It depends a lot on the disease. Many of the nastiest diseases aren’t supposed to be in humans at all. All strains of influenza originally come from birds, where they cause almost no symptoms and live perfectly happily alongside each other. However when they cross into a species they are not evolved for, such as humans, they cause problems, as the mechanisms they evolved to replicate without problems for the host don’t work properly in humans.
This is the case for many (but not all) of the nastiest diseases, Ebola, Covid, etc, which come from bats and cause no symptoms in their original host, as well as HIV, which originated in chimpanzees.
Humans do have many bacteria and viruses that do live inside them and cause no problems at all in most cases. CMV and EBV are common viruses that cause zero symptoms in most people, but sometimes cause bad reactions in those who are immune deficient. Most cases of meningitis are caused by bacteria that live inside the noses of 80% of people perfectly happily, and only rarely decide to cross into the blood and cause problems.
Then you have diseases like colds, which are evolved for humans and cause only mild symptoms, but make you sneeze and cough, allowing you to spread the virus much further and to more hosts than you would normally
The human body is also full of all sorts of other bacteria and viruses that help us in many ways, and could be called the most effective ones to co evolve with us.
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