Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut

Sergio Triana 1 2, Camila Metz-Zumaran 3, Carlos Ramirez 4, Carmon Kee 3 5, Patricio Doldan 3 5, Mohammed Shahraz 1, Daniel Schraivogel 6, Andreas R Gschwind 7, Ashwini K Sharma 3 4, Lars M Steinmetz 6 7 8, Carl Herrmann 4, Theodore Alexandrov 1 9 10, Steeve Boulant 3 5, Megan L Stanifer 11

Exacerbated pro-inflammatory immune response contributes to COVID-19 pathology. However, despite the mounting evidence about SARS-CoV-2 infecting the human gut, little is known about the antiviral programs triggered in this organ. To address this gap, we performed single-cell transcriptomics of SARS-CoV-2-infected intestinal organoids. We identified a subpopulation of enterocytes as the prime target of SARS-CoV-2 and, interestingly, found the lack of positive correlation between susceptibility to infection and the expression of ACE2. Infected cells activated strong pro-inflammatory programs and produced interferon, while expression of interferon-stimulated genes was limited to bystander cells due to SARS-CoV-2 suppressing the autocrine action of interferon. These findings reveal that SARS-CoV-2 curtails the immune response and highlights the gut as a pro-inflammatory reservoir that should be considered to fully understand SARS-CoV-2 pathogenesis.