SARS-COV-2: How we got here and what it means for the future

Ruins of a viking church in Greenland

I want to briefly explain how we got to this point in history and where I expect to see things going during the coming months, in regards to the global pandemic. These are my personal beliefs, based off the evidence I have read. I trust that you’re smart enough to not just take what I say for granted, to look for yourself where the evidence leads you. I’m going to cite my sources where I can find them, but if you wish more explanation of any particular facet of my beliefs, then I’m happy to elaborate and see if I can dig up where I found it.

We start in Wuhan, where a new virus came into existence. This was a lab accident, where a chimeric virus that had been passed through mice with humanized ACE2 receptors ultimately ended up infecting people. My suspicion is that this happened because material was not properly disposed of, the virus ended up in sewage, where workers were carrying out maintenance procedures and subsequently this virus ended up infecting people in Wuhan. Human beings have been carrying out dangerous experiments with viruses for decades, what makes this incident unique is probably mainly the fact that this time we didn’t get lucky, rather than the uniqueness of the experiment itself.

What makes this virus so worrisome is that it is the only one among its near relatives that has a Furin cleavage site. This Furin cleavage site was artificially inserted, as part of the experiment. Furin cleavage sites are not uncommon among corona viruses, but it’s the only one among its relatives that has a Furin cleavage site. Nature gives every one of its critters the bare minimum number of traits that it needs to survive. If you could take a mouse and equip it with the poisonous skin of a frog you’re creating a new mouse plague, because it just lost most of its natural predators that keep its population in check.

Similarly, if you take a coronavirus like this and equip it with a Furin cleavage site, you’re also creating a new plague. These viruses had entered a different path on the tree of evolution to reach the level of fitness required for them to survive. By giving a virus like this a Furin cleavage site, you’re endowing it with a level of fitness far beyond that of its relatives. That’s how it was possible for this virus to spread so rapidly around the globe.

Why were they experimenting with viruses like this? That’s the tougher question. This virus may have been part of an attempt to generate a coronavirus vaccine, useful for military purposes. China, like many other superpowers, has a bioweapons program. The Chinese military likes to experiment with coronaviruses.

The reason for that is relatively simple. East Asian people are the descendants of a genetic bottleneck. Thousands of years ago, a coronavirus decimated the East Asian population, so East Asian people now have genetic traits as well as cultural traits, that make them less susceptible to coronaviruses. They’re less likely to get it, if they do get it they’re less likely to get sick from it and less likely to spread it.

The reason Japan and South Korea were doing so well back in 2020, is the same reason China managed to eradicate this virus in a couple of weeks while we were stuck with it. It’s not because they were wearing masks and contact tracing, as naive Western liberals like to believe. The reason they were doing so well is because they’re East Asian. The number of cases in East Asia and the West will now gradually converge however, because the virus is growing increasingly contagious.

Sometime around late February or March, Western governments began figuring out what had happened, that this is in fact a synthetic virus. That’s when the panic set in. They were trying to get the Chinese government to come clean and admit what had happened, but to admit to this disaster would be the CCP’s Chernobyl moment. It would mean the end of communism in China.

The Chinese communist government knows what they have created, so they were desperate to try to exterminate it. They were spraying disinfectant through the streets. They wanted Zero COVID, because they know very well that they have given birth to a synthetic virus. They told everyone that they had to lock people up in their homes in a desperate attempt to exterminate this virus, without admitting why it is so important to exterminate this virus.

Western governments followed the Chinese government’s example, but it was already too late. With every new person this virus infected, it got a chance to mutate, to try out a new attempt to increase its infectiousness. By November we know this virus was in Brazil, by December 2019 it was in every major Western city. We did not even have the capacity to test for this virus at the scale that was necessary. Zero COVID was not really a viable outcome for humanity when the Chinese government decided to cover up the consequences of this catastrophic experiment.

Most Western conservatives and libertarians are as naive as the liberals. You don’t lock millions of people up in their homes and destroy the global economy to save a handful of nursing home residents. That was never the idea. The lockdowns started out originally as an attempt to eradicate a synthetic virus that had leaked out of a Chinese laboratory, but when that proved impossible, the idea became to use lockdowns to “flatten the curve”. Lock people up in their homes and you can hopefully buy yourself some time to figure out how to deal with what was about to happen.

Unfortunately, there’s a problem that people seem to be missing. When a virus spreads through a population, it builds up genetic diversity. Most of that genetic diversity consists of harmful mutations, some consists of mutations that enhance the virus and allow it to spread more easily. Then, when you try to minimize social interaction, you force a virus like this through a bottleneck. As active cases radically decline, only those lineages of the virus survive that are most contagious. The narrower the bottleneck, the stronger the surviving lineages will be.

That’s what we’ve seen happen since this pandemic began. The version that popped up in England back in fall, now known as Alpha, was more contagious and more lethal than the Wuhan strain. The version that popped up in India, Delta, was more contagious and more lethal than Alpha. At this point, we’re noticing in the United States that young people are being admitted to the hospital at record rates. Hospital admissions for thirty something year olds are now higher than during the winter peak in most of the United States.

This happens for a simple reason. When we try to stop the virus from spreading, only those strains of the virus spread that are best capable of spreading. The strains of the virus that are best capable of spreading, tend to be more lethal too. Why is that? A virus is better capable of spreading when it manages to rapidly make more copies of itself. That’s the same trait that makes it more lethal however. If you look at the mutations in this virus, you’ll find that the same mutations that increase transmissibility tend to increase the risk of hospital admission and death.

This isn’t just true for the coronavirus by the way. It’s true for all the other respiratory viruses too. All of them go through a selection process when we engage in social distancing. This causes all of them to return with a vengeance. In the above graph you can see the Respiratory Synctial Virus outbreak in New Zealand. They caused a problem for themselves, by eliminating all strains of this virus except for a handful of very fit ones, which now spread throughout their population. If this virus keeps going through fitness enhancing genetic bottlenecks like this, the outbreaks will get worse in future years. Why does it seem like everyone has the flu this summer? We relaxed social distancing and so now we’re all getting infected with very fit strains of viruses that were struggling to survive.

If we can agree for a moment that the promise we were given about the vaccine was that it would allow us to move on with our lives after everyone has had a chance to be vaccinated, then I want you to admit right now that the vaccine is not working. You can tell me that it cuts your risk of hospitalization and death by more than 90% compared to unvaccinated people, but it should be clear at this point that the vaccine is not enough for us to return to normal, regardless of whether that is true. To emphasize this point, I’ll give you two graph. The first is deaths in Florida, the second is hospitalizations in Israel:

The numbers are as following: 80.3% of Floridians aged above 65 are fully vaccinated. Israel had fully vaccinated 80% of its adult population by early June. So, here’s the question: Why are their hospitals filling up? If this is all because of “antivaxxers”, shouldn’t hospital occupancy be at less than 20% of what it was back in winter? Remember, it’s not just vaccinated people who should be immune right now: A large number of the unvaccinated people should have immunity from natural infections at this point. Some of the answer can be found in the fact that Delta is more dangerous than the previous strains, but it seems there’s more going on.

Back when this pandemic began, I was very skeptical of the idea that this virus was going to be very dangerous. At this point I have definitely changed my mind. The simple reason for that is because I’m looking at the numbers, I adjust my beliefs when I encounter information that contradicts them.

If we’re in a situation where 80% of the high-risk demographic has been vaccinated, the virus has had more than a year to spread through the population and yet places like Florida are still seeing records in daily deaths, then I am simply left with no other conclusion to draw than the fact that we’re in big trouble. It seems to me that we mainly did this to ourselves, by treating this virus completely differently from how we treat every other virus. By slowing down the speed at which it spreads through the population, we taught it to become increasingly more virulent.

So what’s happening right now? My belief is as following. In recent weeks, we’ve started seeing a rise in breakthrough infections. Most of these infections are not being recorded. However, they’re profoundly dangerous for a simple reason: A strain of this virus that is strong enough to overcome a vaccine induced antibody response against the spike protein is going to be a strain that is unusually strong. With the current leaky vaccines, we have created a situation where once again only highly fit versions of the virus manage to spread through the population.

For vaccinated people, this is unfortunate. For unvaccinated people like me, this is highly dangerous. The vaccines may currently deliver protection for the people who receive them, but it comes at the cost of forcing the virus to become even more contagious to survive. And once again, the same mutations that tend to make the virus more transmissible tend to make it more virulent. I think this is why we tend to see that cases begin to rise when vaccination programs start: If people get infected before the vaccine offers them full protection, the virus undergoes a natural selection process in their bodies.

At some point, the virus reaches a genetic ceiling, where it simply can’t learn new tricks that make it more contagious among unvaccinated people, because it has reached a local optimum. On the other hand, among vaccinated people, this point has not been reached yet. The main reason for that is antibody dependent enhancement.

Among people with antibodies, the virus can acquire mutations that allow it to use the antibodies we produce to its own advantage. These are relatively simple mutations, that can involve deletion, change or insertion of a single codon. The virus is in a constant race, to change itself rapidly enough to allow it to survive. Mutations that allow it to use people’s antibodies to its own advantage will allow it to become more contagious once again.

I respect everyone’s right to make their own decisions when it comes to their own bodies. It is however my firm belief that in the coming months, we will witness the emergence of new strains of this virus, that will continue to reduce the effectiveness of the currently available vaccines, until we eventually end up with strains against which the vaccine has negative effectiveness, that is, strains that will prove to be deadlier in vaccinated than in unvaccinated people.

For most of its brief history, this virus had little genetic diversity. It did not have to change much to spread because nobody had immunity, so relatively little natural selection took place. We saw the same mutations emerge simultaneously in different parts of the world, because only a small number of mutations would be able to enhance its fitness. Because of this, it was possible to make a vaccine against it.

However, the spike based vaccines are now rapidly forcing the virus to change. Unfortunately, this has the effect of causing a rapid and tremendous increase in genetic diversity. The virus is forced to change a handful of places on its spike protein where antibodies can currently bind. It doesn’t really matter how it does that, as long as it pulls this off. Mutations that would previously have decreased its fitness will now enhance its fitness.

When a mutation becomes very prevalent, it opens up an opportunity for new mutations, because some changes to the virus are only possible if intermediate steps can take place on their own. It needs an evolutionary stepping stone for certain changes. People with some degree of immunity against the spike protein create such an evolutionary stepping stone.

What I expect will take place as a consequence is that we’re going to see what evolutionary biologists call an adaptive radiation. History is filled with examples of animals that change very little for a long time, until they conquer a new ecological niche and suddenly evolve into all sorts of different directions as a consequence. With this virus, we have now created a situation where it’s going to branch of into numerous different directions.

This creates a huge problem, when it comes to creating a vaccine against these new strains. With the Dengue virus, we see that you can’t really develop a vaccine, because an immune response against one strain actually has the effect of enhancing the infection with another strain. With this virus, we haven’t reached that point yet, but genetic diversity is rapidly exploding, so we’re likely to see something similar eventually.

The problem you have to understand is as following. Natural immunity is different from spike-based vaccine induced immunity. With natural immunity, you’re extremely unlikely to be infected again. If you do end up infected again, you’re extremely unlikely to pass on your infection to other people. The only people who seemed to suffer second infections tend to be people with rare immune disorders. If reinfections are rare enough, then they don’t play a meaningful role in the evolution of this virus.

On the other hand, in Israel we can see that infections among vaccinated people are now quite common. Those people might not get very sick, but they do create something else: They create a training ground, for this virus to learn how to change its spike protein to avoid both the vaccine induced immune response and parts of the natural infection induced immune response. The viral load studies done so far have shown that CT values among these breakthrough infections are basically equal to those in people who were not vaccinated and got infected for the first time in their lives. In other words, this virus is now spreading among vaccinated people.

This is now setting the stage for the explosion of variants. When this explosion of variants has taken place, it will subsequently become impossible for us to develop any sort of vaccine against the virus, because an immune response against one strain will enhance an infection from another strain. In addition, original antigenic sin means that the first learned immune response will be recalled in a second exposure.

It’s going to be very hard to override the original immune response people learned through the vaccines and the currently administered boosters. This did not have to happen, the mistake that we made was to deploy a leaky vaccine, in the middle of a global pandemic. I think the solution we should have pursued was to deploy a vaccine based on a live attenuated codon deoptimized virus, administered in the upper respiratory tract.

This kind of vaccine would have been able to accomplish what the currently deployed vaccines can not do: They can deliver sterilizing immunity. When you have induced such sterilizing immunity, vaccinated people become effectively irrelevant when it comes to the further evolution of this virus. Right now we’re faced with the opposite scenario, in which vaccinated people are the birthing ground of new variants with different spike proteins against which antibodies don’t function.

The consequence all of this has is that we’re going to be faced with the descendants of this virus for generations to come, with no real viable way to immunize people against them, just as it’s not possible to immunize people against Dengue. You can get infected with one version of Dengue and rather than protecting you against the other versions, your immune response now makes you more likely to get infected with another version and makes the infection more severe.

That is essentially what I expect we’re going to see with the descendants of SARS-COV-2. You can already see this interaction take place between SARS-COV-2 and the other corona viruses. If you get infected with HCoV-OC43, the antibodies you produce against this human coronavirus make you more susceptible to a severe SARS-COV-2 infection. The reverse may very well be true too: It’s perfectly possible that antibodies against SARS-COV-2 make you more susceptible to a severe infection from other viruses.

I know some of you are still of the opinion I had one year ago, that this virus is not a real problem, that it’s merely killing the very old or that people who test positive for it are included in the death count despite having died of other causes. You’re entitled to your opinion of course, but I would like to ask you, to try to explain what we’re seeing in South America now. Why do they have the worst death toll and why is the death toll worse among men than among women?

Human beings differ in the degree to which natural selection has strengthened our protection against respiratory infections. Native Americans are descendants of a genetic bottleneck of hunter gatherers who crossed the Bering strait and because of this happen to be more vulnerable to most respiratory viruses that have decimated Eurasia for generations. This is as true for this novel corona virus as it was for smallpox, influenza and measles.

There are some things we can do to make the situation better. There’s a long list of dietary supplements you can find people preaching about on most obscure corners of the internet, I won’t bother repeating those here. However, my main recommendation would be to learn from the dietary pattern of places where COVID-19 is proving not to be a big problem. In sub-Saharan Africa and East Asia, the death toll is very low. This is largely down to the fact that these people have a plant based diet.

In particular, beans that have been cooked at low temperatures (below 100 degree), still contain protease inhibitors. Plants that produce beans don’t like to have their proteins consumed by insects, so they have inhibitors that make it difficult to break down these proteins. Those same inhibitors make it difficult for viruses like the corona virus to undergo the changes required for them to infect a cell. It’s similarly very useful to eat fermented foods, like people do in East Asia. I recommend eating Kimchi and fermented soybeans, like Natto.

This is not something you’re going to have to do for a winter. Rather, my belief is that we’re entering a bottleneck event as a species, where our population will contract during the years ahead. The people who will survive the bottleneck will tend to be the people who are protected from severe infections with corona viruses. Those people will simply have cultural and dietary practices that are very different from the lifestyle we are familiar with ourselves.

It doesn’t mean the end of regular social interaction, but it does mean that humans will have no other choice than to return to dietary and cultural practices that place us in balance with nature. Our bodies are designed to eat mainly plant material that is either raw or poorly heated. Our bodies are also designed to be in constant contact with a wide variety of natural bacteria. In the slums of India we saw very few deaths from SARS-COV-2, because people live in unhygienic conditions. Social distancing doesn’t eliminate the problem, it makes it worse.

Plants produce terpenes and other volatile organic compounds that have an anti-inflammatory effect in our lungs. We evolved to live in nature, in deep contact with other organisms. We see that people who live in places with a lot of vegetation have low death tolls, whereas forest fires and air pollution increase the death toll. The only reason we were able to create the current lifestyle, in which we live isolated from nature, is because viruses and other pathogens are playing a game of catch-up: They have to learn how to survive in a situation where we practice rigid hygiene and developed antibiotics and other ways of eliminating them.

Long COVID is not a psychosomatic illness. It’s a real disease, a post-viral syndrome that will make you feel exhausted. Long COVID seems to be what happens when the immune system is forced to remove this virus from the body, by generating antibodies that can also bind to your own body’s endogenous proteins. This disease is not unique to SARS-COV-2, but it’s a problem we mostly see with SARS-COV-2 because the virus is more dangerous than regular influenza viruses and because most of the virus very closely resembles human proteins.

All of this isn’t just individual, it’s a collective transition that we’re going to be making, towards simplified lifestyles. If your housemate has a plant based diet, he probably won’t get severely ill from this virus. If he doesn’t get severely ill, he probably won’t make you severely ill by exhaling the virus. Nations with plant based diets, like most of those in Africa, will end up faring much better and see much lower death tolls in the years ahead.

Sometimes a culture chooses to die. That’s the example we often hear about the vikings in Greenland, who died out because they refused to start eating fish when their harvests failed. That’s essentially the decision that not just individuals, but entire nations are going to have to make in the years ahead: Do they want to survive through this global transition, or do they wish to perish together with the old world that isn’t going to return?