SARS-CoV-2 omicron sub-lineages differentially modulate interferon response in human lung epithelial cells

Area of Science:

• Virology
• Immunology
• Molecular Biology

Background:

• SARS-CoV-2 Spike protein mutations are well-studied, but non-Spike mutations also influence viral pathogenesis and immune evasion.
• Omicron sub-lineages (BA.1 to BA.5) possess distinct mutations, including those in proteins interacting with the innate immune system.
• NSP1, ORF6, and Nucleoprotein N are implicated in innate immune antagonism, but their mutation impacts require further investigation.

Purpose of the Study:

• To investigate innate immune modulation by SARS-CoV-2 Omicron sub-lineages.
• To identify viral proteins contributing to virus fitness and pathogenicity.
• To explore the role of ORF6 protein mutations in interferon antagonism.

Main Methods:

• Phylogenetic analysis of Omicron sub-lineages.
• Replication assays in Calu-3 human lung epithelial cells.
• Interferon beta (IFN-β) secretion and transcription level analysis.
• In vitro studies with recombinant mutated ORF6 protein.

Main Results:

• Reduced IFN-β secretion observed in BA.1 and BA.5 Omicron sub-lineages compared to Wuhan-1 strain, with BA.2 being an exception.
• A mutation in the ORF6 protein (D61L) correlated with antagonistic function against IFN-β.
• Recombinant mutated ORF6 protein failed to inhibit IFN-β production in vitro.
• Induced IFN-β transcription in BA.1 infected cells did not correlate with cytokine release, suggesting post-transcriptional regulation.

Conclusions:

• ORF6 protein mutations (D61L) in SARS-CoV-2 Omicron variants contribute to reduced IFN-β secretion, potentially affecting pathogenicity.
• Post-transcriptional mechanisms may play a role in regulating the innate immune response to Omicron infections.
• Non-Spike protein mutations are critical for understanding SARS-CoV-2 evolution and immune system interactions.