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    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.


    Last edited by sharon sanders; October 5, 2020, 11:27 AM. Reason: enlarged size of print for easier reading
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

  • #2
    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.

    Last edited by sharon sanders; October 5, 2020, 11:29 AM. Reason: enlarged size of print for easier reading
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

    Comment


    • #3
      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.
      Last edited by JJackson; October 7, 2020, 05:02 AM.

      Comment


      • #4
        @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/10.1...662v1.full.pdf
        I'm interested in expert panflu damage estimates
        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

        Comment


        • #5
          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.
          ?The only security we have is our ability to adapt."

          Comment


          • #6
            bump this

            Comment


            • #7
              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/

              Comment


              • #8
                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.
                I'm interested in expert panflu damage estimates
                my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                Comment


                • JJackson
                  JJackson commented
                  Editing a comment
                  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
                  Emily commented
                  Editing a comment
                  MIS kids are very low in antibodies for common coronaviruses.
                  https://ars.els-cdn.com/content/imag...70-gr6_lrg.jpg

                  Here's the study:
                  https://www.sciencedirect.com/scienc...92867420311570

              • #9
                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.

                Click image for larger version  Name:	SARS cutaway and bi-layer.JPG Views:	3 Size:	217.4 KB ID:	905846
                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.
                Click image for larger version  Name:	Single S.JPG Views:	3 Size:	107.1 KB ID:	905845

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

                Click image for larger version  Name:	SARS S1-S2 cleavage site..JPG Views:	3 Size:	72.0 KB ID:	905847

                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.

                Click image for larger version  Name:	ACE2 RBD binding.JPG Views:	3 Size:	129.0 KB ID:	905849

                Click image for larger version  Name:	Variants.JPG Views:	3 Size:	315.5 KB ID:	905848

                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.
                Last edited by JJackson; February 2, 2021, 05:50 PM.

                Comment


                • #10
                  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.

                  Comment


                  • #11
                    Even for those of us who are not scientists this was understandable and interesting. Thank you.

                    Comment


                    • #12
                      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.

                      Click image for larger version  Name:	image_33228.jpg Views:	40 Size:	174.6 KB ID:	906531

                      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.

                      Click image for larger version  Name:	image_33227.jpg Views:	41 Size:	50.1 KB ID:	906530

                      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
                      Last edited by JJackson; February 8, 2021, 04:01 PM.

                      Comment


                      • #13

                        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.



                        Click image for larger version  Name:	E484K OVER TIME.JPG Views:	1 Size:	57.6 KB ID:	906789
                        Click image for larger version  Name:	E484K TREE.JPG Views:	1 Size:	340.7 KB ID:	906790
                        Click image for larger version  Name:	cases.JPG Views:	1 Size:	75.5 KB ID:	906791

                        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 28th 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.
                        Last edited by JJackson; February 10, 2021, 06:48 PM.

                        Comment


                        • gsgs
                          gsgs commented
                          Editing a comment
                          > 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)
                          Last edited by gsgs; February 20, 2021, 12:38 AM.

                        • JJackson
                          JJackson commented
                          Editing a comment
                          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.

                      • #14
                        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.


                        Click image for larger version  Name:	B cell maturation.JPG Views:	9 Size:	199.0 KB ID:	907704

                        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.


                        Click image for larger version  Name:	dendrictic cell.JPG Views:	9 Size:	85.6 KB ID:	907703

                        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.


                        Click image for larger version  Name:	Lypnatic system.JPG Views:	9 Size:	112.0 KB ID:	907705Click image for larger version  Name:	Germinal center.JPG Views:	9 Size:	147.1 KB ID:	907702


                        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.
                        Last edited by JJackson; May 21, 2021, 07:22 AM.

                        Comment


                        • Emily
                          Emily commented
                          Editing a comment
                          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.

                      • #15
                        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

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