Synchronous co-infection drives lineage representation in influenza A virus populations.

Lineage enrichment in influenza A virus populations predominantly occurs during synchronous co-infection, when multiple viral genomes occupy the same cell, alongside increased viral output.

• Why it matters: Replication-driven diversity is constrained by antiviral responses and by influenza-specific limits on reassortment, complementation, and infection heterogeneity, yet adaptation persists in nature.
• What they did: The authors paired in vitro single-cell transcriptomics with viral lineage tracking to link infected cellular environments to viral output dynamics.
• The result: They identify a timing-dependent condition that can shift lineage representation and predict that traits increasing burst output or synchronous co-infection likelihood may disproportionately shape population composition.