Stringent selection drives convergence toward omicron-like SARS-CoV-2 receptor-binding motifs

Area of Science:

• Virology
• Molecular Biology
• Evolutionary Biology

Background:

• The SARS-CoV-2 spike protein's receptor-binding motif (RBM) is crucial for binding human ACE2, initiating viral infection.
• Understanding the evolutionary pathways of the RBM is key to predicting viral adaptation and developing countermeasures.

Purpose of the Study:

• To explore the evolutionary trajectories of the SARS-CoV-2 spike protein RBM under different selection pressures using in vitro protein evolution.
• To investigate the role of receptor-binding constraints in shaping viral adaptation and compare in vitro findings with global mutation trends.

Main Methods:

• In vitro protein evolution experiments were conducted on the SARS-CoV-2 spike protein RBM.
• Stringent and mild selection pressures were applied to protein-coding sequences from Wuhan or non-Omicron variants, and Omicron variants.
• Evolutionary patterns were analyzed, focusing on mutations related to receptor binding and immune evasion.

Main Results:

• Stringent selection pressures rapidly drove convergence towards Omicron-like mutations in the RBM.
• Mild selection resulted in fewer Omicron-like mutations at lower frequencies.
• In vitro evolution mirrored global SARS-CoV-2 mutation trends and in silico simulations, highlighting the importance of receptor-binding constraints.

Conclusions:

• The Omicron RBM represents a highly humanized binding motif, likely shaped by high-stringency selection.
• In vitro protein evolution demonstrates predictive power for viral adaptation, particularly concerning receptor-binding constraints.
• Immune evasion mutations were not significantly selected under these experimental conditions.