Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency

Abstract

After endocytic uptake, influenza viruses transit early endosomal compartments and eventually reach late endosomes. There, the viral glycoprotein hemagglutinin (HA) triggers fusion between endosomal and viral membrane, a critical step that leads to release of the viral segmented genome destined to reach the cell nucleus. Endosomal maturation is a complex process involving acidification of the endosomal lumen as well as endosome motility along microtubules. While the pH drop is clearly critical for the conformational change and membrane fusion activity of HA, the effect of intracellular transport dynamics on the progress of infection remains largely unclear. In this study, we developed a comprehensive mathematical model accounting for the first steps of influenza virus infection. We calibrated our model with experimental data and challenged its predictions using recombinant viruses with altered pH sensitivity of HA. We identified the time point of virus-endosome fusion and thereby the diffusion distance of the released viral genome to the nucleus as a critical bottleneck for efficient virus infection. Further, we concluded and supported experimentally that the viral RNA is subjected to cytosolic degradation strongly limiting the probability of a successful genome import into the nucleus.

Multiple mechanisms drive phage infection efficiency in nearly identical hosts

“…Briefly, in phage studies, the term "efficient" is used to describe either infections or phages that lyse the most cells the fastest [28,29], have the shortest LP/best growth rate [104], display better intracellular capabilities (e.g., in DNA replication [105] or gene transcription [37], or are proficient at hijacking host RNAP [37]). In contrast, the eukaryotic viral literature evaluates whether each step of the complex viral infection, from attachment to dispersion, is efficient [106][107][108][109][110][111][112][113].…”

Stochastic Model of Acidification, Activation of Hemagglutinin and Escape of Influenza Viruses from an Endosome

“…Cytoskeleton retrograde flow plays a key role for the Influenza virus transport inside the endosome toward the cell nucleus and to ensure a safe delivery of its genome near the nucleus, before replication [9,10]. During this transport, the endosome can fuse with lysosomes, leading in that case to viral degradation.…”

Microtubules in Influenza Virus Entry and Egress

“…The importance of microtubules in progressive endosome acidification has been previously demonstrated [66]. Mathematical modelling further suggests that coordinated endosome acidification and microtubular transport serve as limiting factors during influenza virus infection [93]. Viral transport by microtubules to a perinuclear fusion site represents an optimal condition for successful infection since premature exposure of invading virions to the cytosol can enhance vRNP degradation [93].…”

“…Mathematical modelling further suggests that coordinated endosome acidification and microtubular transport serve as limiting factors during influenza virus infection [93]. Viral transport by microtubules to a perinuclear fusion site represents an optimal condition for successful infection since premature exposure of invading virions to the cytosol can enhance vRNP degradation [93]. Thus, the trafficking of IAVs along microtubules within endocytic vesicles serves not only to protect incoming viruses from immune detection [94], but it is also optimal for perinuclear fusion, at sites where LEs concentrate.…”