Rapid SARS-CoV-2 Adaptation to Available Cellular Proteases

Area of Science:

• Virology
• Molecular Biology
• Genomics

Background:

• SARS-CoV-2 variants like Alpha, Delta, and Omicron exhibit spike mutations linked to increased pathogenesis.
• Coronaviruses possess significant adaptation and evolution potential, even with stable consensus genotypes.

Purpose of the Study:

• To investigate the dynamics and mechanisms of SARS-CoV-2 rapid adaptation in Vero E6 cells.
• To understand the role of spike protein mutations in viral adaptation and evolution.

Main Methods:

• Passaging SARS-CoV-2 in Vero E6 cells to observe adaptation.
• Analyzing spike protein cleavage efficiency by host proteases (cathepsins, furin, TMPRSS2).
• Investigating the influence of heparan sulfate (HS) binding on virus growth.

Main Results:

• Adaptation to Vero E6 cells is driven by increased S1/S2 cleavage efficiency by cathepsins.
• Vero E6-adapted virus shows defective entry into human cells due to poor spike processing by furin/TMPRSS2.
• Subdominant variants lacking furin cleavage sites rapidly dominate in Vero E6 cells but wild-type sequences persist, enabling reverse adaptation.

Conclusions:

• The SARS-CoV-2 spike protein rapidly adapts to available proteases, demonstrating significant evolutionary potential.
• Deep sequence surveillance is crucial for identifying novel SARS-CoV-2 variants with adaptive capabilities.
• The maintenance of subdominant variants within the viral population facilitates rapid adaptation to changing selective pressures.