Wed. Aug 4th, 2021

(Oh, and mandatory masking in public places.)

There’s been a lot of information going around since Monday about why what the government is doing is a “bad idea,” or conversely, why it is “the only thing that it can do, because we will never be rid of the virus.”

Much of the discourse around the issue has been highly politicised – and correctly so, because the government has made some extremely stupid decisions over the handling of this pandemic, and was not prepared  – witness Operation Cygnus – for any similar situation. But not all of that politicisation is helpful, because it obscures what actually happens with viruses.

We hear a lot of conversation around the virus mutating, and herd immunity, and the R number, and vaccine escape, and the potential for disaster when the virus is rife (in a high incidence) in the population, and we are told that the more we open up and the higher the virus levels in the population rise, the likelier we are to reach a situation where the vaccines we have received do not function against the virus any longer, but that if we can reach “herd immunity” then we will all be ok, and this situation will simmer down to the type of situation we have with flu: we will all be relatively resistant and only some people will die.

Sometimes this gives rise to people advocating herd immunity, and the anti-vaxxers have a field day with the “vaccines don’t work so we should rely on natural immunity” and attempt to focus us on the dangers of vaccines compared to relying on natural immunity. Sometimes it gives rise to suggestions of completely isolationist policies designed to reach zero-covid, which suggestions are then used politically to beat some particular drum.

But do we actually know what viruses are, and how they work when we are talking about all of these issues? Do we actually understand what we are dealing with here? I’m not sure.

Viruses are not necessarily living things, that’s for starters. They straddle the border between the biological and the chemical, and the argument about whether they are “living” has been going on since they were first isolated. (And is still going on today: read this if you’d like to see arguments for and against: ) If you look at the “seven life processes” that we are all taught about – or should be taught about – at school, then they fail certain basic tests. They do not, for example, reproduce independently outside a host cell, which could be used to argue that if they are incapable of independently reproducing they are not alive. The thing is, viruses reproduce in a specific and peculiar way.

The Microbiology Society – which should know what it is talking about – defines viruses thus:

“Viruses are the smallest of all the microbes. They are said to be so small that 500 million rhinoviruses (which cause the common cold) could fit on to the head of a pin. They are unique because they are only alive and able to multiply inside the cells of other living things. The cell they multiply in is called the host cell.

A virus is made up of a core of genetic material, either DNA or RNA, surrounded by a protective coat called a capsid which is made up of protein. Sometimes the capsid is surrounded by an additional spikey coat called the envelope. Viruses are capable of latching onto host cells and getting inside them.

H3N2 influenza virus particles

© CDC / Science Photo Library H3N2 influenza virus particles, coloured transmission electron micrograph (TEM).

Each virus consists of a nucleocapsid (protein coat) that surrounds a core of RNA (ribonucleic acid) genetic material. Surrounding the nucleocapsid is a lipid envelope that contains the glycoprotein spikes haemagglutinin (H) and neuraminidase (N). These viruses above were part of the Hong Kong Flu pandemic of 1968-1969 that killed approximately one million people worldwide. H3N2 viruses are able to infect birds and mammals as well as humans. They often cause more severe infections in the young and elderly than other flu strains and can lead to increases in hospitalisations and deaths.

Viruses only exist to make more viruses. The virus particle attaches to the host cell before penetrating it. The virus then uses the host cell’s machinery to replicate its own genetic material. Once replication has been completed the virus particles leave the host by either budding or bursting out of the cell (lysis).

(Budding: As the newly formed viral particle pushes against the host cell’s plasma membrane a portion adheres to it. The plasma membrane envelops the virus and becomes the viral envelope. The virus is released from the cell. This process slowly uses up the host’s cell membrane and usually leads to cell death.

Lysis: The virus particles burst out of the host cell into the extracellular space resulting in the death of the host cell. Once the virus has escaped from the host cell it is ready to enter a new cell and multiply.)

And this, of course, is how they make you sick and ultimately kill you: they are disrupting your cells from the inside, killing them, again and again and again.

What about vaccines?

In whatever form they are made – and there are many different ways of creating them – vaccines make it possible for your cells to recognise the attack of the virus, and defend you against it. In a very, very simple way of looking at it, if the virus uses a specific prod to open a way into your cell, then what the vaccine does is to teach your body to recognise that prod and disarm it.

Here is the World Health Organisation’s explanation about pathogens. (A virus is a pathogen: in the original Greek etymology, literally this means “a begetter of suffering”: the “pathos” is “suffering” and the “gen” bit is the same root as “genesis” and “genome” and derives from the Greek “gignesthai,” to be born.)

“A pathogen is a bacterium, virus, parasite or fungus that can cause disease within the body. Each pathogen is made up of several subparts, usually unique to that specific pathogen and the disease it causes. The subpart of a pathogen that causes the formation of antibodies is called an antigen. The antibodies produced in response to the pathogen’s antigen are an important part of the immune system. You can consider antibodies as the soldiers in your body’s defence system. Each antibody, or soldier, in our system is trained to recognize one specific antigen. We have thousands of different antibodies in our bodies. When the human body is exposed to an antigen for the first time, it takes time for the immune system to respond and produce antibodies specific to that antigen. (This is where we are with Covid.)

In the meantime, the person is susceptible to becoming ill.

Once the antigen-specific antibodies are produced, they work with the rest of the immune system to destroy the pathogen and stop the disease. Antibodies to one pathogen generally don’t protect against another pathogen except when two pathogens are very similar to each other, like cousins. Once the body produces antibodies in its primary response to an antigen, it also creates antibody-producing memory cells, which remain alive even after the pathogen is defeated by the antibodies. If the body is exposed to the same pathogen more than once, the antibody response is much faster and more effective than the first time around because the memory cells are at the ready to pump out antibodies against that antigen.

This means that if the person is exposed to the dangerous pathogen in the future, their immune system will be able to respond immediately, protecting against disease.”

Look carefully at the picture, because it is important. The whole point about a vaccine is that it teaches the body to deal with a specific pathogen by producing a specific antibody. But then the picture shows us that a new pathogen doesn’t have an antibody to counter it.

And it’s not just a new pathogen. A mutated pathogen – a virus that has changed its shape, for example – will also not trigger the antigen because the antigen doesn’t recognise its shape any more.

And this is where it gets tricky. When we use language such as “fighting the virus” or “defeating the virus”, or “winning against the virus” we anthropomorphise – and politicise – the whole issue of what viruses are and what they do in a way that impedes our understanding of how we can deal with the virus that is currently causing so much death and suffering worldwide. We imply that this is a fight against a wily and aggressive predator, and that if we are strong enough, plucky enough, powerful enough, and in this country, given its emerging social narratives, patriotic enough, we can “defeat” the virus. The virus, it is implied, is almost deliberately producing different variants to defeat our attempts to defeat it.

But we are not fighting a predator. We are not fighting an enemy. This is not a battle we can win with any glorious defence, because what we are fighting against is chemistry and mathematics, and they are impervious to any human emotion. They cannot be swayed, they cannot be influenced, they cannot be persuaded or bludgeoned or argued with. They can be countered, yes, but only chemically and mathematically.

All viruses mutate. They can do this because they contain their own DNA, and a mutation is a change in a DNA sequence. Mutations can result from DNA copying mistakes made during cell division, exposure to ionizing radiation, exposure to chemicals called mutagens, or infection by viruses. Germ line mutations occur in the eggs and sperm and can be passed on to offspring, while somatic mutations occur in body cells and are not passed on.

(The picture below, from the National Human Genome Research Institute, shows some ways in which viruses can mutate.)

Can you will a cell to mutate? No. Can a virus deliberately cause its DNA to mutate in order to evade a vaccine? No. A virus has no “intent” or “will.” It does not even have an intent or a will to replicate, but it will do it as expeditiously and frequently as possible given a readily available source of host cells. So why do mutations happen?

As the NHGRI says “Mutation has been the source of many Hollywood movies, but it’s really a simple process of a mistake made in a DNA sequence as it’s being copied. Some of that’s just the background noise that DNA copying is not perfect, and we should be glad of that or evolution couldn’t operate. But mutation can also be induced by things like radiation or carcinogens in a way that can increase the risk of cancers or birth defects. But it’s pretty simple; it’s basically an induced misspelling of the DNA sequence. That’s a mutation.”

So here’s a thing. Mutations happen when viruses copy themselves. This is where things get mathematical. (The numbers are for illustrative purposes only. They do NOT reflect actual incidence. Please do NOT get hung up on the numbers.)

If 10,000 people have Copy Alpha of a virus, in 9,997 of them, Virus Copy Alpha may replicate itself without making any mistakes. That’s 9,997 copies of virus Alpha, all ready to go off and do what they do best: invade host cells to replicate themselves. (And again, see how easy it is to use language that anthropomorphises, that implies intent, that ascribes agency. We are human; it’s natural that we should do it. But really, it all comes down to mathematics and chemistry.)

In Copy 9,998, a mistake, one of the mistakes in the picture above, happens. The virus shape changes. Maybe it has duplicated a bit of DNA. But whoops, the change has made the virus so faulty that it cannot enter a cell to reproduce itself. Copy 9,998 could have become a “strain” of the virus, but it’s doomed, because it can’t enter a host cell to reproduce. It “dies.” (And that is in quotes because if something isn’t living it’s questionable that it can die: now, however, we’re talking philosophy.) Goodbye, Copy 9,998: the virus strain we never knew.

Now let’s take Copy 9,999. Copy 9,999 also has a mistake in it. It’s not the same as the mistake in Copy 9,998: it’s perhaps a translocation, rather than a duplication, say. (Look at the picture.) Copy 9,999, however still functions as a virus, so it continues to reproduce. But until or unless – and actually, it’s always until – it  makes a mistake in copying itself, thus giving rise to Copy 9,999.1 what it will reproduce is not Copies 1 to 9,997, like the virus that it was copied from, but itself: Copy 9,999.

And finally, let’s take Copy 10,000. Copy 10,000 also makes a mistake copying itself. It might make two: viruses can. It might make a deletion and a substitution, or a translocation and an inversion. In any case, it is no longer the same as copies 1 to 9,997, nor the same as poor, doomed Copy 9,998, nor the same as Copy 9,999. It is different. Let’s assume, however, for the purposes of our illustration, that it can still reproduce, always remembering that what it will reproduces – until it itself mutates, is its own altered DNA for Copy 10,000, not the DNA of Copies 1 to 9,997.

Does this matter? Do DNA mutations matter? Yes, they do. It’s your DNA and mine that makes me short, and you tall. It’s your DNA and mine that gives me grey eyes, and you brown. It’s your DNA and mine that predisposes me to e.g. obesity and gives you cystic fibrosis. Genotype – what the genes encode for –determines phenotype – what we look like. (Yes, environment also plays a factor: if I am well fed my whole life I might achieve my maximum encoded height, whereas you, malnourished from birth, might never achieve the height that your genotype would allow. Nurture as well as nature plays a part here, but we are talking about viruses, which are simpler than we are.)

So when a virus mutates, it changes shape. Its little spiky proteins might look, microscopically, very different. So here’s the thing with the vaccines, and our randomly mutated virus copies. The vaccine teach our cells to recognise specific shapes of the virus. But what if those shapes are different?

Back to Virus Copy Alpha. Let’s assume it’s Virus Copy Alpha we’re vaccinated against.

Imagine that your vaccine has taught your body cells to recognise Virus Copy Alpha. Of the 500 or so of the 9,997 correctly copied copies of Virus Copy Alpha you accidentally, by happenstance, meet floating around – delivered by aerosol – you inhale about 350 – again, numbers are illustrative, remember. Your vaccinated body recognises them and produces antigens, and those virus copies, villains that they are, slink off, defeated. Ha, villain! Foiled you again.

Later, you meet Copy 9,998. Whoosh! Down it goes into your lungs. But wait: it can’t get into any of your body cells, so it can’t reproduce, and dies a lonely and unlamented death.

Coincidentally – in real life of course, you would never be this unlucky, or at least one hopes so  – you meet Copy 9,999. You inhale. “What’s this?” say your antigens. “It’s like those other 350 copies of Virus Alpha we met and mopped up the other day. Let’s kill this one too!” (Remember the WHO says that “Antibodies to one pathogen generally don’t protect against another pathogen except when two pathogens are very similar to each other, like cousins.” Copy 9,999 is kissing cousins with Copies 1 to 9,997.) You’re safe.

But – and here you really are unlucky – you also meet Copy 10,000. Copy 10,000 is not at all like Copies 1 to 9,997, and it’s not like Copies 9,998 and 9,999 either. It is sufficiently different in shape that your vaccinated body does not recognise it. Your vaccine is useless, Copy 10,000 enters one of your cells, and merrily reproduces. You sneeze, hack, cough and splutter, and thousands of correctly copied copies of Copy 10,000 enter the air as aerosols – especially if you’re not wearing a mask to trap them, or protect anyone else – ready to infect anyone they come across – including people who have had the same vaccine as you.

Now, replicate that scenario thousands of times. Hundreds of thousands of times. Millions of times. Hundreds of thousands of people, all maskless, coughing, spitting and spluttering out copies of Copy 10,000 (we call it the “Delta Variant” now, by the way) all of them infecting vaccinated and unvaccinated people alike.

In this scenario you, as a Copy 10,000 infected person, have the courtesy to wear a mask, thus reducing, if not more or less eliminating, the copies of Copy 10,000 that you’re emitting. The rest of your friends, however, when they get it, don’t. And while I am a) vaccinated and b) wearing a mask, what my mask mostly protects me from – unless it’s an extremely expensive FFP2 or FFP3 mask, worn correctly and with excellent biosecurity protocols into the bargain, is from me infecting you. It doesn’t stop you or your friends infecting me, if you’re not wearing a mask, and you’re reproducing and emitting a virus copy that my antibodies don’t recognise.

Oh, and let’s think mathematically again, shall we?

The more people spreading a virus – the more copies of that virus in circulation – the more copies of that virus that reproduce, then the greater the chances are of one of them having a mutation or two, and the greater the chances are of one of those mutations – which can already evade the vaccine, remember – are of becoming even more different not only from Copy 10,000, but from the original Virus Copy Alpha against which we are all vaccinated. (Except we’re not, are we? Not everyone can be. Spare a thought here especially for the people who are depending on waiting for plasma therapy to achieve their release into a normal life, please!)

What’s the answer?

The more the virus reproduces, the greater the chances are of random mutations. The greater the chances are of mutated viruses that enter the body and are not recognised by its defences. The greater the chances are of escalating infections, some of which will spawn more mutated viruses that may be more lethal (and also less lethal, of course, and also less infectious, and also less capable of reproducing, just like Copy 9,998. It goes both ways).

The government positions this as a war that we can win. It isn’t. Mathematically speaking it isn’t, because we’re talking about coming into contact with millions and billions of individual virions, all of which might carry a mutation.

The higher the number of infections, the more potentially mutated virions we come across, the greater the environmental viral load, and the greater the chances of mutations that enable vaccine escape. In order to reduce the probability of new variants which escape our vaccines we need to reduce the reproduction of the virus because as long as it’s reproducing it’s mutating, and as long as it’s mutating it will keep producing new variants. It’s doing that as we speak.

Yes, the environmental and social costs of the pandemic have been huge. We need to get back to “normal” – not that it was a good “normal” for many by any stretch of the imagination – whatever “normal is. Fine, if you want to, Johnson, Javid, open up society. Allow people to make some “personal choices”, knowing as you do that some will make stupid personal choices, some will make careless personal choices, and some will be so stressed and miserable by the mere fact of making their way in the unkind world that this government has created that they’re barely conscious of making any choices at all: driven from pillar to post, harried and harassed, they do what they must and what they can to survive.

But if you’re going to do anything at all, anything that will make a difference to this, at least continue with mandatory mask wearing. At least attempt to reduce the transmission of the virus. At least deny it the possibility of reproducing and mutating. At least ensure that the vaccines scientists worked so hard to create continue to work, while we have a chance to assess the situation and create better ways of preventing damage from, dealing with, healing ourselves from, what is not a monster – because it has neither will, not intent, nor malice – but an act of nature, one which has happened many times before and will happen many times again.

But what you’re doing now, Johnson? What your plans are, Javid? This complete abrogation of responsibility? The immediate switch from total governmental control to total individual freedom? That is willed. That is intentional. That is malicious.

One could almost call it deliberate democide. Eugenics by stealth. A huge sociological experiment with us as the unwitting and unconsenting guinea pigs; experimental subjects in a global laboratory. Subjects, unwillingly, in an experiment that the world is now watching not with interest, but with horror, revulsion, pity and concern.

5 thought on “Viral Basics: What Happens With Variants, And Why This Is An Issue Of Chemistry, Mathematics and Copy 10,000.”
  1. Thanks so much for your deeply researched and thoughtful article. If only Johnson and co cared enough for the population to maintain mask-wearing, instead of being scared of the anti-maskers

  2. Would it be appropriate to send this link to my (infortunately) Tory MP? She isn’t a scientist and is a strng adherent of any Party Line. She is also nmot the brightest button in the box when it comes to logic. She has a child-like faith in vaccines/people’s common sense and altruism/ BJ’s wisdom and motives.
    Will take your advice Joanna
    Mary May

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