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Articles often state that certain SAR-COV-2 strains are more transmissible, e.g:

Most studies indicate Delta is 50-60% more transmissible than the Alpha variant

How dangerous are covid-19 Delta and Delta Plus variants?

I believe that these studies are all based in statistics of people infected — that higher transmissibility has something to do with changes in the virus attachment and entry into human cells — but without much further detail. Is it known which changes lead to a virus strain becoming more contagious, and whether one can predict that when certain molecular changes appear in a virus strain it will be more contagious, or is our knowledge based solely on observation? Is it known which molecular changes make certain SARS‑CoV‑2 strains more contagious?

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  • $\begingroup$ Aside from changes in virus attachment and entry, other changes affecting transmissibility would include those affecting number of viruses given off by the infected and in what form (e.g. aerosolized), survival of the virus outside an infected individual, mutations affecting course of disease once virus enters a cell, and so forth. Some of those mutations can be studied in the lab in animal models or in tissue culture. Mutations affecting structure such as in the S protein can be modeled and can be tested to see if convalescent serum or monoclonal antibodies will still bind to them. $\endgroup$
    – Armand
    Jun 27 at 17:06
  • $\begingroup$ There are many approaches as described above -- it's worth looking into them if you're interested. $\endgroup$
    – Armand
    Jun 27 at 17:07
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    $\begingroup$ Pablo, two things. 1. Infectologist is not an English word. 2. Questions of the sort “Do experts know?” are unnecessarily contorted. This site is for questions about biology, not biologists. Your title would be better if you deleted the first three words. Likewise in your last sentence. $\endgroup$
    – David
    Jun 27 at 18:46
  • $\begingroup$ @RoniSaiba The important thing is not whether virologists know, but whether it is known on the basis of peer-reviewed published science that is supported by other findings. The paper could be published by a Nobel Laureate or an Undergraduate student. Emphasis on status has no place in science. I therefore feel obliged to edit the post in the way I hoped the poster would. He will not learn if you do it for him, especially if you do it wrong. $\endgroup$
    – David
    Jun 27 at 19:13
  • $\begingroup$ @David sure. Feel free to edit as you see fit. "Infectologist" was too much of an eyesore so I suggested an edit. $\endgroup$
    – Roni Saiba
    Jun 27 at 19:26
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We can only see this in retrospective. So here are some mutations that have enhanced the transmissability of the virus:

  • ORF1b:P314L in combination with S:D614G (Pango lineage B.1 and all subsequent lineages)
  • S:N501Y Most prominent mutation of Alpha, Beta, and Gamma. It often licences S:E484K which on its own does not seem to boost transmission.
  • S:P681R The key mutation in the Delta variant, enhancing the Furin cleavage site

In order to be efficient the mutations need to be embedded in a fitting virus, the same mutation may enhance transmission for a certain variant, but being inefficient in another variant with different co-mutations.

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  • $\begingroup$ To improve this answer, you could 1) provide links to references for your points. 2) discuss why retrospective analysis is not the only method we can use to see these sorts of things, and 3) what sort of changes are seen in similar viruses that also lead to enhanced transmission (cough polybasic cleavage site cough). $\endgroup$
    – bob1
    Oct 10 at 7:47

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