California Institute of Technology Finds Yet Another New SARS-CoV-2 Variant B.1.526 With The Immune Evasive Mutation E484K Circulating In New York!
Researchers from the California Institute of Technology while using a newly developed software tool by the institute called the Variant Database (VDB) to monitor the rapid changing landscape of spike mutations, chanced upon an emerging lineage of viral isolates in the New York region that shares mutations with previously reported variants.
The most common sets of spike mutations in this new variant (now designated as the B.1.526 variant
) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V.
This B.1.526 variant appeared in late November 2020, and alarmingly isolates from this lineage account for about 5% of coronavirus genomes sequenced and deposited from New York during late January 2021 and scientists are worried that this number is growing exponentially.
The study findings were published on preprint server and are currently being peer reviewed. https://www.biorxiv.org/content/10.1101/2021.02.14.431043v1
Since the fall of 2020, numerous SARS-CoV-2 variants
are emerging with newer characteristic including increased infectivity and transmission, and some with immune evasive properties.
Many of these new variants contain multiple mutations, mostly focused on the spike protein.
Multiple lines of evidence support escape from antibody selective pressure as a driving force for the development of these variants.
Growing concerns about the potential effects of these mutations on the effectiveness of passive antibody therapies and on the ability of vaccines to prevent mild or moderate COVID-19 have driven genomic surveillance programs to monitor the evolution of SARS-CoV-2.
Utilizing the vdb tool,the study team detected several clusters of isolates of this new variant with spike mutations at sites known to be associated with resistance to antibodies against SARS-CoV-2 .
The new software can find clusters of isolates sharing identical sets of spike mutations, and then these patterns can be used to find potentially related isolates.
The most notable cluster of isolates was collected from the New York region. There are two main branches of this lineage, one having E484K and the other including S477N, both located within the receptor-binding domain (RBD) of spike. Regarding four of the mutations in isolates in this cluster:
-1) E484K is known to attenuate neutralization of multiple anti-SARS-CoV-2 antibodies, particularly those fou
nd in Class 2, and is present in the South African variants B.1.351 and Brazil’s variant P.1/B.1.1.248 ,
-2) D253G has been reported as an escape mutation from antibodies against the N-terminal domain,
-3) S477N has been identified in several earlier lineages, is near the binding site of multiple antibodies, and has been implicated to increase viral infectivity through enhanced interactions with ACE2, and
-4) A701V sits adjacent to the S2’ cleavage site of the neighboring protomer and is shared with variant B.1.351.
The overall pattern of mutations in this cluster suggests that it arose in part in response to selective pressure from antibodies. Based on the dates of collection of these isolates, it appears that the frequency of these isolates is increasing and is of concern.
The United States is facing lots of emerging new variants of its own in recent weeks besides those being imported for elsewhere.
Some like the B.1.1.7 variant from UK is expected to becoming the dominant prevailing strain in America by March while many more are quickly circulating around.
All these new variants are challenging current vaccination efforts and worse it is expected that reinfections and disease severity coupled with increased mortality is expected to accompany the dynamics of these variants’ circulation and their increasing prevalence.
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