Sunday, 14 March 2021

Malevolent Designer News - Study Shows SARS-CoV-2 Transfer From Bats to Humans Was Relatively Easy

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

Creationist mode:

Well, it looks like the intelligent [sic] designer really thought it through before it created the bat virus that was to become the SARS-CoV-2 virus and cause a global pandemic to kill 2.6 million humans and infect 119.6 million more (latest figure at 14 Mar 2021).

According to scientists at the University of Glasgow Centre for Virus Research, Glasgow, United Kingdom, and colleagues, the move from bats into humans was relatively easy, all the heavy lifting being done in the ancestral bat virus.

As the PLOS press release explains:
How much did SARS-CoV-2 need to change in order to adapt to its new human host? In a research article published in the open access journal PLOS Biology Oscar MacLean, Spyros Lytras at the University of Glasgow, and colleagues, show that since December 2019 and for the first 11 months of the SARS-CoV-2 pandemic there has been very little 'important' genetic change observed in the hundreds of thousands of sequenced virus genomes.

The study is a collaboration between researchers in the UK, US and Belgium. The lead authors Prof David L Robertson (at the MRC-University of Glasgow Centre for Virus Research, Scotland) and Prof Sergei Pond (at the Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia) were able to turn their experience of analysing data from HIV and other viruses to SARS-CoV-2. Pond's state-of-the-art analytical framework, HyPhy, was instrumental in teasing out the signatures of evolution embedded in the virus genomes and rests on decades of theoretical knowledge on molecular evolutionary processes.

This does not mean no changes have occurred, mutations of no evolutionary significance accumulate and 'surf' along the millions of transmission events, like they do in all viruses...

This stasis can be attributed to the highly susceptible nature of the human population to this new pathogen, with limited pressure from population immunity, and lack of containment, leading to exponential growth making almost every virus a winner.

Dr Oscar MacLean, Joint lead author
MRC Centre for Virus Research,
University of Glasgow, Glasgow, United Kingdom
First author Dr Oscar MacLean explains, "This does not mean no changes have occurred, mutations of no evolutionary significance accumulate and 'surf' along the millions of transmission events, like they do in all viruses." Some changes can have an effect; for example, the Spike replacement D614G which has been found to enhance transmissibility and certain other tweaks of virus biology scattered over its genome. On the whole, though, 'neutral' evolutionary processes have dominated. MacLean adds, "This stasis can be attributed to the highly susceptible nature of the human population to this new pathogen, with limited pressure from population immunity, and lack of containment, leading to exponential growth making almost every virus a winner."

Pond comments, "what's been so surprising is just how transmissible SARS-CoV-2 has been from the outset. Usually viruses that jump to a new host species take some time to acquire adaptations to be as capable as SARS-CoV-2 at spreading, and most never make it past that stage, resulting in dead-end spillovers or localised outbreaks."

[W]hat's been so surprising is just how transmissible SARS-CoV-2 has been from the outset. Usually viruses that jump to a new host species take some time to acquire adaptations to be as capable as SARS-CoV-2 at spreading, and most never make it past that stage, resulting in dead-end spillovers or localised outbreaks.

Professor Sergei L. Kosakovsky Pond, Joint lead author
Institute for Genomics and Evolutionary Medicine,
Temple University,
Philadelphia, Pennsylvania, USA
Studying the mutational processes of SARS-CoV-2 and related sarbecoviruses (the group of viruses SARS-CoV-2 belongs to from bats and pangolins), the authors find evidence of fairly significant change, but all before the emergence of SARS-CoV-2 in humans. This means that the 'generalist' nature of many coronaviruses and their apparent facility to jump between hosts, imbued SARS-CoV-2 with ready-made ability to infect humans and other mammals, but those properties most have probably evolved in bats prior to spillover to humans.

Joint first author and PhD student Spyros Lytras adds, "Interestingly, one of the closer bat viruses, RmYN02, has an intriguing genome structure made up of both SARS-CoV-2-like and bat-virus-like segments. Its genetic material carries both distinct composition signatures (associated with the action of host anti-viral immunity), supporting this change of evolutionary pace occurred in bats without the need for an intermediate animal species."

Interestingly, one of the closer bat viruses, RmYN02, has an intriguing genome structure made up of both SARS-CoV-2-like and bat-virus-like segments. Its genetic material carries both distinct composition signatures (associated with the action of host anti-viral immunity), supporting this change of evolutionary pace occurred in bats without the need for an intermediate animal species.
Spyros Lytras, Joint first author
PhD Student
MRC Centre for Virus Research,
University of Glasgow, Glasgow, United Kingdom
Robertson comments, "the reason for the 'shifting of gears' of SARS-CoV-2 in terms of its increased rate of evolution at the end of 2020, associated with more heavily mutated lineages, is because the immunological profile of the human population has changed." The virus towards the end of 2020 was increasingly coming into contact with existing host immunity as numbers of previously infected people are now high. This will select for variants that can dodge some of the host response. Coupled with the evasion of immunity in longer-term infections in chronic cases (e.g., in immunocompromised patients), these new selective pressures are increasing the number of important virus mutants.

[T]he reason for the 'shifting of gears' of SARS-CoV-2 in terms of its increased rate of evolution at the end of 2020, associated with more heavily mutated lineages, is because the immunological profile of the human population has changed.

Professor David L Robertson, Joint lead author
MRC Centre for Virus Research,
University of Glasgow, Glasgow, United Kingdom
It's important to appreciate SARS-CoV-2 still remains an acute virus, cleared by the immune response in the vast majority of infections. However, it's now moving away faster from the January 2020 variant used in all of the current vaccines to raise protective immunity. The current vaccines will continue to work against most of the circulating variants but the more time that passes, and the bigger the differential between vaccinated and not-vaccinated numbers of people, the more opportunity there will be for vaccine escape. Robertson adds, "The first race was to develop a vaccine. The race now is to get the global population vaccinated as quickly as possible."
In summary, the original bat virus that became SARS-CoV-2 did not need extensive modification to allow it to infect humans and, once it did so, there was little or no resistance to it in the population, hence the rapid spread and exponential growth in people infected. However, once the number of people with antibodies from having been infected before, began to increase, there was selection pressure in it natural environment for new variants which could evade that resistance, so we saw and are still seeing, an increase in the number of new variants.

Importantly, while there is still a large pool of people who have not been vaccinated, there will be a large population of viruses in which mutations can arise, some of which may be more virulent or more contagious than others. resistance does not need to arise in people with antibodies but so long as there is a pool from which they can be re-infected, variants which can evade the antibodies will prosper.

The way to reduce this is to deny it supply, by vaccinated as many of the world's population as possible. It is in all our interests to roll out the vaccines are widely as possible.

The group pubished their findings open access in PLOS Biology a couple of days ago:

Abstract


Virus host shifts are generally associated with novel adaptations to exploit the cells of the new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little to no significant adaptation to humans since the start of the Coronavirus Disease 2019 (COVID-19) pandemic and to October 2020. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus the early SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects evidence for significant positive episodic diversifying selection acting at the base of the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in these ancestral bat hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor about 1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. While an undiscovered “facilitating” intermediate species cannot be discounted, collectively, our results support the progenitor of SARS-CoV-2 being capable of efficient human–human transmission as a consequence of its adaptive evolutionary history in bats, not humans, which created a relatively generalist virus.

I've explained before how the intelligent [sic] designer designed the immune system of bats so they could act as testbeds for new viruses before unleashing them on humans and other species. It looks like that foresight really paid off here, enabling it with just a few tweeks to inflict a devastating pestilence on human beings, though quite how that fits in with the notion of al all-loving god can only be guessed at. As things stand, the intelligent [designer] is looking either incompetent or malevolent.

Creationist mode:

Well, that's a problem for creationists to explain. As for science, the explanation is perfectly simple and involves no planning or forethought, malevolent or mysteriously somehow 'all-loving', including inflicting mass random death on people.

The answer practically shouts out to anyone willing to read what the scientists said. There was no magic or malice involved. It was all due to a perfectly rational, natural, evolutionary process - an explantion which Creationists feel compelled to reject.

But it's worth asking yet again, in the hope that one day a Creationist will find the courage to give an honest answer:

Why is evolution by natural selection the only explanation for the SARS-CoV-2 virus that doesn't make Creationism's putative designer god look like a pestilential, genocidal, misanthropic sadist who hates its creation and wishes to make it suffer and die?








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