Dynamics in disease: establishment of the human lung SARS-CoV-2 infection model and multiple viral variants competition system

Abstract

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), targeting human alveoli, caused a coronavirus disease 2019 pandemic (COVID-19), and multiple viral variants of the virus, such as Alpha, Delta, and Omicron, continuously emerged. However, the lack of models mimicking the cellular physiology of hAT2 cells and systems to simultaneously compare the infectivity of multiple viral variants limits understanding of infection dynamics. I aim to build systems of (1) understanding pathogenesis of the virus and (2) comparing the infectivity of multiple viral variants. In the first part, I established a human lung alveolar organoid infection model for SARS-CoV-2. With successful establishment of alveolar organoids, I infected the organoids with the virus and demonstrated robust infection through imaging-based and transcriptome- analysis. I revealed rapid viral replication during 24 hours after infection and robust innate immune response, including interferon-associated and proinflammatory genes in alveolar organoids. In addition, using unique mutation, I identified a single viral entry can fully infect an alveolar cell. I established human physiology mimicking infection model and it could be applied to investigate the pathogenesis of SARS-CoV-2. In the second part, I integrated human alveolar organoids and single-cell transcriptome sequencing to compare relative infectivity of multiple viral variants. As a proof-of-concept study, I chose four highly transmissible SARS-CoV-2 variants, including GR (B.1.1.119), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (BA.1). With unique genomic mutations of each viral variant, a rapid evaluation of the relative infectivity in controlled experiment was possible. My system demonstrated that the Omicron variant is 5- to 7-fold more infectious to human alveolar cells than the other SARS-CoV-2 variants at the initial stage of infection. To my knowledge, the system measures the relative infectivity under multiple virus competition and provides new experimental procedures monitoring newly emerging viral variants.