IAV_FITNESS

Scope

Influenza fitness determinants, conserved noncoding RNA elements, segment-specific viral biology, fidelity, packaging, and innate-sensing consequences.

Working Model

IAV fitness is shaped by RNA-level regulatory circuitry, fidelity errors, segment completeness, splicing outcomes, and co-infection complementation, not only polymerase activity or canonical immune antagonism.

Key Concepts

• Conserved viral noncoding RNAs as regulatory determinants.
• Segment completeness and Segment 8/NS1 sufficiency.
• Rare IFN-positive sentinel cells.
• Defective genomes.
• Co-infection rescue of incomplete viral states.
• Early-cycle virus-intrinsic fitness.
• RNA velocity/MOI titration.
• Late-stage barcoding at the M2 3' splice junction.

People

• Fiorella Chacon: HA/membrane project tied to influenza host response.
• Abigail Korenek: NS1 multifunctionality.
• Ben tenOever

Known Outputs

• Remembered 4-figure IAV paper:
• Fig. 1: defective genomes / Segment 8 loss / rare IFN-positive cells / IRF7.
• Fig. 2: late-stage barcoding at M2 3' splice junction.
• Fig. 3: co-infection rescue of segment completeness and boosted transcription.
• Fig. 4: early-cycle virus-intrinsic fitness, host-state independence, RNA velocity/MOI titration, reassortment framing.
• Keystone abstract: “Fidelity Errors as the Nexus of Innate Sensing, Viral Fitness, and Evolution.”

TODO

• Add raw single-cell datasets, barcoded library design, figure drafts, and manuscript status.