The Unnatural Evolution of the SARS-CoV-2 Variants

This article discusses the research showing that the evolution of the SARS-CoV-2 variants is unnatural and could be manufactured.[1]

Two authors from Japan specializing in viral genetics and evolution made the astounding claims.

Atsushi Tanaka from the Division of Research Animal Laboratory and Translational Medicine of the Osaka Medical and Pharmaceutical University.

The other is Takayuki Miyazawa, an associate professor at the Resilience Research Unit at Kyoto University in Japan.

Tanaka and Miyazawa work at the Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences in Kyoto.

Miyazawa has co-authored other papers about viral evolution, namely Genome Evolution of SARS-CoV-2 and its virological characteristics and Dynamic Evolution of Retroviral Envelope Genes in Egg-Laying Mammalian Genomes.

I mentioned his previous research to show that Miyazawa most likely knows the natural patterns of viral evolution that should be expected.

Introduction

The SARS-CoV-2 Virus

SARS-CoV-2 uses human cells to multiply and thereby cause an infection. It injects its RNA into the cells to make viral proteins like the spike protein.

The replication process happens very fast and is prone to errors called mutations.

Synonymous and Non-synonymous mutation

Synonymous and non-synonymous mutations are frequently mentioned in the paper, so let us differentiate.
Synonymous mutations tend to produce the same amino acid and do not affect the function. At the same time, non-synonymous mutation can lead to another amino acid and change the property of the protein. If the non-synonymous mutation happens at the beginning of the protein, it can become lethal and make the protein nonfunctional.

Typically, synonymous and non-synonymous mutations in SARS-CoV-2 viruses occur together at a rate of 1.28. This tidbit will be pertinent later.

SARS-CoV-2 variants

  1. The first SARS-CoV-2 detected in Wuhan is called the Wuhan H1.
  2. It acquired the D614G mutation and quickly spread worldwide.
  3. Alpha B.1.1.7: 20I (Alpha, V1) appeared in September 2020) and became predominant in early 2021.
  4. Beta showed up in October 2020.
  5. Alpha variants B.1.351: 20H (Beta, V2) was identified in October 2020
  6. Gamma, V3 in December 2020
  7. Delta (B.1.617.2) (January 2021)
  8. Mu was discovered in January 2021
  9. Omicron B.1.1.529, or BA.1, showed up on November 24, 2021, with more than 50 amino acid changes compared to the first reported strain, Wuhan-Hu-H1. It also has 39 amino acid changes in the spike protein.
  10. Omicron BA.2, initially detected on December 5, 2021, has 31 amino acid changes in the spike protein compared to the Wuhan -Hu-H1.

Method

The authors compared the sequences of 129 Omicron BA.1-related isolates, 141 BA.1.1-related isolates, and 122 BA.2- 28 related isolates to know the order in which the mutations led to the formation of the SARS-CoV-2 Omicron variants.

The second objective is to know if homologous recombination happens.
Homologous recombination occurs when genetic information from the two becomes recombined to form a new variant. It can happen when two variants infect the same person.

Three Reasons Why the SARS-CoV-2 Variants are Unnatural

After their analysis and lots of bioinformatics work, they arrived at the reasons why the SARS-CoV-2 variants are artificially synthesized.

1. There are Omicron variant-associated isolates, with one mutation site being Wuhan-type.
Some mutations in the subtypes of BA.1 and BA.2 variants are present in older variants. The mutations seemed to skip a generation, making it hard to know the chronological sequence of the Omicron mutations.

The presence of these isolates refutes the establishment of Omicron strains through a continuous evolutionary process by accumulating mutations.
So, we could not determine which mutation occurred first or last in forming the Omicron variants.

page 7-8. Unnaturalness in the evolution process of the SARS-CoV-2 variants and the possibility of deliberate natural selection.

The explanation they offered on how mutations from the Wuhan type can also be seen in the Omicron variants is that non-synonymous mutations were artificially made, and once released in the natural environment, synonymous mutations occurred within the variants.

2. The almost complete absence of synonymous mutations in the Spike protein in the isolated variants.

Typically, seasonal human coronavirus, like the 229E, has a synonymous–non-synonymous mutation ratio of 1.28.

Their work shows that the Alpha, Beta, Gamma, Delta, or Mu variants have no synonymous mutations.

The fact that most of these mutations occurred without synonymous mutations suggests that none of these mutations arose as a result of trial-and-error random mutations in nature.

page 13. Unnaturalness in the evolution process of the SARS-CoV-2 variants and the possibility of deliberate natural selection.

The Omicron variant (BA.1 lineage), which shows the most significant accumulation of mutations in the S protein, is primarily non-synonymous in the S protein and has only one synonymous mutation.

Recall that the BA.1 has more than 50 amino acid changes compared to the Wuhan, with 39 in the spike protein.

3. Some Omicron variants were already present in Puerto Rico as early as 2020.

This was discovered somehow by accident. They hypothesized that the Omicron BA.1 and BA.2 may have infected the same person and recombined their RNA in a homologous recombination process.

Next, they made a hypothetical spike protein sequence of an Omicron BA.1 and BA.2 recombination.

To their surprise, the theoretical recombination was already present in 2020 among 35 isolates in Puerto Rico 2020!

How can that be when Omicron first appeared in November 2021?

The study of 35 recombinant isolates of Omicron variants BA.1 and BA.2, confirmed that Omicron variants were already present in 2020.

The table below shows two isolates from Puerto Rico in 2020 that are shaded purple in the leftmost column.

The other columns are the color-coded mutations from the BA.1 and BA.2 recombination that appeared much later in 2021.

Notice the exact colors of the mutations in the same columns depicting that Omicron recombinants were present in 2020 before the Omicron was officially announced to be circulating.

This should not have happened if the Omicron naturally evolved.

Source: Unnaturalness in the evolution process of the SARS-CoV-2 variants and the possibility of deliberate natural selection. 2023. DOI: 10.5281/zenodo.8216373

Apologies for the microscopic font in the table. If you want to see the expandable table, it is on page 39 at this link.

Is it possible that a new way of natural evolution happened? The authors answered.

One idea, the hypothesis that these viruses were artificially generated, is more reasonable than proposing a novel mutation acquisition mechanism.

However, they did not speculate on any malevolent reason why a lab-made virus is released.

However, is there any reason to artificially create these mutants, which are unlikely to have occurred naturally, given the current SARS-CoV-2 epidemic?

Tanaka and Miyazawa did not limit their conclusion to the Omicron variants. Instead, they raised the bar and included the earlier variants.

Suppose the SARS-CoV-2 Omicron variant and its one amino acid reversion mutants were artificially and systematically generated.
In that case, we should suspect that the other variants (Alpha to Delta) may also be artificially generated viruses.

In their closing remarks, they pointed out that they were not espousing any conspiracy theories and played it safe.

Furthermore, we do not conclude that these viruses were artificially synthesized and distributed based on malicious intent.
This paper aims to point out that SARS-CoV-2 has undergone unthinkable mutations under conventional coronavirus mutation mechanisms, and we hope that the possibility of artificial theory should be included in the discussion seriously as to the formation of SARS-CoV-2 variants.
Nonetheless, the analysis we have shown here concludes that the Omicron variants are formed by a completely new mechanism that cannot be explained by previous biology.
The way how the SARS-CoV-2 280 mutations occurred should prompt a reconsideration of the SARS-CoV-2 pandemic.

What do you think? Is there a secret organization with a bio lab that churns out SARS-CoV-2 variants to sell more vaccines?

Let me know what you think.

Truth heals. Lies kill. Don’t Get Sick!

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References:

  1. Atsushi Tanaka and Takayuki Miyazawa. Unnaturalness in the evolution process of the SARS-CoV-2 variants and the possibility of deliberate natural selection. 2023. DOI: 10.5281/zenodo.8216373
  2. Scoville, Heather. “Synonymous vs. Non-synonymous Mutations.” ThoughtCo, January 26, 2021, thoughtco.com/synonymous-vs-nonsynonymous-mutations-1224600.

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