[WSMDiscuss] COVID-19: Virology and Conspiracy Theories: Origins of SARS-CoV-2: 'Coronavirus from lab? Bat or pangolin more likely'

[Sukla Sen]

[It's on Dec. 31 2019, the world was alerted by Chinese authorities that in
China 27 suspected cases of severe acute respiratory syndrome (SARS) have
been reported by then.
(Ref.: <
https://www.worldaware.com/suspected-sars-cases-reported-hubei-province>.)

The causal agent would, however, not be identified until a week later, on
Jan. 7  2020.
A new type of coronavirus was isolated by Chinese authority.
The genome sequence of SARS-CoV-2 (WH-Human_1) was first released and
shared by China on Jan. 10."
(Ref.: <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7098030/>.)

The first case from outside China would be reported from Thailand on Jan.
13 - a woman who had earlier arrived from the ground zero - Wuhan, the
capital of the Hubei province in Central China.
"Authorities in the US, Nepal, France, Australia, Malaysia, Singapore,
South Korea, Vietnam and Taiwan confirmed cases over the following days."
(Ref.: <
https://www.aljazeera.com/news/2020/01/timeline-china-coronavirus-spread-200126061554884.html
>.)

As the disease started spreading globally - threatening lives and
lifestyles, triggering widespread panic, varying and divergent conspiracy
theories started doing the rounds.
Much of these being a part of the geopolitics, the accusing fingers,
mostly, pointed at either China or the US.
Here is a pretty useful and fairly comprehensive account: <
https://en.wikipedia.org/wiki/Misinformation_related_to_the_2019%E2%80%9320_coronavirus_pandemic
>.
In India, deviating somewhat from the dominant norms, it's "Corona Jihad" -
in order to weaponise the crisis, regardless of its impact on the grim
fight on hand, in order to further intensify polarisation of the society,
into combating camps, across religious divides.
(Ref.: <https://time.com/5815264/coronavirus-india-islamophobia-coronajihad/
>.)

In the midst of all, the more than half a century ol prestigious scientific
journal 'Nature' has on its March 17 issue carried a genomic study of the
SARS-CoV-2: <
https://www.nature.com/articles/s41591-020-0820-9?fbclid=IwAR1ftpSQLzMhiJJ73Xv64le7Hciaa8toUTy165n5XMzhqLjljne4nE6meME
>.
It has, in effect, debunked the claims that the virus is one engineered in
a biological lab - whether meant to be a bioweapon or even otherwise.

This study says:
I. It "is not derived from any previously used virus backbone".
II. It has a counterintutive feature that makes its binding capacity with
the human receptor lower than ideal.

Both taken together, "(i)t is improbable that SARS-CoV-2 emerged through
laboratory manipulation of a related SARS-CoV-like coronavirus."

It also hints at the likelihood of the virus jumping from a pangolin to a
human and, then, therefrom being transmitted to humans.
(Ref.: "All SARS-CoV-2 genomes sequenced so far have the genomic features
described above and are thus derived from a common ancestor that had them
too. The presence in pangolins of an RBD very similar to that of SARS-CoV-2
means that we can infer this was also probably in the virus that jumped to
humans. This leaves the insertion of polybasic cleavage site to occur
during human-to-human transmission.")

About a month later, the UN Secy General has issued a pointed appeal
against campaigns of misinformation on COViD-19: <
http://www.unodc.org/unodc/en/press/releases/2020/April/message-on-covid-19-and-misinformation.html
>.
Much before that, on February 2, the WHO had warned of a massive
‘infodemic’: <
https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200202-sitrep-13-ncov-v3.pdf
>.
Never mind.

<<Further, scientific work revealed that pangolin coronaviruses are similar
to human SARS-CoV-2. How similar? In subsequent scientific investigations,
the letter-by-letter identity estimates between the genomes of the novel
human and pangolin coronaviruses were between 90 and 92 per cent.

But what is more remarkable is that all of the alterations in the RBD that
confer a high efficiency on the SARS-CoV-2 to bind to human ACE2 are
present in the pangolin coronaviruses.

The logical conclusion is that the pangolin coronavirus jumped to humans.
The pangolin coronavirus loved humans easily via the ACE2 protein and
multiply happily there.

At some stage, the virus — possibly because of one or two other changes
within its genome — acquired the capability of human-to-human transmission.
This is a clear case of Darwinian natural selection.>>

(Excerpted from the analytical comment reproduced below.
The comment is by a domain expert in a very accessible format - presumably,
anchored in the genomic study carried by the 'Nature'.)

A rider, however, needs be issued here to the effect that very much unlike
religious scriptures, which remain unalterable over centuries and
millenniums and are not open to questioning by mere mortals, a scientific
"truth" is pretty much acknowledged as tentative.
It holds till it's negated or modified in terms of new evidences and/or
rational analyses.]

https://www.telegraphindia.com/india/coronavirus-from-lab-bat-or-pangolin-more-likely/cid/1766392?fbclid=IwAR3gf9s-K9qFmR4rpgeUAz6ikK7yFlABERUz6PJpnXRwKmJars4PFgfA3RM


Coronavirus from lab? Bat or pangolin more likely
The outbreak rapidly become a pandemic and has already killed over 150,000
people worldwide

By Partha P. Majumder

Published 20.04.20, 2:56 AMUpdated 20.04.20, 5:40 PM
4 mins read

State Rep. Matt Shea, R-Spokane Valley, listens to testimony on the House
floor at the Capitol in Olympia, Washington, in photo taken on February 19.
Prominent state lawmaker Shea says the coronavirus is a foreign bio-weapon
and claims Marxists are using the pandemic to advance totalitarianism.
AP

Soon after the novel coronavirus outbreak, scientists identified an
alteration in the virus’s RNA sequence.

Compared to other coronaviruses, this alteration helps the novel
coronavirus (nCoV or more technically SARS-CoV-2) spread more efficiently
in humans.

Immediately, politicians went into a frenzy. Former Iran President Mahmoud
Ahmadinejad declared that the nCoV is a bio-weapon from a military
laboratory.

“It is clear to the world that the mutated coronavirus was produced in a
lab,” he said.

US Senator Tom Cotton suggested the virus was a biological weapon released
on purpose.

Our own MP, Manish Tewari, national spokesperson for the Congress, tweeted
on March 13: “Coronavirus is a bio-weapon… an act of terror. International
investigation conducted either under auspices of ICJ or ICC is necessary to
unearth the truth and bring focus back on eradicating biological weapons.”

Within the past week, many claims have been made on social media and in
articles placed in the public domain that Bill Gates helped create the nCoV
with the idea of selling a particular vaccine.

Can the novel coronavirus be a human creation?

The outbreak was detected in Wuhan, China, as we all now know. The Chinese
authorities informed the World Health Organisation on December 31 last year
that the outbreak was that of a novel coronavirus that was causing severe
illness.

The outbreak rapidly become a pandemic and has already killed over 150,000
people worldwide.

Shortly after the outbreak, Chinese scientists determined the RNA sequence
of SARS-CoV-2 and made the sequence available in the public domain.

This has facilitated research on the evolution of the novel coronavirus and
led to the firm conclusion that the virus was not engineered by humans but
arose naturally by evolution from another coronavirus.

Before the emergence of SARS-CoV-2, six other coronaviruses had been known
to infect humans. All of them cause clinical symptoms.

Two of them, SARS-CoV and MERS-CoV, cause severe disease and often death.
The remaining four (HKU1, NL63, OC43 and 229E) cause mild clinical symptoms.

The RNA sequences of these six coronaviruses had been determined before the
current outbreak. Different portions of the RNA of these viruses are
associated with different functions.

A virus cannot live independently. It needs to get into an organism’s cell
— host cell — and multiply there. We humans are not the favourite host of a
virus. Viruses usually live in other animals.

In the process of getting into a host cell, living and multiplying there, a
virus uses many biological features of the host cell aside from its own.
The coronavirus has spike proteins on its surface that help it gain entry
into a host cell, first by grabbing and then penetrating the outer wall of
the host cell.

The spike protein has two major components: the receptor-binding domain
(RBD), which is like a molecular hook that helps the virus grab the
host-cell surface, and the cleavage site, which helps it penetrate the host
cell.

The genome of an organism accumulates changes as it evolves. A change is
usually harmful to the organism. But sometimes a change can be beneficial,
because it helps the organism survive better and longer. It may also help
the organism reproduce more.

A genome has several portions, not all of which are equally important to
the organism. Some portions are so critical to its survival that the
organism dies if an alteration takes place in that region.

The not-so-critical portions are usually found to harbour many alterations.
The RBD portion of a coronavirus genome — it’s most variable portion —
accumulates many alterations during its evolution over time.

The genome sequence of the novel coronavirus (SARS-CoV-2) is remarkably
similar — letter by letter through its about 30,000 letters (nucleotides) —
to those of SARS-CoV and other SARS-like coronaviruses found in other
animals, including bats.

SARS-CoV-2 is therefore a descendant of, or has evolved from, other SARS or
SARS-like coronaviruses. There are, however, some notable differences.

The RBD portion shows five alterations in the SARS-CoV-2 genome compared to
SARS-CoV. These alterations are remarkable. Because of these alterations,
the novel coronavirus can bind very efficiently to a protein present on the
surface of human cells, especially in some cells of the lung. This protein
is ACE2, or angiotensin-converting enzyme 2, which regulates blood pressure.

Of course, SARS-CoV also binds to ACE2, but the descendant virus (CoV-2)
binds much more efficiently. Patients suffering from heart disease and
diabetes are often treated with ACE inhibitors. These medicines actually
help increase the amount of the ACE2 protein in the body.

The presence of more ACE2 protein enables more coronavirus particles to
enter the lungs, because more coronaviruses find protein molecules to latch
on to.

The cleavage site of the novel coronavirus too exhibits a novel alteration
compared to SARS-CoV. However, it is still unclear whether this alteration
results in better penetration into the host cell.

Bats and pangolins

How do these findings help refute the claim that the novel coronavirus is a
man-made bio-weapon, created through genetic manipulation?

There is no direct evidence against the bio-weapon claim. But the indirect
evidence derived from studies of the genomes of coronaviruses is
overwhelming.

The genome of a bat coronavirus (RaTG13) is about 96 per cent identical to
that of SARS-CoV-2. Interestingly, the similarity between SARS-CoV-2 and
SARS-CoV is only about 79 per cent; with MERS-CoV it is even lower, about
50 per cent.

Thus, the novel coronavirus is more similar to the bat coronavirus than to
other human coronaviruses (SARS and MERS). This indicates that SARS-CoV-2
is more likely to have arisen from a bat coronavirus than from a
pre-existing human coronavirus.

However, there is considerable dissimilarity between SARS-CoV-2 and bat
coronaviruses relating to the receptor-binding domain (RBD). The bat
coronavirus, therefore, cannot bind as efficiently to human ACE2 as
SARS-CoV-2.

Coronaviruses were also found in pangolins — commonly known as the “scaly
anteater”, now an endangered species — around the Wuhan area. Pangolin meat
is a delicacy in China. The scales of the pangolin are much sought after
for their presumed medicinal properties. Therefore, the pangolin is poached
and trafficked.

Just before the Covid-19 outbreak in Wuhan, two dead pangolins were
discovered in the nearby Guangdong Wildlife Rescue Centre. The lungs of
these dead pangolins were filled with a frothy liquid. Coronaviruses were
found in these pangolins.

Further, scientific work revealed that pangolin coronaviruses are similar
to human SARS-CoV-2. How similar? In subsequent scientific investigations,
the letter-by-letter identity estimates between the genomes of the novel
human and pangolin coronaviruses were between 90 and 92 per cent.

But what is more remarkable is that all of the alterations in the RBD that
confer a high efficiency on the SARS-CoV-2 to bind to human ACE2 are
present in the pangolin coronaviruses.

The logical conclusion is that the pangolin coronavirus jumped to humans.
The pangolin coronavirus loved humans because it could get into human lungs
easily via the ACE2 protein and multiply happily there.

At some stage, the virus — possibly because of one or two other changes
within its genome — acquired the capability of human-to-human transmission.
This is a clear case of Darwinian natural selection.

There is no need to accuse ourselves of having engineered a coronavirus to
a novel form and made it more infective for its use as a bio-weapon.

Partha P Majumder is president, the Indian Academy of Sciences, and
president, the West Bengal Academy of Science & Technology.
-- 
Peace Is Doable




-- 
Peace Is Doable
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