SARS-CoV-2 productively infects human gut enterocytes

SARS-CoV-2 productively infects human gut enterocytes Jefferson T, Spencer EA, Heneghan C.

Published on July 28, 2020

Reference Lamers MM, Beumer J, van der Vaart J, et al. SARS-CoV-2 productively infects human gut enterocytes  Science. 2020;369(6499):50-54. doi:10.1126/science.abc1669
Study type
Country Netherlands
Setting Non Applicable
Funding Details ERC Advanced Grant and by Lung Foundation Netherlands to HC, and by NWO Grant 022.005.032; funding from the Dutch Technology Foundation STW and from European Union’s Horizon 2020 Programme.
Transmission mode Orofecal

Bottom Line

SARS-CoV-2 infects enterocyte lineage cells in a human intestinal organoid model.

Evidence Summary

SARS-CoV-2 can infect airway and gut organoids

Virus was added to organoid *-derived human airway epithelium cultured in 2D and SARS-CoV and SARS-CoV2 infected differentiated airway cultures.

  • Immunostaining revealed that the viruses targeted ciliated cells, but not goblet cells.
  • SARS-CoV-2 productively infected Human small intestinal organoids (hSIOs) assessed by qRT-PCR for viral sequences and by live virus titrations on VeroE6 cells
  • Viral RNA was detected readily in culture supernatants and  correlated with the infectious virus levels within hSIOs 

*Organoids are 3D structures, that can be grown from adult stem cells (ASCs).

SARS-CoV-2 can infect enterocyte lineage cells

Comparable rates of viral infections were observed in the organoids At 60 hours, the number of infected cells had dramatically increased. At 60 hours, apoptosis became prominent in both SARS-CoV and SARS-CoV-2 infected enterocytes.

Ultrastructural analysis of the viral life cycle in enterocytes

Two hSIOs, selected from 42 imaged hSIOs at 60 hours differed in the state of infection: 

Organoid 1: cellular organization still intact.

Organoid 2: many disintegrated cells seen, with viral particles of 80-120 nm occurred in the lumen of the organoid, at the basolateral and apical side of enterocytes. 

RNA expression changes in infected enterocytes

Infection with SARS-CoV-2 elicited a broad signature of cytokines and interferon-stimulated genes (ISGs) attributed to type I and III interferon responses RNA sequencing analysis confirmed differentiation of DIF organoids into multiple intestinal lineages, including ACE2 up-regulation. 

What did they do?

To determine the target cell type, they performed confocal analysis on hSIOs cultured in EXP, DIF, or EEC conditions. And stained for viral dsRNA, viral nucleocapsid protein, KI67 to visualize proliferative cells, actin (using phalloidin) to visualize enterocyte brush borders, DNA (DAPI) and cleaved caspase 3 to visualize apoptotic cells.

Unsupervised transmission electron microscopy was performed on selected highly infected samples.

mRNA sequence analysis was performed to determine gene expression changes by SARS-CoV-2-infection of hSIOs cultured continuously.

  • DIF: differentiation medium
  • EXP: high expansion medium
  • EEC: enteroendocrine cells

Study reliability

Limited information is available on coronavirus pathogenesis and transmission.

Clearly defined setting Demographic characteristics described Follow-up length was sufficient Transmission outcomes assessed Main biases are taken into consideration
N/A N/A N/A N/A Yes

What else should I consider?

The regulation of SARS-CoV-2-induced genes in SARS-CoV infected organoids. This induction was similar to infections with other viruses like norovirus [Hosmillo], rotavirus [Saxena] and enteroviruses [Drummond, Good]. 

Hosmillo M., Chaudhry Y., Nayak K, et al. Norovirus replication in human intestinal epithelial cells is restricted by the interferon-induced JAK/STAT signaling pathway and RNA polymerase II-mediated transcriptional responses. mBio 11, e00215-20 (2020). 10.1128/mBio.00215-20 [PubMed

Saxena K., Simon L. M., Zeng X. L., et al. A paradox of transcriptional and functional innate interferon responses of human intestinal enteroids to enteric virus infection. Proc. Natl. Acad. Sci. U.S.A. 114, E570–E579 (2017). 10.1073/pnas.1615422114 [PubMed

Drummond C. G., Bolock A. M., Ma C., et al. Enteroviruses infect human enteroids and induce antiviral signaling in a cell lineage-specific manner. Proc. Natl. Acad. Sci. U.S.A. 114, 1672–1677 (2017). 10.1073/pnas.1617363114 [PubMed

Good C., Wells A. I., Coyne C. B., Type III interferon signaling restricts enterovirus 71 infection of goblet cells. Sci. Adv. 5, eaau4255 (2019). 10.1126/sciadv.aau4255 [PubMed]

About the authors

Carl Heneghan

Carl is Professor of EBM & Director of CEBM at the University of Oxford. He is also a GP and tweets @carlheneghan. He has an active interest in discovering the truth behind health research findings

Elizabeth Spencer

Dr Elizabeth Spencer; MMedSci, PhD. Epidemiologist, Nuffield Department for Primary Care Health Sciences, University of Oxford.

Tom Jefferson

Tom Jefferson, epidemiologist.