What Science Tells Us About the Future of the Pandemic

umair haque · Dec 28 · Medium.com

Is Omicron just Covid evolving to become the common cold? Right about now, you’re hearing that from a dozen places or more. Here, here, here, here, and here. But is it true? Or is it just a myth? I want to share with what science — actual science — has to say. You can form your own conclusions. I am not going to take a “side.” If you’re the kind of person who wants to pick sides, then you are politicising science, and in my estimation, you are a fool. Please go where fools go. Read pundits at the New York Times, who fly into a rage every time I write things like this, and call me names, instead of engaging with the science.

I am not on any side. I am only here to try and think through the science. That is all I am going to do, and you can join me if you want to learn something, too. If not, please don’t read this, and go away.

Let’s begin at the beginning.

Do viruses “evolve to become less severe”? That is the pop theory this particular one — Omicron is evolving into the common cold — is based one.

“There is a widespread belief that infectious diseases evolve to become less virulent, leaving many hopeful that Omicron will be less severe for everyone, regardless of age or vaccination status. This is false. Viruses do not necessarily get selected to be milder or more severe.”

That’s Dr William Hanage, professor of the evolution and epidemiology of infectious disease at Harvard and the co-director of the Center for Communicable Disease Dynamics. He is saying that the pop theory is false. It is a myth that viruses “evolve to become less severe.”

You should note that plenty of the people spreading this myth are not epidemiologists. They are pundits, or talking heads, or doctors, or all three. But they appear to have a poor understanding of epidemiology and virology.

Wait, you might say. Come on. That’s not right. Viruses do evolve to become less severe. Don’t they?

Think it through. If “viruses evolve to become less severe,” we would never have needed vaccines. Remember all the terrible diseases of…not so long ago. Polio was nearly eradicated in the 70s. The eradication of smallpox — probably humanity’s greatest achievement — only happened in 1977. They’d been around for millennia. And they had never evolved to “become less severe.” They just went right on killing and crippling and disfiguring people.

If you think about it, in fact, just using the knowledge in more or less everybody’s mind, there is no example whatsoever of a virus “evolving to become less severe.” Go ahead, just think about what you already know about any virus there is. Did any of the following evolve to become “less severe”? HIV? Nope. Hepatitis? Nope. Rabies? Nope. In fact, HIV and Ebola grew to become more severe over time. What Dr Hanage is trying to point out — despite the myth pundits are peddling — is precisely correct. Viruses don’t evolve to become less severe.

So why do we think they viruses “evolve to become less severe”? Well, it appears to be wishful thinking, which ends up making us fall prey to selection bias. We see a milder wave of a pandemic, and we interpret it as “evolution.” But when a worse wave arrives, we tend to discount that one. In this case, we see the movement from Delta to Omicron as evidence of “evolution.” But evolution is not what is happening here. At least not scientifically — it just appears to be. So what is happening here?

Wait. So why don’t viruses “evolve to become less severe?” Here’s Dr Hanage again. “If virulence (the severity of the disease) is not connected to transmission (the factor that makes a virus successful or not) there’s no real link between the two in most real situations. The great majority of Covid transmission occurs before people become seriously ill, and so the virus has already moved on.”

Now think about polio and smallpox. If you got polio, you’d get crippled years or decades later. You’d get the virus in childhood, but not get disfigured until adulthood. The virus had “moved on.” Smallpox was different — it proceeded swiftly in terrible outbreaks which would kill scores of people in towns or villages or cities, and then rise again and again. Those are two poles of viruses not “evolving to become less severe” for different reasons — because the virus “moves on,” as Hanage says, or because the outbreak burns itself out, but not before travelling elsewhere. Both mean that the selection pressure on the severity of the virus is relatively small, and so it does not evolve to become less severe.

Viruses don’t evolve like we do. This myth is easy for us to believe in because we apply our own understanding of evolution to viruses. But viruses are not like us. We don’t need a host. They do. They aren’t sexually reproducing to seek some kind of fitness advantage. They’re just out there replicating and recombining. Not just in us, but sometimes with us — that is what retroviruses do, write themselves into our DNA.

And “there is little evidence that recombination is favoured by natural selection to create advantageous genotypes.” That is, viruses recombine because it’s what they do. It’s not because recombination is “favoured by natural selection.” That is what they are.

That is what I mean when I said viruses are not like us. It’s a really alien concept to wrap your head around. Viruses just swap genes, in a kind of alien free for all. Sure, there are chemical preconditions and so forth. The point is that are really not like us. We can’t and don’t recombine. We have kids — two of us. Viruses? The “virosphere,” as virologists call it, is an alien world, of beings which are existentially Schrodingeresque, not really alive but not not alive either, recombining in the quadrillions, each of them able to acquire stuff from others, and then jump across species. Viruses aren’t like us at all. And that is why they don’t evolve like us — meaning cellular organisms, especially vertebrates — at all, either. Our primary evolutionary mechanism is sexual reproduction and mutation. Theirs is recombination. We couldn’t be more different.

In fact, viruses evolve…us. If you really want to understand evolution and viruses — and us — then the slightly creepy but also weirdly cool fact is that viruses evolve us.

“Viruses have been proven to be drivers of evolution (Villarreal and Witzany, 2010), including the human genome, which by at least 45% is composed of sequences related to retroviruses. In addition, endogenized retroviruses supplied the syncytin genes that are essential for the development of the mammalian placenta, and allowed the growth of embryos without its rejection by the maternal immune system (Dupressoir et al., 2012).”

This is related to the fact that viruses don’t “evolve to become less severe.” If anything, the opposite happens. We evolve to outcompete or cooperate with them, sometimes by fusing with them. Think of how those “endogenized retroviruses” literally allow us to have kids, allowing the maternal immune system not to reject embryos.

In the really big picture, we co-evolve with viruses. Viruses don’t evolve to “become less severe.” That is a far more accurate view of how evolution really works.

Now let’s come back to Covid.

So why does it look like Omicron is just Covid becoming the common cold? Are my eyes lying to me?!

Think of the flu. Even that hasn’t “evolved to become less severe.” It still affects millions people a year, killing almost a million. People at risk. Like elderly people and the immunocompromised. What saves their lives? Flu shots. The virus didn’t evolve to become less severe. We just developed vaccines. And we have to redevelop them every single year.

A big, big part of why Omicron appears to be Covid “evolving to become less severe” is that we have vaccines. So for those who are vaccinated, it does not end up producing severe symptoms, on average. But that isn’t “evolution,” it’s science.

And it’s science that has a few implications, too. One is that we need our shots to keep on holding against new variants.

You probably think that a booster shot protects you from Omicron forever. You’re wrong. You probably don’t know what the latest data says. I don’t blame you. It’s brand new. Even booster shots hit under 50% efficacy in ten weeks. Presumably, after that — which is all the data we have so far — it falls farther and faster.

Let me say it again. Covid boosters hit 50% efficacy in ten weeks — which is all the data we have so far. In other words, there’s evidence of rapid declines in the efficacy of boosters.

Meanwhile, we have plenty of evidence that you can be reinfected with Omicron. Add those two facts up, and it means that people will keep on getting Omicron after their booster efficacy wanes. Every three or four months or so, because, just as boosters had lower efficacy than first doses, so even fourth and fifth shots will offer less and less protection, too.

Until we have a vaccine specifically against Omicron, we’re going to face reinfection. Even if it’s “mild,” or just like a “cold,” because many of us are vaccinated, not because of “evolution,” we’re going to keep getting it.

And by that time…maybe you can guess what I’m going to point out next…there’s probably going to be another variant.

Why is that? Because the danger of every Omicron case isn’t just that you get ill. I’ve had Omicron, and for me, it was….weird. I woke up with a bad case of vertigo. The room was spinning. Then I proceeded to have something like the flu for about a week. But what science tells me is that the problem here isn’t just that — how sick (or not) I get. It’s that every case of Omicron helps produce the next variant.

And if you understand the science above, because Omicron isn’t Covid “evolving to become the common cold,” the next variant could go either way.

Here’s what Dr William Haseltine, doctor, PhD, and former professor at Harvard Medical School, has to say in his new book, Variants. He is perhaps the single smartest mind on this topic, and I’m going to show you why.

“The existing literature on coronaviruses already tells us they can recombine…in fact, this process is likely how SARS-CoV-2 came to be born, in the ant-eating mammals knowns as pangolins. There are unpublished reports that recombination among SARS-CoV-2 variants occurs.”

“Give the high prevalence of both SARS-COV-2 and other cold-causing viruses at this time, I suspect all the events above have either already occurred or inevitably will.” Did you get that? Dr Haseltine seems to have predicted Omicron.

Now that’s shockingly smart. Haseltine figured out something that affected the entire world, as far as I can tell, first.

Where will the next variant come from, and what will it be like?

So where does the man when who predicted Omicron think the virus will go? He’s monitoring immunocompromised patients. Because they are where new variants appear to emerge, something like — and I hate to say this, but there is no other way to put it — petri dishes for mutation and recombination.

“In some instances of Covid infection, lingering symptoms may last for months, often in immunocompromised individuals. This allows the virus to effectively adapt within a single patient over time, resulting in potent mutations to the Spike protein and larger genome, particularly in cases when the patient receives any sort of antiviral drug. Here we examine one such case of a 72-year-old patient who was infected continuously for two months, as detailed by Truffot et al.”

You should read that article — it’s published in Forbes, of all places. It’s very detailed, and you’ll come away with a much, much better understanding of the science — and the stakes. Here’s what Dr Haseltine goes on to say.

“Position 493 is interesting as well. Until recently, Q493R in the Spike protein was an uncommon, highly antigenic mutation. Gideon Schreiber described a number of receptor-binding domain mutations for antigenicity, one of which was at positions 493. He described Q493H as a highly antigenic mutation. The Q493R and Q493H mutations are both neutral to positive charges, indicating Q493R should have a similar effect. This means transmissibility for variants that carry this mutation is much higher. The only instance of Q493R in variants of concern is the current Omicron variant which is reigniting Covid-19 infections throughout the world. Its observation in an individual immunocompromised patient is notable, to say the least.”

Haseltine is literally watching new variants be born in immunocompromised people.

“This is not the only instance of dangerous mutations developing within an immunocompromised individual. There is a long history of these patients, many of which we have analyzed, including the London, Boston, Pittsburgh, and Italian patients. Recently a 58-year-old patient who underwent a six-month-long infection developed a few questionable mutations in the Spike protein as well, in this instance, E484G and F490L in the receptor-binding domain and several deletions in the N-terminal domain. These mutations all aid in the transmissibility and immune resistance of major variants.”

Emphasis mine. What is Dr Haseltine watching for? Well, understanding viral evolution, he understands that a new variant could go either way. It could be relatively benign, or even milder than Omicron. Or it could be really deadly, recombining, as he warned recently, with elements of MERS and SARS, which have mortality rates of 40% and 15%. Or it could be something entirely novel — like the mutations described in the above paragraph, which appear to elevate transmissibility and severity.

Haseltine is monitoring immunocompromised patients as patient zeros for new variants of Covid. Precisely because there is no guarantee whatsoever — certainly not by “evolution” — that a new variant will be milder. That is because Covid is not “evolving to become the common cold.” It is just evolving. And we can’t say what direction — or jump, leap, sudden recombination or mutation — it’s evolution will take.

That’s the science. As far as I’ve read it and know it. Virologists and epidemiologists are welcome to weigh in. I’ve tried to be careful not to take a side. To commit the fool’s mistake of politicising science. Science is the closest thing we have to eternal, objective truth in this fragile world. None of us should sully it with the callow stupidity of politics, as our leaders do — and pundits do, too.

Read the above carefully. Reflect on it. I’m not telling you anything. I’m just sharing science with you, my reading of it, my interpretation of it. I have no motive or agenda. I would rather have fewer people who really engage to read this post, than more who don’t. I care about disco and art and fashion — but I also read and love science. Here is what it tells me.

It seems it’s a myth that Omicron is Covid “evolving to become the common cold” or “evolving to become less severe.” That is not how viruses evolve. It isn’t how any of them, from polio to smallpox, ever have.

The danger now is of complacency. We will assume that Omicron is Covid evolving to become the common cold, hear that myth repeated back to us a hundred times a day, believe it because it’s what we want to be true, and then get angry and defensive when it’s challenged.

Meanwhile, our leaders, being who they are, irresponsible, imbecilic, incompetent, will seize on this comfortable narrative, which acquits them of a problem to solve. Pundits will force it along, grinning all the while, because they are to science what clowns are to libraries. The world will assume that “Covid is over” because it’s “become the common cold” — and few will question whether that’s actually true or false.

But believing that myth is an error and a mistake. It’s sheer dumb luck — or recombination probability — that Omicron is milder, not the invisible hand of “evolution,” and we’re probably not going to get lucky forever.

Meanwhile, wiser minds, like Drs Haseltine and Hanage will stay vigilant, for the next variant. Because having actually understood the science, they know there is no guarantee it will be better — or worse. There is only the guarantee it will come, and that guarantee is Omicron itself, spreading, mutating, recombining explosively. Our boosters decline in efficacy, and our protections weaken. They are guarding all of us from the uncertain future into which we blindly walk. We should be listening to the wise among us, not the callow, the ones who tell us what we want to hear.

But we’re human. When have we ever done that?

Umair
December 2021

WRITTEN BY

umair haque

Eudaimonia and Co

Eudaimonia & Co