Influenza makes millions of people ill every year, placing a large burden on the healthcare system and the economy. To develop a treatment against influenza, we combined virucidal sialylated cyclodextrins with interferon lambda and demonstrated, in human airway epithelia, that the two compounds inhibit the replication of a clinical H1N1 strain more efficiently when administered together rather than alone. We investigated the mechanism of action of the combined treatment by single cell RNA-sequencing analysis and found that both the single and combined treatments impair viral replication to different extents across distinct epithelial cell types. We showed that each cell type comprises multiple sub-types, whose proportions are altered by H1N1 infection, and assessed the ability of the treatments to restore them. To the best of our knowledge this is the first study investigating the effectiveness of an antiviral therapy against influenza virus by single cell transcriptomic studies.

Influenza makes millions of people ill every year, placing a large burden on the healthcare system and the economy. Combination therapies with two or more compounds hindering different mechanisms of viral replication represent a suitable approach to not only enhance the effectiveness of the individual drugs, but also to reduce the likelihood of resistance emergence. To develop a novel treatment against influenza, we combine virucidal sialylated cyclodextrins with interferon lambda and demonstrate, in ex vivo human airway epithelia, that the two compounds inhibit the replication of a clinical H1N1 strain more efficiently when administered together rather than alone. We investigate the mechanism of action of the combined treatment and its effects on the host cells in absence of infection, by performing single cell RNA sequencing analysis. We find that both the single and combined treatments impair viral replication to different extents across distinct epithelial cell types. We also show that each cell type comprises multiple sub-types, whose proportions are altered by H1N1 infection, and assess the ability of the treatments to restore them. To the best of our knowledge this is the first study investigating the effectiveness of an antiviral therapy by transcriptomic studies at the single cell level.