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State of Mankind

Coronavirus Pandemic – A Holistic View (3)

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A Holistic View:
Are We Able to Prevent Another Disaster
Like Coronavirus Pandemic?

— Part 3: A Mysterious Virus — How Did It Start?

May 28, 2020 | By Tong Gen and Wuxian, (

(Continued from Part 2)
Chapter 5: Man-made Theory

So far, the main arguments that support the man-made theory about the origin of the virus are centered around the sequence of its spike protein (S-protein), as well as a piece of sequence insertion that appeared to come from an artificial vector used for DNA manipulation.

1. The spike protein of the new virus contains a unique cut site not present in its close relatives.

Scientists have found that the S-protein of the new coronavirus has a special fragment of sequence that can be cleaved by a special protein in the host cell. After the sequence was cut by the protein called furin, the virus gains the ability to enter the host cell and infect multiple organs.

Some people argued that the furin cleavage site in the virus is unique and hasn’t been found in its close relatives of other coronaviruses, but some scientists also point out that such sequence does exist naturally in other viruses, including some coronaviruses not directly related to the new virus.

While one could argue that the insertion of the furin cut site to the virus is through genetic manipulation, as it’s a well-established bioengineering process, one can’t completely rule out the possibly that the virus takes up the sequence from the environment itself, given the fact that coronavirus is a RNA virus, which isn’t stable and is constantly mutating and taking in sequences from the environment (a process called genetic recombination).

As a result, the furin cut site alone isn’t enough to conclude that the virus was a product of lab manipulation.

2. Indian researchers claimed the virus contains HIV sequences

There are also some other arguments about the virus’ S-protein containing HIV sequence. A preprint of an article from Bishwajit Kundu and others at the University of New Delhi was published in bioRxiv in late January. The Indian team noticed four insertions in the virus S-protein are unique. They are not present in other coronaviruses, and amino acids are actually identical or similar to proteins in HIV. The Wuhan virus “is unlikely to be fortuitous in nature,” wrote the authors. Two days later, however, the Indian team withdrew this paper.

3. The new virus contains sequence similar to that from an artificial p-Shuttle SN Vector

Another argument that claims the Wuhan virus to be a lab-engineered strain was based on an article published on January 30, 2020, by James Lyons-Weiler, who formerly worked at the University of Pittsburgh as a bioinformatician.

In his article, Lyons-Weiler wrote that he observed a gene sequence in the Wuhan virus being 67% identical to the p-Shuttle SN Vector, which has been used in many labs to produce SARS vaccine. He then speculated that the novel coronavirus was a man-made virus used for SARS vaccine research.

Another researcher, Steven Salzburg, a computational biologist and professor at Johns Hopkins School of Medicine, searched the virus sequence against the database on NCBI (National Center for Biotechnology Information), only to see the top hits were sequences from other bat coronavirus, but not the vector.

Salzburg argued that if the virus sequence did come from the vector, it would be “near-identical,” not [67%] “distantly related.”

Chapter 6: Natural-origin Theory

Given above rebuttal to the man-made theory, no solid evidence could support the argument that the virus was actually generated in a lab. Many scientists agree that the new coronavirus was probably a naturally occurring virus that originated in bats.

1. Bat virus has closest relationship with the new coronavirus, but needs intermediate hosts to facilitate mutation

On February 3, 2020, Shi Zhengli published a paper on the prestigious journal Nature, titled “A pneumonia outbreak associated with a new coronavirus of probable bat origin.”

In this paper, Shi reported that through whole genome sequencing, her team has identified a bat coronavirus named RaTG13, sharing 96.2% identity with the novel coronavirus. This is the closest strain to the novel coronavirus reported so far.

The 96.2% similarity does not mean that the bat virus would directly infect humans and be responsible for the current pandemic. According to Trevor Bedford, a bioinformatics specialist at the University of Washington, it would usually take 25-65 years for the bat virus to mutate enough to become 100% identical to the current coronavirus.

However, the new coronavirus broke out only a few months ago, and there was not enough time for the bat virus to eliminate the 3.8% difference (=100% – 96.2%) and become the coronavirus if it had directly infected humans.

The only possibility for the bat virus to quickly mutate into the coronavirus was through intermediate hosts. In other words, if the bat virus had infected an intermediate host, which then spread the virus to humans, that’d greatly accelerate the mutation speed. Richard Ebright of Rutgers University argued that “the mutation rate may have been different as it passed through different hosts before humans.”

The quest is on to identify the intermediate host(s). In previous zoonotic outbreaks (diseases spread from animal to human), both the 2003 SARS in China and the 2012 MERS in Saudi Arabia were found to result from bat viruses that used palm civets and camels as intermediate hosts, before jumping back to human and causing diseases.

By the time the virus broke out in Wuhan in the winter of 2019, bats have already gone into hibernation and there were no bats sold at the wet market. So it’s possible that the virus has been around in the environment for months or even longer and has gone through a comprehensive mutation process before developing the deadly traits.

Several candidates came up in the search of the intermediate host, including mink, ferrets and even turtles. Although the list was narrowed down to pangolin as a hot contender, it soon proved to be impossible too.

The pangolin lives in a warm environment and has to stay in a subtropical environment unlike Wuhan. Its diet is limited to ants and termites. It also has a weak digestive and respiratory system. Pangolins get sick easily and the illness is often lethal. Because of these reasons, pangolin is not suitable for captive breeding. In fact, China does not approve its trading, so pangolins come from smuggling and very few of them are alive.

Had pangolins been an intermediate host, the first patients would have been smugglers. The outbreak would have also spread in various locations, since Wuhan is not a distribution center of the smuggling.
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