Embryonated chicken eggs clear systemic H3N2 influenza without RIG-I: transcriptomic evidence for innate sufficiency and brain immune privilege

1An apparent paradox drives this study: H3N2 influenza virus concentrates in the brain of infected 10-day chicken embryos while kidney and lung, which express the same viral entry receptors (ST3GAL3 and other sialic acid receptors), are essentially virus-free. Using mRNA-seq on brain, kidney, and lung from H3N2-infected 10-day chicken embryos, we resolve this paradox identifying immune privilege rather than neurotropism as the cause; circulating macrophages clear the virus from peripheral tissues but cannot cross the embryonic brain barrier. The innate response is robust despite lacking RIG-I: MDA5/IFIH1 and TLR3-TLR7-IRF signaling compensate fully, driving complete viral clearance in peripheral organs. At 48 h post-infection, kidney and lung are in a post-clearance M2 macrophage state; complement is activated but lacks both the H3N2-specific antibodies and the terminal C9 component for productive effect. These findings directly challenge the hypothesis that RIG-I loss renders chickens susceptible to influenza, and identify the embryonic brain as an immune-privileged viral sanctuary with implications for influenza neurological disease in young hosts.