Saturday, August 14, 2021

Pandemic of the Unvaccinated

Here is a heat-map showing percentage of Black population in each county in the U.S.:


Original Source: https://www.reddit.com/r/MapPorn/comments/gdwty5/percentage_of_black_population_in_the_us_by_county/

I have highlighted areas of particularly dense concentration in green.

Here is a heat-map showing percentage of Hispanic population in each county in the U.S.:

Original Source: https://en.wikipedia.org/wiki/File:2010_US_Census_Hispanic_Population_by_County.svg

I have highlighted most of the areas of particularly dense concentration in purple.  For reasons I'll explain in a bit, I've left out California.  I've also highlighted one county in Oregon that has a particularly low concentration of Hispanics.

Now here is a heat-map showing the current spread-rate of Covid per county.  I have transferred those same highlights from the previous two maps to this map (by hand, in Paint, so excuse the crudity of my model):




Original Source: https://twitter.com/EricTopol/status/1426549915581251590/photo/2


My highlights from the previous maps are covering the bulk of the high-transmission counties.  So then the last piece of data is the vaccination rates of Black and Hispanics:

Original Source: https://kff.org

These vaccination rates are only national averages, and are thus not the whole story.  Vaccination rates of Blacks in the south seem particularly bad, when I look at them.  In Florida, they're terrible--high 20s if I remember correctly.

So obviously, I'm driving at a pattern here.  My hypothesis is that a very significant portion of this surge in Covid is being driven by Black and Hispanic communities with low levels of vaccinations.  Remember: diseases don't actually spread geographically so much as they spread through socially connected networks of people.  Therefore, it doesn't matter that Florida actually has an above-average vaccination rate if there exists within Florida a community of socially connected people having a shared low vaccination rate.  In this case, Covid will spread through that specific community at a rate that is high concomitantly with their lack of vaccination.

A few anomalies on the combined map

There are a few things on the Covid heatmap that might seem a bit anomalous, given my hypothesis.

  1. California and Wyoming maybe seem a little reversed compared to what you would expect.  California should maybe have more Covid spread based on its high percentage of Hispanics, and Wyoming seems anomalously high, maybe.

    But California also has had one of the strictest anti-Covid regimes of any State in the Union, fairly consistently from early on in the pandemic.  I think we can maybe see the result of this type of policy in the heatmap.  Other places where I might see the result of public policy are Virginia--which has an interesting clear demarcation from North Carolina, and also has been more Covid-cautious in its public policies--and New York, which became much more Covid-cautious after early disaster.

    And as for Wyoming, I don't think it actually fits that badly with the hypothesis--its most infected county is, after all, also its county with the highest percentage of Hispanics, and the state overall does have a fair share of Hispanics.

    I also suspect that if you really dug into the statistics (if you could get them), you would probably find that there was an inverse correlation between social "class" and low vaccination rates, as well.  I do know that Wyoming is ranch-heavy and therefore hires an awful lot of migrant worker, and I suspect vaccination rates among them are *quite* low.

  2. There is that one area in Oregon which has a very low percentage of Hispanics, but a very high Covid transmission rate.  This, it turns out, is the exception that proves the rule.  This area is comprised of two counties: Douglas and Josephine counties.  And although those two counties may not have high percentages of Hispanic populations, for whatever reason they are considerably less vaccinated than other counties around them:

    Vaccination Rate per 10,000: Taken from the Oregon Health Authority COVID-19 Site
    So this just highlights that the problem here isn't race or ethnicity per se: the problem is vaccination rate among socially connected persons.
So, what we have been told is in fact correct: this is--now--a pandemic of the unvaccinated.

What does this imply?

I think the implications of this reality are pretty straightforward: the highest priority for ending this pandemic in the United States should be increased vaccination, and the area where this most needs to happen is in Black and Hispanic communities.  How we increase vaccination in these communities . . . I have no idea myself.

Furthermore, I think we need to be particularly concerned with the vulnerable people in those communities: the elderly, the sick, and the immunocompromised.  Greater effort should now be exerted, I believe, to seek out those individuals for vaccination.

One thing that has puzzled me recently is how the death rate from Covid compared to infections has not really decreased *that* much since vaccination.  Data is still sketchy on this, but my initial estimations put it at 1/2 to 1/3rd what it used to be before the vaccines.  That's better--but it doesn't match up very well with the great efficacy we have been seeing in the vaccines preventing hospitalization and death, *and* the relatively high rates of vaccination among those most in danger.  If 80% of the elderly are vaccinated and the vaccines are 95% effective at preventing death, then you wouldn't expect the death rate among the elderly to drop just by 1/2 or 2/3rds--it should be a lot more.

But if the spread is happening primarily in communities in which vaccination is low, this now makes a lot more sense.  In fact, deaths from nursing home residents have fallen drastically as a percentage of overall Covid deaths since vaccinations (see New COVID-19 Cases and Deaths Among Nursing Home Residents Have Dropped Since Vaccinations Began).  But not all elderly and infirm live in nursing homes; plenty of them live at home with family among these vulnerable communities.  I believe it very likely that the bulk of the deaths from this latest surge of Covid are coming from these people: elderly, hesitant unvaccinated parents of hesitant unvaccinated children.

So none of this gives us a way forward, per se.  But I think it *does* give us a focal point and I would like to start hearing more discussion about how we are going to solve this specific problem.

Sunday, August 8, 2021

Efficacy, Effectiveness, and the Prevalence of Vaccinated among the Hospitalized: Part 2

Now let's look at an example case in which the efficacy of the vaccines in preventing infection and hospitalization has seemed to be inadequate.  It has been reported (see This 900-person delta cluster in Mass. has CDC freaked out—74% are vaccinated) that an outbreak of Covid in Barnstable County, Massachusetts was a key datapoint in the CDC reversing its recommendation on mask wearing for vaccinated people.  The CDC report on the outbreak is available here, and the key worrisome facts about this outbreak is that a full 74% of the people who became sick were vaccinated, 4 out of the 5 people who were hospitalized were vaccinated, and the Ct values (i.e., roughly how many particles of virus were found from nasal pharygeal swabs of the infected) of the vaccinated and non-vaccinated were "similar".

These numbers do make it seem, on the face of it, that the vaccines aren't doing very much to limit infection spread among the vaccinated.  However, as we saw in the previous post, it is possible for those overall numbers to be misleading, especially if there is a chance that a significant proportion of those people who became infected or hospitalized were immunocompromised.  And it turns out that this is likely to be the case.

The nature of the outbreak in Barnstable County

According to the CDC paper, the outbreak in Massachusetts was the result of "multiple summer events and large public gatherings were held in a town in Barnstable County, Massachusetts, that attracted thousands of tourists from across the United States".  The Massachusetts Department of Public Health, when they interviewed people associated with the outbreak found that people "reported attending densely packed indoor and outdoor events at venues that included bars, restaurants, guest houses, and rental homes."  But the CDC paper also contains this line in the discussion on limitations of its findings at the end of the paper: 

Third, demographics of cases likely reflect those of attendees at the public gatherings, as events were marketed to adult male participants; further study is underway to identify other population characteristics among cases, such as additional demographic characteristics and underlying health conditions including immunocompromising conditions.

What sorts of events are "marketed to adult male participants"?   It turns out that Barnstable County, MA, is the most popular summer vacation destination on the East Coast for LGBT+ vacationers.  It has the highest rate of gay marriage in the entire country.  In the middle of July, they host something called "Bear Week", which is essentially a week-long party for gay men.  During this period, the town population increases 20-fold (from 3,000 people to as high as 60,000) as a result of out-of-town LGBT+ vacationers.  (Wikipedia: Providencetown, Massachusetts)

Neither the CDC report nor the Massachusetts July Covid Update (July 30, 2021 | Update: COVID-19 Cluster in Provincetown) say how many of those who fell sick were gay men.  However, the Massachusetts report *did* show that a full 89% of the people who were sick were male, mostly young.  While Covid has been shown to impact men more seriously than women if they get sick, both genders will get sick at approximately the same rate.  For the natural balance to be upset to that degree, something like 728 of the 934 people who got sick (or 78%) would have to have been gay men.

The CDC report does mention a fairly small number of the patients (30) from the outbreak whom they had already confirmed had an HIV diagnosis--but this was mentioned as being a *preliminary* finding, and they only confirmed by cross-indexing the Massachusetts index of people registered with HIV.  Given that most of the people who got sick were from out-of-town, and given that registering as HIV positive is optional, this number is certain to be too low.

In fact, it's been found in random surveys that more like 1 in 5 of young gay men who frequent bars have HIV, and about half of those people don't even know it yet: (cf: 1 in 5 Gay/Bi Men Have HIV, Nearly Half Don't Know).  So this means that something more like 146--not 30--of the patients in the outbreak are likely to have been immunocompromised.

How many vaccinated people in Barnstable should we have expected to be hospitalized?

The answer to this question depends very much on how many of the out-of-town vacationing gay men were fully vaccinated.  I would *think* that this number would be very high.  If I were a gay man looking to party for a week in crowded settings with other gay men, I would want to make sure I were vaccinated ahead of time.  So I think that my estimate of 90% vaccination rates from Part 1 seems very reasonable.  I admit; this is a guess.  But let's assume this is true for now.

In Part 1, the various multipliers for hospitalization that we came up with work out to a 450x greater likelihood of hospitalization for immunocompromised vaccinated individuals compared to immunocompetent vaccinated individuals.  If you applied this multiplier to the 146 likely immunocompromised people in Barnstable, then you would expect to see about 80 vaccinated patients hospitalized from that group for every single patient hospitalized outside that group.  The actual proportion of vaccinated to unvaccinated was 4 to 1.  So based on my numbers from Part 1, the vaccines seem to be working more effectively than I would have expected.

The difference is so great, in fact, that I suspect my assumptions from Part 1 are wrong.  In particular, I think that my assumption from the South African Novavax study--that the vaccines would be not effective at all for the HIV positive--might be incorrect.

If you expect 80 people to be hospitalized, but only 4 are, this translates to a vaccine efficacy of about 95%.  And indeed, this is roughly what the CDC has been reporting--that the vaccines remain something like 95-96% effective in preventing hospitalization.  So I see the numbers of hospitalized in Barnstable, even given how many immunocompromised were likely in that population, as tending to confirm the efficacy of the vaccine--as far as it goes.  There will still be more immunocompromised people being hospitalized from Covid than immunocompetent, but if you compared immunocompromised to immunocompromised only, the vaccinated will have roughly the same comparative advantage against the unvaccinated.

How many immunocompromised would we have expected to get sick?

So much is good for the issue of hospitalization.  However, the CDC did not look at the Barnstable results and say that the vaccines weren't preventing hospitalizations: they worried (apparently) that the vaccines weren't preventing infection and spread.  So let's look at the reported numbers of the symptomatic infected more closely.  

I estimated in Part 1 that immunocompromised people were twice as likely to catch a disease (at least, symptomatic disease) in the first place compared to the immunocompetent.  This, however, was just taking into account their diminished capacity to fight off a disease rapidly.  In the case of the Barnstable County outbreak, you also have a large group of people that includes (most likely) many immunocompromised people who are also engaging in much higher risk behavior: packing themselves into crowded bars and restaurants for a week-long party.  In this specific scenario, what effectiveness of the vaccine for the immunocompromised would have to obtain in order for the vaccinated to make up 74% of the infected?

I have put together another section of the spreadsheet (link again here: Efficacy vs. Effectiveness) that attempts to model this scenario.  The key assumptions for the Barnstable County outbreak that I am making are as follows:

  • 50,000 visiting LGBT+ vacationers.
  • 90% of visiting LGBT+ vacationers are vaccinated (compared to 69% of the locals, which was the value reported).
  • A baseline vaccine efficacy of 80%
  • A reduced vaccine effectiveness for HIV positive people of 50% the baseline (i.e., 40% in this case)
  • A 2x multiplier for HIV positive people to come down with symptomatic Covid if they are infected.
  • An 8x "exposure rate" for the vacationers compared to the locals to account for the crowded party activities.
Given these assumptions, I can come up with a percentage of the vaccinated among the total infected of 73%, which is right in line with what actually happened.  In other words, it is not necessary to conclude that vaccine effectiveness at preventing disease spread has fallen very far at all in order to see large numbers of vaccinated become ill, in this specific scenario.

VERY Important caveat on interpreting statistical results of models

If you are not very experienced with this sort of analysis, you might mistakenly think that this result is amazingly accurate and therefore must reflect reality.  That I should be able to so accurately reproduce the real-life numbers with some reasonable inputs into a model might seem proof-positive that the immunocompromised are the real reason for the vaccinated making up 74% of the infected people from the Barnstable County outbreak.  But if you thought this, you would be very wrong.

In reality, I had to tweak many of the inputs in this model in order to come up with a percentage very close to the observed percentage.  I constructed the spreadsheet, put in some initial numbers, and then tweaked those parameters that I thought could be realistically tweaked, until my end result finally said "73%".

Since none of my parameters are outlandish, but all could potentially be realistic and true, it is correct to say that my theory (that immunocompromised are almost completely the cause of the scary proportion of vaccinated individuals from Barnstable) is consistent with the available data.  "Consistent with" is a very different statement from "proof of", and it is important to be aware of the difference between a study claiming one and a study claiming the other.

Sensitivity Analysis

It is for this reason that whenever I do a rough-model like this, I provide the link to the spreadsheet, and I encourage anyone who reads my estimates to look at the spreadsheet and make changes--play around with different parameters to see what sorts of result are generated with the new numbers.

When you do this formally and rigorously, this sort of thing is called "sensitivity analysis": you systematically change each parameter--individually and in groups--and determine which parameters are the important ones that actually make a difference on the outcome.  Good statistical packages can do this for you automatically nowadays--though you have to be sure you include all of the relevant parameters as inputs to the program!  "Garbage In, Garbage Out" is still a very true dictum.

Understanding the dynamics of which parameters make a difference to the outcome can do several things for you:

First, it allows you to see what aspects of the problem are more important to get clarity on.  For example, in my toy model, I found that although I accounted for the difference between the local population and the vacationing population, I really didn't need to bother.  The vacationing population is so much bigger, the effects of the local population on the outcome doesn't really matter.  This tells me that the "69% vaccinated" rate of Barnstable County that was reported in the CDC paper and in a lot of news outlets, is really irrelevant. 

Second, it allows you to see how reliable your result is.  In the case of my toy model, I am able to see that my result is not very reliable at all--I have some excessively sensitive parameters that are also too much of a raw guess on my part.  The key number here that makes all the difference is the vaccination rate of the vacationers.  I set that at 90%; if instead you set if lower (to 80%, for example), you have to set the effectiveness of the vaccine way down (to somewhere around the 40% level) in order to still end up in the neighborhood of 74% vaccinated among the infected, if you keep all the other parameters the same.

Likewise, the proportion of HIV positive individuals among the vacationers has a huge impact on the result, and my proportion of 1/5 is taken from a single study of general trends, not any sort of specific survey of this particular population.

Therefore, what this model really proves is only that the events of Barnstable County are currently capable of multiple interpretations.  If we want to know what is really going on in this outbreak, we need more information.  In particular, the prevalence of both vaccination and HIV in the vacationing population are very important for a correct interpretation: both of which might be very difficult to obtain at this point.

Bottom Line

The bottom line conclusion of this must be that we cannot make firm conclusions about the real-world effectiveness of the vaccines from the Barnstable data as it has been reported to us so far.  We would need a far better knowledge of other variables at play--other risk factors--in order to know which variables aside from vaccination effectiveness may have caused different people to end up infected or in the hospital.

This conclusion is especially true in the case of the Barnstable data given that the outbreak there occurred under circumstances far from normal for the national population in ways that are materially relevant to disease spread and vaccine efficacy.  But the conclusion is also true for a lot of other data that has been bandied about by many people.  In general, the prevalence of vaccinated among the hospitalized is a very bad statistic on which to make conclusions.  There are far too many confounding variables that are in play--far too many risk factors which dramatically change the likelihood of hospitalization independently of vaccination status--for this bare statistic to be of any use without a whole lot of other data about those people.

The gold standard for judging the effectiveness of a vaccine is the ability to compare vaccinated people versus unvaccinated people when you are able to control for all other variables.  You want to compare vaccinated sick old men with unvaccinated sick old men, vaccinated teenage girls with no health problems with unvaccinated teenage girls with no health problems, vaccinated middle-aged gay party-goers with HIV to unvaccinated middle-aged gay party-goers with HIV.  And so forth, and so on.

Simply comparing the raw numbers of hospitalized vaccinated to hospitalized unvaccinated people--with no differentiation--is going to be comparing apples to oranges with a vengeance.


Monday, August 2, 2021

Efficacy, Effectiveness, and the Prevalence of Vaccinated among the Hospitalized: Part 1

There has been a lot of angst, recently, over how many vaccinated people are coming down with Covid, even to the extent of being hospitalized.  A lot of people are coming to the conclusion that vaccine effectiveness has been waning--either because the new Delta variant is escaping suppression, or because the vaccines are losing effectiveness over time, or both.

There is some truth to those fears, for sure.  However, I believe that neither fear plays as much a role in uncomfortable numbers of vaccinated people getting sick as a lot of people think.  A third factor that you need to consider when you look at the number of people who are vaccinated who are also getting sick or being hospitalized is the difference between vaccine "efficacy" and vaccine "effectiveness".

I am going to explain what the difference is between these terms and why it matters in Part 1.  In Part 2, I am going to look at an important case study in which this distinction might be very important.

Efficacy vs. Effectiveness

These two words--"Efficacy" and "Effectiveness"--are technical terms in immunology.  Briefly, "efficacy" refers to how well a vaccine reduces disease in an ideal, properly balanced clinical trial.  "Effectiveness" refers to how well a vaccine reduces disease in the real world, given a distribution of recipients that is limited by real world constraints rather than the artificial constraints of a clinical trial.

When a vaccine (or any other medication, for that matter) is tested in a clinical trial, the goal is to identify how well the vaccine works compared to non-vaccination, all other things being equal.  A well-designed clinical trial will identify all characteristics of a subject that might have an effect on the outcome of the trial.  The trial runners will then balance the trial vs. the placebo groups so that an equal proportion of each characteristic appears in each group.  That is, both the placebo and trial groups should contain the same proportion of elderly to young people, of each race and gender, of sickly vs. healthy people, and so forth.  If there is a certain population that is more (or less) susceptible to the disease in your trial, and you do not balance that population properly between your trial and placebo groups, then your final results will be biased by the properties of this particular population.

If a clinical trial is properly balanced, then you can take the difference between how many people get sick in the vaccinated group vs. how many get sick in the unvaccinated and calculate your vaccine *efficacy*.

In the real world, however, there is no one balancing out the vaccinated vs. the unvaccinated populations.  People get vaccinated or not for reasons other than balanced, random chance.  Therefore it is quite possible (and actually inevitable) that, in the real world, the group of people who are vaccinated will have different characteristics from the group of people who are unvaccinated.  This means that you should not expect that the difference between the vaccinated and the unvaccinated who get sick in the real world to reflect the same efficacy as was found in the clinical trials.  What you get from this calculation is the *effectiveness*, and this can be skewed from the "efficacy" number for a lot of reasons.

Risk Averse Behavior

The most critical reason effectiveness can be skewed from efficacy (or at least the reason that *I* think is the most important) is the very nature of human behavior relating to risk.  Simply put, it is pretty obviously true (if you think about it), that those people who are more naturally at risk from a disease will choose to take a vaccine against that disease at a much higher rate compared to people who do not feel similarly at risk.  Given that this is true, you should expect, in the real world, that the group of all vaccinated people will contain many more naturally at-risk people that the group of all unvaccinated people.

How large of an effect will this have?  Well, it could actually have quite a large effect, depending on the specifics.  I think there are, broadly, two different types of person this distinction applies to, which I will now describe.  Then I will try to estimate the magnitude of this effect with some reasonable guesses and a spreadsheet.

At-Risk of Exposure

One type of person is more at risk of catching Covid because of an occupation.  This type of person may have a job that brings him into close contact with a lot of potentially sick people on a regular basis.  The classical example here is health care workers; they are obviously exposed to Covid (at least potentially) a lot more than other people are.  Now, some early studies showed that health care workers weren't getting sick all that more often than other people (see Prevalence of SARS-CoV-2 Infection Among Health Care Workers in a Tertiary Community Hospital)--but those studies were done during a time in which rather extreme Personal Protective Equipment (PPE) practices were in place.  Nowadays, practice has tended to relax a lot further and we are looking at close to business-as-usual behavior.  So I think it is fair to say that healthcare workers will very likely be exposed to a lot more Covid virus than other people.

For this type of person, both natural immunity and vaccination would be expected to work as well for them as for anyone else.  However, given that they will be exposed so much more, the vaccination will be given much more opportunity to fail for these people than for others.

At-Risk of Infection

Another type of person is not necessarily more exposed to Covid, but might be more naturally at risk of catching the disease when they are exposed.  The most important group here, I think, is the immunocompromised.  This is a larger group of people than most realize: it includes the HIV positive, people on a whole array of immunosuppresive drugs, people undergoing cancer treatment, and people with Down syndrome--to name just a few.  Randomized surveys have shown that a full 2.7% of Americans at any given time have been diagnosed as immunosuppressed. (Prevalence of Immunosuppression Among US Adults, 2013).  And I think this number might be understating the total effect, because there are certain conditions that typically don't get you outright diagnosed as "immunocompromised", but which actually do have some compromising effects on immunity.  The two most important of these conditions are age and obesity, both of which are known to exert some suppressing force on immunity (see Impact of Obesity and Metabolic Syndrome on Immunity) and which are together the two most important "comorbidities" for Covid.

How much effect immunocompromising conditions might have on the effectiveness of vaccines is not completely known--but it might be rather severe.  The Novavax study in South Africa included a cohort of known HIV positive test subjects in its vaccine trial.  The sample size was not large--which makes its results here uncertain because of lack of statistical power--but insofar as the results are reliable, they indicate that the Novavax vaccine was not at all effective in the HIV cohort (Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant).  The trial found the vaccine pretty effective for other people, but did not see any effectiveness for the HIV positive--in fact, slightly more vaccinated HIV subjects came down with Covid than unvaccinated HIV subjects.

Immunocompromised also have a two-fold problem: not only are they more prone to catching a disease, since their bodies are not well equipped to fight a disease once it gains a foothold, they are much more likely to be hospitalized from a disease once they catch it.

How much of an effect could these special cases have?

But, you might say, even if the vaccines don't work very well for the immunocompromised, that's only roughly a 3% portion of the population.  That couldn't mess up the numbers that badly, could it?  Yes, it could.  Covid attacks people very unevenly; the more vulnerable people aren't just a little bit more likely than everyone else to suffer badly from Covid, they are far more likely to suffer badly from Covid.  This uneven distribution of adverse effects means that even a pretty small population of very vulnerable people can have a very substantial effect on the makeup of the total hospitalized and dead.

To illustrate this, I have put together this spreadsheet with what I considered simplified but still reasonable numbers, here: Efficacy vs. Effectiveness

In this spreadsheet, I setup a group of 1 million people, and then determine who gets sick and who gets hospitalized based on various parameters.

Here are the assumptions I make for this spreadsheet:

  • The average person will have a 1% chance of catching Covid.
  • 5% of the population will be in "high exposure" occupations, which I set to 4x the regular exposure to the virus.
  • 3% of the population will be immunocompromised.
  • The immunocompromised will be 2x as likely to catch the disease compared to everyone else (a guess, but I think reasonable based on my experiences with an immunocompromised daughter).
  • The vaccine will be 88% efficacious for normal people.  
  • It will be 0% efficacious for immunocompromised people.  (This is consistent with the Novavax trial results even if not proven by them.)
  • 5% of unvaccinated people with functional immune systems who catch Covid will end up hospitalized
  • The vaccine will be 96% effective at keeping people who come down with Covid from being hospitalized.
  • 40% of immunocompromised who catch Covid will end up being hospitalized.
  • 80% of people in high-exposure occupations will be vaccinated.
  • 90% of immunocompromised people will be vaccinated.
  • 60% of everyone else will be vaccinated.
These are all reasonable assumptions.  They may not be quite accurate and some of them are fairly bald guesses, but nothing here is outlandish and nothing contradicts anything I actually know to be true.

With these assumptions, what you will see as far as numbers of actual infections and hospitalizations is that 1394 people who are vaccinated will become infected, whereas 4140 who are unvaccinated will be.  This translates to an effectiveness of approximately 66%.  Meanwhile, 218 vaccinated people will be hospitalized, whereas 228 unvaccinated people will be--which makes it seem as if the effectiveness of the vaccine at preventing hospitalization is basically 0%.

And remember--these results are assuming a very robust protection from the vaccine for 97% of the population: 88% protection against infection and 96% infection against hospitalization over and above that protection.  So we have a seemingly paradoxical result that even with a vaccine that is highly effective, as many vaccinated as unvaccinated are seen to be suffering badly from the disease.

Bottom line conclusion: It is very easy for important sub-groups of your population to completely throw off your bottom-line numbers if you do not interpret the results correctly.  So make sure you understand the sub-groups of your population and account for their characteristics in any study that you do.

In the case of how many people are vaccinated yet also hospitalized, we need to pay careful attention to what other risk factors these people have.  It is not necessarily the case that high numbers of vaccinated people in the hospital implies inefficacy of the vaccine.

Saturday, July 24, 2021

Decrease of Vaccine Efficacy against the Delta Variant?

There have been some worrisome headlines recently to the effect that the vaccines are not very effective against the Delta variant of Covid.  Here's one example reporting the "39%" number that Israel has been reporting:  https://www.cnbc.com/2021/07/23/delta-variant-pfizer-covid-vaccine-39percent-effective-in-israel-prevents-severe-illness.html.

I'd like to put my oar in and give an opinion on what I think may be going on.  I'd like to stress that this opinion is less well formed than some of my other opinions, so if anyone has contrary evidence, I'd be happy to hear it so that I can revise what I think.

To explain what I think is happening, first I need to explain some basics--(be warned that this is a dramatic oversimplification):

How immunity works

I think maybe "Immunity" is an unfortunate word, because it has an absolute feel to it: as if whoever is "immune" has an absolute invulnerability to a disease.  This isn't how immunity to disease works, however.  It's important to realize that immunity is the result of specific cellular functions and therefore operates in a specific way that can offer various degrees of protection.

Let's start at the beginning: when a virus first enters the body of an individual who has never before encountered one of its kind.  At this time, it enters a cell, replicates and spreads to other nearby cells.  Fairly soon, it will start to encounter cells that form part of the body's innate immune system--but successful viruses are able to spread an multiply fairly well for a time before triggering a powerful system-wide immune response.  So for a time, the virus is able to spread exponentially from cell to cell without a lot of opposition.

The *timing* is important here: how fast does the body mount an immune response (elevated temperatures, increase immune cell production, etc.), compared to how fast can the virus replicate throughout the body?  In a typical case of first-time Covid, the virus is replicating throughout the body ("incubating") for maybe 3-7 days before the body's defenses really begins noticing things and starts to kick-in with the defense.  This is why Covid can spread so quickly throughout a population--those last few days of non-defended replication can make a person a font of virus particles for other people before they feel ill themselves.

In addition to mounting a systemic immune response, the human body also begins producing a virus-specific response: neutralizing antibodies.  These are tailor-made particles of just the right shape and properties to stick to the invading viruses and de-activate them (mostly, as we know, by gumming up the spike protein and thus preventing the viruses from entering cells in order to replicate).  The initial production of these antibodies, however, takes some time to ramp up--it's something like 7-14 days before we see any of these of note.

Typically, the combination the innate immune system and neutralizing antibodies will be enough to clear the system of the virus before very long.  The person can be sick for some time afterwards (for reasons I'm not clear on and I don't know if anyone *else* is clear on either).  One thing that has been seen for Covid, however, is that people can test positive for Covid for some time after they have been mostly free from symptoms but that these people very rarely spread Covid to other people.  After the body starts producing neutralizing antibodies, those virus particles that are shed by the sick person tend to come out pre-coated with those antibodies--meaning they don't have much capability to infect others.

How immunity continues after illness or vaccination

Once the body has fought off the disease, the innate immunes system settles down.  However, those specific neutralizing antibodies are still produced at a high level for some time--the body remains "alert", as it were, to the presence of the disease.  This doesn't mean that there is some magic shell around the body repelling the virus, however: if another copy of the virus makes it into your nasal mucus membranes, they will again begin to reproduce.  Immunity isn't some chemical property that infuses all of your cells--it's a "herd immunity" of a collection of cells.  So infection will begin to spread again just fine.  The presence of the antibodies, however, means that the infection will not get very far--some cells will be infected, but enough replicated virus particles will become coated with antibodies that the colony of infection will not spread robustly, but rather will die out.

How quickly this happens depends on several factors: how innately good the virus is at spreading, how many antibodies are being produced by the host, and how effective those antibodies are at impeding the growth of the virus.  For some diseases, the antibodies we produce in response to the virus are incredibly effective at stopping the spread of the virus, so that even a small presence of those antibodies are sufficient to very rapidly halt the progression of a viral infection from cell to cell.  The medical field calls immunity to diseases of this sort "sterilizing immunity", because it is as if the body is completely impervious to a disease after getting it.  In reality, there is still some very small level of infection and replication inside the body if the particular virus gets in--it's just that the spread is *so* small that it is not noticeable and produces no relevant results.

With other diseases, however, the neutralizing antibodies are not quite as effective.  And this starts to matter after a while, because the body doesn't keep up production of neutralizing antibodies for a specific disease at a high level, permanently.  It always keeps some around, but it is normal for the levels of these neutralizing antibodies to drop over time.

What the body relies on, after some time has passed, is the ability to ramp up production of these neutralizing antibodies again.  The immune system has a memory mechanism, by which once it has produced antibodies to a particular virus, it can remember and ramp up production of that same antibody if ever the virus comes back.

All that has been said here applies essentially the same for illness and for vaccination.  The bodily responses are not identical, but the basics here are the same.

The Dynamics of the Immune Response

How your body responds to a virus when you have been reinfected after you have developed an immunity therefore depends on several circumstances.

First, what are the remaining levels of neutralizing antibodies in your system?  If they are currently still high, the virus may never have a decent shot at colonizing your body a second time and the infection will rapidly die, likely without you even noticing it.  Since you have a bunch of antibodies in your system, while the infection is progressing inside you, you are less likely to be infectious as virus particles you expel will tend to be coated in antibodies.  So you could test positive for Covid, but not be a risk to anyone around you.

If your levels of neutralizing antibodies are lower, however, the virus might start successfully spreading throughout your body, up until the point where your body takes notice of it and decides to start activating the innate immune response and ramping up production of the antibodies it already knows how to produce.

How sick you get and how infectious you will be to others now depends on timing.  It becomes a race between the virus becoming established and the body ramping up production of the neutralizing antibodies.  Factors for how this will end up include how healthy your immune system is and how effective your antibodies are against the new viral invader; so the outcomes can range widely.

What I think is happening with Delta and the vaccines

I believe that the dramatically decreased reported effectiveness of the vaccines against the Delta variant are principally due to this dynamic and not principally due to the genetic drift between Delta and original Covid.  It has been shown that neutralizing antibodies produced against original Covid do not work quite as well against Delta as against the original--but I believe this translates into a decrease of vaccine effectiveness something like from 95% to 88%, not all the way down to 39%.

Instead, what I believe is happening is that immunized individuals are getting reinfected with Covid after their neutralizing antibodies have waned somewhat.  There is then a period of time in which the virus is able to colonize their bodies before immune memory kicks in.  This triggers both the emergence of symptoms (which are what get noticed) and rapid uptick of production of neutralizing antibodies.

This is why Israel has been seeing a large increase in infections, but not a correspondingly large increase in hospitalizations or deaths.  In fact, I believe the symptoms that are being reported in Israel as "symptomatic Covid" are primarily immune response symptoms, very similar to what the vaccinated experience on their second dose of the vaccine.

I think evidence for this theory is reflected in the different experience that the U.K. has been having with Delta and the vaccines.  They have been seeing an effectiveness against symptomatic Covid with Delta in the vaccinated more like the 88% range.  But the crucial difference here is that the U.K. pursued a strategy in which they significantly delayed the second dose of the vaccine.  Therefore, most of those fully vaccinated individuals in the U.K. have not had the second dose until fairly recently.  Therefore their levels of neutralizing antibodies are still rather high, and the Delta variant is thus dealing with individuals who do not need a ramp-up time to fight it off.

What does this mean for infectiousness?

Does this mean that Covid is going to be able to spread well among people who were vaccinated back in December / January?  Is the time that the virus is able to reproduce in the body of people whose neutralizing antibody levels have waned somewhat enough time where it can then also spread to other people.

I think the answer to this question must be, yes, at least a bit.  I have a hard time thinking that this won't increase somewhat the ability of the virus to spread from vaccinated individuals.  However, that doesn't mean that I think that this will be a major factor.

The issue is, again, the timing.  While it has been shown that in some cases, Covid can incubate and spread as quickly as in a single day, this is not very common.  More commonly, a person becomes significantly infectious 3-5 days after becoming infected themselves.  Meanwhile, we have carefully watched antibody levels during the vaccine trials, and we see from that that whereas it takes the body a full 7-14 days to start making any antibodies at all after the first shot of vaccine, the second shot of the vaccine produces an almost immediate spike of antibody production--within a single day.

I therefore think that it is likely that in the large majority of cases, a vaccinated individual with lower levels of antibodies will begin producing antibodies and thus become mostly non-infectious before the virus gets a chance to truly blossom.  Presence of symptomatic Covid in vaccinated individuals is therefore usually a sign of delayed but operational immunity, and not necessarily a danger of infectiousness.



Friday, June 18, 2021

Myocarditis after the Pfizer Vaccine: Uncertainties

I wanted to do a quick post about incidents of myocarditis (inflammation of the heart muscle) in young men after the Pfizer vaccine.  This has been in the news for a bit, but I don't think the uncertainties involved in this issue have been properly explained.  Ultimately, I'd like to be able to fit this risk into my risk analysis framework, but we have to deal with the uncertainties first, and in this case they make for a very difficult risk to assess.

Background Rate

Whenever I hear a report of a possible complication associated with one of the vaccines, the first thing I do is research to find out, what is the background rate of that complication?  I then look at the rate at which this complication is being reported by vaccine takers, try to adjust based on how much I think this complication might be underreported, and then the difference between background rate and the adjusted rate for vaccine takers is the increase of risk or this complication that can be imputed to the vaccine.

With myocarditis, however, I found that there isn't a simple answer for determining what the background rate of myocarditis is, especially among young men which is the demographic of concern.

The most up-to-date summary on myocarditis incidence rates I know of is "Epidemiological Impact of Myocarditis", published just this past February.  It describes the current state of knowledge as follows:

Myocarditis was considered a rare disease until intensified research efforts in recent decades revealed its true epidemiological importance. While it remains a challenge to determine the true prevalence of myocarditis, studies are underway to obtain better approximations of the proportions of this disease. Nowadays, the prevalence of myocarditis has been reported from 10.2 to 105.6 per 100,000 worldwide, and its annual occurrence is estimated at about 1.8 million cases. This wide range of reported cases reflects the uncertainty surrounding the true prevalence and a potential underdiagnosis of this disease.

"Between 10 to 105 cases per 100,000" is a very wide range.  There are several reasons for this:

Variability of Severity and Symptoms

Myocarditis is a generic description of any sort of inflammation of the heart muscle.  It can have a number of different causes, and it can be more or less serious, depending on the cause and the degree.  The noticeable effects of myocarditis can range anywhere from "none" (as in, you have myocarditis but just don't notice anything) to "mild chest pains" (which I think is the most common manifestation) all the way up to "sudden death" (see Myocarditis in Clinical Practice).

It is this last part that has caused the medical world to try harder, in recent years, to get a handle on how often myocarditis is happening.  What they have noticed was that in autopsies of people who died suddenly and unexpectedly from heart failure, myocarditis was frequently present even though the patients had not exhibited any of the classical observed symptoms (see Myocarditis and Sudden Death).  If myocarditis is capable of being present with little or no symptoms and yet still causing or contributing to death, there must be many more people who have it at any given time and do not know it, nor suffer any obvious consequence from it.  There would be no reason for these people to come to the attention of the medical world, so the conclusion has been that we don't really know how often myocarditis happens, but we know that it is very under-diagnosed.

One possible measure of how much it is under-diagnosed comes from a study of post-Covid athletes, Prevalence of Clinical and Subclinical Myocarditis in Competitive Athletes With Recent SARS-CoV-2 Infection.  There, they evaluated patients just from symptoms first but later followed up with an MRI.  When they did the MRIs, they identified 7.4 times as many incidences of myocarditis than they did by just symptoms alone.  Now, this study was just for a very particular demographic in a very particular circumstance, so I'm not sure how well it generalizes to the population as a whole.  However, it does mean that a difference between actual rates of myocarditis and reported rates of myocarditis all the way up to, say, 10x are within the realm of possibility.

Variability of Understanding

Given that the medical world has fairly recently recognized myocarditis as being under-diagnosed, increased effort has been put into understanding its spread.  This has led to better tests and procedures developed to detect it in patients who come in with relevant symptoms.  Indirectly, this also leads to a variety of answers to the question of "how prevalent is myocarditis?", depending on how old the specific paper is.  Recently, I have seen this paper cited in support of an incidence rate of myocarditis in children at 1.13 per 100,000: The Incidence of Pediatric Cardiomyopathy in Two Regions of the United States (cited in this NPR article: Pfizer's COVID Vaccine In Teens And Myocarditis: What You Need To Know).  However--crucially--this study was published in 2003.  There are more recent studies that have reported some very different numbers, and I think that's important to recognize.

Variability by Age and Gender

One of the things we know for sure is that there is an age and a gender component to myocarditis: at least, reported myocarditis.  Importantly for the current discussion, the demographic that is most susceptible to myocarditis is young men.  This is something that has also been revealed more clearly in recent years.  The 2003 study I mentioned above did see a slightly higher incidence rate of myocarditis in teenage boys compared to other children, but only by a bit less than 2x as much.  A newer Finish study (2014), on the other hand, has identified a much higher difference--closer to 18x higher prevalence in teenage boys compared to other children (Occurrence and Features of Childhood Myocarditis: A Nationwide Study in Finland).  In what might be considered a companion study of adults, the Finns discovered that the peak incidence occurred in mean aged 16-20 years, declining steadily by age after that (The effects of gender and age on occurrence of clinically suspected myocarditis in adulthood).  Here's the key graph from the first study so that you can appreciate the dramatic difference that occurs for this age group specifically (unfortunately, I don't have access to the full data of the second study):


I don't believe it's completely understood why boys in particular have these higher rates of myocarditis, but I know testosterone levels are suspected.

When you have this level of variability in a specific sub-group, this can lead to higher variability in end-results of a lot of studies, because it then becomes a question: how many of a particularly susceptible sub-group did you include within this study compared to that study?  Especially when we don't know the exact mechanism which causes teenage boys to be more susceptible to myocarditis, this can make it difficult to get consistent results across studies.

Variability by Region and Viral Background

In the first study I mentioned, there was a reported rate as high as 105 cases per 100,000 people.  This specific rate was reported for a particular region: Albania.  Are Albanians particularly susceptible to myocarditis?  Well, maybe--but on the other hand, it may have had more to do with the types of diseases that had been recently prevalent in Albania at and before the time of that regional study.

The majority of cases of myocarditis in the developed world are thought to be caused by viral infections: a virus attacks the heart muscle in some way, and then the immune system triggers inflammation of the damaged tissue.  It's known that certain specific viruses are more prone to causing myocarditis than others, and some of the viruses that have this property are otherwise not very serious.  The incidence rates of myocarditis, then, can fluctuate greatly depending on what specific diseases were recently going around in the region under study.  This may well have been what happened to Albania here.

Here it is relevant to point out that Covid is one of those viruses that has been shown to cause myocarditis--at a rather high rate, as well (possibly even as high as 25%, depending on the study you look at).  Further, we know that Covid has spread much more rapidly among young adults than was earlier appreciated (see here: Difference in Severe Acute Respiratory Syndrome Coronavirus 2 Attack Rate Between Children and Adults May Reflect Bias), and we know that it spreads in this demographic very often undetected.  So we have at hand here in the United States a plausible, ready provider of large amounts of occult myocarditis in young adults.

Combined Variability

When you add up all these sources of variability, you get a lot of uncertainty, because each of the causes of uncertainty I've described so far are independent of each other.  For example, the 105 cases per 100,000 were only from reported cases.  Multiply that by 7.4 as a very plausible ratio between actual and reported, and you get a rate of 777 per 100,000.  And if you were looking for the incidence rates for just the young men in that area, well, you could easily multiply that number by 2 or 3 as well because of the increased prevalence in that group.  So we are looking at plausible ranges of background myocarditis at anywhere from 2 per 100,000 all the way up to *2300* per 100,000, depending on various things that we don't have a great way of knowing.


Rate of Myocarditis Among Vaccine Takers

Ok, so on that very unsatisfactory note, we now we have to move to the rate of myocarditis that we're actually seeing in young men taking the Pfizer vaccine.  The best numbers I've been able to get for the States so far has been from this news report: CDC confirms 226 cases of myocarditis after COVID-19 vaccination in people 30 and under

The CDC is still going through cases they've found on VAERS (as of the time of that news article, they were about half way done), but what they've found so far is:
79 cases of myocarditis/pericarditis reported in teens ages 16 or 17 years after a second dose of vaccine, while the expected number was two to 19 cases, according to Dr. Shimabukuro. There were 196 cases in young adults ages 18-24 years, while eight to 83 were expected.

I know that the first number (79) is out of about 7 million teens who have so far been vaccinated over the course of about 1 month.  If they were expecting 2-19 cases from 7 million people over one month, that means that they were expecting myocarditis at a rate of 0.3 - 3.4 per 100,000 per year.  That corresponds OK with the older 2003 report I mentioned above, but it does not correlate well with the Finnish data.  So I wonder if whoever is analyzing this for the CDC has good updated numbers on myocarditis prevalence, or whether they are using dated information.  Then again, it could be argued that the 2003 study, while not as recent as the Finnish study, at least was a study done in the States, and as we have seen, there can be dramatic regional differences in background rates.


Meanwhile, Israel has reported that "between one in 3000 and one in 6000 men ages 16 to 24" who have been vaccinated have developed myocarditis (news story here: Israel reports link between rare cases of heart inflammation and COVID-19 vaccination in young men).  That's between 17 and 34 per 100,000.  The scientist (Mevorach) is quoted as saying that his is between 5 and 25 times the expected rate, which implies that he thinks the expected background rate is 1.4 to 3.4 per 100,000.  That tells me, again, that he might be behind the times when it comes to background rates of myocarditis in young men, as those numbers don't agree with the Finnish study in the least.  He might well be using the same numbers the CDC is using?  That would seem less valid for Israeli data, though.  Anyhow, compared to the Finnish study, the rates reported are more like 1x-2x the expected background rate.  That's suggestive of a difference, but given the other possible variabilities here, hardly what I would call conclusive.

Europe has also reported some numbers, but as their vaccine program is heavily behind and still heavily targeting the elderly, their numbers are a lot less relevant.

Adjusting the Reported Rate

So, given the bare rates reported above, how would we need to adjust them to get closer to the true number of cases of myocarditis after vaccination?  Unfortunately, this is going to be very difficult to do.

Since VAERS is a self-reporting database, there are likely to be other cases that happen that are unreported.  However, no one really has a great handle on what this ratio between reported and unreported incidents is.

We have done research on VAERS in the past that makes it quite clear that the more serious the side-effects are, the more likely they are to be reported in VAERS.  About 76% reporting for the more serious side effects was the highest that particular report found (see here: The reporting sensitivity of the Vaccine Adverse Event Reporting System (VAERS) for anaphylaxis and for Guillain-BarrĂ© syndrome )

But that high rate of reporting was during the swine flu epidemic, and the researchers rightly pointed out that the high levels of media reporting on the pandemic may have increased reporting percentage in that case.  So what are we to expect in the age of Covid, in which media reporting and public concern about possible side effects of a vaccine under an unprecedented Emergency Use Authorization rollout?  Especially given the fact that the official guidelines for reporting Covid vaccine related side-effects are much more stringent and inclusive than they ever have been for any other vaccine (see the special "Covid-vaccine-only" official guidelines here: https://vaers.hhs.gov/faq.html )

I think it's very reasonable to expect that side-effect reporting for the Covid vaccines will be much higher than normal, and probably higher than they have ever been.  But in reality, no one has actually studied or measured this, and we can only go from intelligent guesses.  Personally, I think the rate is likely to be all the way up to 90% or higher--but I don't have much to back that number up aside from feeling.  Lower numbers are plausible--for the most trivial of side-effects and for other times, reporting rates as low as 1% have been seen.

So I could see plausible ranges of reporting ratios here all the way from 10% to 90%, given that the symptoms of mild myocarditis are frequently very mild and could be dismissed as no big deal.  So instead of 17 to 34 cases per 100,000, maybe we are actually seeing more like 170 to 340 cases per 100,000.

Bottom Line: What can we say about vaccines causing myocarditis?

Unfortunately, I think the honest answer to this question is, "not a lot".  Given the numbers that I am seeing, it is entirely plausible that the vaccines have no causal link to myocarditis at all.  It is also entirely plausible that the vaccines are causing myocarditis in young men, maybe even at a rate as high as about 1 in 3000.  The problem is that there is too wide a range of plausible answers for us to say for certain what is actually the case.

There can be other clues aside from mere numerical prevalence: for example, there is some coincidence of timing, where apparently there are clusters of cases around 4 days after the second dose.  However, I have seen things like this appear chimerically in data on an initial analysis, only to vanish after longer vigilant analysis, so I don't trust this datapoint yet.

I, personally, am very suspicious that this link between vaccination and myocarditis didn't become evident until after the vaccine was approved for 12-16 year olds--precisely the age group that the latest studies are showing to be much more prone to myocarditis than anyone else.  I think it's quite likely that this is a false signal based on an underappreciation of the true background rate of myocarditis in young men.  However, other more expert people than myself have held that there is *probably* something here, so I admit my opinion is not a consensus.  Also, I think that the contrary to my opinion is very possible as well.

So what should we do, in practice?  Well, the first thing not to do is avoid taking the vaccine.  At a very worst case, the vaccine would be causing myocarditis at a rate of something like 1 in 300--that's multiplying the Israeli number by 10x for all of the very mild, asymptomatic cases we assume might be happening without being caught.  If you also account for the same sort of thing on the Covid side, however, you get a rate of myocarditis at 1 in 4.  In other words, if you get Covid, you are at least about 100x as likely to get myocarditis than if you got the vaccine, and probably more like 200x-500x more likely.  You would have to be *really* certain you were not going to get Covid in order to make those odds work out in your favor.

Another reason to get the vaccine is that the cases of myocarditis we have seen from the vaccine have definitely been on the mild side, and again, that is less the case with what we've seen from the virus.  So the incidence numbers alone don't tell the whole story.

The one practical thing that I believe we can take away from this is a single recommendation: for teens and young men who get the vaccine, I would personally recommend avoiding strenuous exercise for the week following the second dose, just in case.  Strenuous exercise is the single most common circumstance that is seen in conjunction with myocarditis that leads to a serious attack.  In case there is any increased risk of myocarditis with the vaccines, abstaining from strenuous exercise for the likely critical period seems to me to be a prudent decision.

Saturday, May 1, 2021

[Draft] Is it an Abuse of Power for the Government to Mandate Vaccination?

DRAFT


This post is a continuation of a discussion from Facebook.  The question we are debating here is:

Is it ever allowable for the government to mandate that a citizen submit to a medical procedure, such as vaccination?  Or, on the contrary, does an unwanted medical procedure--something done to the body of the individual--always violate the personal integrity of the recipient, such that even if it would be for the common good of the nation, a government must respect the wishes of any individual refusing vaccination as inviolate?

1. Summary of the Argument So Far

Here are some of my key take-away points from the initial discussion:

1.1. We are here asking whether there is an intrinsic and necessary bar from the government enacting a vaccine mandate--whether it is permissible for the government to make such a law under any circumstance, or whether instead the nature of personal responsibility or the inviolateness of conscience or some such thing makes it this wrong for the government to do this under any circumstance.

1.2. It is admitted that if such an inviolate freedom exists, it might only apply to the innocent, and that there could be some crimes that would result in the forfeiture of this right to medical self-determination.  This is not on-topic; we're talking about laws that apply to all or most citizens.

1.3. It is also established that there could be other, prudential, reasons for not wanting such mandates to be enacted.  Some such reasons discussed were wanting to avoid the temptation of the government to intrude unnecessarily into the private life of citizens, and wanting to limit government's power to forestall the slide into tyranny.  We are not discussing arguments of this sort now; this discussion is about the logically prior question of the intrinsic possible powers of government.  If it is wrong per se for any government to make laws of this sort, the prudence of such laws for our current world situation is irrelevant.

1.4. The distinction has already been made between laws that impact the common good and laws that are directed solely to the private good of individuals, and it has already been conceded that laws should not be passed that only affect the private good of individuals.  But it was also conceded that vaccination laws do affect the common good, so the claim which we are contesting is that the individual right to medical self determination pre-empts the responsibility of the government over things affecting the common good, in this case.

1.5. I'll point out here that most of the examples given so far as moral parallels haven't been very satisfactory.  Most of the things pointed out as "you wouldn't expect the government to be able to mandate X, would you?" have been things that only affect the private good, whereas the things pointed out as "we already admit that the government can mandate Y, right?" have been things that are done to people's properties and not to their bodies.  Vaccination might be a singular thing in that it is performed on individual's bodies, and yet also has a very clear impact on other people and on the common good.  Or maybe we just haven't thought of other good parallels.

1.6. One parallel that was raised but hasn't been answered yet is the example of a suicidal mother with an unborn baby, starving herself to death.  I think we would all agree the State would be right to force intravenous hydration in this case--but the point was mentioned and then the discussion moved on with anyone directly addressing it.

1.7. The attempt is being made to use the principle of the union of the soul and the body to claim that self-determination over the body is as inviolable as self-determination over the soul.  So far, this is the heart of the current disagreement, I think.


2. On "Personal Bodily Integrity"

The claim is that government mandated vaccines would violate an unalienable right of citizens in some way: maybe you could call it the "right to medical self-determination".  Another way this was put is that man's "moral stewardship" over his own body is absolute, at least insofar as decision making about it can't be compelled by the State.

So first off, I grant that there are certain aspects of the human person which are inviolate and about which the government should not legislate, even if they have a bearing upon the common good.  After thinking about these aspects of human life that I would agree are out-of-bounds, I think there are three very closely related concepts here at play here: dignity, responsibility, and integrity.  In none of these, however, do we see that absolute freedom from the State is accepted.

2.1. Dignity

I have two examples related to dignity:

2.1.1. The ability of man to choose his own individual life "path" and to choose his own way in life is a reflection of his being created in the image and likeness of God, and is hence a matter of high dignity.  This is reflected in the fact that it is considered a sacred and inviolate right of people to choose whether or not they wish to marry and to whom.  It would be a grievous overstepping of government authority to mandate marriages to its citizens.

Nevertheless, this doesn't mean that the choice of matrimony is entirely free from government regulation.  The government validly makes laws to prohibit near relations from marrying, for example, to prevent inbreeding.  The sovereign choice of whom to marry is thus still subject to laws, insofar as their choices have an impact on the common good.

2.1.2. There is no higher aspect of man's dignity than his relationship to God.  Therefore, conscience provisions prohibiting governments from dictating man's beliefs are the hallmark of a good and free society.

Nevertheless, freedom of conscience and freedom of religion are not unbounded, and are still subject to limiting laws for the sake of the common good.  In Thomistic thought, this fact is expressed in terms of whether or not the State has the right to punish heresy (it does).  This sounds quaint, but is not so far off from American jurisprudence as you might think; the rationale by which Thomas justifies the right of the State to do this is the damage to the peace and well-being of society that heresy can cause.  Likewise, freedom of religion in American thought does not give one license to preach any and every thing you want.  Openly preaching sedition or openly calling for the assassination of politicians, for example, is illegal no matter how much you justify the talk with your religious beliefs.  In both cases, the limiting factor on freedom of religion is the genuine common good.

Conclusion: If these two aspects of human life--self-determination in a family and freedom of religion--which are of the very highest human dignity, are not on that account free from all government regulations, then medical self-determination (which is clearly a lesser thing than those), is not therefore free from government regulation on account of dignity.


2.2 Responsibility

Aside from dignity, we also believe in that responsibility of rule follows the principle of subsidiarity: laws should be made by those responsible authorities who are closest to the subject matter of the law.  Therefore it seems that decisions about one's body should most properly be taken by the person himself, who is obviously closer than anyone else possible to the body in question.

You can enumerate the reasons behind subsidiarity as follows:

  1. Those who are closest to the subject matter of a law know the most about the subject matter.  They are therefore the best able to make good decisions about how that thing should be ruled.
  2. Those who are closest to the subject matter of a law are affected by the consequences of the law most directly.  Therefore, they have a stake in the correctness of the law, and are incentivized to avoid capricious rule.
  3. Those who are closest to the subject matter of a law are often naturally fit to rule about said subject matter.  For example, parents are the proper rulers of their children, as ordained by nature.

But do these reasons apply to laws regulating the body in all cases?  We will see that they do not, and that when they do not apply, we do accept that the government can step in as the more appropriate lawmaker.

2.2.1 Knowledge

While individuals are usually the most well-informed about their own personal health, there are a number of things in which it is unreasonable to assume that the average person is best aware of, even regarding his own body.  For example, controlling bacteria growth in the food chain is a complicated process that involves very specialized knowledge and experience.  If you were to ask most people, "how do you ensure that you don't get botulism by eating the wrong foods?", they wouldn't have the first idea how to describe all the steps that need to be taken to do this.  It is therefore unwise for a State to leave the health of the publicly available food chain to personal, individual responsibility only, even though the ultimate end of all activities being regulated is what individuals put into their own bodies.  This is properly a State responsibility, not an individual one.

Likewise, individual citizens are often ignorant of even basic facts about immunology and epidemiology.  They usually don't have a very good idea of the relative risk to either themselves or to others by vaccinating vs. not vaccinating.  This is not a natural knowledge that just comes from being human and living a regular life; it is a specialized knowledge which previously didn't even exist in the world, and that only came about due to the long efforts of many scientists, and which is still increased regularly by a discipline carried out by specializing scientists who spend entire careers studying and improving this knowledge. 

Just as the public health of the food and water chains are the responsibility of the State rather than the individual, then, so to should be the public health of citizens as regarding vaccinations.

2.2.2. Scope of Effect

You might expect that because a law has to do with the body of an individual, that for that reason no other person could be as affected by the law as the individual to whom the law directly applies.  However, with vaccination this is not true.

Vaccinations work against infectious diseases, and these (by definition) spread.  Infectious diseases spread by growing; in other words, in order for a disease to spread throughout a community, each infected person must in turn infect more than one person (on average).  If the average person who catches the disease doesn't pass it on to more than one person, the disease will never grow and it will never be able to spread through a community.

Therefore, for any spreading infectious disease, the average individual who makes decisions that affect his susceptibility to disease is always in the minority of the people whom his actions will impact.  His decisions will impact himself, and more than one other person who is likely to become infected as a result of his actions, plus all the people they may infect, and so forth.

This same principle is operational in the military, where we grant that government has the authority to override the natural instincts of self-preservation over the health of the body inherent in every human, and order soldiers to do dangerous or unhealthy things, or difficult but healthy things that they would rather not do, except that they are so ordered.  This is because the actions and state of health of members of the military affect the lives of many more people than are in the army, because they are the guarding principle of the entire nation.  Therefore whatever individual health preference they might have is "outvoted" by the greater needs of the common good.

In the same way, the impact that  susceptibility to infection has on society is greater than the impact it has on the individual.  And therefore the proper responsible body is society and the State and not the individual.

2.2.3. Natural Fittingness

It may seem that nobody is more naturally fit to make decisions about a body than the person for whom that body is an integral part of their whole being.  

However, when God designed the human person, he did not give rule over all aspects of the body to the human person.  Some operations of the body are independent of our own rule, exempted from that rule by God Himself: involuntary actions.  Disease spread and vaccination involve entirely such involuntary human actions.  We can't choose whether or not to breath; we can't decide how many water droplets we will expel in each breath.  We can't tell our immune system to make this antibody or that antibody at will.

Furthermore, we cannot (in general) choose to change our social interactions so entirely as to preclude the possibility that we will become vectors of disease spread.  Governments may temporarily impose harsh restrictions on social interaction, but since man is by nature a social animal, these things can never last for very long.

Vaccination therefore is directed towards a part of human life that involves the confluence of a completely involuntary action of the human body (susceptibility to infection) with an essential and necessary part of human nature (close-quarters physical interaction).  While everyone participates in these things as individuals, they do not--as individuals--have the power to abrogate or essentially alter these things.  Therefore they do not, de facto, have natural fittingness as rulers over these things.

Conclusion: While most decisions regarding an individual's body do belong to the individual, by virtue of the rules of subsidiarity, none of those usual rules apply specifically to the question of vaccination.  In both knowledge, scope of effect, and natural fittingness, society or the State has a higher competency than the individual.  Therefore responsibility for decision-making regarding vaccination is appropriately given to the State and not to the individual.

2.3 Integrity

A final aspect of the human body that might make it off-bounds of government regulation is its integration with the soul into the whole human. 

2.3.1. While other laws might be validly written that affect the body accidentally, these only regulate how the body exist.  It seems, on the other hand, that a medical procedure effects what the body is.  By affecting the very nature of the body, such a law would touch on the identity of the human being itself.

Supposing, for example, in some small country there were a severe imbalance between men and women.  Could the State mandate (given technology that doesn't really work this way yet) that a certain percentage of the population accept a sex change operation so that the common good of procreation  could be better attained?  Pretty clearly, no, the State does not have the right to do this, even for the sake of the common good.

2.3.2. Another way to see that vaccination is more intrusive into the human integrity than other laws concerning the body is to see that while other laws require men to do something "with" their bodies (go to here, do this thing) or prohibit men to do something "with" their bodies (don't go here, don't do that), mandatory vaccination is almost the only type of law that requires people to do something "to" their body.

However, these arguments are faulty in several respects.

2.3.3. First, the association between any bodily change and identity / personhood is faulty.  While the soul is the form of the body, this does not imply that any bodily change therefore touches on the identity or soul of the person.  In fact, the relationship goes in the other direction: the essence of a man comes from the soul and not from the body.  Since the active principle is the soul and not the body, any modifications done to the body can only, at worst, hinder the actuation of the man's essence.  They cannot add to it.

Mutilations, such as sex change operation, can hamper the soul's ability to completely properly inform the body with its due purpose.  But nothing done to the body actually affects either the essence or the personhood of the subject of such a change.  Amputating a limb, for example, does not make the amputee any less of a person, nor decreases in any way that person's soul.

Mere bodily changes, therefore, do not affect what a person is, as a body/soul composite.  They can only affect how well the body/soul composite exists, if there is severe damage to the body.  Bodily changes that are not also mutilations, then, cannot affect the essence of the person at all.

2.3.4. Second, the above arguments misunderstand the nature of the bodily change brought about by vaccination.  Different types of bodily change affect different aspects of human life, and touch on different aspects of the human essence, because not only is the human being a composite of body and soul, but there soul itself is a composite of different levels and types of souls.  The human essence is composed of sub-essences which are unified into one.

Aristotle, and Aquinas after him, clearly distinguished between those actions that followed from deliberate choice and involuntary actions.  Only the first kind of actions were admitted to be properly human actions.  A man is a rational animal, and it is in his nature to deliberate and choose actions.  Those bodily functions that happen on their own without deliberate reason are called "actions of a man", or also, actions flowing from the vegetative soul of a man.  These involuntary operations are clearly of lesser importance in defining the nature of a man, as they are excluded entirely from the consideration of ethics, as being not relevant to the proper activity by which a man follows his true nature.

Even within the involuntary operations of a man, we can see a distinction between different components, depending on how closely they are related to the essential nature of man.  For example, the reproductive organs have a necessary link to procreation, and hence to the social and familial nature of man.  There are therefore more restrictions on the physical modifications that are allowed to these organs compared to other organs which don't have a function so closely related to the essence of man.  Or also the brain is the organ tied to the intellectual powers of the soul, and therefore must be treated with utmost respect and delicacy, given that reason is the very thing that is properly human.

The immunological functions of man are not in the same way tied to anything uniquely or specially human, but is a mere basic biological function of health which we share with all animals.  Modifications done to it, therefore, do not have anything like the import that modifications to other body parts might.

2.3.5.  Third, the above arguments are wrong to characterize the change caused by a vaccination as a change of what, even purely from the perspective of the immune system.  

In fact, the immune system is a nearly infinitely malleable system that is designed to learn how to recognize invasive particles, to remember which antibodies render those particles inert, and to recall and produce those antibodies when those invasive particles are again detected.

With a vaccine, an antigen is presented to the immune system, but is then processed by the immune system and eliminated from the body.  What is left over is not the vaccine, but the memory of the vaccine in the immune system.  While the immune system after a vaccination is in a different state than what it was before the vaccination, it has not suffered a change of nature.  Rather, it has simply operated in accordance with its nature and now has a bio-physiological memory of a previous experience.

When we learn something intellectually, we do acquire the forms of the new thing we learned as quasi-additions to our own essence.  But it is never said that learning something changes the nature of our mind, or that by learning something new we now are something different than we once were.  Rather, the mind is designed to learn an infinitude of possible forms, and after learning new ones, it has actuated its potency more perfectly than it previously did.

What happens to the immune system after a vaccination is exactly parallel, and is hence not a change of essence at all: it is an actuation of latent potency.

2.3.6. The argument that vaccination is a more intimate and invasive change because it is forcing us to actively do something "to" our bodies also fails.

Boethius, in the "Consolation of Philosophy", discusses the relative happiness of himself, suffering many privations to his body, to that of his captors, who were inflicting those privations on him.  Considered rationally, he concludes that his happiness is the greater.  For while many things were being done to his body against his will, none of those privations compared with the evil actions of his captors, who by their actions were distorting their very soul.  The evil they were inflicting on him was only surface level, whereas the evil they were inflicting upon themselves went to the very root of their being.

In other words, things done to your body can never compare in significance to things you do which have serious moral implications.

But can the government legitimately compel us to do things which have serious moral implications?  If it can, then the argument that compelling us to do something morally neutral to our bodies is too invasive fails.

And, in fact, it can.  For example, the government has the right to compel regular citizens who might have knowledge of a crime to come forward, to swear an oath to God that they will tell the truth, and then to tell the truth about their knowledge of that crime. Or if a citizen happens to have special knowledge that would be of aid in the pursuit of justice in a court, he could be compelled to come forward and offer expert testimony for the sake of justice.

These are actions that all admit that the government can compel us to take, and which have serious moral consequences.  By Boethius' principles, these compelled actions strike much more closely to the core of human nature than does the reception of a vaccine.

2.3.7.  As a further example, I will again point out that the very closest analogy to vaccination that exists outside of the medical world is the act of learning, as becoming immune through vaccination is essentially forcing your body to learn a physical shape in a physical way.

But the mind is in all respects a superior and higher aspect of man than the body.  If the government can mandate mental education for its citizens, which it does for the sake of the common good in order to have a more highly educated populace, then a fortiore, it must have the right to also mandate the physical education of the immune system, in this case for the sake of the physical common good of the population.

Conclusion: Vaccination involves no essential change to a person's body, imparts no change that has an import on functions of the body that are tied to essential characteristics of man-as-man, and is in every respect a less integral and fundamental part of human being and selfhood than other things which do admit of government control.  Therefore, it is appropriate for the State to mandate vaccination, and this in no way represents violence to the makeup of the individual's personal humanity.

3. Overall Conclusion

Mandated vaccination is clearly in the just scope of government authority.  There is no aspect of what vaccination does to a person, whatsoever, which is not matched or exceeded in significance by other things over which we all admit government does have legitimate authority.  Therefore, the argument that the State is violating inviolable rights or transgressing its proper boundaries by mandating vaccination is false.