Tuesday, 17 May 2022

Malevolent Designer News - Why Creationism's Beloved Malevolence Has Its Work Cut Out

Even as the structure of SARS-CoV-2 changes with different variants of the virus (gray), the J08 antibody (blue) can still bind it, Scripps researchers showed.
Credit: Scripps Research
Scripps Research scientists explain what makes COVID-19 antibody “J08” so potent | Scripps Research

Creationist mode:

Creationism’s beloved malevolence is going to have its work cut out it it is to outdo bio-medical science in their search for a definitive cure for the COVID-19 virus it created to cause the current COVID-19 Pandemic. So far, it has come up with several variants, the latest being the Omicron variant that is much more contagious than earlier variants, but, at least in a population where a large proportion of the people have been vaccinated, is mostly, though not always, a relatively mild infection.

Nevertheless, it has managed to achieve nearly 6.3 million deaths worldwide, 1 million of them in the USA where, due to the incompetence and narcissistic Dunning-Kruger stupidity of the president when the pandemic started and was most dangerous in 2020, and because of the opposition to measures to control it by fundamentalist Christians and the super spreader events they insisted on holding in their churches, deaths were far in excess of anything seen in most other advanced economies.

But now, a collaborative effort between scientists at the Scripps Institute and scientists in Italy and France may have found an antibody to the SARS-CoV-2 virus that not only treats and prevents known variants of COVID-19 but will probably be effective against future variants. The antibody is currently undergoing stage II/III clinical trials in Italy. The antibody, known as J08 was isolated from the blood of people who had recovered from COVID19 by scientists at the Scripps Institute and Toscana Life Sciences.

The question creationist devotees of the magic, pestilential sky man whom they believe designs these things, is just how is it going to find a way round this new prevention/treatment so it can continue the chaos and suffering it created? Only time will tell.

Creationist mode:

Even though we can’t predict what variants of COVID-19 will emerge next, understanding the details of J08 reveals what works against the virus, and perhaps how we can engineer antibodies to be even more potent.

Professor Andrew Ward, PhD, senior author
Professor of Integrative Structural and Computational Biology
Scripps Research, La Jolla, CA, USA
Their research is published, open access, in the journal Proceedings of the National Academy of Sciences (PNAS), where the researchers claim that, because of it's flexibility it will likely remain effective against future variants.

As the Scripps news release explains:
When a person is exposed to a virus like SARS-CoV-2, their body generates a variety of antibodies that bind to different sections of the virus to clear it from the body. Scientists designing vaccines and treatments against COVID-19 are interested in what makes some of these naturally produced antibodies—like J08—more effective than others. In the months after Ward and his collaborators first identified J08, it became clear that the antibody, unlike many others, was potent against a variety of COVID-19 variants.

With variants other than Omicron, this antibody binds quickly and doesn’t come off for hours and hours. With Omicron, we were initially happy to find that it still binds, but it falls off very quickly. We identified the two structural changes that cause this.

I think we’re pretty confident that future variants won’t necessarily have both of these two critical mutations at the same time like Omicron, so that makes us hopeful that J08 will continue being very effective.

Gabriel Ozorowski, co-first author
Senior staff scientist
Professor Ward’s Laboratory
Scripps Research, La Jolla, CA, USA.
In the new work, the researchers determined the three-dimensional structure of J08 as it bound to the spike protein of SARS-CoV-2. They confirmed that J08 successfully attached to the Alpha, Beta, Gamma and Delta variants and neutralized the viruses—preventing them from replicating. However, J08 attached to the Omicron variant about 7 times more slowly, and then rapidly came off. About 4,000 times more J08 was needed to fully neutralize Omicron SARS-CoV-2 compared to the other variants.

This small, flexible footprint is part of why J08 is able to withstand so many mutations—they don’t impact the antibody binding unless they happen to be in this one very small part of the virus.

Jonathan Torres, co-first author
Lab manager
Professor Ward’s Laboratory
Scripps Research, La Jolla, CA, USA.
The team showed that, for all the variants, J08 binds to a very small section of the virus—a section that generally stays the same even as the virus mutates. Moreover, J08 could attach in two completely different orientations, like a key that manages to unlock a door whether it is right side up or upside down.

The Omicron variant of SARS-CoV-2, however, had two mutations (known as E484A and Q493H) that changed the small area of the virus that directly interfaces with J08, anchoring it in place. Ward and his collaborators found that if just one of these mutations is present, J08 still manages to bind and neutralize the virus strongly, but mutations in both are what make it less effective against the Omicron variant.
The team have published their results in the journal Proceedings of the National Academy of Sciences (PNAS):
Clinical candidate monoclonal antibody J08 binds the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S-protein independent of known escape mutations and is able to potently neutralize most variants of concern (VoCs). Here, we explore these properties using cell-based assays and structural studies. A relatively small epitope footprint high on the receptor binding domain (RBD) ridge and the ability to bind multiple conformational states of the S-protein contribute to strong neutralization across several variants.
As the coronavirus disease 2019 (COVID-19) pandemic continues, there is a strong need for highly potent monoclonal antibodies (mAbs) that are resistant against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs). Here, we evaluate the potency of the previously described mAb J08 against these variants using cell-based assays and delve into the molecular details of the binding interaction using cryoelectron microscopy (cryo-EM) and X-ray crystallography. We show that mAb J08 has low nanomolar affinity against most VoCs and binds high on the receptor binding domain (RBD) ridge, away from many VoC mutations. These findings further validate the phase II/III human clinical trial underway using mAb J08 as a monoclonal therapy.
If this antibody proves as effective as early indications seem to show, and if it can be produced in sufficient quantities, and if it can be made available world-wide regardless of national wealth, then it might be possible to irradicate this nasty little virus in the human population altogether.

However, in the past, the process which produces new variants has proved to be amazingly creative. With a world-wide population of the virus probably numbering in the trillions or quadrillions, the probability of a novel combination of mutations arising by chance alone is a virtual certainty. And of course, as with any zoonotic species of parasite, the potential for breeding a novel variant in some other species can't be ruled out.

The likelihood is that science will always be playing catchup until a generic vaccine against all coronaviruses is found and measures to get it into the arms of everyone aren't hampered by the same superstitious, credulous fools who believe in magic designers, because people who study only the fantasies of Bronze Age hill farmers told them it was real science, and threatened them with eternal torture if they didn't believe it.

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