.atlantis-press.com/journals/jegh/125946349
2.https://academic.oup.com/jid/advance...iab104/6144906
3.https://www.jbc.org/article/S0021-92...208-8/fulltext