Infection of 3D Brain Organoids with Human Pathogenic Viruses Under Biosafety Level-3 Conditions with Subsequent Inactivation to Study Viral Replication, Pathomechanisms, and Other Viral Infection-Mediated Effects

Viral infectious diseases may cause neurological symptoms primarily in two nonexclusive ways. Infection may lead to an excessive inflammatory response that damages the neuronal system, which is referred to as immunopathology, or the pathogen is able to infect brain cells, such as neurons or nonneuronal glial cells, like oligodendrocytes, microglia, and astrocytes. Viruses that target and infect cells of the CNS, in general, are called neurotropic. 3D brain organoids provide favorable conditions to study target cells and induced pathomechanisms associated with such viral neurotropism. In the context of highly pathogenic viruses, strict safety precautions (safety level-3 laboratory) must be taken if infectious laboratory strains or strains from clinical samples are to be used for infection experiments. Likewise, safe inactivation protocols must be used for subsequent analysis. This chapter will discuss appropriate protocols, focusing on methodological aspects for each of these steps, and discuss advantages and disadvantages when working with 3D brain organoids while handling biosafety level-3 pathogens based on our work with severe acute respiratory virus type 2 (SARS-CoV-2).