Malevolent Designer News - How SARS-CoV-2 Mutates to Escape Antibody Binding

How SARS-CoV-2 Mutates to Escape Antibody Binding - University of Pittsburgh School of Medicine.

It's time to play at being intelligent [sic] design creationists again to see what mental summersaults are needed to believe in it.

This time it involves looking at how it is coping with the fact that human medical science has found a way to make the immune system it designed to protect us from the viruses like SARS-CoV-2 it creates to make us sick, actually do the job it would have done if only it had been competently designed in the first place.

Remember, one of the rules of the game is to pretend that nothing happens without the personal intervention of a perfect, omniscient god. The corollary to that is that whatever happens is exactly what that god intended to happen, nothing more and nothing less. Oh! And we have to pretend that this god is the god of the Christian Bible whom Christians believe is an omni-benevolent god, worthy of worship and praise.

Now we come on to the first mental summersault - we have to believe this all-loving god designed and created the SARS-CoV-2 virus responsible for the current devastating pandemic that is killing people by the hundreds of thousand, making millions sick, some of whom will end up with long-term disabilities, and wrecking economies and ruining business the world over.

The first mental summersault is thus to believe that this virus was the creation of of an all-loving deity.

Now we have to explain the fact that, no sooner has medical science come up with vaccines to kick-start our immune systems into pre-emptively producing antibodies and other immune responses to the virus, than the intelligent [sic] designer had to start trying to find work-arounds in the form of mutations that mean the anti-bodies don't work, and so the vaccines need to be re-designed.

And to help us with this we have the results of research by scientists at the Pittsburgh University School of Medicine (UPMC). They have found how the SARS-CoV-2 virus evolves by deleting small sequences in it genetic sequence in the parts of it that carry the instructions for assembling these 'spike' proteins. These proteins are what the antibodies the vaccines cause us to produce look for, so they can bind to the viruses and neutralise them if we are unlucky enough to be infected.

Although the scientists call this evolution, because they are scientists and understand how evolution works, we are pretending this is the intended outcome of the intentional redesign of the virus by the intelligent [sic] designer, so we can't assign these changes to a mindless, unplanned natural process where mutations that give the virus an advantage in its environment will increase in the vurus genepool until they come to dominate it.

That doesn't happen, otherwise it would mean the Theory of Evolution by Natural Selection is true; it was all intentional, remember!

The scientists, however, claim to have found that this happens because the SARS-CoV-2 virus' genome doesn't come with a built-in error correcting mechanism that can spot deletions, so it doesn't 'notice' these accidental deletions and correct them.

As they explain in the UPMC press release:

Histology: Multiple antibodies (green and red) bind SARS-CoV-2 spike protein within cells (blue) when there are no deletions (LEFT). Spike protein deletions stop neutralizing antibody from binding (absence of green) but other antibodies (red) still attach very well (RIGHT). Recurrent deletion generates variants that escape from neutralization.

Credit: Kevin McCarthy and Paul Duprex

Duprex’s group first came across these neutralization-resistant deletions in a sample from an immunocompromised patient, who was infected with SARS-CoV-2 for 74 days before ultimately dying from COVID-19. That’s a long time for the virus and immune system to play “cat and mouse,” and gives ample opportunity to initiate the coevolutionary dance that results in these worrisome mutations in the viral genome that are occurring all over the world.

Since these deletions happen in a part of the sequence that encodes for the shape of the spike protein, the formerly neutralizing antibody can’t grab hold of the virus, the researchers report today in Science. And because the molecular “proofreader” that usually catches errors during SARS-CoV-2 replication is “blind” to fixing deletions, they become cemented into the variant’s genetic material.

“You can’t fix what’s not there,” said study senior author Paul Duprex, Ph.D., director of the Center for Vaccine Research at the University of Pittsburgh. “Once it’s gone, it’s gone, and if it’s gone in an important part of the virus that the antibody ‘sees,’ then it’s gone for good.”

But, the spike protein isn't just there for decoration; it plays a vital part in the virus' ability to gain access to the host's cells where it can use the cell's replication machinery to make more copies of itself, so obviously, it the deletion is not to prove fatal to the virus and so be quickly eliminated from the population gene-pool, it must be in a section of the protein that doesn't unduly damage this function, and in this case functionality depends on shape and the distribution of electrostatic charges over the surface of the protein, which depends on amino acid sequence.

Protein Structure: Deletions in the SARS-CoV-2 spike protein sequence (horizontal cyan bar) affect the shape of different parts of the protein (cyan). Bar graph at left shows the relative frequency of recurrent deletions in the correspondingly colored part of the spike protein. Deletions tend to occur outside the region that binds to cells at the beginning of the infection.

Credit: Kevin McCarthy and Paul Duprex

What the team noticed, when they search through the massive database of SARS-CoV-2 genomes that have been sequenced sine the pandemic began is that these deletions in different serotype varieties repeatedly occur in the same part of the RNA, so affect the same part of the spike protein. Its as though somethign is selecting mutations that occur in a part of the spike protein that are minimally harmful to the virus and maximally good at evading our defences!

Among the sequences McCarthy identified as having these deletions was the so-called “U.K. variant”—or to use its proper name, B.1.1.7. By this point, it was October 2020, and B.1.1.7 hadn’t taken off yet. In fact, it didn’t even have a name, but it was there in the datasets. The strain was still emerging, and no one knew then the significance that it would come to have. But McCarthy’s analysis caught it in advance by looking for patterns in the genetic sequence.

Reassuringly, the strain identified in this Pittsburgh patient is still susceptible to neutralization by the swarm of antibodies present in convalescent plasma, demonstrating that mutational escape isn’t all or nothing. And that’s important to realize when it comes to designing tools to combat the virus.

“Going after the virus in multiple different ways is how we beat the shapeshifter,” Duprex said. “Combinations of different antibodies, combinations of nanobodies with antibodies, different types of vaccines. If there’s a crisis, we’ll want to have those backups.”

Although this paper shows how SARS-CoV-2 is likely to escape the existing vaccines and therapeutics, it’s impossible to know at this point exactly when that might happen. Will the COVID-19 vaccines on the market today continue to offer a high level of protection for another six months? A year? Five years?

“How far these deletions erode protection is yet to be determined,” McCarthy said. “At some point, we’re going to have to start reformulating vaccines, or at least entertain that idea.”

The Pittsburgh team's findings were published yesterday in Science:

Abstract

Zoonotic pandemics, like that caused by SARS-CoV-2, can follow the spillover of animal viruses into highly susceptible human populations. Their descendants have adapted to the human host and evolved to evade immune pressure. Coronaviruses acquire substitutions more slowly than other RNA viruses, due to a proofreading polymerase. In the spike glycoprotein, we find recurrent deletions overcome this slow substitution rate. Deletion variants arise in diverse genetic and geographic backgrounds, transmit efficiently, and are present in novel lineages, including those of current global concern. They frequently occupy recurrent deletion regions (RDRs), which map to defined antibody epitopes. Deletions in RDRs confer resistance to neutralizing antibodies. By altering stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution.

McCarthy, Kevin R.; Rennick, Linda J.; Nambulli, Sham; Robinson-McCarthy, Lindsey R.; Bain, William G.; Haidar, Ghady; Duprex, W. Paul
Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Science 03 Feb 2021: eabf6950; DOI: 10.1126/science.abf6950

© 2021 The American Association for the Advancement of Science
Reprinted with kind permission under license #5001961165267

Of course, if the scientists are right, it means that, as the number of people in the world population who have been vaccinated increases, so the likelihood of a mutation which enable the virus to escape the antibodies also increases, meaning that we will probably have to keep redesigning the vaccines to keep up with the evolutionary arms race, or, in intelligent [sic] design terms, the manoeuvrings and machinations of what looks for all the world like a malevolent designer.

So, the last summersault we needed to perform to complete our little 'intelligent [sic] design' game is tell ourselves that not ascribing all this to a mindless, amoral, natural process of evolution by natural selection, but instead insisting that the god of the Christian Bible nust have done it in full knowledge of what it was doing, somehow leaves that god looking like an all-loving god worthy of worship and praise, and not the pestilential, genocidal, malevolent monster people might rationally be tempted to see it as.

Anyone who can perform those self-deluding mental gymnastics with ease is probably fully qualified to be a Creationist, complete with the perverse notion of the meaning of 'benevolence' that that entails.

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