Previous studies revealed both genetic and environmental factors contribute to the Crohn’s disease pathogenesis. ATG16L1, an essential component of autophagy, is one of the susceptibility genes of the disease. We previously showed that mice with decreased expression of ATG16L1 and Crohn’s disease patients homozygous for the ATG16L1 risk allele develop Paneth cell abnormalities in the intestinal epithelium, and the abnormalities were dependent on murine norovirus (MNV) infection. MNV is a single stranded RNA virus that persistently infects the gastrointestinal tract.