The Origin of SARS-CoV-2: Lab-Made or Natural Evolution?

Madison Pascual Munar has a Doctorate degree in Molecular Biotechnology.

Curiosity Killed the Cat, But the Satisfaction Brought It Back

Reading headlines about the discovery of gene sequences with high similarity with HIV-1 genes in the SARS-CoV-2 genome, a Nobel Laureate testifying that SARS-CoV-2 is an engineered strain, and publications about the creation of a chimeric SARS virus by a Chinese virologist, made me think whether there is basis on the speculations about the origin of SARS-CoV-2.

I won't deny that I myself got curious whether SARS-CoV-2 was a result of genetic engineering or simply a product of natural evolution. Curiosity killed the cat, but the satisfaction brought it back. I found this proverbs inspiring to delve deeper into my own curiosity. Hopefully with this article, I can bring some clarity on these scientific conundrums.

SARS-CoV-2 is A New Strain

Where Did SARS-CoV-2 Come From?

Generally, viruses have a primary host where it naturally exists without causing any adverse problems. In case of the SARS-CoV-2 virus, the identified primary host was the horseshoe bat (Rhinolophus hipposideros). The secondary host or intermediate host which is the transitory reservoir prior to the infection of humans for SARS-CoV-2 is still unknown. However, several publications pointed out that Sunda or Malayan pangolins (Manis javanica) are the most likely intermediate host, based on genetic analysis.

Scientists from South China Agricultural University in Guangzhou reported their findings about the 99% similarity of the SARS virus genome from Malayan pangolins with the SARS-CoV-2. Moreover, recent studies identified recombination events within the Receptor Binding Domain (RBD) in the SARS-CoV-2. This suggests that SARS-CoV-2 is a possible product of recombination events involving the bat-CoV viral genome as the backbone and new genetic insertions from the Pangolin-CoV RBD.

Spillover Events Led to SARS-CoV-2 Infection in Humans

Horshoe Bats As the Primary Host of SARS-CoV-2

Sunda/Malayan Pangolins As Probable Intermediate Host of SARS-CoV-2

Pangolin originated from the Malay word penggulung which means to roll. Pangolins tend to roll into a ball when threatened.

Phylogenetic Analysis Revealed 99% Homology of SARS-CoV-2 with Pangolin-CoV

The Scientific Controversy

The controversy emerged from the publication of some scientists from the Indian Institutes of Technology regarding the occurrence of four gene insertions with high sequence similarity with HIV-1 gp120 and HIV-1 Gag amino acid sequences.

Upon close investigation, the presumed HIV-1 gp120 and Gag amino acid sequences in the SARS-CoV-2 genome were very small, less than 10 amino acid residues, and has truncated sequences. Truncated amino acid sequences may not be able to retain the original function of the protein showing sequence homology. More so, if the sequence similarity is very low. This alone is a strong basis to debunk these claims.

The preprint of the publication was already withdrawn in the Biorxiv preprint server by the authors.

Presumed HIV-1 Amino Acid Sequences in SARS-CoV-2 Genome

HIV-1 gp120

HIV-1 Gag Protein

High Human to Human Transmission

Unlike other SARS-related viruses, the SARS-CoV-2 have a notable high human to human transmission. This in particular was the reason why some scientists doubt of the possible origin of this new strain.

Different spillover scenarios were proposed, including the possible release or contamination from the Wuhan Institute of Virology, a Level 4 Biosafety Laboratory (BSL). BSL-4 is the highest Biosafety Level where researches on aerosol-transmitted pathogens like viruses that could cause fatal human diseases are allowed.

The presence of Wuhan Institute of Virology, and studies on bat viruses, specifically on SARS-CoV, at the center of the outbreak is also incontrovertible.

In depth epidemiological studies on human SARS pathogens will aid in determining the culprit of the outbreak, and predict future re-emergence of this deadly disease.

SARS-CoV-2 Phylogeny Validated New Strain Status

At least two independent studies on the phylogenetic relationship of SARS-CoV-2 with other SARS-related viruses agreed that the causative agent of COVID-19 is from a new coronavirus strain. Based on the phylogenetic analyses, distinct clustering of the SARS-CoV-2 genome sequences isolated from COVID-infected patients were observed. This is a concrete evidence that SARS-CoV-2 is a new strain.

The Real Price of Wildlife Trade

The unknown spillover events that have transpired and allowed for the transmission of the SARS-CoV viruses from animals to humans is a direct consequence of illegal poaching and wildlife trade.

Pangolins were reported to be poached at an alarming rate, which also put these species on the brink of extinction. Their meats are advertised as aphrodisiac and as a status symbol, and their scales are used in traditional Chinese medicines.

The real price of illegal wildlife trade has rebounded towards us. These illegal activities must be stopped or future pandemic outbreaks will roll one after another.

Pangolins: The Most Trafficked Mammal in The World

The only way to prevent a future pandemic is by paying respect to nature. The world is round, what goes around comes around.

References

• Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2 - Volume 26, Number 7—July 20
  

• Did pangolins spread the China coronavirus to people?
  

• Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins | Nature
  

• Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag
  

• Implications for viral capsid assembly from crystal structures of HIV-1 Gag(1-278) and CA(N)(133-278
  

• Molecular architecture of native HIV-1 gp120 trimers
  

• Phylogeny of SARS-like betacoronaviruses including novel coronavirus SARS-CoV-2
  

• Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China
  

• Pangolins: The Most Trafficked Mammal You've Never Heard Of | National Geographic - YouTube