SARS-CoV-2 evolution enhances endocytic uptake while preserving TMPRSS2-dependent fusion.

Area of Science:

• Virology
• Molecular Biology
• Infectious Diseases

Background:

• Omicron, a SARS-CoV-2 variant of concern, exhibits increased transmissibility and infectivity but reduced pathogenicity.
• This shift in virulence is linked to altered viral entry mechanisms, favoring endocytosis over direct fusion.

Purpose of the Study:

• To compare the entry mechanisms (endocytosis vs. direct fusion) of various SARS-CoV-2 variants, including Omicron.
• To investigate the role of specific mutations in determining viral entry pathways.

Main Methods:

• Analyzed nine clinical SARS-CoV-2 isolates (wild-type, Alpha, Delta, Omicron) in four human cell lines.
• Used TMPRSS2 inhibitors (camostat) and cathepsin inhibitors (aloxistatin) to differentiate entry pathways.
• Determined full-length viral genomes via next-generation sequencing.

Main Results:

• Alpha and Delta variants primarily used TMPRSS2-dependent fusion.
• Omicron variants showed a significant shift towards endocytosis, especially in specific cell types.
• Certain mutations (Δ69/Δ70, L452R, F486V) were associated with increased reliance on endocytic uptake.

Conclusions:

• Omicron variants broadened their cell tropism by retaining fusion activity while enhancing endocytosis.
• Increased upper airway replication and transmissibility are observed, but lower respiratory tract infection capacity is maintained.
• Specific mutation combinations may confer a selective advantage, contributing to their prevalence.