A lot of pathogens (viruses, bacteria, parasites) initially get into humans with a transmission from animals.
It is transmission of Ebola virus in a bat to a little boy in West Africa that led to the Ebola epidemic that infected more than 20,000 people. Researchers look at reports of all the earliest cases and then follow these clues back to try to identify the first case. Here is some more information about that work:
Some pathogens spread in similar ways. Mosquitoes of various sorts spread malaria, dengue virus and Zika virus. Ebola is spread through bodily fluids. Influenza is spread through virus in droplets that are breathed out of one person and into another. These mechanisms are very important to understand. Some diseases spread mostly when those infected are showing symptoms of disease – harder is when a lot of people don’t show signs of infection but still spread the infection on to others. We try our best to use equations that take into account these important differences.