Analysis on the Coronavirus Disease 2019 Documentary

– Viperae

Disclaimer:
The article was written out based on the writer's personal research about the said issues raised.

Heads up, long article ahead!

Everybody loves a good conspiracy theory but in this crisis, it is not. For weeks now, a lot of rumors and theories already spawn on the social media and science communicators are doing their best to refute them with the help of experts who specialized with this kind of situation.

Probably you've watched the said documentary that leaks what is supposed to be the pandemic we're experiencing is a bioengineered from a Chinese Research Laboratory and a Chinese Espionage happened. The theory has been up for weeks but there are no concrete evidence for that. The video investigated the origin of the virus but as soon the video was released, intrigued of what could be the video's content and after watching it several times and decided to do some review on that said vide.

1. Misleading Headline and Video Title

–The first thing probably not everyone noticed. The video's headline and title is not appropriate. World Health Organization already announced the proper name for the pandemic, Coronavirus Disease 2019 or COVID-19 and the causative agent, SARS-COV-2.

To further understand where the name came from, Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, responsible for the nomenclature and classification of new viruses under the Family Coronaviridae. CSG-ICTV assessed the new human pathogen which was formerly called 2019-Novel Coronavirus based on the phylogeny, taxonomy and established guidelines, CSG recognizes the novel coronavirus on the sister clade of the Bat and Human Severe Acute Respiratory Syndrome Coronaviruses. In addition, CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. As we can see there are a lot of missing information thus we need to extend our researches to fully understand and will help us for further to end this pandemic.

The lone title can have a viewer's effect when presenting an investigatory report and prolly what happened when the outbreak began, Chinese were discriminated as people called the disease as Wuhan Virus or Chinese Virus. People tend to ask as well, if we can't call it that way, why are we calling other past pandemics such as Spanish Flu, would that discriminate them? Priority of how such news is reported, media has something to do, that's the norm but it is should not be used. The 1918 Pandemic is called 1918 H1N1 Pandemic Flu as well as the causative agent was similar to the 2009 H1N1 Pandemic.

2. The Seafood Market

–The controversy began with where the concluded origin of the virus for now. While we can agree that until this time there are uncertain on the origin of it. The epidemiological links of the earliest patients with the ground zero of the pandemic became the basis to further support the claim but this does not mean that a virus created from the lab. In the recent studies which shows the ancestral phylogeny of the virus, majority of them really are not linked to the seafood market and contracted the disease elsewhere.

In the earlier cases reported by Chinese health officials and even the WHO said that the first patient had onset symptoms on December 8, 2019 and most of those cases had link to the seafood market. This raises the question further more that if it is accurate data then human to human transmissions must be earlier as the incubation time of where a patient contracted it to the onset of symptoms shown. The near possible hypothesis for this scenario is that there are a lot of silent spreaders from Wuhan or even elsewhere before the sudden rise of cluster of infection to Wuhan. This scenario also happened to the MERS-COV outbreak began from a patient in Saudi Arabia but later studies traced it back to an outbreak of similar pneumonia in Jordan in April 2012. Other scenarios were added such as a group of infected animals came into the marketplace and the other one is that an unknown intermediate host before jumping to humans.

In my previous article as well, I pointed out that the genomic epidemiology of the pandemic, bat are the suspected primary hosts and before reaching the humans, there's a missing link. Earlier papers show snakes as the intermediate host but quickly rejected as snakes does not infected by coronaviruses thus they focused into the pangolins which gene sequences has high relativity.

3. The S protein Argument

–The part where everyone should be at least aware as it hints again pangolins as intermediate hosts. In the video, it was discussed as well that and likely used this piece to gather evidence that it is lab created. The video pointed out the S protein of SARS-COV-2 shows the similarities among other coronaviruses and argues that virus could not have come from natural reservoirs.

While it is worth noting that the samples presented actually exists which I will provide them below this article, there is a misinterpretation happened on that part.

S protein or spike protein, a protein inserted in the outer membrane of coronaviruses that serves as key in a lock. Protein binds to protein present on the surface of the host's target cells and thus allowing the virus to enter and infect cells. The protein's amino acid serves as the dictating program of what receptor protein it can only bind to and determining the host species type of tissue the virus it can infect. The S protein of SARS-COV-2 upon entrance to the body targets the epithelial cells in our lungs.

The similarities of S protein of SARS-COV-2 and other previous isolated strains is closely related to the viruses found in wildlife such as bat virus RaTG13, the controversial CoVZC45 and CoVZXC21. In Jan of this year, various experts I've come across of discussing and sharing their findings as well on the genomic and phylogeny analysis compared to the available library of coronaviruses we have at present. A lot of them pointed out a possible recombination event occurred.

When these experts compared the SARS-COV-2 genetic sequence with a library of viruses, authors found that the most closely related viruses were two SARS-like coronaviruses of bat origin: bat-SL-CoVZC45 and CoVZXC21 which shared 88% of the genetic sequence.

In addition it was more genetically distant to the human SARS virus which shared about 79% of the genetic sequence and the Middle East respiratory syndrome (MERS) virus which shared about 50% of the genetic sequence. Reports of similarities in the genetic sequences between SARS-COV-2 and its close relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21 were less than 90%, meaning these two bat-derived coronaviruses are not direct ancestors of the current virus.

In the case of the S protein, six amino acids have been shown to be crucial for the protein to bind to the receptor ACE2 of human cells and infect them. COVID-19 virus, SARS-CoV-2 has exactly the same six amino acids as the pangolin coronavirus, and only one out of six with the SARS-CoV-1 S protein. This means that the SARS-COV-2 S protein is more closely related to coronaviruses infecting wildlife animals such as the pangolin.

The results as well suggest that recombination events are complex and are more likely occurring in bat coronaviruses than our current virus we're experiencing. Recombination is probably not the reason for emergence of this virus, although this inference might change if more closely related animal viruses are identified.

4. HIV Insertion Argument

–In the later part of the video as well pointed out that a part of the virus came from HIV. Before the video was released, there is one paper uploaded in BioRXiv that discussed and also used in the video.

The paper titled "Uncanny similarities of unique inserts in 2019-nCoV spike protein to HIV-gp120", questioned these so called insertions on the virus.

The 4 insertions that the paper mentioned gathered criticisms from various experts and the researchers failed to check the allegedly insertion's similarities to other species hence it disproves their research as well. The paper now as well is withdrawn due to the criticisms.

One of those experts who criticized the paper was Trevor Bedford, faculty member at the Fred Hutchinson Cancer Research Center who studies viral evolution. He re-analyzed the gene and protein sequences used by the authors and found that the so-called “unique” inserts appeared in many other organisms, including Cryptosporidium and Plasmodium malariae.

5. The Source

–I have to step up as well with these misinformation spread in the social media. An investigatory report must be factual and reliable but in other aspects the reporter/s should at least be critical thinker which was not shown in the video.

Here's a quick review on the media outlet:

I checked their credibility and found out that in the past, they are known to published numerous unsupported conspiracy theories and was banned from advertising in Facebook after they were found to operate a network of fake profiles and a consistent anti CCP/Pro-Trump.
(Does it remind of you of something similar?)

Further more one of the speakers in the video, Judy Mikovits, had actively research on viruses but not on coronaviruses prior to 2012. She was the director of the non-profit Whittemore Peterson Institute, a medical research institute affiliated with the University of Nevada, Reno.

Mikovits was reported as well she was fired amid the controversies on the reproducibility of her research.

There are tons of false, inaccurate information laid down on the said documentary that reflects how critical information is spread faster than the virus itself. Some of my colleagues as well pointed out that there are papers that are retracted or withdrawn for questionnable research like the HIV argument.

#EnigmaReadera

References and Sources:

Menachery et al. (2016) SARS-like WIV1-CoV poised for human emergence. Proceedings of the National Academy of Science. (https://www.pnas.org/content/113/11/3048)

Forster et al. (2020) Phylogenetic network analysis of SARS-CoV-2 genomes. Proceedings of the National Academy of Science. (https://www.pnas.org/content/early/2020/04/07/2004999117)

Andersen et al. (2020) The proximal origin of SARS-CoV-2. Nature Medicine. (https://www.nature.com/articles/s41591-020-0820-9)

Liu et al. (2020) No Credible Evidence Supporting Claims of the Laboratory Engineering of SARS-CoV-2. Emerging Microbes and Infections (https://www.tandfonline.com/doi/full/10.1080/22221751.2020.1733440)

Xiao et al. (2020) HIV-1 Did Not Contribute to the 2019-nCoV Genome. Emerging Microbes and Infections. (https://www.tandfonline.com/doi/full/10.1080/22221751.2020.1727299)

Ge et al. (2013) Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. (https://www.nature.com/articles/nature12711)

Cohen (2011) Chronic Fatigue Syndrome Researcher Fired Amidst New Controversy
(https://www.sciencemag.org/news/2011/10/chronic-fatigue-syndrome-researcher-fired-amidst-new-controversy)

Pradhan et al. (2020) Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag (https://www.biorxiv.org/content/10.1101/2020.01.30.927871v2)

Letko et al. (2020) Functional assessment of cell entry and receptor usage for lineage B β-coronaviruses, including 2019-nCoV
( https://www.biorxiv.org/content/10.1101/2020.01.22.915660v1.full)

https://www.nytimes.com/2020/02/05/technology/epoch-times-youtube.html

https://twitter.com/trvrb/status/1223666856923291648