Dispersal of influenza virus populations within the respiratory tract shapes their evolutionary potential.

Summary

Barcoded H1N1 infections in ferrets revealed that the nasal cavity and trachea maintain highly diverse viral populations conducive to adaptation, whereas the lungs exhibit pauci-clonal, genetically distinct populations due to seeding bottlenecks. Inoculation route modulated lung population structure, and barcode diversity declined over time as de novo variants arose locally, driving divergence across sites.

Key Findings

• Nasal turbinates and trachea harbor similarly diverse barcode compositions regardless of inoculation route, indicating minimal constraints on upper airway establishment and descent.
• Lung infections are pauci-clonal with genetically distinct populations, reflecting strong seeding bottlenecks; aerosol inoculation yields distinct populations at each lung site.
• Barcode diversity declines over time across the tract, while de novo mutations arise locally, leading to spatially heterogeneous evolutionary trajectories.

Clinical Implications

Supports surveillance strategies that consider sampling site, highlights aerosol route implications for lung seeding and bottlenecks, and informs models of resistance emergence and transmission.

Limitations

• Ferret model may not fully recapitulate human respiratory tract dynamics
• Short follow-up window (1–4 days) limits long-term evolutionary inference

Future Directions

Extend to human clinical sampling and longer timeframes; integrate immune microenvironment profiling to link spatial evolution with selective pressures.