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How is the Omicron variant genetically

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Since the emergence of the pandemic caused by the SARS-CoV-2 virus, there have been variants that the World Health Organization called worrisome. These worrisome variants are five (as of today, December 18, 2021) and were named 20I (Alpha, V1) or B.1.1.7,  20H (Beta, V2) or B.1.351,  20J (Gamma, V3) or P.1,21A (Delta) or B.1.617.2 and  21K (Omicron) or B.1.1.52. One of them is currently in full swing is the Ómicron variant.

What does the coding of the different names mean?

Sometimes biology becomes for profane people a gibberish of meaningless names. I have to tell those people that science is structured in a logical way, therefore everything has a reasonable explanation and is named following some kind of proper coding. In the scientific names of animals and plants formerly bore names of the person who discovered them or were an occurrence of the discoverer. For example, the bivalve Abra cadabra, was later renamed.

The CoVariants website uses the Nextstrain naming  system  for variants. It is a bit confusing since there are several coding systems as can be seen in Fig. 1. The most used is the simplest, that is why it usually uses the label of the World Health Organization, that is, it is called by the corresponding Greek letter. Therefore, what is heard in the media is Omicron variant, instead of 21K variant (Omicron), which is less commercial.

omicron
Figure 1. Variants of the SARS-CoV-2 virus

Entry of the virus into the cell

Much has been said about the mechanism that the virus must enter the host cell. Viruses, on their own, cannot survive in any medium. They are like a replication machine, only looking to use what a host provides them to replicate non-stop. The SARS-CoV-2 virus fits like a glove into a human cell receptor called ACE2.

As it has mutated, changing its sequence, it turns out that it is increasingly appropriate to bind to that receptor and therefore the virus becomes more contagious. The mechanism can be seen in Fig. 2.

Figure .2 How the SARS-CoV-2 virus enters the cell

21K (Omicron)

Also known as 21K B.1.1.529, Omicron appeared in November 2021. Early sequences of this variant come mainly from South Africa, but it was also detected in Botswana and Hong Kong. Africa has been a breeding ground and laboratory for the virus and poor vaccination has led to the proliferation of variants such as this hyper-contagious one.

21K(Omicron) is a cause for concern because of the large number of mutations it has in the Spike gene (the spicule). Many of these variants are in the receptor binding domain and the N-terminal domain and can therefore play key roles in ACE2 cell receptor binding and antibody recognition.

Phylogeny

The phylogeny, the kinship relationship between the different variants of the SARS-CoV-2 virus can be seen in Fig. 3, extracted from nextstrain.org.

Figure 3. Phylogeny variant 21k Omicron, source: https://nextstrain.org/groups/neherlab/ncov/21K.Omicron

Genetics

The genetics of a virus is the most important thing. In its genes are instructions to replicate and create copies of itself non-stop using the biosynthetic machinery of the host.

The RNA sequence of the original genome of the SARS-CoV-2 coronavirus, isolated from Wuhan-Hu-1, whose complete sequence of 29,903 ribonucleotides of single-stranded RNA  was deposited in GenBank(MN908947.3)and with a sequence of amino acid encoded from glycoprotein S corresponds to  QHD43416.1. The genome of the Omicron variant is different from that of the original variant in having  29684 ribonucleotides.

The SARS-CoV-2 peak glycoprotein is a trimer (3 units shown,) in complex with the ACE2 receptor of the human host cell (shown 1-unit, green ribbon). Positions with changes in lineages B.1.1.529 + BA.1 are indicated as colored balls in Fig. 4. Changes with phenotypic effects documented from the literature are light orange or cyan for insertions/deletions (elimination), while others without documented phenotypic effects are colored in green.

omicron
Figure 4. 3D structure of the spike protein with changes in amino acids. Source: https://www.gisaid.org/hcov19-variants/

A similar representation in gif format of the protein model for 21K can be seen in the following figure made through GISAID.

Figure 5. Protein model. Source: https://covariants.org/variants/21K.Omicron

References

  • https://covariants.org/variants/21K.Omicron
  • https://covariants.org/shared-mutations
  • https://nextstrain.org/blog/2021-01-06-updated-SARS-CoV-2-clade-naming
  • https://nextstrain.org/groups/neherlab/ncov/21K.Omicron
  • https://www.nature.com/articles/s41564-021-00954-4
  • https://www.gisaid.org/hcov19-variants/
  • https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern

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