The Three Phases of Any Pandemic — Back to Basics

Arab Dhow, taking on cargo at The Creek in Dubai

Just so folks understand, I can’t believe I have to write the piece I’m going to write down. You’d think that there would be some cogent narrative regarding COVID, that the epidemiological community would settle on, and the press would forward. But unfortunately, we’ve inherited communities whose social structures are far more damaged than we care to admit — rigid hierarchies, ruled by people with OCD, and psychopaths — that basically are possessed only with dichotomous thinking modes. And that means we’re either ON or OFF with COVID. And in that context, the only messages during ON times are that everyone is going to die, or at least Grandma is going to die.

It’s utterly absurd.

So, in the interest of curing this toxic ignorance, I’m going to write down my take on any virus. Let’s get going.

The Three Stages of Any Viral Epidemic

Any pandemic can be roughly broken up into three stages. These are:

  1. Containment — where the virus is either fenced into a particular geographic area, or alternately fenced out.
  2. Mitigation — where spread across a given landscape can be constrained or delayed with some set of human actions.
  3. Endemic — the virus is functionally everywhere, and while some spread actions may or may not affect who get the disease, it’s largely futile to worry about who’s going to infect who, barring the usual concerns of sanitation of keeping people from coughing on each other (viral dose concerns.)


Containment of a virus is the first part of any pandemic. We jumped this shark in the US likely back in late January 2020, or earlier. Wuhan practiced a provincial lockdown that worked only moderately well (they DID end up shipping enough people around the world to infect everyone else!)

Containment is largely a function of the boundary being considered, as well as the structure of the interface (the permeability of the boundary.) Obviously, if you’re an island nation like New Zealand, you are far more likely to have a longer period of containment/exclusion of a given virus than if you have a situation like New York City, with multiple airports, lax virus security (especially at the beginning of the pandemic) and an attached super-spreader network like the New York subway system. The problem with containment is that it is absolutely inevitable that it WILL end, because living creatures serve as viral reservoirs, and no testing can find a given virus once it is dormant inside a human system.

We can see great examples of failures of containment down through history, with past pandemics like the Black Plague, and the smallpox epidemics that devastated the Americas during the Columbian Exchange. Looking at the situation with a very neutral eye, we might conclude that total social isolation is the only thing that will keep a sufficiently infectious agent out of a population over historic time. And once that collapses, because there is no built-up immunity from exposure, bad things are going to happen.

Containment phases also imply NO exposure to the virus. When that ends (the virus, somehow, gets through) the results aren’t pretty. In COVID, we’ve seen the higher Case Fatality Rates in institutional settings, since no virus was allowed to circulate until it came knocking on the door. People’s immune systems were completely unprepared, and those have been the places with the highest fatality rates.


Mitigation is the phase where potential social actions can be taken to limit the spread of a given virus, before it is established in the myriad biological reservoirs available to it that help it on the path to becoming endemic.

Mitigation is largely a function of network topology of (in our case) a nation. A country like the United States, with its hyper-connected road and other transport systems, is essentially going to have an impossible time during any mitigation phase. Since between any two points on the map in the U.S. contain multiple pathways, each with some assigned time due to population health, various Non-Pharmaceutical Interventions of various efficacies, and especially in the U.S., passage through different climatic zones, what you do on one path only delays the inevitable.

Countries with more simplified topologies, like Canada (essentially a straight line, once the border was shut off) are likely to see more limited success in some kind of mitigation efforts. But of course, these will fail as well. It’s also poorly studied whether mitigation helps or hinders long-term Population Fatality Rates (PFR). An argument might be made that slowing circulation of the virus might help build up human immune systems through low exposure (breaking down containment, essentially, more slowly) or help other systems like hospitals prepare for endemic levels of exposure. At the same time, all mitigation efforts always come at a price of other social goods, like businesses, health, including mental health, and a host of other factors poorly considered.

Understanding mitigation also requires some understanding of viral dose, as well as how this indexes to viral exposure. Maybe I just didn’t get the memo, but this has been one of the most under-studied part of COVID. Feel free to correct me in the comments, and I will add those insights.

After a minimum of one seasonal cycle, and potentially two, it should be assumed that mitigation efforts are ineffective and should be discontinued. In the U.S. , a hyperconnected topology with two seasons under our belt, it is a fair assessment that COVID is everywhere and mitigation no longer works. Don’t believe? Look at the US case map on Google. Or look at this blog post by Ian on Substack. Comparing various areas with mitigation (like masks, which are worthless anyway, but still) next to those without, and seeing identical results, can mean two things. First is that the mitigation measure is weak, and cannot positively affect the numbers of cases/deaths. Or — it can mean that the virus is so well-established with viral reservoirs that we’ve transitioned out of that stage.


I wrote a funny piece about endemicity here, using the example of alligators in Florida and Louisiana. Go read it.

When a virus is endemic, it means that spread is no longer an issue because the virus is literally everywhere. Recently, we’ve seen research on COVID in deer. COVID has also been found in dogs, according to the CDC. I do know from personal experience that airlines won’t let you fly your dog in cargo because of fear of COVID exposure to their employees. Because all of this is just crazy-making, you can indeed fly your small dog under the seat in a compartment. In order to keep this a friendly piece, I really have to hold my fire in discussing the CDC. If you’re an absolute germophobe, you should realize that your cat or dog that is likely the only thing keeping you modestly sane in this pandemic is likely also harboring COVID.

Boo Boo had to be driven across the country last October because Delta said No No to Boo Boo in the Cargo Hold

Seasonality drives all respiratory viruses. That means, once a virus is established and endemic, the only thing that can protect you is your own immune system. Wearing a mask isn’t going to help (not that they work anyway) and if anything, likely forces re-dosing of your respiratory system. We exhale freely for a reason, folks, and the “experts” that seem to trumpet these kinds of measures don’t realize is that wrapping your face in a piece of cloth is not the way the system has evolved to work.

One thing I do know — we likely won’t see a movement to exterminate our pets. I wonder about how far all this will go, but I think that Fido and Fi-fi are probably safe. People may refuse to accept endemicity as an actual thing for people, and wrap those of lesser social status (including children!) in useless masks. But they will not tolerate anything severe for pets. How do I know this? There are two things I’ve written about that have generated the most controversy in my ridiculous, semi-pro career as an op-ed writer. One is masks, during COVID. The other? Killing off feral cat colonies. Lordy.

In Closing

There is a lot of research out there on viral reservoirs. I Googled up this piece in about 5 seconds on RSV. Note date. This is not a new insight. It’s actually an interesting blurb, and I recommend reading it. Basically one can draw from the conclusions that in a modern world, it is functionally impossible to maintain containment over time. Just so you realize, with both the Black Plague, as well as the 1918 Flu, it was ALSO impossible. Once a disease has some combo of factors that increase its virality past a critical level (and hopefully we can agree that COVID is such a disease) everyone’s gonna get it. Anyone with a kid in daycare has experienced this phenomenon.

Virus can hide at undetectable levels in all sorts of living creatures. So China, New Zealand or Australia really don’t look that smart now, do they? They’re just people that jumped off a building and declared they were flying. And we all know what happens next. At the same time, competing for ignorance are people saying “well, I wore a mask this year and didn’t catch a cold.” No one really knows about endemic spread, and sure, contact with other humans may have something to do with viral dosing. But folks — it’s an undiscovered country out there. Or rather, it’s a discovered country out there — by the virus. Demand the right studies. And I’m guessing that the results, in the end, won’t involve our latest version of a St. Christopher medal.

What we are really witnessing is the same old viral phenomenon we’ve experienced as humans (regardless whether it was invented in a lab– that’s an issue but not relevant here) over literally millions of years. But what is new is the memetics. Now we have institutions stuck primarily back in the containment/exclusion – mitigation phase, who have taken unchangeable stances because of their addiction to status. Or you could just say ‘fame’.

These two pieces are here, and really, they’re far more insightful than this one. Once again, I can’t believe this isn’t in a basic epidemiology textbook. But here we are.

The Structural Memetics of Masks

Elite Risk Minimization

2 thoughts on “The Three Phases of Any Pandemic — Back to Basics

  1. Re ” we’ve inherited communities whose social structures are far more damaged than we care to admit — rigid hierarchies, ruled by people with OCD, and psychopaths — that basically are possessed only with dichotomous thinking modes.”

    Yes, a bunch of psychopaths are ruling but that’s only ONE part of the equation. The true, WHOLE, but “politically inconvenient” and “culturally forbidden” reality is more encompassing. Read “The 2 Married Pink Elephants In The Historical Room –The Holocaustal Covid-19 Coronavirus Madness: A Sociological Perspective  & Historical Assessment Of The Covid “Phenomenon”” by Rolf Hefti at

    Without a proper understanding, and full acknowledgment, of the true problem and reality, no real constructive change is possible.


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