Researchers followed the signal from the wastewater treatment plant through the sewage system, checking various manholes along the way. After sampling about 50 manholes, they pinpointed the source to a single building housing a company with about 30 employees.
I did some more research and apparently for signal tracing and hypothesis testing a ton of data sampling techniques were utilized here. Especially, sub ground sampling techniques and kriging to interpolate the directions to investigate more samples. This is because genetic sequencing is a very costly process. This is how they were able to do only 50 samples between the wastewater plant and the building where Patient Zero was working.