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Updated: Jun 26, 2026
06:08
Application of Ha-CoV-2 Pseudovirus for Rapid Quantification of SARS-CoV-2 Variants and Neutralizing Antibodies
Published on: September 8, 2023
Computational Study of Antibody Binding to SARS-CoV-2 Variants
Carolyn Chiu1, Muhammad Zaki Jawaid2, Daniel Lee Cox1
1Department of Physics and Astronomy, University of California, Davis, CA 95616, USA.
Antibodies (Basel, Switzerland)
|June 25, 2026
Summary
Viral evolution generally weakens antibody binding to SARS-CoV-2 spike proteins, but some antibodies show a "re-entrant" binding strength. This suggests a balance between maintaining ACE2 binding and escaping immunity.
Area of Science:
- Immunology
- Virology
- Structural Biology
Background:
- SARS-CoV-2 spike protein mutations impact antibody binding.
- Understanding viral immune escape and human immunity co-evolution is crucial.
Purpose of the Study:
- To simulate antibody-spike protein binding dynamics.
- To analyze the impact of SARS-CoV-2 variants on antibody efficacy.
Main Methods:
- Utilized YASARA for molecular dynamics simulations of six SARS-CoV-2 variants and ten antibodies.
- Employed YASARA and HawkDock MMGBSA to measure binding energies and hydrogen bond counts.
- Analyzed hydrogen bond populations over time using VMD.
Main Results:
- Interfacial hydrogen bond counts accurately proxy binding energies.
- Viral evolution generally decreases antibody binding strength.
- A modest re-entrance of binding strength was observed for most antibodies.
Conclusions:
- "Re-entrant immunity" may arise from balancing ACE2-spike binding with antibody escape.
- This balancing act can maintain or even strengthen immunity against later viral strains.
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