For total RNA extraction from mouse ileum, three pieces (1-cm-long segment) of the ileum with Peyer’s patches (~3-mm each in length) were retrieved from the distal ileum (distal 1/3 part of the ileum), opened, cleaned by washing with PBS to remove fecal matter, and homogenized in 1-ml PBS. Similarly, total RNA was recovered from MLNs. Total RNA from cells or culture media was extracted with TRIzol or TRIzol LS reagent (Invitrogen, Carlsbad, CA, USA), respectively. Norwalk virus and MNV-1 RNA copy number was determined by RT-qPCR as described previously68,69. Quantification of mRNA was carried out by RT-qPCR using SYBR Premix ExTaq (Takara, Japan). The specific primer sets used are listed in Supplementary Table 1. Specific primers for human IFN-β and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were as described previously70. The expression levels of all the target genes normalized with the expression level of GAPDH mRNA were quantified using the ΔΔCt method71.