The evolutionary genetics of SARS-CoV-2 and the murderous stupidity of the bourgeoisie

The ruling class is doing everything in its power to assist the evolutionary development of SARS-CoV-2, to become more infectious and vaccine resistant. In their myopic incompetence and sheer disregard for human life and scientific evidence, the capitalists are helping to ensure this pandemic drags on for years and continues to wreak havoc on billions of lives. 

There appears to be a correlation between the worst outbreaks of the COVID-19 pandemic and the presence of right-wing politicians closely aligned with religious fundamentalists. These fundamentalists often reject the ideas of Darwinian natural selection. However, while they may not be interested in evolution, evolution is very interested in them. The short generation time of the virus means we can see natural selection occurring in real time rather than thousands of years. These stupid capitalist politicians have been totally incapable of understanding the evolution of the novel coronavirus, with the outcome of millions dead. The threat of new variants is a direct result of this failure.

Donald Trump, Jair Bolsonaro, Narendra Modi and Boris Johnson, amongst others, all followed some form of “herd immunity” plan, or purely relied upon vaccines. They let infection run wild in the population. However the trouble with this approach is that vaccines are designed to work on last year’s version of the virus. This is like World War II generals fighting with horses. Evolution has been likened to the Red Queen in Alice Through the Looking-Glass who said, “It takes all the running you can do to keep in the same place.” Natural selection results in a permanently moving target, while our hapless rulers are stuck in the trenches trying to win the last war, with no concern for the number of casualties their troops are suffering.

A brief lesson in natural selection

Natural selection is nothing more or less than a method of explaining how populations of organisms change in relation to their environment, and for describing how the structures and strategies used by living things came to pass. Evolution by natural selection is a blind and undirected process that will occur in any population that has the following three things:

1. Variation
2. Selection
3. Heredity

Variation means that there must be a variety of different structures or strategies in a population. If there is no variation there is nothing for natural selection to act upon. Selection means that a subset of these strategies are preferred and have increased survivability or fecundity (fertility, reproduction rate) relative to other varieties. And heredity means that individuals in the following generation must be more similar to the preferred types than the previous generation.

For example, an ancestor of elephants adapted to Africa finds itself in a colder climate. There may be a variation in hairiness between individuals. Those individuals with more hair tend to survive and produce more offspring than those with less hair. The average hairiness of the population will increase until either the available variation is exhausted or the energetic or other physical limitations of extra hair become more detrimental than the benefits of thermal insulation.

Figure 1: Natural selection

However, we can also envision situations where natural selection does not occur: eye colour in humans, for example. Here is a situation where there is variation and heredity, but as far we can tell there is no selection. Alternatively, imagine plants growing in areas of varied sunlight. The plants with more sunlight grow larger than those in darker areas. Here there is variation and selection, but no heredity as the differences are environmental and not genetic. 

We apologize for repeating what for many may be ABC, but these important first principles are clearly not understood by the rich and powerful in capitalist societies.

Real-world evolution is often more complex than the above simple situation. Genes often encode proteins that do a specialized job. For example, the novel coronavirus has genetic information that specifies the structure of its spike protein that allows it to enter a host’s cells. Such proteins are typically highly adapted to a task and almost all changes in structure will lead them to be non-functional. This leads to a contradiction: while genetic variation is the raw material of natural selection, in an adapted population 99.9 per cent of mutants are less fit than their parents. An organism that can lower its mutation rate will have more successful progeny than an organism with many mutant offspring. Organisms with lower mutation rates will therefore tend to increase in frequency in the population.

Evolutionary geneticists use the term “fitness” to measure the success of an organism or an adaptation. Adapted populations have a low degree of variation around a mean of maximum fitness. But what if there is another arrangement of the spike protein that is potentially more efficient in entering cells than the old arrangement? And what if this protein structure is not a simple change from the previous structure (as we saw in the example of more hair versus less hair)? This brings us to the concept of fitness peaks and fitness valleys, otherwise known as a rugged fitness landscape.

In Figure 2 we see that there are two genotypes (genetic makeups) that for example could encode two differently arranged spike proteins that are local fitness peaks. But one fitness peak is higher than another. Envision three different populations (A, B, and C) that start with different genotypes. The size of the circles denotes the degree of variation within the population.

Figure 2: Rugged fitness landscape

Population A is close to its peak and if it has low variation it cannot evolve because all mutant individuals will have lower fitness than the average. Population B is away from the peak, but can only evolve in the direction of the lower peak. It is impossible for population B to go in the other direction because it is a contradiction in terms to evolve to “lower fitness”. Population C is on the other side of the fitness valley and is free to evolve to the highest fitness peak. In these three populations with low variation only one is free to evolve to the highest peak. If this is SARS-CoV-2 the higher peak could mean an increase in infection and spread in a human population. 

To achieve maximum potential fitness and jump the fitness valley populations A and B need to increase their variation. This would give them individuals on the other side of the valley. One way to increase variation is to increase the mutation rate. But as previously explained, a high mutation rate tends to be deselected as almost all mutants are less fit than their parents. How is our viral population to solve this problem and go on to ruin the lives of millions of people?

The virus seeks the help of right-wing politicians who allow massive spread of the old variant. Increased population size is the way for the virus to produce more extreme individuals and jump over the fitness valley.

Figure 3 shows two populations with the same average genotype, the same mutation rate, and therefore the same statistical deviation around the mean genotype. One population is large and the other population is small. As can be seen, the large population has more extreme individuals who may be on the other side of a fitness valley. They can then proceed to evolve to be a new more infectious variant of the virus.

Figure 3: Increased population and extreme individuals

The way to stop the occurrence of new variants that go on to kill far more people is to stop natural selection. The easiest way to stop evolution is to keep population sizes low. We need to limit the variation that is the raw material of natural selection and prevent the occurrence of extreme individuals. Politically this means prioritizing reducing the spread of the virus over corporate profits. This is a choice that capitalist politicians are just not willing to make.

Life cycle of SARS-CoV-2

The coronavirus’s genetic material consists of a single strand of RNA, only 30,000 bases long (approximately 10,000 times smaller than a mammalian genome, or 100 times smaller than bacteria). It only contains 12 functional genes which produce proteins that help replicate the virus’s RNA, form a membrane to enclose the RNA, a “spike” protein to enter host cells, plus other proteins that help the virus evade host immune response and spread more efficiently. All of these genes are possible areas where natural selection can act, and the proteins they encode are possible targets for vaccine-promoted immune response.

Genome sequencing has revealed that the virus that causes COVID-19 is 98 per cent similar to a bat virus. Bats and the coronavirus have likely had thousands of years of parallel evolution and mutual adaptation. Therefore when bats become infected, they probably get no more sick than humans do with the common cold. But having jumped the species barrier to humans, we are a new environment for the virus and its presence creates a new environment for us. The increased lethality relative to influenza, for example, is related to the fact that we have little pre-adaptation to SARS-CoV-2.

Trumpite conspiracy theorists and Sinophobic racists have peddled the myth that COVID-19 was created in a Wuhan lab, or from eating bats. Lately, such garbage has been picked out of the trash by Joe Biden for imperialist strategic purposes. This “theory” is highly improbable, as a lab-made virus splicing together a bat-virus and a human-virus genome would be clearly recognizable upon analysis. It is also unlikely that humans caught the virus directly from bats. Cats and dogs can also become infected, going on to infect humans.

The main method of human infection appears to be close contact with aerosolized virus particles by being in an enclosed environment with an infectious individual for a period of time. Factories, warehouses, public transport, and poor-quality crowded housing are perfect environments for spread, and these are the environments the capitalist class forces the working class to live and work in. 

Once inside the body, virions must evade the host immune response. This response can be both broad-based and general against all invaders, or additionally there can be antibodies targeted against specific virus antigens. The virus enters the host cell by its spike protein “key” attaching to a cell receptor “lock”. Once inside, the virus hijacks the host cell machinery and resources to produce more viral protein and RNA. Newly created virions either bud off to infect other cells or the entire cell bursts releasing large numbers of virions. The infected individual then breathes out these particles which go on to infect others. 

Natural selection potentially acts on all phases of the virus life cycle: from increased aerosolization, to immune system evasion, to more efficient cell entry, to more speedy replication. For example, the virus could produce a molecule that irritates the lungs to promote coughing and increased spread. Disrupting the steps of the virus life cycle is the goal of the immune system, antiviral drugs, and vaccines. 

Figure 4: Life cycle of SARS-CoV-2 / Image: Colin D. Funk, Craig Laferrière, and Ali Ardakani  

It is important to note that the virus isn’t actively trying to kill us, in the same way capitalists aren’t trying to destroy the environment—it is just an unfortunate side effect of profiteering. The virus is just replicating as fast as it can, and we are their environment. In fact a virus that is too lethal may be selected against as hosts that die too quickly will not go on to infect others. Asymptomatic individuals can be ideal hosts for the virus, as these people have no idea they are infected and can go on to infect many others. But as explained previously, neither humans nor the virus are currently well adapted to each other and therefore there is initially a high lethality rate. This lethality rate is increased in poor individuals, and individuals facing racism, living in substandard housing with poor nutrition and irregular sleeping patterns due to shift work. All these impacts of capitalism result in worse outcomes based upon class.

How do vaccines work?

Vaccines have been developed in order to beat back the virus. There are two main types of vaccines, those based on messenger RNA (e.g. Moderna, Pfizer) and those based on genetically modified attenuated DNA-based virus (e.g. AstraZeneca, Johnson & Johnson). Both vaccines target the SARS-CoV-2 spike protein. The DNA vaccine works by inserting the code for the spike protein into a weakened cold virus. This mostly harmless virus infects your cells and produces spike protein mRNA, which then go on to produce spike protein. The mRNA vaccines just produce the spike protein directly without having to be carried by a cold virus. 

In contradiction to anti-vax conspiracy theories, there is no way for either of these vaccines to alter your DNA. However, there are common flu-like symptoms in the days after injection, and rare blood clots in the DNA-vaccines due to some unfortunate people having an overreaction of their immune system to the attenuated cold virus. 

Once vaccines have introduced spike protein into the body, these proteins are literally displayed on the surface of cells. Immune cells interact with these displayed proteins to learn what they look like, and to prepare to attack them whenever they are seen again. Most of the vaccines currently require two doses in order to make sure there is a lasting immune response that does not forget what the spike protein looks like. 

Corporate propagandists hail the rapid production of vaccines as due to the innovation of capitalism. Nothing could be further from the truth. More than 90 per cent of the funding and research to develop these vaccines occurs in publicly funded universities. It is only the final step that is privatized and given over to corporate profit. What is more, capitalist governments pre-pay for the vaccines regardless of efficacy and therefore there is very little risk to the corporation. To top it all off, these private corporations deliberately restrict intellectual property rights and production, in order to limit supply and push up prices. They make billions by holding the lives of working class people hostage. This is in direct contradiction of all the tenets of scientific discovery, which relies upon sharing knowledge and collaboration. Additionally, across the globe there are thousands of potential production sites sitting idle because they are not being given the licences to produce vaccines. 

While corproate propagandists celebrate the private production of vaccines, in reality 90 percent of the funding and research is organised via the state / Image: U.S. Secretary of Defense

The capitalist-created bottleneck of vaccine production, combined with the profiteering of corporations and governments forcing workers into infectious environments, plus vaccine nationalism that limits immunization in poor countries, means that virus populations have continued to explode in various countries. This large population size, as we explained before, is the way for the virus to win the race of natural selection. And that is why we continue to see the occurrence of new variants of concern.

One may think that new variants that out-evolve their vaccines is a worry for the pharmaceutical giants. Precisely the opposite: under the murderous logic of capitalism, it is part of their business plan. In reports to investors these corporations have predicted strong profits on developing booster shots to respond to new variants. It is not in their financial interest to eradicate the virus. In a modern take on evolution, one can conceptualize a symbiotic relationship between SARS-CoV-2 and biotech investors, both united in their parasitism of the bodies of working class people. 

The danger of new variants

A number of new variants have been discovered that have evolved to be more infectious than the original strain. The Alpha variant was originally discovered in Britain, the Beta variant in South Africa, the Gamma variant is from Brazil, and the Delta variant is believed to have arisen in India. To mitigate racism exploited by Trump and others using terms like “China virus”, the World Health Organization is moving to name variants after letters of the Greek alphabet. However, it is clear to see the pattern of newly evolved variants coming from countries with right-wing governments that allowed the highest infection rates. 

The infectiousness of a variant can be measured by a virus “R” value. R stands for reproduction rate and is a description of the number of people each infected individual will go on to infect. For example 100 people infected by a virus with an R value of 2 will go on to infect 200 people, who will infect 400, then 800, etc., in a process of exponential growth. A variant with an R lower than 1 will steadily diminish. R is determined by both biological/genetic and social/environmental factors. Lockdowns, mask-wearing, social distancing, and vaccines serve to suppress R. Evolution, profiteering, and stupidity serve to increase R. It is quite amazing that capitalist politicians who have no problem understanding the concept of compound interest repeatedly act like an outbreak with an R greater than 1 will spontaneously fix itself without any measures taken to suppress the spread. 

For example, the Alpha variant has an R approximately 40 to 50 per cent higher than the original strain. This, combined with government negligence, was a major driver of the third wave in countries like Britain and Canada in early 2021. In the space of four to six weeks, the Alpha strain went from 10 per cent of infections to 90 per cent. In a situation where the original strain had an R of 1, Alpha had an exponentially growing R of 1.5.

Recent research into the Alpha variant has revealed it to have 23 mutations relative to the original. This fact corresponds to the rugged fitness landscape model, as the chance of an individual spontaneously having 23 mutations that end up beneficial is incredibly low. And if each mutation in isolation was beneficial, then the original strain would have contained them from the start. Nine of these 23 mutations are believed to alter the structure of the spike protein, potentially enabling the variant to enter the host cell quicker, or evade the immune response to the old spike protein. But interestingly, many of the other mutations are in non-structural proteins and are thought to suppress the innate immune response, allowing the virus to “pass under the radar” without triggering an alarm. 

Now the world is threatened by the Delta variant that contains an additional 13-17 mutations. This variant has an R approximately 50 per cent higher than Alpha, and is responsible for the devastating second wave in India. There has been an attempt to block travel from India, but it is already too late. In the rich countries there is currently a race between vaccination and the variant, but there is no hope that poor countries with few vaccines will win this race. Worryingly, Delta appears not to be significantly slowed down by single doses of the vaccine, and there are even reports of outbreaks amongst fully vaccinated individuals. It is probable that mutations to the spike protein mean that it looks different than the spike protein included in the old vaccines. While it is possible that rich countries will be able to contain Delta with a combination of vaccination and maintaining restrictions, it is sure to run wild in Africa, Asia, and Latin America. And then we all face the prospect of an as-yet unnamed Omega variant evolving out of these outbreaks. 

How capitalists help pathogens evolve

It is probable that the policies employed by right-wing governments to allow premature reopening of the economy facilitated the fact that Delta is not particularly impacted by a single dose of vaccine. Countries like Britain and Canada adopted a “delayed second dose” strategy with the supposed aim to have partial immunity in the population to suppress spread sufficiently so corporations could get back to making profits. This was risky in a number of ways. It could have led to a reduced immune response, but thankfully that did not happen. But it did provide the ideal environment to allow the virus to out-evolve the vaccine.

The murderous stupidity of the capitalists is promoting the virulence and vaccine-resistance of new strains of COVID-19 / Image: Pixabay

This process is analogous to antibiotic resistance. Antibiotics are a wondrous discovery that have improved human health immeasurably in the last century. Prior to the use of antibiotics people used to die from infections all the time. But of course capitalists are ruining this advance by using antibiotics in frivolous ways. Apart from over-prescribing them to people who do not need them (while boosting the bottom line of pharmaceutical giants), corporations also give antibiotics to cattle, to achieve five per cent better growth rates. This leads to a permanent low concentration of antibiotics in the environment. Such sub-lethal doses provide perfect conditions for bacteria to evolve immunity, and are increasingly making antibiotics useless. In the coming decades we could be back to 19th century death rates due to infection and resistance.

The delayed second dose strategy provides an environment to the virus of partially immunized individuals. These partially immunized individuals are sub-lethal to the virus which can infect them, adapt to the vaccine, and then go on to infect others. This is the lesson of every horror movie: don’t wound the monster—kill it dead or it will come back stronger! Again, the drive for profits before people is killing us.

Rich countries seem to be moving away from the delayed second dose strategy and are changing policy to get people fully vaccinated. But this is a case of closing the stable door after the horse has bolted. Delta already exists and is running rampant.

Repeatedly politicians and corporations take a static strategy ignoring the evolution of the virus. Faced with the beginnings of a new rise in Delta we are informed that data shows vaccinated individuals have better outcomes and are less likely to be hospitalized than non-vaccinated. This may be true currently, but it is the equivalent of saying, “Don’t worry if you get sick—you probably won’t die!” These are very easy gambles for the rich to make with the lives of others. They are perfectly happy to play Russian roulette with working class people while they collect their profits in comfortable isolation. 

Let’s assume that vaccines do prevent hospitalization with regard to the Delta strain. They are again forgetting evolution, and are providing perfect conditions for the evolution of a new strain that can overcome the vaccine. The “Red Queen” is running rings around their static backward-looking policy, and vaccine nationalism is allowing infection to run wild in poor countries. 

Murderous stupidity of the capitalists

Scientists can sometimes be guilty of letting their fascination for inquiry cloud their appreciation for the social repercussion of the things they are studying. From an abstract viewpoint, one cannot help but be impressed by the adaptive speed and ingenuity of SARS-CoV-2. That is until one remembers that the virus is ruining the lives of millions of human beings. But one cannot fault the virus. It has no emotions, it has no intelligence, it has no consciousness. The coronavirus is merely 30,000 RNA bases blindly following the laws of evolution—variation, selection, and heredity—in order to most successfully adapt to the environment it finds itself in. 

It is not the virus’s fault that we are ruled by a sociopathic oligarchy that does not care about the people they rule over. You can’t blame SARS-Cov-2 for the fact that our ruling class is doing everything in its power to give it an environment that assists it to evolve. You can and you must blame the bourgeoisie for their profit-driven system that has led society to this disaster. The parasites in suits are far more culpable than the parasites with spike proteins. And the parasites in suits are providing the ideal conditions for a new more infectious and potentially more virulent Omega variant in the months to come. But none of this is known. It is also possible that the coronavirus has evolved to maximum transmissibility and society will finally overcome the pandemic. But if this happens it will be no thanks to the rich and powerful. It will be despite them and not because of them. And it is vital that we understand and remember the murderous role of the bourgeoisie so we can eradicate the capitalist virus after we have eradicated the RNA virus.

Originally published 16 June at marxist.ca |