Unbiased, Cell-free Profiling of Single Influenza Genomes at High-throughput

Area of Science:

• Virology
• Genetics
• Epidemiology

Background:

• Influenza A virus (IAV) segmented genome facilitates reassortment, generating novel strains with pandemic potential.
• Previous studies of IAV reassortment were limited by low throughput and infection-based assays, restricting analysis to permissive reassortment.
• Understanding reassortment propensity is critical for predicting pandemic strain emergence.

Approach:

• Developed DE-flowSVP for ultra-high throughput (10^5 particles/day) direct profiling of IAV particles.
• Enabled quantitative analysis of reassortment propensity between divergent IAV strains.
• Investigated reassortment between low-pathogenicity avian IAV strains.

Key Points:

• Confirmed molecular incompatibility drives preference for within-strain mixing.
• Revealed that 2-3 particle aggregation is the primary mechanism (75-99%) for IAV genome mixing.
• Demonstrated genome mixing is sensitive to co-infection timing, segment abundance, and viral surface proteins.

Conclusions:

• DE-flowSVP offers a powerful tool for large-scale IAV reassortment potential surveys.
• Particle aggregation provides a secondary pathway for IAV genome mixing, bypassing co-packaging fitness costs.
• Findings inform pandemic preparedness by characterizing reassortment dynamics across diverse IAV strains.