Mutations of OMICRON and DELTA strain spike protein! COVID-19

Dear citizens and associates,
The appearance of the new Botswana SARS CoV variant, Omicron strain on November 24, 2021, has been described as the most feared strain of the virus known to experts so far and is an intriguing phenomenon for research, especially by molecular biologists, virologists and other professional staff.

The new strain systematized as VOC B.1.1.529 has in its genome all the “worrying mutations” already present in other COVID strains, as well as additional mutations that contribute to the infectivity and resistance to vaccines currently available. The new “super strain” has appropriated all mutations from the Delta strain, which gives scientists the right to expect more intense transmission and dominance in the infectious process at the human population level, compared to previously emerging strains.
Omicron also carries genetically specific alterations in the Beta strain, which are responsible for resisting artificially acquired immunity with available vaccines, as well as the mutation characteristic of the Alpha strain. In total, the new strain carries more than 50 mutations throughout the viral genome (positive sense ssRNA), of which only 32 mutations are located in the gene encoding the spike protein. Due to a large number of mutations in the S gene, its functional protein product – Spike protein acquires a completely different three-dimensional conformation and becomes unrecognizable for antibodies artificially induced in a given organism, ie under the action of a vaccine, which was created specifically for the initial 3D structure of S protein. The three amino acid substitutions H665Y, N679K, and P681H allow easier internalization of the virus in the host cell, while substitutions R203K and G204R are retained in the Omicron proteome, and are present in all pre-existing strains defined by the WHO as a concern (VOC – Concern).
The laboratory chain of specialized diagnostic laboratories BIOTEK in Skopje and through the cooperation it has at the national and international level with other diagnostic centers involved in screening during the COVID pandemic, monitors every incident and offers a complete solution for the new diagnostic strain by RT-PCR method at a genetic level. Specifically, compared and analyzed based on available bioinformatics data on mutations in strain B.1.1.529 of the coronavirus, it was defined that the above-elaborated mutations in the genome of the new strain do not affect the diagnostic properties of the SARS CoV-2 / SARS CoV Multiplex test. Real-Time PCR manufactured by DNA Technology, Russia.

Namely, the multiplex panel construction of the test is precisely intended for detection and differentiation of 3 genes, 2 of which are highly specific and low mutable for SARS CoV-2 and 1 gene characteristic for the whole family of Coronaviridae which includes all newly formed mutant strains.

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