Guest post: Pedram Razghandi on vaccination and resurgent pathogens

There’s a heated discussion of vaccinations on a Facebook thread of mine, on which Pedram made such informative comments in response to a claim that whooping cough was coming back because of “over use of vaccination” that I requested and got permission to quote them here. The rest is Pedram.

No, high vaccination rates in the population means that a pathogen cannot replicate as quickly–many fewer hosts will be available. Vaccination is just a way of inducing a regular adaptive immune response (the adaptive immune cells are exposed to antigens that mark the dead or inactivated pathogen used in the vaccine, without the danger of an infection). If this is done extensively enough, the pathogen can quickly be suppressed or even (mostly) eradicated. Preventing new infections is a very fast way of stopping a disease in a population.

And, those few people who cannot get vaccinated (those with severely weakened immune systems, lymphoma, or very rare autoimmune conditions) can be protected by the ‘herd immunity’–if others aren’t being infected, no one can spread it to them. Now if vaccination rates are low, the pathogen has a chance to replicate again, starting with the unvaccinated people. After enough rounds of new infections, that suddenly expanding, once-small population of pathogen strains would be carrying a *lot* of low-frequency new mutations, and gradually, increased exposure of vaccinated individuals to non-vaccinated individuals (who are basically walking microbial culture vats at this point) means more chances for the resurgent pathogen to spread to them. That in turn gives a significant selection pressure–those variants among the myriad low-frequency mutants which differ in key antigens will slip unnoticed past the vaccine-primed immune systems (which were adapted to the old strains), and the fast spread will begin anew. **And even worse, those low-frequency mutants will still be among a whole bunch of medium-frequency ‘freak’ mutants, since the previously severely contracted population of pathogen would have left various strains that possibly differ substantially from the wild type of the past, just by sampling error (i.e. genetic drift), but now supplemented with this explosion of new mutants.

Antibiotic overuse is totally different. It is most often the problem when they’re being misused–‘stretched’ in low doses, or the dosing is terminated prematurely. Most mutations which confer resistance to an antibiotic (or antivirals, for that matter) are also costly in terms of replicative fitness, since they involve changes in structure of key receptors or overactivity of some metabolic enzyme, so fully-resistant strains are extremely rare. Strong, sustained antibiotic dosing regimens kill off infections. But decreased antibiotic concentration means that partially-resistent strains (shitty replicators, but better against antibiotics than the wild type strain) can outcompete their nonresistant counterparts. Once enough of them survive, more replicative generations means more chance for some other mutation to appear which compensate for the resistance traits’ effects on replication, or complete the resistance without further reproductive cost, so the resistant strain takes off. Vaccines on the other hand aren’t killing off robust and diverse populations of pathogens–rather, they prevent new infections by small founding populations, which are overwhelmed by the vaccine-primed immune system’s fast adaptive response.

Nature doesn’t choose how to adapt. Adaptations happen because of changes in average genetic variants in the population, due to some variants replicating more frequently than other variants.


  1. rorschach says

    Strong, sustained antibiotic dosing regimens kill off infections.

    Not in the case of whooping cough, where all the antibiotic does is to reduce the rate of transmission from the host to other people. It does not hasten the person’s recovery.

  2. Pedram says

    ^^True, that was a simplification. Some antibiotics (and some antivirals for that matter–e.g. for herpes) only control the infection enough to decease shedding of pathogen from the host, but the infection goes on internally. Or, the pathogen itself is causing less damage than the violent, dysregulated immune response triggered by the large amount of antigens if the infection is not controlled early (most common colds [though these are quickly self resolving and there’s little hope in controlling it before you know you have it], as well as cytokine storms in sepsis and some types of flu). That’s part of why prevention of *new* infections is so important. Then there are some pathogens for which it is difficult to make effective vaccines, since they have many different equally fit antigen variants, or they are masters at immune evasion. Influenza and HIV are excellent examples of the latter.

    I should have said “strong sustained antibiotic dosing *can* kill off infections”, but it was a rapidly-typed Facebook post at around 5am :/

  3. says

    (actually, the antivirals for herpes do also control symptoms for the patient, luckily, but they won’t rid them of the provirus, which has been programmed into enough cell genomes to comprise a big latent pool of hidden virus, alas)

  4. theobromine says

    One other thing that might be worth addressing* (even if it is based on an article from Natural News) is the statement that people who are vaccinated against measles are more likely to contract the disease.

    One example given was of a 1984 measles outbreak in a school where “all 400 students were vaccinated”. Since everyone admits that the vaccine is not 100% effective (especially the earlier versions that were given in the 1970s through early 1980s), why would anyone be surprised about this?

    The second case cited referenced a PubMed article (, which to my reading of the abstract seems to be actually supportive of vaccination.

    Vaccine failures among apparently adequately vaccinated individuals were sources of infection for at least 48 per cent of the cases in the outbreak. There was no evidence to suggest that waning immunity was a contributing factor among the vaccine failures. Close contact with cases of measles in the high school, source or provider of vaccine, sharing common activities or classes with cases, and verification of the vaccination history were not significant risk factors in the outbreak. The outbreak subsided spontaneously after four generations of illness in the school and demonstrates that when measles is introduced in a highly vaccinated population, vaccine failures may play some role in transmission but that such transmission is not usually sustained.

    [emphasis added]

    But nonetheless, Natural News provides this as an argument for antivaxxers to bolster a claim that vaccination increases the chance of contracting a disease. They can do this because most people are really bad at statistics (hence the success of casinos and government lotteries). Let’s take a hypothetical population of 2001 students, of which 2000 are vaccinated and 1 is not, and expose them to measles. For this example, assume that the probability of contracting the disease is 0.1% for a vaccinated person, and 50% for an unvaccinated person. So, the 1 unvaccinated person has even odds of escaping the disease, while it is very likely that at least 2 of the 2000 vaccinated people will get sick. So, it would not be surprising if the unvaccinated person stayed healthy, and only vaccinated people got sick. But if you had 2000 unvaccinated and 1 vaccinated, the vaccinated person would have a 99.9% chance of not getting sick, while the expectation would be that *~1000* people would come down with measles, one of whom would likely get encephalitis resulting in permanent brain damage or death (not to mention the risk of a few dozen having other complications such as pneumonia, or permanent deafness and blindness).

    *also posted on FB in case the antivaxxer is still reading)

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