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In vitro evolution predicts emerging SARS-CoV-2 mutations with high affinity for ACE2 and cross-species binding.

Neil Bate1,2, Christos G Savva3, Peter C E Moody3

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|July 18, 2022
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Scientists identified specific mutations in the SARS-CoV-2 virus, S477N and Q498H, that significantly increase its binding to human ACE2. These mutations could impact viral transmission and inform the development of new COVID-19 therapeutics and vaccines.

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Area of Science:

  • Virology
  • Molecular Biology
  • Structural Biology

Background:

  • Emerging SARS-CoV-2 variants pose significant challenges to the COVID-19 pandemic response.
  • Predicting mutations that enhance viral transmissibility or immune evasion is crucial for developing effective countermeasures.

Purpose of the Study:

  • To identify mutations in the SARS-CoV-2 receptor-binding domain (RBD) that increase binding affinity to human ACE2.
  • To understand the structural mechanisms underlying enhanced ACE2 binding.

Main Methods:

  • In vitro evolution experiments to select for SARS-CoV-2 RBD mutations.
  • Cryo-electron microscopy to determine the structure of mutant-RBD:ACE2 complexes.
  • Binding affinity assays to quantify RBD-ACE2 interactions.

Main Results:

  • A double mutation (S477N and Q498H) was found to increase RBD-ACE2 binding affinity by 6.5-fold, primarily driven by Q498H.
  • The Q498H mutation enhances binding to human ACE2 and enables high-affinity binding to rat ACE2.
  • In the presence of the N501Y mutation, Q498H binding is inhibited; Q498R serves as an alternative for similar affinity gains.
  • These identified mutations are emerging in current SARS-CoV-2 variants.

Conclusions:

  • SARS-CoV-2 RBD can achieve significant affinity gains and cross-species binding through alternative mutational pathways involving Q498.
  • The selection of these pathways is influenced by the presence of the N501Y mutation.
  • These findings have implications for understanding viral transmission dynamics and developing broad-acting medical interventions.