Variable susceptibility of intestinal organoid–derived monolayers to SARS-CoV-2 infection

Abstract

Gastrointestinal effects associated with Coronavirus Disease 2019 (COVID-19) are highly variable for reasons that are not understood. In this study, we used intestinal organoid–derived cultures differentiated from primary human specimens as a model to examine interindividual variability. Infection of intestinal organoids derived from different donors with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) resulted in orders of magnitude differences in virus replication in small intestinal and colonic organoid–derived monolayers. Susceptibility to infection correlated with angiotensin I converting enzyme 2 (ACE2) expression level and was independent of donor demographic or clinical features. ACE2 transcript levels in cell culture matched the amount of ACE2 in primary tissue, indicating that this feature of the intestinal epithelium is retained in the organoids. Longitudinal transcriptomics of organoid-derived monolayers identified a delayed yet robust interferon signature, the magnitude of which corresponded to the degree of SARS-CoV-2 infection. Interestingly, virus with the Omicron variant spike (S) protein infected the organoids with the highest infectivity, suggesting increased tropism of the virus for intestinal tissue. These results suggest that heterogeneity in SARS-CoV-2 replication in intestinal tissues results from differences in ACE2 levels, which may underlie variable patient outcomes.

Antiviral response mechanisms in a Jamaican Fruit Bat intestinal organoid model of SARS-CoV-2 infection

“…To determine whether the JFB intestine supports SARS-CoV-2 infection, organoids were dissociated and then inoculated with SARS-CoV-2 at MOIs of 0.1, 1 and 10. We selected distal intestinal organoids for these experiments, based on several previous publications that demonstrated SARS-CoV-2 replication in human ileal organoids 43,44,45 . Quantitative PCR analysis of viral genomes in JFB organoid cell lysates revealed a signi cant, concentration-dependent increase (> 1 log, P ≤ 0.05) in SARS-CoV-2 gene E RNA at 48 and 72 hours post infection (hpi, Fig.…”

Development of a high-throughput barrier function assay using primary human gut organoids

“…A number of organoid-derived monolayer systems have been described recently [17][18][19][20][21][31][32][33][34][35][36][37][38] .…”

SARS-CoV-2 Omicron BA.1 variant infection of human colon epithelial cells

“…Up to 70% of COVID-19 patients experience GI symptoms, including nausea, vomiting, and diarrhea. We and others have previously shown that human small and large intestines express high levels of ACE2 and TMPRSS2/4, the host receptor and proteases, respectively, required for SARS-CoV-2 cell entry into host cells 4 . Here, we show that in the context of donor intrinsic genetic heterogeneity, the SARS-CoV-2 Omicron variant infects human colonoids similarly, if not less effectively, than the ancestral WT (WA1) strain or the Delta variant.…”

“…To date, only one study has compared infectivity of SARS-CoV-2 variants in human enteroids. Using spike-pseudotyped lentiviral viruses and a luciferase-based reporter assay to quantify infection, the authors observed a 2.5- and 5-fold higher infection of colonoids with the Omicron pseudotype spike compared to Delta and D614G spikes, respectively 4 . Our study’s use of authentic SARS-CoV-2 virus and quantitation of both viral RNA and infectious particles may help explain this potential discrepancy.…”