American scientists studying how influenza viruses replicate within cells “accidentally” discovered that different flu viruses use distinct strategies to infiltrate cells in the first place, they reported in The Journal of Virology.
They also found that it is possible to target specific molecules to prevent the viruses from entering new cells, thereby stopping their replication.
The findings provide fundamental insights into how seasonal flu viruses infect people, and illuminates a path for developing better medications to prevent infections in the future.
“The hope is that curiosity-based research like this helps to pave the way for novel strategies to treat and prevent influenza infections,” said principal investigator Emily Bruce, PhD, assistant Professor of Microbiology and Molecular Genetics at the Larner College of Medicine, University of Vermont.
A variety of different flu strains can cause illness, with H1N1 and H3N2 influenza A viruses being the most common. Current flu tests do not differentiate between the two viruses, and clinical treatments are the same for both.
While flu vaccines can help prevent infection, and antiviral drugs can shorten the illness and prevent complications in high-risk individuals, there is a dire need for better medications to prevent the viruses from replicating and infiltrating new cells in the human body.
Bruce’s research team examined H1N1 and H3N2 viruses isolated from the nasal passages of people who tested positive for flu in 2022. Their study initially aimed to learn how viral proteins move within cells and enable viruses to replicate themselves, which is what causes people to become ill.
“You don’t get sick when a virus is in one cell. You get sick because a virus replicates itself and goes into many more cells,” said Bruce. “We were looking at how influenza virus RNA segments are transported within cells to the right place at the right time to make new virus particles.”
During this investigation, Bruce’s team unexpectedly discovered a cellular pathway that blocked the viruses from entering lung cells. The data revealed that H3N2, but not H1N1 viruses, failed to enter human lung cells when a particular protein called Rab11B was depleted.
Using reverse genetics, the team mapped this Rab11B-dependent defect and found a novel and H3N2-specific role for Rab11B during viral entry into a lung cell. This fortuitous discovery suggests that H1N1 and H3N2 viruses enter lung cells via different routes – and it can inform therapeutic targets to prevent viral entry.
“Viruses are like pirates from different countries hijacking someone’s ship. Different viruses, like different types of pirates, use different methods to get onboard,” Bruce said. “We had previously thought that all flu viruses used the same way to get into a cell, but we discovered that this is not true. H1N1 and H3N2 need different proteins to get in, and if you get rid of the right protein, a specific virus can’t get in.”
This discovery can help scientists think about new ways to prevent distinct flu viruses from entering cells.
The next steps will seek to determine whether Rab11B-dependency is a fundamental property of H3N2 that no one realised previously, or whether it is new to currently circulating H3N2, in addition to understanding the precise Rab11B is playing during H3N2 viral infection at the molecular level.
Study details
Rab11B is required for binding and entry of recent H3N2, but not H1N1, influenza A isolates
Allyson Turner, Sara Jaffrani, Hannah Kubinski et al.
Published in Journal of Virology on 2 June 2026
Abstract
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.
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