Animal models are a dominant method used to study pathogenesis in a complete organism. Using an animal model requires the organism to be infected with the pathogen of interest, which can result in the death of the organism from the infection. This has many ethical concerns; it is the only way (at the moment) to study the impact of a pathogen on an entire organism. Using animal models is complex, due to the regulatory requirements, as well as ensuring the animals do not experience undue suffering (given they are being infected with a pathogen it is likely they will experience negative effects from it).
Cell lines are mammalian cells that can be grown indefinitely in vitro, and a typically derived from cancerous tissues. These are normally human cells, and can be genetically modified to express specific surface proteins, etc…. Some cell lines were obtained in questionable ways, such as HeLa cells (which were taken without the patient’s knowledge), and some people have religious objections to their use. Cell lines reflect one type of cell found in an organ, and so cannot be used to study the impact of an infection on an entire organism.
Organoids are clones of an organ, typically from donated tissue, accurately reflecting the real anatomy of that organ. These are donated consensually, and allow the effect of an infection on different types of tissue found in an organ. However, organoids are only a single organ, and it is not possible to study the effect of an infection on an entire organism. Some individuals will have ethical qualms with organoids, however it will likely be fewer than with cell lines and animal models.
Cell lines are the cheapest method of study, then organoids, and animal models are the most expensive. However, there may be costs with the purchase of equipment specific to each method, and that could make switching from animal models to organoids, for instance, more expensive. Some research labs may continue using a method (such as animal models) because of institutional inertia – where it is done that way because it always has been. The use of animal models will likely decrease as welfare regulations become stricter, and alternative models become more representative.