Russia – Germany are affected by the new variant B.1.1.523 SARS-CoV-2 which combines many spike mutations

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected millions of people during the pandemic 1,2.

During this pandemic, various variants of this virus were detected in surveillance and were linked with increased infectivity or immune evasion 3,4.

Data of these variants are shared via the GISAID (Global initiative on sharing all influenza data) database that helps to understand spread and evolution of SARS-CoV-2.

The Centers for Disease Control and Prevention (CDC) and European Centre for Disease Prevention and Control (ECDC) assign certain variants as “variant of concern” (VOC) because of an increase in transmissibility, more severe disease, or immune evasion 5,6. Current VOC are B.1.1.7 (alpha-variant), B.1.351 (beta-variant), P1 (gamma-variant), and B.1.617.2 (delta-variant).

These VOC harbor several spike protein mutations linked to immune evasion. The receptor-binding domain (RBD) and N-terminal domain (NTD) are frequently targeted by neutralizing antibodies mostly directed to the NTD 7,8.

In addition, a so called antigenic supersite is described in the NTD with three regions. Potent neutralizing antibodies in convalescent plasma target this antigenic super site.

Still, mutations in the RBD are important as for example E484K mutation is also strongly linked with immune evasion 3,4. This short communication describes a new variant with a new combination of various concerning spike mutations shared with VOCs and is already spread across many countries.

The pangolin lineage of this variant is B.1.1.523 and is recognized as a variant under monitoring since 14th of July 2021 9

“This type of B.1.1.523 coronavirus allegedly appeared on the territory of Russia in February of this year.
It began to actively spread only in May – June.
In the genome of this species there are many mutations characteristic of the “beta” and “delta” strains of the virus and associated with an increase in infectivity and a decrease in the effectiveness of vaccines “

Then, in the genome of this strain, biologists have discovered the E484K mutation and three other characteristics of the South African variation of the virus, which help it “bypass” immunity.
The shell of this strain has undergone changes and has acquired greater infectivity than the “delta” strain, the researchers specified.

Importantly, the number of carriers of this coronavirus variation in Russia and Germany grew rapidly in early summer amid outbreaks of alpha and delta strains.
This suggests that the B.1.1.523 strain variety is very dangerous, therefore doctors around the world should closely monitor its spread.

Discussion

In this short communication we report a variant (B.1.1.523) with a new combination of concerning spike mutations that are shared with current VOCs.

Many of these mutations are linked with immune evasion that could lead to less effective vaccines. This variant has been reported in various different countries and continents and likely originates in Russia. In addition, the number of cases appears to increase despite the dominant variants B.1.1.7 (alpha) and B.1.617.2 (delta).

Mutations that are shared with VOC or linked with immune evasion were S:E156del, S:F157del, S:R158del, S:E484K, and S:S494P 5,6,11. Two mutations are in the RBD of the spike protein, positions 484 and 494, and are both linked to immune evasion in B.1.1.7 (alpha) variant. E484K mutation is also present B.1.351 (beta) and P.1 (gamma) variants that are strongly linked with reduced efficacy of vaccines 3,4.

These findings are supported in studies where the effect of spike mutations on efficacy of monoclonal antibodies and convalescent plasma was investigated 12. Similar studies were performed to investigate the antigenic super site of the NTD 7,8.

In the β-hairpin region of the antigenic super site the B.1.1.523 variant has a deletion (position 156-158) similar to the currently dominant B.1.617.2 (delta) variant (S:E156G and 157-158del) 5-8.

Other VOC also have deletions in one of the regions of the antigenic super site, B.1.1.7 (alpha-variant) position 144 and B.1.351 (beta-variant) position 241-243. As the mutations observed in this B.1.1.523 variant are strongly linked to immune evasion and disseminated to different continents, despite the dominance of both the B.1.1.7 (alpha) and B.1.617.2 (delta) variants, this could be a variant of interest and should be monitored closely.

However, as this is the first study that describes this variant of the B.1.1.523 lineage, there is yet no information on transmissibility that contributes to the need of actions required to prevent dissemination.

reference link : biorxiv.org/content/10.1101/2021.09.16.460616v1.full


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