Rab11Bis required for binding and entry of recent H3N2, but not H1N1, influenza A isolates.

Influenza A virus (IAV) depends on host proteins to complete several important functions, including trafficking viral proteins throughout the cell. Previous work has established a critical role for the cellular vesicular trafficking protein, Rab11A, in transporting the viral genome segments to the site of budding at the plasma membrane. While the role of Rab11A in IAV assembly is relatively well understood, very little is known about the function of a closely related isoform (Rab11B) during influenza virus infection. We have shown that both Rab11A and Rab11B are required for successful IAV infection by current H1N1 or H3N2 isolates. Cells in which either Rab11A or Rab11B were depleted failed to efficiently produce virus, with significant reductions in infectious titer. Surprisingly, our data revealed that recent (2022) H3N2, but not H1N1, isolates failed to efficiently produce viral proteins in single-cycle infections when Rab11B (but not Rab11A) was depleted. Flow cytometry analysis suggests that the defect in protein production is driven by a reduction in the total number of infected cells, rather than a decrease in viral protein production at the single-cell level. Using reverse genetics and "7+1" reassortant viruses, we mapped this Rab11B-dependent early defect in recent H3N2 isolates to the HA gene. RT-qPCR analysis of H3N2 virions bound to the cell surface showed a ~50% decrease in virus binding to the surface of cells depleted of Rab11B, but not Rab11A. Analysis of cell surface α2,6 and α2,3 sialic acids revealed no significant global change in sialic acid profile upon the depletion of Rab11B. As H3N2 virions could be removed by exogenous neuraminidase, the totality of these data suggests that the H3N2 failure to bind is the result of a loss of one (or more) specific sialylated cell surface protein(s) upon Rab11B depletion, rather than a decrease in bulk α2,6 sialic acid levels. These data suggest a novel role for Rab11B during viral entry that is specific to H3N2 isolates.IMPORTANCEInfluenza A is a major human pathogen, which poses risks through both the continuous circulation of "seasonal" influenza viruses (H1N1 and H3N2 subtypes) as well as the emergence of novel pandemic strains from animal hosts. Here, we demonstrate that contemporaneous H3N2 (but not H1N1) subtypes enter human lung cells through a Rab11B-dependent mechanism. This is distinct from the well-known role of Rab11A later in the life cycle, where it mediates the transport of viral ribonucleoprotein complexes to the site of virion assembly. These findings are relevant for assessing the risk that recently emerged zoonotic influenza viruses can enter human lung cells. Our work suggests that H1N1 and H3N2 viruses enter via different routes, which are not dependent on sialic acid levels. Our data provide important foundational information for the growing number of Rab11-dependent viruses, as it suggests that the Rab11 isoforms can affect both viral entry and viral exit.