Intestinal organoids expose heterogeneity in SARS-CoV-2 susceptibility

Organoids generated from primary human specimens facilitate investigation of the intestinal barrier by recreating the complex cellular composition of the epithelium. Although the significance remains unclear, intestinal organoid lines display heterogeneity in their growth and morphology. We hypothesized that organoids will also display variability in the degree to which they are susceptible to infectious agents. Using SARS-CoV-2 as a model, we found orders of magnitude differences in the amount of SARS-CoV-2 recovered from small intestinal and colonic organoids generated from different donors. SARS-CoV-2 burden did not correlate with demographic or clinical features associated with donors, but rather reflected the expression level of the virus receptor ACE2 . Remarkably, organoid ACE2 transcript levels matched the amount of ACE2 detected in primary tissue from the same individual, indicating that certain properties of the intestinal epithelium are retained during ex vivo differentiation. Longitudinal transcriptomics of organoids identified a delayed yet robust interferon signature, the magnitude of which corresponded to the degree of SARS-CoV-2 infection. These results suggest that intestinal organoids display substantial heterogeneity in their ability to support viral infections and can potentially inform mechanisms behind interindividual differences in susceptibility to infectious disease. ### Competing Interest Statement K.C. has received research support from Pfizer, Takeda, Pacific Biosciences, Genentech, and Abbvie. K.C. has consulted for or received an honoraria from Puretech Health, Genentech, and Abbvie. K.C. holds U.S. patent 10,722,600 and provisional patent 62/935,035 and 63/157,225.