The clinical presentation of COVID-19-related illness ranges from asymptomatic to mild respiratory symptoms resembling influenza infection to acute symptoms including pneumonia requiring hospitalization and admission to the intensive care unit. COVID-19 starts in the upper airways and lungs, but in severe cases can also affect the heart, blood vessels, brain, liver, kidneys and intestines. Understanding the functional characteristics and cellular tropism of SARS-CoV-2, as well as the pathogenesis leading to multi-organ failure and death, has driven unprecedented adoption of organoid models. Successful drug discovery and vaccine development rely on preclinical models that faithfully recapitulate the viral life cycle and host cell response to infection.

Organoids are defined as three-dimensional structures grown from stem cells and composed of organ-specific cell types that can self-organize to recapitulate key and functional features of tissues in a dish. Organoids can be started from two main types of stem cells: (1) pluripotent embryonic stem (ES) cells or synthetically induced pluripotent stem (iPS) cells and (2) organ-restricted stem cells.

In vitro models of SARS-CoV-2 infection are critical for understanding the host and viral factors that support cellular tropism and the viral replication cycle. They are also needed to prepare viral inoculum for further research and preclinical evaluation of medical countermeasures against COVID-19. Early in the pandemic, virologists used classical cell lines such as immortalized Vero cells and human continuous cell lines. A severe limitation of these simple tissue culture models is that they are not human or derived from human cancers and thus do not faithfully replicate healthy human physiology.

The Vero cell line has been widely used by virologists because these cells have a homozygous gene deletion resulting in the loss of the type I interferon (IFN-1) gene cluster and the cyclin-dependent kinase inhibitor gene . These cells are permissive to different viruses, producing high titers of virus particles in the culture supernatant. However, infection of Vero cells by SARS-CoV-2 resulted in adaptations of the viral genomes to optimize their replication in these cells. MBCS is mutated or deleted in Vero cells. MBCS facilitates TMPRSS2-mediated entry, and given that this is the mode of entry into primary human epithelial cells, viral stocks produced by Vero cells do not reflect the true viral amplification/replication cycle and may not recapitulate true infection.

Many other organoids derived from tissue stem cells or human pluripotent stem cells have been used in SARS-CoV-2 research to define cell tropism and understand pathogenesis and transmission patterns. These include tonsils and oral cavity, saliva as a potential mode of transmission, pancreas, alveolar macrophages and gastric epithelium.

The SARS-CoV-2 pandemic has resulted in unprecedented advances in several areas: genomic epidemiology and modeling, vaccine and drug development, preclinical models, and public health, among others. And, as measures are taken to contain the pandemic, it has exposed its inadequacy on every front. In the early stages of the pandemic, the focus was on non-functional traits such as the genomics, phylogeny, and evolution of SARS-CoV-2. It soon became apparent that COVID-19 was more than just a respiratory infection, and that functional features such as mechanisms of cell entry and cell tropism, host cell responses to infection, and the development of vaccines and drugs to treat COVID-19 have become and remain.

The need to understand the underlying drivers of SARS-CoV-2 mutations, the clinical impact of emerging variants, and the multiorgan clinical sequelae of severe COVID-19 has led to the exponential adoption of organoids from diverse tissues. Through organoid technology, we understand potential viral entry points (nose, eyes), possible loss of epithelial barrier function to enter the brain/central nervous system (choroid plexus, olfactory bulb), and begin to understand the role of comorbidities

Early studies of autopsy tissues identified organs harboring SARS-CoV-2. Tissue- and region-specific organoids help identify target cells within tissues of affected organs (e.g., lung, liver, kidney, brain, and vasculature).

The limitations of classical virological tissue culture models were quickly revealed, leading to the use of more predictive organoid-based cultures in drug discovery and vaccine feasibility studies. Diverse preclinical models of human organoids provide insights into transmissibility and pathogenesis. The next stage is more complex organoid models, including components of the cellular and physical microenvironment of infected cells. For example, understanding the long-term effects of COVID-19 remains a challenge that will undoubtedly drive further adoption and advancement of organoid models.