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Actually, that is a bogus comparison. For several reasons


I guess you missed the most important factor (in this case) in the spread of infectious disease:
Distance

Infection transmissibility in the case of viral infection is dependent on three factors:
Viral Burden
Time of contact
Distance

South Dakota has the same population as San Francisco living in an area of 77,184 mi² compared to San Francisco with 874,961 people living in 46.87 mi²
The spread of communicable disease has always been more rampant in congested cities than rural country-side; this has been consistently observed going all the way back to the Black Plague in Europe.
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