Elucidating coronavirus and virus-host interaction in bat and human intestinal organoids

Abstract

A novel coronavirus SARS-CoV-2 has caused the COVID-19 pandemic since December 2019. Full-genome sequence analysis reveals that SARS-CoV-2 demonstrated high homology with SARS-related coronaviruses identified in bats, suggesting the bat origin of SARS-CoV-2. Bats are the natural reservoirs of many viruses associated with human diseases, especially coronaviruses such as SARS-CoV, MERS-CoV, and SARS-CoV-2. However, in contrast to various pathologies in human coronavirus infections, bats appear to host coronaviruses in an asymptomatic manner, indicating a distinct profile of virus-host interaction in bats. Moreover, coronaviruses show enteric tropism in humans and animals, especially in bats, as most bat coronaviruses were identified from fecal specimens. Indeed, many COVID-19 patients had gastrointestinal symptoms in addition to respiratory manifestations. Yet no direct evidence showed SARS-CoV-2 infection in human and bat intestinal cells. The lack of a robust and biological-relevant in vitro model has been a hurdle for studying numerous bat coronaviruses and elucidating virus-host interactions in human and bat cells. We conducted a series of studies to investigate coronavirus infections and virus-host interaction in bat and human intestinal organoids. Firstly, we demonstrated the establishment, optimization, and characterization of long-term expandable intestinal organoids from the primary intestinal tissues of Chinese horseshoe bats Rhinolophus sinicus. The derived bat intestinal organoids faithfully simulate the native bat intestinal epithelium. Secondly, we found that bat intestinal organoids are susceptible to SARS-CoV-2 infection and sustain robust viral replication. We also showed active replication of SARS-CoV-2 in human intestinal organoids. Thirdly, we provided evidence that bat organoids are susceptible to a bat coronavirus CoV-HKU4, but resistance to EV-71, an enterovirus of exclusive human origin, indicated that bat organoids adequately recapitulated the authentic susceptibility of bats to certain viruses. Furthermore, we investigated the cellular mechanism(s) underlying bat tolerance of coronavirus infections by comparing the innate immune response in bat and human organoids. Firstly, basal expression levels of IFNs and IFN-stimulated genes were higher in bat organoids than in their human counterparts. Secondly, bat organoids mounted a more rapid, robust, and prolonged antiviral defense than human organoids upon Poly(I:C) stimulation. TLR3 and RLR might be the conserved pathways mediating antiviral response in bat and human intestinal organoids. Last but not least, TLR3/RLR inhibition in bat organoids boosted viral growth in the early phase after SARS-CoV-2 or CoV-HKU4 infection. Collectively, we established the first expandable organoid culture system of bat intestinal epithelium and provided evidence that SARS-CoV-2 and CoV-HKU4 can infect bat intestinal cells. The robust SARS-CoV-2 replication in human intestinal organoids suggests that the human intestinal tract might be a transmission route of SARS-CoV-2. The analogous comparison in bat and human organoids suggested that the higher basal expression of antiviral genes, especially more rapid and more robust induction of innate immune response, prepared bat cells to respond to viral infections instantly, which restricted, rather than prevented, viral infections. The more potent host defense gave bat cells an edge to curtail virus propagation in the early phase of infection, which may largely obviate the virus-induced inflammation and immunopathology commonly seen in human coronavirus infections.