Influenza A virus surface proteins determine the spatial structure of viral spread

Influenza A virus (IAV) is an enveloped RNA virus responsible for the seasonal flu. The IAV genome encodes two surface proteins with competing activities: hemagglutinin (HA), which binds to sialic acid (Sia) on the cell surface; and neuraminidase (NA), which cleaves Sia. To enable viral attachment to naïve cells while still permitting the release of new virions late in infection, IAV requires functional balance between HA and NA. While prior work has provided valuable insights into the genetic and biochemical basis, it remains unclear how HA-NA functional balance influences viral replication and spread. To address this gap in knowledge, we investigated the in situ activity of NA on the cell and viral surface during productive infection. Using a chemical approach to quantitively label Sia in cell monolayers, we show that NA on the surface of infected cells cleaves Sia on both the infected cell and the adjacent uninfected neighbors. The extent of this cleavage does not necessarily follow the intrinsic NA activity as determined by traditional assays (e.g., MUNANA). Using fluorescence microscopy to track the spread of individual virions from initial sites of infection, we find that the Sia depletion from neighboring uninfected cells leads to a reduction in virus binding and uptake by these cells. Performing these measurements in the H1N1 strain A/California/04/09 in the presence of NA inhibitors, exogenous sialidase, or genetic replacement with the enzymatically weaker NA from A/WSN/1933, we find that the efficiency of localized virion spread is inversely correlated with in situ NA activity, leading to differences in multiplicity of infection and efficiency of multicycle spread. Thus, the activity of cell surface NA represents a viral intrinsic mechanism that can tune cellular multiplicity of infection, with implications for virus evolution and cross-species transmission.