Abstract: The COVID-19 pandemic has intensified the urgency for new tools for modeling respiratory infections and screening therapeutic candidates, given the poor predictive power of animal models and immortalized cell culture. Despite this urgent and ongoing need, human primary cell-based organ-on-chip models have been slow to respond. Common barriers associated with most microphysiological systems (MPS) include low throughput, operational complexity, and lack of access or function within high containment facilities such as biosafety level 3 (BSL-3) labs. Here we present successful demonstration of the applicability of the PREDICT96-ALI (Air-Liquid-Interface) platform technology, cultured with human primary tracheobronchial epithelial cells in a physiologically relevant microenvironment, to operation in a BSL-3 laboratory, with modeling of multiple variants of SARS-CoV-2 and screening of known efficacious and non-efficacious compounds to develop in vitro – in vivo correlations. This system supports robust viral replication of SARS-CoV-2 through an array of complementary readouts including RT-qPCR, viral plaque assays, TCID50, tissue transcriptomics and Immunofluorescence. Routine and high efficiency operation of the 96-multiplexed platform in a BSL-3 lab enables highly reproducible and statistically significant experiments across a range of viral strains, input titers, therapeutic compounds and administered doses. This capability greatly extends prior MPS studies of SARS-CoV-2 infections and therapeutic screening that were limited to the study of viral entry of pseudoviruses due to operational constraints in conventional BSL-3 operational settings. The demonstrated application of this technology toward SARS-CoV-2 infection modeling and therapeutic screening can be extended to other pathogens that require high containment operation, not only other respiratory infectious diseases, but also viral and bacterial infections of other tissues and organs compatible with investigation in the PREDICT96 platform.
Here we report findings for multiple experiments with Washington, Delta and Omicron strains of SARS-CoV-2 across several sources of human donor tissue in the PREDICT96-ALI platform, recapitulating clinical observations regarding the rate of viral replication for the different strains, and revealing mechanistically relevant behaviors regarding cytopathic effects across the strains. Therapeutic screening of established treatments such as nirmatrelvir, remdesivir and molnupiravir are ongoing, and show an excellent correlation between clinically observed efficacy (for instance hospitalization rates following treatment.) Additional studies with known non-efficacious compounds also compare well with results of ongoing clinical trials, providing a level of confidence in the ability of the PREDICT96-ALI system to faithfully recapitulate key aspects of the SARS-CoV-2 infection and its response to antiviral medications. Future studies are aimed at integration of immune components in this platform to further extend these capabilities toward a powerful new tool in rapid and predictive drug development.