Nov 17 2011

Vaccine Questions

I recently received the following question, which contains some common misconceptions about vaccines so I thought I would answer here instead of just in a private e-mail. The e-mailer writes:

Hello, I’m a new listener to the show. A few times now I’ve heard the subject of vaccinations come up on the show and I’m not sure I understand.

I fully understand that the “anti-vac” folks are wrong, and that vaccinations are very helpful in eradicating disease. I also understand that a certain portion of the population needs to be immune to a disease in order to protect the rest of the population from it. But I don’t understand – why does everyone need to get them, every year, and isn’t it possible that doing so weakens our natural immune system? If my body can fight off the flu quite easily, then why get the shot? Won’t the net effect (my body killing the virus) be the same?

Is there something I’m missing?

The e-mailer refers initially to herd immunity – once a certain percentage of the population is immune to infection (for whatever reason) there will not be enough susceptible hosts for the bacteria or virus to spread, and therefore there will likely not be an outbreak. The exact percentage of the population that needs to be immune varies depending on the infecting agent, but around 90% is typical. This means that for most vaccine-preventable diseases we would need vaccine rates to be above 90% in order to achieve herd immunity (some people may be immune because of prior infection, but this number is low for diseases for which there has been a vaccine available for decades).

Further, the 90% figure applies to local populations, not the country as a whole. So if there are pockets of low vaccine compliance then herd immunity will be compromised and outbreaks can occur. We are seeing this happen now with mumps, measles, and pertussis in communities with an large anti-vaccine sentiment.

The e-mailer next asks, “But I don’t understand – why does everyone need to get them, every year?” I assume they are referring to the flu vaccine. The reason for this is simple – the flu virus comes in many strains. Every year a few different strains are dominant, and the CDC and other organizations have to make their best guess as to which strains are likely to come around. They essentially look at the rest of the world to see what strains are making the rounds, and then try to anticipate which strains will hit their region.

This is a difficult guessing game, and sometimes they get it right and the flu vaccine is very effective, while other years the strains change between the time they start vaccine production and flu season, and the flu vaccine is less effective.

Strains are largely defined by the HN system – this refers to two glycoproteins: hemagglutinin and neuraminidase. So H1N1 (swine flu), for example, has the first variation of both hemagglutinin and neuraminidase, while the bird flu is H5N1.

Flu vaccines have activity against specific strains. Usually they include three strains out of the many possibilities. In the last two years H1N1 has been incorporated into the flu vaccine. There is also evidence that after getting the flu vaccine for many years a person can develop fairly broad resistance to many flu strains, and they are less susceptible to the flu in general.

The holy grail of flu vaccines, however, is to develop a universal flu vaccine, one that targets structures on the flu virus that are conserved or common across all strains, instead of targeting structures that are specific to one strain. Researchers are working on the universal flu vaccine, and recently announced progress in this area. It is possible that we could have a universal flu vaccine by 2016. Until then, it is recommended that you get the flu vaccine every year. (Now would be a good time if you have not gotten your vaccine yet this year.)

The last question is this, “isn’t it possible that doing so weakens our natural immune system?” This is a common claim of the anti-vaccine movement (the e-mailer is clearly not anti-vaccine, but you can see how misinformation spreads). Vaccines do not weaken the immune system, they strengthen it. The concept behind vaccines is that they expose the immune system to proteins, killed viruses, parts of viruses or bacteria, or attenuated viruses or bacteria (which are alive but not virulent). The immune system will react as if there is an infection, making antibodies against the structures, including the memory cells that will be able to react the next time the immune system sees the same proteins or structures. Therefore, when the host is exposed to the infecting organism they can mount a much more vigorous immune response and fight off the invader before a clinical infection occurs.

The immune system is therefore strengthened, not weakened. I have never been able to figure out what the reason is to believe vaccines can weaken the immune system. It seems that some people may believe the vaccines fight off infection without using the immune system, as is suggested by the e-mailer’s reference to the “natural immune system,” as if the vaccine represents an artificial immune system. Vaccine works through the immune system – it does not replace it.

There is a real question about the strength and duration of the immune response from vaccines vs a natural infection. Infections do often produce greater and longer lasting immunity from vaccines, because the immune response is often in proportion to the duration of exposure, and an infection can produce more exposure than a vaccine. But scientists track the immune response to vaccine by measuring antibody levels. For many vaccine types sufficient antibody levels last for decades or even a lifetime, so even when they are not as long as the infection they are still robust and long lasting. For others booster shots are required.

In any case this is all better than getting the actual infection. The e-mailer’s suggestion that we can easily fight off infections (again, I assume they mean the flu) is not accurate. Most healthy individuals will weather the flu just fine, but will be miserable for a week or so. For me avoiding a week of the flu is worth getting a shot. But also the flu causes hundreds of thousands of hospitalizations in the US every year, and from 3-49 thousand deaths (it varies greatly from year to year). Also, there are many people in the community who are not healthy, or cannot get vaccinated, so getting the vaccine can help them as well.

The flu vaccine, and vaccines in general, are a safe and effective public health measure. There are some common misconceptions, however, that need to be cleared up on a regular basis. Further, there is a dedicated campaign of ideologically motivated misinformation about vaccines, requiring an equal campaign of public education about the true state of the science.

31 responses so far

31 thoughts on “Vaccine Questions”

  1. Just a couple of points/ nitpicks:

    I know it’s generally difficult to strike a balance between technical depth and accessibility, but I still bristle a bit when I see the flu strain used in a vaccine referred to by only its subtype classification.

    I won’t nitpick much regarding your referring only to Influenza A type viruses and leaving out mention of others like Influenza B type (which don’t use HN classification) for which one strain is usually included in the trivalent vaccine. I’m mostly OK with that simplification considering the intended audience.

    Every year, the seasonal influenza vaccine contains three influenza virus strains – one influenza A (H3N2) virus, one influenza A (H1N1) virus, and one influenza B virus.

    While I don’t expect anyone trying to communicate to a lay audience to use the specific strain name , such as A/California/7/2009 (H1N1), I think it’s important for the reader to know that not all H1N1 strains are the same and that being vaccinated against one H1N1 strain doesn’t necessarily confer protection against any other strains of H1N1.

    When I talk to people about the flu vaccine this year, I usually say that this year and last year’s vaccines include the 2009 pandemic strain of H1N1 or sometimes I will just call it 2009 H1N1, but never just H1N1.

    Also, I think it’s important explicitly to stress one of the key benefits of vaccination and heard immunity and a major reason to get vaccinated: Even if YOU have a robust immune system and can fight off the flu after a few days and suffer no major complications, while infected, you may transmit the virus to someone who is not so lucky. A flu infection is a much more serious deal for someone who is elderly or immune compromised, such as a transplant recipient on immune suppressing drugs or someone infected with HIV, etc.

    In rereading the post, I see you do mention this, but it didn’t come off to me as a key point, coming almost as an after thought, passing mention in the last sentence of the second to last paragraph. I’m not tying to be a jerk on this point, but it’s a key point for anyone who says, “The flu’s never a problem for me, so I don’t benefit from it, why bother?”

    Just like it’s polite to not litter by throwing your trash on the ground in public places, it’s also polite to do your best to not litter by spreading your diseases around public places as well. One of the best ways to do this is to get vaccinated and prevent getting the disease in the first place. It protects you and those around you was well.

  2. ChrisH says:

    It has been a long time since I read Flu: The Story of the Great Influenza Pandemic of 1918 and the Search for the Virus that Caused It by Gina Kolata, but I remember she has a section that describes how the viruses change between birds, human, pigs and other animals. It is where I remember reading how the influenza virus changes, mostly because it was written for a general audience.

    I would suggest that the e-mailer read that book, and then follow it up with John Barry’s book on the 1918 influenza epidemic. The latter has some interesting perspectives on the evolution of modern medicine and medical schools.

    (now here is the weird thing, I mostly remember reading those two books in a music studio during my daughter’s violin lessons)

  3. WayneR says:

    Could it be that vaccine skeptics are confusing vaccines with antibiotics? In my layman’s understanding, antibiotics and antivirals kill the bugs for you while vaccines strengthen the immune systems ability to kill them naturally. This distinction seems to be lost on some people and could benefit from some education. Am I correct?

  4. mindme says:

    I used to not get vaccinated. My assumption was I’d enjoy a couple days off of work if I had a legit flu but my thinking changed when it was pointed out to me (I think by SGU) that it’s about herd immunity and me not getting it and passing it on to a stranger who is elderly/pregnant/etc. I don’t want to be responsible for a death because I picked the wrong Starbucks table to sneeze on.

    There seem to be many things we put ourselves out for: we clean up our camp site so strangers can enjoy it later. We walk an extra block to toss our garbage instead of throwing it onto the street or leaving it on a bus seat. We partially do these things because of shame. I don’t want to be thought of as s dirty litter bug. I don’t want to make the indian cry. Littering ain’t cool.

    However much Phil Plait argues “don’t be a dick” is there room for shame in increasing vaccinations?

  5. mindme,

    My thought is that strong wording != bring a dick. Sometimes it takes strong wording to encourage others to not be dicks. Don’t be a dick, get vaccinated.

    Some people would consider it less than civil and dickery to say “Don’t be a dick” in such blunt language, but Phil was just using strong wording to get people’s attention.

  6. Typo “!= bring a dick.” should be “!= being a dick.”

  7. thequiet1 says:

    “My thought is that strong wording != bring a dick”

    Agreed 🙂

  8. In regards to the first commenter pointing out herd immunity as an extremely important point to be made (and I absolutely agree), but one which he felt Dr. Novella failed to properly stress, I would like to say, in his defense, that vaccines being a common topic on his blog he has stressed its (herd immunity) importance many times in the past in many different ways.

    At any rate, a little overstressing of this point is never a bad thing.

  9. VRAlbany says:

    “If my body can fight off the flu quite easily, then why get the shot?” Because the shot is even easier! I hadn’t had the flu for a long time until a bout with it last winter. Yes, my body fought it off quite easily, but not after a few days of feeling like death. This year, I made sure to get my flu shot, and it only took 15 minutes on a regular work break to walk in the pharmacy and walk out. Didn’t even feel feverish or have any side effects or anything. Will do it every year from now on (until that wonder shot comes out).

    I hope the emailer finds the above blog entry and comments enlightening.
    I especially like the “Don’t be a dick, get vaccinated” sentiments above. Getting your shots is not just about you.

  10. VRAlbany says:

    *not before a few days of feeling like death*

  11. eean says:

    I guess the other misconception here is that the body isn’t constantly fighting off infection so it needs the “training” from the flu. The viruses and bacteria which have nice short names are the exceptions that manage to cause a problem. However there nameless billions of denizens of our body which are immune system just takes care of.

  12. eean says:

    Also I wonder how much this whole conversation is colored by people not knowing what the flu is. The term ‘flu’ is used for so many ailments. I had the flu once in high school, it kicks your ass for a week. It’s not a tummy ache.

  13. Donna B. says:

    Caution: Anecdata, n=1 follows.

    For several years (2003 to 2008) I had two or three bouts per year of severely painful sinus infections that always turned into several weeks of bronchitis so severe my ribs ached. After rounds of antibiotics, opiate cough syrups, and steroids, all this would clear up in 3 weeks or so. Late 2008, I changed primary care docs and my new one suggested a flu shot on my first visit.

    I didn’t question the suggestion thinking all I needed was the flu right after recovering from one of those bronchitis bouts. Plus I was not aware of any anti-vaccine movement then and probably wouldn’t have questioned it anyway.

    The amazing thing for me is that I’ve not had a serious sinus infection/bronchitis episode since. This is in part probably due my fear of them and not hesitating to treat the slightest sign of one with more cooperation from my current doctor. But I wonder if it might also be due to the flu shots I’ve been getting.

    Is it unreasonable to wonder if the various ‘influenzas’ out there might cause something else besides full-fledged flu in some people? I’ve never had the flu. Call it superstition if you want, but I’m not about to skip the flu vaccine and part of the reason is that I think it wards off sinus infections and bronchitis. I’m not going to skip it even if it ‘stops’ doing that as I want to keep saying I’ve never had the flu.

  14. Mostly Harmless says:

    I can actually second your anecdote Donna. I had a similar history of chronic bronchitis once or twice a year like clockwork that stopped 3 years ago at the same time I started getting the flu shot on a routine basis. When I was sick it was rarely severe enough for my doc to prescribe anti-biotics, but for the 5-6 years prior to getting the flu shot regularly I would have to take some kind of expectorant or suppressant for about two weeks until it cleared up.

    I did get the full fledged flu one year in that span, but other than that one time all I ever had was a cough and congestion. Now its been almost 3 years since I’ve been sick more than a day at a time.

  15. BillyJoe7 says:

    Interesting anecdotes but please remember they mean nothing.

    Anecdotes are useful only insofar as they lead to hypothesis testing.
    Otherwise they are actually worse than useless in that they can lead to believing things that have almost no chance of being true.

  16. Mostly Harmless says:

    I agree, and I don’t hold my experience as evidence of anything, but seeing someone with a similar set of circumstances does make me interested in looking at what evidence there is regarding whether symptoms like my “chronic-bronchitis” can actually be a low grade flu. I’ll never be able to roll back the clock and know that was the case for me even if there is actual evidence in other people, but I’m curious as to whether there is any information out there along those lines. If true, it could serve as another motivator for people to get vaccinated if they realize that other low grade conditions they don’t associate with the flu are actually treatable by the flu shot.

  17. Donna B. says:

    Gee, thanks for the unnecessary reminder BillyJoe7. Did you not read far enough to get to the “I wonder if” part? If “wondering if” about something is not part of science and/or skepticism then just what is?

    Clarify please. Are you saying that there is almost no chance that flu viruses cause any other ailments besides the flu? Is this so certain that it’s not even a question worth investigating? If so, educate us and tell us how you know that.

    I acknowledged that superstition — not fact — plays a role in my getting the vaccination. That’s “a” role and not one big enough to sway me not to get the shot if I do get bronchitis again.

    Anyway, I should have googled it myself instead of posting a meandering “I wonder” comment here. It’s apparently already known that bronchitis is sometimes caused by flu viruses.

    A yearly flu shot is the 2nd recommended action to prevent bronchitis.

  18. BillyJoe7 says:

    Donna B.,

    Sorry, I was only trying to help.
    If you think I’m not helping, well then I’ll just crawl away again.

    I’m saying that the following has almost zero chance of being true:

    – That you had two or three bouts per year of severely painful sinus infections from 2003 to 2008.
    – That these episodes were caused by a flu virus.
    – That every one of these sinus infections were followed by several weeks of bronchitis
    – That the sinus infections were the cause of these episodes of bronchitis.
    – That the infections cleared up because of the antibiotics; or opiate cough drops; or the steroids.
    – That the flu shots played any role in terminating these attacks.

    The reason I am saying this is threefold. Firstly, memory is known to be very unreliable (points 1 and 3), and there are many reasons for this. Secondly, any hypotheses, even a very well constructed one, is very unlikely to be true – most end up in the dustbin, and very few survive the rigors of the scientific method. Finally, and unfortunately, the flu vaccine is not THAT effective.

    ” Call it superstition if you want, but I’m not about to skip the flu vaccine and part of the reason is that I think it wards off sinus infections and bronchitis.”

    I think you got the superstition bit right. ;):)
    You should have the flu shot though – not because of your anecdote, but because it helps prevent you from getting the flu and from spreading it.

    “A yearly flu shot is the 2nd recommended action to prevent bronchitis.

    They don’t say so explicitly, but they mean bronchitis as part of the illness caused by the flu.


  19. Donna B. says:


    You’re not helping.

  20. BillyJoe7 says:


    All I can say is that was my intention.
    I’m sorry if it looked like a personal attack.

  21. Diane says:

    My understanding is that while the flu virus usually causes a pretty nasty disease that knocks you flat on your back for several days, it can sometimes present as nothing more than a bad cold. Also, viral respiratory infections (flu, cold, and others) increase the chance of subsequent bacterial bronchitis or sinus infections, by damaging the physical barriers to bacterial invasion and also maybe by inhibiting the anti-bacterial immune response.

    So it seems plausible to me that Donna and Mostly Harmless could have been getting the flu and not knowing it, and then been getting the sinus infections and bronchitis as sequelae to the viral infections, so for them getting the flu vaccine could indeed reduce the frequency of sinus infections and bronchitis. It’s very unlikely–they’d have to have been getting multiple flu infections with a highly atypical presentation every year–but it’s not impossible.

    Still, I’d say the most likely explanation for their experiences is chance.

    In case you’re wondering, I’m not a doctor. I am a biomedical microbiologist, but I don’t work on viruses or respiratory diseases, so I don’t have any real expertise in this area.

  22. BillyJoe7 says:

    “It’s very unlikely–they’d have to have been getting multiple flu infections with a highly atypical presentation every year–but it’s not impossible. ”

    A highly atypical presentation three times a year for six years of is not impossible, but it’s pretty close to impossible. Add to that the fact that the flu vaccine that supposedly terminated these attacks completely, is not actually very effective….

    But anyway.

  23. PerpetualLearner says:

    As a nurse practitioner I offer and encourage the flu vaccine frequently, and it’s stunning how often I get the response, “No way! The last time I had a flu shot I got the worst flu of my life. Never again!” I then talk about how the vaccine actually works, and about the individual’s contribution to the greater good, but I have yet to convince anyone who has already drawn their cause and effect conclusion. I am not going to argue with my patients, but it would be great to have an effective rejoinder to this frustrating response. Any gentle thoughts out there?

  24. Donna B. says:


    Your interpretation of my comment read a lot into it that simply WAS NOT there. I merely wondered if there was a connection and you went all crazy like I’d said I was absolutely certain it was a flu virus causing all my problems and absolutely certain getting the flu vaccine ended them. I noted that my new doctor was cooperative in helping me combat the first signs of bronchitis. I should have put more emphasis on that, but you should have noted that meant I was still getting some kind of infection even after starting to get the yearly flu shot.

    I’m also having trouble understanding why you are stating and re-stating that the flu vaccine is not very effective as if that refutes the advisability of wondering about its effectiveness.

    Is this based on the recent study finding that it’s only 59% effective? Is that ineffective enough to post that it’s “not very” effective? Is there any vaccine that is 100% effective? Is there a chart somewhere defining effectiveness of vaccines into say… not at all (0-20), a little bit (20-40), effective (40-60), very effective (60-80), and super-duper effective (80-100)?

    On that made up scale, 59% would be darn close to being considered very effective. Of course, I could change the words to make it not so. Perhaps you’d like to be a little more precise with your statement as I should have been with mine?

  25. BillyJoe7 says:


    Th flu vaccine is certainly not effective enough to stop your three times a year for six years in a row attacks of supposed flu infection stone dead. Not by a long shot.

    And I didn’t go all crazy, I was just trying to help.
    But, instead of getting appreciated for my efforts, I get dumped with a load of anger.

    But, hey, if I’ve somehow misread you, I apologise and I’ll be on my way.


  26. Donna B. says:


    You are again misrepresenting what I wrote and ignoring my subsequent attempts to explain it to you. You are battling a strawman. And that does not help.

    It is difficult to appreciate a misrepresentation. And yes, you have misread me as I’ve tried to explain several times. And that’s a non-apology — a backhanded attempt to make it look as if I owe you one.

  27. BillyJoe7 says:


    Okay, I re-read your original post a couple of times and, in the light of your subseqent posts, I think I did mis-read it. Your story contained a little more circumspectness than I realised. Sorry.


  28. dave7444 says:

    If you get flu and you haven’t had a vaccine doesn’t the process have to search for the correct response to the virus. If you have a vaccine isn’t this part of the process bypassed and if you have had enough vaccines and not suffered enough enough viruses and this part of the process avoided too often couldn’t the immune response it be damaged through some kind of atrophy?

    Regarding having the vaccine I haven’t had it because of assuming I am fairly unlikely to catch it, I am healthy enough to survive the flu and the cost and difficulty in getting a flu jab in the UK, if you are not in the defined risk groups.

  29. SimonW says:

    The Common Cold Research place in Wales notes that ~10% of common colds are caused by Influenza viruses.

    So highly likely as Diane suggests that a lot of people who “never get flu” just never get it especially badly, or get it but don’t recognize it for what it is.

    The other side of the flu vaccine is that it isn’t especially effective at stopping cold like symptoms, probably because it only causes ~10% of cold like illnesses. Which rather depressingly means the vaccine stops a lot of problems in aggregate, but may not make much noticeable difference to the individuals who receive it.

    Then again the retail price of the influenza vaccine is about $10 in the UK currently, so you don’t need to avoid much illness to justify the expense (and a lot of people can get it free of charge in the UK).

    I looked at one of the less common common cold virus groups, adenoviruses, and there was a wonderful story of how the US DoD use to vaccinate against some forms to save on training expenses, but eventually struggled to find a manufacturer. Seems adenovirus vaccine manufacturing restarted this year, so perhaps there is a story here for the skeptics guide. Anyway I found the background to this really interesting, but maybe that is just me.

    To make an impact on “cold like symptoms” we really want a Rhinovirus vaccine, progress is being made but it is slow. An RSV vaccine would save a surprisingly large number of babies and prevent a huge number of babies being hospitalized.

    I suspect the “hug me I’m vaccinated” message gets the “don’t be a dick” message across, plus you might get the odd hug, which seems less likely with the “don’t be a dick” message. I’m thinking “too few – too late” might be worth a shot for getting money from the evidence based thinkers for vaccine research.

    Oh and in the bickering above I think someone failed to account that the 60-70% effectiveness of the vaccine is an average, and that the vaccine may be much more effective in particular individuals (no doubt the reason why some people swear by the flu vaccine and some swear at it), and that breakthrough disease is often more mild. Hence the Cochrane review finding 75% reduction in hospitalisation for a vaccine which is less that 70% effective (according to CDC research). The effect on deaths appears to be even more marked than for hospitalisations.

  30. dave7444 – I don’t think this is correct. Essentially you are getting the vaccine instead of the flu. Both expose the immune system to antigens and stimulate it, one without an infection and one with.

    But even if it were – the immune system is exposed to many novel invaders daily. It is getting a regular work out, have no fears. The addition of a few strains of flu are negligible in terms of immune system exposure.

    The only time this becomes a concern – immune system atrophy due to lack of exposure – is not through vaccines but rather when someone lives in an obsessively clean and antiseptic environment, avoiding as much exposure as possible. Even then the concept is controversial, but is the subject of research.

    Ironically the antivaxer claim that vaccines give the immune system to much of a workout – overloading it.

    Neither claim is correct. Vaccines have a negligible impact on the total number of antigens that the immune system gets exposed to. They simply target a few specific virulent illnesses.

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