Estimating and explaining the spread of COVID-19 at the county level in the USA

The basic reproduction number, R₀, determines the rate of spread of a communicable disease and therefore gives fundamental information needed to plan public health interventions. Using mortality records, we estimated the rate of spread of COVID-19 among 160 counties and county-aggregates in the USA at the start of the epidemic. We show that most of the high among-county variance is explained by four factors (R² = 0.70): the timing of outbreak, population size, population density, and spatial location. For predictions of future spread, population density and spatial location are important, and for the latter we show that SARS-CoV-2 strains containing the G614 mutation to the spike gene are associated with higher rates of spread. Finally, the high predictability of R₀ allows extending estimates to all 3109 counties in the conterminous 48 states. The high variation of R₀ argues for public health policies enacted at the county level for controlling COVID-19.