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In terms of cause and effect, a root cause is the cause of symptoms and a symptom stemming from a root cause is the effect of the root cause. There is no entity disease involved in cause and effect.
A pathogen is a biological agent, or germ, that causes disease to its host by interrupting normal body processes. Bacteria, viruses, fungi and parasites are all common types of pathogens that can cause pathogenic, or infectious, diseases.