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4bases’ paper of the month – February 2022 – Omicron variant (B.1.1.529) of SARS-CoV-2: Mutation, infectivity, transmission, and vaccine resistance

Our team’s reading recommendation for this month goes to “Omicron variant (B.1.1.529) of SARS-CoV-2: Mutation, infectivity, transmission, and vaccine resistance”[1] by Shi-Yan Ren et al., an extremely interesting paper just published in “The World Journal of Clinical Cases”.

The paper reminds us of the panic responses at the time of emergence of the Omicron variant, mostly related to its very high transmission rate and to its high number of mutations, and it proposes a review of the highly mutated regions. Fortunately enough, we found out in the meantime that, although Omicron has been spreading faster than any previous variant, it generally caused less severe symptoms than those previous variants.

The human antibodies that neutralize the SARS-CoV-2 virus can be grouped in three classes, each of them targeting a slightly different site on the spike protein of SARS-CoV-2. With more than 50 mutations, the Omicron virus’ spike protein has 26-35 amino acids that are different from the original SARS-CoV-2 virus or the Delta. A mutation called E484K changes the shape of the site that class 2 antibodies recognize, making them less potent. The Omicron harbors E484A mutation in this site and similar changes in the sites for the other two classes of antibodies.

This also affects the efficacity of vaccines, without cancelling it completely, and the of previous infections in protecting patients against new infections.

Furthermore, one of the three target genes encoding for the spike protein is not detected, which is called S gene dropout or S gene target failure (SGTF) and can be detected in the three-target RT-PCR assay. Then, SGTF samples are sequenced for whole genome of the Omicron.

In the “How is the Omicron tracked from the potential infected people?” chapter, the paper explains that “The SARS-CoV-2 variants carrying the spike (S) deletion H69-V70 (ΔH69/ΔV70) and RBD mutations are screened with RT-PCR followed by whole genome sequencing.”  

As variants can generate significantly different epidemiological scenarios and impact our health and wellness in many different possible ways, whole genome sequencing of SARS-CoV-2 and its future variants is expected to play an important role in the upcoming years. 

We at 4bases are proud to develop and offer molecular diagnostic tools to identify, in real-world clinical settings, SARS-CoV-2 gene mutations thanks to a brand-new whole-genome sequencing COVID panel.  Stay tuned!!!!

[1]Ren SY, Wang WB, Gao RD, Zhou AM. Omicron variant (B.1.1.529) of SARS-CoV-2: Mutation, infectivity, transmission, and vaccine resistance. World J Clin Cases. 2022 Jan 7;10(1):1-11. doi: 10.12998/wjcc.v10.i1.1. PMID: 35071500; PMCID: PMC8727245.

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