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Is there a model of how the B-cell-antibody pool in the lymphoid organ evolves during the first two weeks of infection by a new virus ? With a model I mean something like this

At first we have $10^6$ different antibodies binding weakly to 4-5 amino acid motives and through somatic hypermutation and selection the pool converges to a few dozen of antibodies binding strongly and specifically to some 8-10 amino acid motives in the most numerous antigens presented by T cells (mostly motives found in the viral protein sequence since they must be in the peptide presented by antigen presenting cells).

This is what would make sense from the algorithmic point of view, which is often valid in biology, but not always. I have a few refs 1 2 3 but they stay elusive on that point.

If there is no such model then please make a few expert guesses.

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There are plenty of papers with models for this. For instance, check a few hundred here.

Edit: I'm not an expert in modeling these particular processes. However, I do know about mathematical models in biology more generally. The OP asked if there is "a model" of how the B-cell antibody pool matures ('evolves'). The short answer is 'no'. There is not 'a model', because anyone can make their own model, with their own assumptions, parameters, methods, etc. The 'algorithmic point of view' is not something that is valid on itself, it is only useful (sometimes). It is the job of the modeler to navigate the nuances of her/his own model so that it ends up being useful for some particular purpose or question at hand. Thus, there is no simple answer to this question, or any other modeling question (take, for instance, all the talk about epidemic models in the COVID-19 case: even experts differ about the relevance of some particular details/assumptions). This is my long answer.

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  • $\begingroup$ Tks, most of them are a little too specialized or hard to read, if you are an expert in this field, can you choose one and enumerate the 3 or 4 concepts you find relevant to the low affinity of the antibody pool at first and how (TCR-antigen engulf?) leads to increasing affinity and specificity, finally recognizing a few dozen of AA motives ? $\endgroup$ – reuns Apr 7 at 10:31
  • $\begingroup$ @reuns check out my answer edit. In short, you are asking a hard question, because whether a model is useful or not, depends on many things, including the purpose of the model. If you want me to ennumerate '3 or 4 concepts', I could do that, but why would these be the relevant ones? No one knows but me. You need to decide by yourself, because there is no absolute truth here. You asked if there is 'a model', and I can say, in short: there are as many 'models' as you can imagine. Find one (or build one) that is useful for you. Good luck! $\endgroup$ – TumbiSapichu Apr 7 at 12:13

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