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I am curious to know if the original SARS‑CoV‑2 virus, or any of its variants, can mutate in people who have been fully vaccinated. I am referring to those people who have received all the recommended vaccinations and booster vaccinations since the worldwide outbreak of COVID-19 back in November 2019.

Can SARS‑CoV‑2 mutate in people who have been fully vaccinated?

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  • $\begingroup$ I wonder if we also can say something about expected mutation rates between vaccinated and unvaccinated, or even the kind of mutations that are likely to happen in each case. $\endgroup$ Nov 27 '21 at 13:42
  • $\begingroup$ Most likely there is little effect. See last (new) ¶ of my answer. $\endgroup$
    – Ben Bolker
    Nov 27 '21 at 17:53
  • $\begingroup$ @leftaroundabout: Please see my comment on Ben's post. $\endgroup$
    – user21820
    Nov 28 '21 at 13:06
  • $\begingroup$ I don't know "anything" in mutation, but if a virus is not "killed" (with or without vaccination), mutation can occur and can be transmitted ... It is a logical "defensive" reaction. Do we know all about "virus"? No, and in reality, about "nothing". $\endgroup$
    – Antonio51
    Nov 28 '21 at 17:23
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Since vaccination is not 100% protective against infection (i.e. the virus can sometimes succeed in establishing and replicating in a vaccinated host's body), the answer is yes. Furthermore, since vaccination is also not 100% protective against transmission — although it does lower the probability of transmission from infected individuals — such mutations could also be transmitted to other hosts.

However, vaccination greatly reduces the probability of infection and onward transmission. It might also be expected to reduce the duration and intensity (viral load) of infection, which would further reduce the probability that a mutation arises in an infected person (because the total number of mutations is proportional to the population size of the virus within the host).

Singanayagam et al. (2021) found that the peak viral load was not greatly reduced in infected, vaccinated people infected with the delta variant (relative to unvaccinated people), but that the decline from the peak was faster; with more effort/re-analysis of these data, we could estimate the magnitude of the change in the expected total number of viral replications over the course of an infection, which would in turn tell us the expected proportional difference in overall mutation probability due to changes in the within-host dynamics of the infection. (Also see this answer for more detail on viral load in vaccinated vs. unvaccinated individuals.)

Responding to a comment: the mutation rate (i.e. per base pair per viral replication, or per genome per viral replication), and the mutational spectrum (i.e. what kinds of mutations occur) are not expected to change much under vaccination - these are determined by the biochemistry of viral replication, and are probably not affected by what the host's immune system is doing.

(Disclaimer: my background is in ecology/evolution/epidemiology, not virology or immunology or biochemistry.)


Singanayagam, Anika, Seran Hakki, Jake Dunning, Kieran J. Madon, Michael A. Crone, Aleksandra Koycheva, Nieves Derqui-Fernandez, et al. “Community Transmission and Viral Load Kinetics of the SARS-CoV-2 Delta (B.1.617.2) Variant in Vaccinated and Unvaccinated Individuals in the UK: A Prospective, Longitudinal, Cohort Study.” The Lancet Infectious Diseases 0, no. 0 (October 29, 2021). https://doi.org/10.1016/S1473-3099(21)00648-4.

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    $\begingroup$ +1 - Of course you are aware of this, but it seems like the OP may not be - but it may be worth clarifying that viruses mutate whenever they replicate, entirely independently of whether they are in a host that has been vaccinated - the vaccine doesn't precent mutations, just (as you said) reduces the opportunity for them to replicate and mutate. $\endgroup$
    – user438383
    Nov 27 '21 at 11:55
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    $\begingroup$ If someone wants to leave a reason for their downvote I would be happy to try to respond. $\endgroup$
    – Ben Bolker
    Nov 27 '21 at 17:52
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    $\begingroup$ I did not downvote but I do not agree with your claim that "the mutational spectrum [...] are not expected to change much under vaccination - these are determined by the biochemistry of viral replication, and are probably not affected by what the host's immune system is doing.". That is completely false; because of course the mutational spectrum depends on the immune system; if it is good at destroying a certain viral strain then of course the virus population would mutate away from that strain! $\endgroup$
    – user21820
    Nov 28 '21 at 13:06
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    $\begingroup$ @user21820, what you are describing is within-host selection, not a change in the mutational spectrum. Perhaps that process should be included in my answer, but it's not technically mutation. $\endgroup$
    – Ben Bolker
    Nov 28 '21 at 13:59
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    $\begingroup$ @user21820: The mutational spectrum isn't affected by the characteristics of the host's immune system. The ways in which the virus mutates are totally unaffected - the only thing that changes is which of those mutations are selected for or against once they appear. $\endgroup$
    – Vikki
    Nov 28 '21 at 18:30

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