Longitudinal and Spatial Analyses Reveal Distinct Immune Response Landscapes in Lung and Intestinal Tissue of SARS-CoV-2-Infected Rhesus Macaques

The pathological and immune response dynamics in the lungs of individuals with COVID-19 have been broadly studied and characterized. Besides, it is noteworthy that SARS-CoV-2 also causes complex gastrointestinal symptoms and has a long period of rectal shedding. SARS-CoV-2 initially infects the upper airways, and the differential tissue response between the intestines and lungs remains unclear. To better understand how nasal infection leads to subsequent modulation of the intestinal mucosal immune system, we depicted the spatial single-cell transcriptional atlas of longitudinally collected lung and intestinal tissue samples from SARS-CoV-2-infected rhesus macaques 3 to 10 days post infection. We found a decrease in alveolar macrophages (AMs) caused by viral infection, with involvement of neutrophils and monocytes infiltration and an increase in alveolar epithelial cells (ATs) and endothelial cells (ECs) related to pathological changes. In-depth of understanding, we demonstrated that intestinal enterocytes (IECs) were degraded at 3 days post infection (dpi) but recovered rapidly at 7 and 10 dpi, revealing that viral infection mildly impacted the intestine. Crucially, we observed suppression of the inflammatory response and tissue damage related to B cell and Paneth cell accumulation in the intestines, although T cells were activated in the early and middle stages of SARS-CoV-2 infection. Comparing with lung, expression of genes related to the interferon response was inhibited and inflammatory factor secretion was lower in the intestines. Further analysis of SARS-CoV-2 receptors revealed the widespread distribution of ACE2+/TMPRSS2+ cells in intestinal tissues, and expression of IFN-γ response markers was detected in ACE2-expressing cells at 3-7 dpi. The above findings show that intestinal mucosal immunology is in a state of dynamic imbalance during SARS-CoV-2 infection, which may underlie the ongoing rectal viral shedding and mild tissue damage.Funding: This work was supported by National Natural Sciences Foundations of China (82041017,32070923,32000133), Basic Scientifc Research Funding of National Colleges and Universities (3332020066), Basic Research Project of Science and Technology of Yunnan Province (202001AT070143).Declaration of Interests: The authors declare no conflict of interest.Ethics Approval Statement: The experiments associated with infectious SARS-CoV-2 was performed in biosafety level-3 (BSL-3) and animal biosafety level-3 (ABSL-3) laboratory, which has been approval from the Institutional Biosafety Committee of Institute of Medical Biology (IMB) & Chinese Academy of Medical Sciences (CAMS). The work with infectious virus were performed in a certified Class IIB Biosafety Cabinet in a BSL-3 facility. All staff members armed with scrubs, 3M or Tyvek suits and waterproof gowns for carrying out monkey experiments, along with powered air-purifying respirators, shoe covers, and double gloves. Animal experiments of this study were approved by the Institutional Animal Care and Use Committee (IACUC) of the IMB & CAMS.