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Updated: Sep 9, 2025

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Mutation profiling, evolution analysis, molecular dynamics simulation, and functional characterization of Omicron

Tian Gong1, Xuan Zhang1, Haiyan Lin1

  • 1Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang 330209, China; Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 DongYue Dadao, Nanchang 330209, China.

Virus Research
|September 2, 2025
PubMed
Summary
This summary is machine-generated.

SARS-CoV-2 evolution drives new variants with altered binding and immune escape. Researchers analyzed Omicron sub-strains, finding mutations impact receptor binding and antibody response, informing future strategies.

Keywords:
Immune escapeMolecular dynamics simulationOmicron variantsReceptor binding forceSARS-CoV-2selection pressure

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Area of Science:

  • Virology and Molecular Biology
  • Immunology
  • Computational Biology

Background:

  • SARS-CoV-2 continuously mutates, leading to variants like Omicron with significant global health implications.
  • Understanding the functional impact of these mutations is crucial for effective pandemic response.

Purpose of the Study:

  • To analyze selection pressures on SARS-CoV-2 Omicron sub-strains.
  • To investigate the impact of mutations on the binding affinity between the viral Receptor Binding Domain (RBD) and human Angiotensin-Converting Enzyme 2 (ACE2).
  • To evaluate the immune escape capabilities of RBD mutations against monoclonal antibodies (mAbs).

Main Methods:

  • Analysis of selection pressure at gene and amino acid levels across 49 Omicron sub-strains.
  • Molecular dynamics simulations on eight representative Omicron sub-variants (B.1.1.529, BA.2, XBB.1.5, BA.2.86, JN.1, KP.2, KP.3, and KP.3.1.1).
  • Assessment of RBD binding affinity to ACE2 and interaction with monoclonal antibodies.

Main Results:

  • Identified 12 positive selection mutation sites on the viral S protein, with 11 in the N-terminal domain (NTD) and RBD.
  • Accumulated mutations increased receptor binding affinity in B.1.1.529 and BA.2.86, with BA.2.86 showing maximal binding affinity.
  • The E484K mutation demonstrated the highest binding affinity in BA.2.86 and its descendants; some mutations affected binding affinity, while others did not.
  • RBD mutations and altered epitopes may facilitate immune escape in BA.2.86 variants.
  • The ABBV-47D11 monoclonal antibody showed broad binding to RBD mutation sites across various strains.

Conclusions:

  • SARS-CoV-2 evolution, particularly in Omicron sub-strains, significantly alters viral properties like receptor binding and immune evasion.
  • Specific mutations, such as E484K, play a key role in enhanced binding affinity.
  • Findings provide insights into viral evolution and support the development of targeted therapeutic strategies, including broadly effective monoclonal antibodies.