High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing

Significance Influenza A viruses (IAVs) represent a major worldwide health threat. Wild aquatic birds are the natural reservoir of IAVs, which also infect other species including domestic poultry and mammals. Pigs are “mixing vessels” where IAVs from different strains can reassort, posing a continuous threat of zoonotic infections, and animal–human reassortant IAVs episodically generate severe pandemics. We demonstrate large-scale quantitative assessment of reassortment between two circulating human IAVs using high-throughput droplet microfluidics. Our method will enable i) a better understanding of the rules underlying reassortment and ii) scrutinization of reassortment between zoonotic animal viruses and human seasonal viruses, to identify those representing a threat to human health. This provides an additional predictive parameter to complement existing Pandemic Influenza Risk Assessment Tools.