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Some covid SAQ NAFE and GP


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It has been mentioned a few times, so I thought I'd start a new thread.

Covid Seldom Asked Questions, Not Asked For Explanations and General Pontifications.

I might put some posts from other threads up here just to keep them in one place. 

Feel free to challenge and ask technical questions -- because without challenge and query we have nothing...

...but perhaps keep chitchat to the main threads.


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I'll start with this from today:

  11 hours ago, Pinkpanther said:

Thanks for that 

I have one question that has been bothering me and I was wondering if you could enlighten me or point me in the right direction.

If the immune system in the vaxxed is not controlling the virus. Then what stops the virus replicating? 

My limited knowledge of this area would lead me to conclude that the virus would replicate (because that what they do) until all the cells that it can replicate in have been used. Or in other words it would take over and kill you. But obviously not.


The way the immune system responds to viral infections is rather complex, particularly for respiratory infections, and involves innate* antibodies, a variety of innate cellular responses some of which involve the creation of chemical responses and others that are directly cellular, adaptive cellular responses and adaptive system antibodies, most of which are used to signal cellular responses but some of which neutralise the virus.

[* innate means there anyway and not linked to a memory of a prior infection; adaptive means arising as a result of a prior infection]

Part of our problem here is the unfortunate way government 'education' has simplified this into 'antibodies! antibodies! antibodies!', mainly because the covid vaccines mainly work by priming the body to produce antibodies by the bucketful (a much stronger response than you'd get with natural infection) and don't do that much else (there is also a limited adaptive-cellular response, which appears to be a much smaller response than you'd find with a natural infection).  I don't understand why they've had this single-minded response to medically-responding to covid, other than 'if the only tool that'll make me money is a hammer, it is in my interest to make people think that all problems look like nails'.


When you get a respiratory tract infection your body responds with the innate immune system -- this allows the body to limit the spread of the infection and also produces the symptoms we're familiar with ('having a cold').  These symptoms can* last for some time, as these processes don't clear up the infection on their own.

[* I'll come back to this]

The adaptive immune system does clear up the infection, but takes a while to get up to speed.  In coronavirus infections this is 'about a week', which is why colds typically last as long as they do.  In the upper respiratory tract the main mechanism appears to be antibodies that bind to any viral proteins and signal the cellular immune system to act.

Note, signalling antibodies that don't neutralise the virus on their own.  There are also neutralising antibodies, that bind to 'important bits' of the viral proteins and stop it working.  For the covid vaccines this is the single target, which is strange because it appears to be the least important part of the immune responses to respiratory tract infections in general, including coronaviruses.

It is also interesting to note that the antibody response to coronaviruses (in general, as well as other upper respiratory tract infections) is rather short lived -- it is as if the body tries to get rid of the antibodies because they're not that helpful in the end.

So really your question should be 'what are the vaccines doing anyway?', or, perhaps, 'how do they work at all?'.

I think they're doing a number of things:

  • Neutralising antibodies in the upper respiratory tract do have some direct impact on controlling infection, but not much.  These do reduce viral load by some margin and will help stop infection in the first place.
  • However they also compete with the innate immune system, suppressing it and stopping it from working so well.  This will reduce 'cold like' symptoms (because it is the immune system that creates the symptoms, not the virus), but will also likely make the infection last longer.  Note that the virus is still there and replicating 'enough', so the individual will be infectious and able to transmit even without symptoms -- this is different from a normal infection where lack of symptoms generally means that the virus hasn't taken hold (hasn't stimulated the innate immune system to act).
  • If the virus moves from the lungs to the whole body (particularly the blood) then the neutralising antibodies that are floating around really do stop the infection (this is their forte) -- this then significantly reduces the risk of serious covid (which is a whole-body problem, not a respiratory problem).

This is exactly what we see as a result of vaccination:  reduction of risk of infection, strong reduction in mild symptomatic disease and highly significant reduction in serious disease.  

But the other consequences of this will also mean longer infectious periods in the vaccinated infected, and a higher level of asymptomatic transmission.

Note that this might result in a weird pattern in the response of the body to coronaviruses (in general, and perhaps other upper respiratory tract viruses).  When a naive individual gets 'a cold' they should clear it up in about a week.  If they're reinfected within a timescale of 'about a month' they should fight off the infection (primed innate and adaptive immunity).  If they're reinfected after about 6 months they should just have a 'normal cold' (normal innate immunity and no adaptive immunity).  But if they're reinfected in a time scale of about 6 weeks to 3 months they should get longer lived but very mild symptoms such as a 'not that annoying' persistent cough that just doesn't go away (primed adaptive immunity and suppressed innate immunity).

Finally -- why does the body try so very hard to produce an immune response to coronaviruses (in general, 'colds'), but then 'forgets' all about it so rapidly?  I believe that this is a function of man's natural social habitat and issues with coronavirus antibodies.  Humans evolved in relatively small 'extended family' tribes -- when these were infected with a cold (maybe from casual contact with a person from a neighbouring tribe) it would rapidly move through the entire tribe but then run out of hosts as everyone would have had an infection and generated a level of protective immunity (by various mechanisms).  Thus immunity wouldn't need to last long -- only as long as it took for all potential hosts to become infected and to clear up the infection -- there would then be no virus in the community and no need for a protective immune response.  But why make the antibodies go away?  I see four possible 'reasons'*; because structural similarities between viral proteins and human proteins meant there was a risk of an autoimmune response (eg, the body creating blood clots) so it was best to get rid of them if they weren't being useful; because mutations in the viral proteins by the next time it came around (6-12 months) meant that there was a risk of the antibodies to the first variant actually assisting the viral variant that comes around next (eg, ADE); because having those antibodies hanging around at the time of next infection introduces selective pressure for the virus to mutate 'at important bits', increasing the risk that it will mutate to get around the immunity and, because of original antigenic sin, the body would struggle to produce antibodies to this new form in the future; increasing the risk that it will mutate to get around the immunity and happen upon a more virulent form.

I don't know if this is true or which of those potential mechanisms might be important -- but very kindly the world's politicians have just designed an experiment to find out. 

[* this means 'selective pressure for humans to evolve to have a different immune response to some viruses, where they don't produce a long lived antibody response']

I'll add that there are more explanations for antibody decline -- the most important one is 'it is just that way and there's no reason' -- this always has to be considered.  And there's also 'the virus has evolved to trick the immune system into lowering defences so that it can reinfect more easily' -- this is certainly plausible; immunity is a merry dance between the body building defences and pathogens evolving to get around the defences.

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Mental Floss

Ooooh can I have one! There appears to be an implied superiority of vaccination protection vs infection acquired immunity.

Is there any scientific rationale for this? 

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I'll break my own rules about no chitchat because it is my thread and I can do what I like.

But looking at the text I just posted I'm reminded of Cgnao -- he was far more sensible than me and would have distilled the above into:

WTPZ31 KNHC 150851

SARS-COV-2 Advisory Number   5   

EP062021 200 AM PDT Thu Jul 15 2021









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8 minutes ago, Mental Floss said:

Ooooh can I have one! There appears to be an implied superiority of vaccination protection vs infection acquired immunity.

Is there any scientific rationale for this? 


Vaccination offers very high levels of neutralising antibodies, either circulating in the body or produced by B cells on infection.  These are highly protective and significantly reduce the impact of infection.  

Except in upper respiratory tract infections, where innate and cellular immunity is more important.

Covid vaccines are very good at producing neutralising antibodies to the very specific proteins that are in the vaccine.  These antibodies are also very long lived, compared with antibodies created in response to natural infection.  But they're rather poor at producing a cellular response (other than B cells creating new antibodies).  Thus the actual protective impact of the vaccines will be inferior to natural infection.  Any protective effect from the antibodies is also time-limited because high vaccination levels create immense selective pressure for the virus to evolve vaccine escape, making the fact that the antibodies are still circulating a moot point.  In addition, Original Antigenic Sin will make the immune response to future infections biased towards the original (vaccine) spike protein and thus suppress the ability of the immune system to respond adequately.

I find it rather concerning that the pharma companies have negotiated that in future, clinical trials of vaccine candidates will only have to show an immune (antibody) response, rather than having to go to the effort of showing protective impact on the population.  I find this extraordinarily short-sighted and liable to result in significant problems.


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