This is a daily updated tracker website providing time-varying estimated reproduction numbers for COVID-19 in California, based on both daily case counts and wastewater readings.

We estimate transmission rates of COVID–19 using reproduction numbers. A time-varying reproduction number, commonly written R, is the average number of cases infected by a given case over the course of that individual’s disease progression. Of particular interest is the question of whether transmission is supercritical, meaning that R > 1, in which case the epidemic can increase in size, or is subcritical, meaning that R < 1, in which case it will fade out. To eliminate a disease locally, it is not necessary to reduce R to zero, only to reduce it below one for a sustained period.

We use raw data from three sources: new cases by county from California Health and Human Services, (“Cases”, below); wastewater readings from the Cal-SuWers network (“Cal-SuWers”), WastewaterScan (“WWScan”), and BioBot Analytics (“BioBot”).

For more details see the Methods section below.

Recent

R estimates

This is a plot of estimated reproduction numbers in the Bay Area. The latest estimates are as follows: in Alameda County, from WasteWater Scan, 0.99 on February 04, 2025, from the state, 1.00 on February 04, 2025; in Contra Costa County, from the state, 1.03 on February 03, 2025; in Marin County, from WasteWater Scan, 1.02 on February 05, 2025, from the state, 1.00 on February 04, 2025; in Napa County, from WasteWater Scan, 1.01 on February 05, 2025; in San Francisco County, from WasteWater Scan, 1.02 on February 06, 2025; in San Mateo County, from WasteWater Scan, 1.01 on February 06, 2025, from the state, 1.00 on February 04, 2025; in Santa Clara County, from WasteWater Scan, 1.00 on February 06, 2025; in Solano County, from WasteWater Scan, 1.01 on February 05, 2025, from the state, 0.99 on February 02, 2025; in Sonoma County, from WasteWater Scan, 1.02 on February 02, 2025, from the state, 1.01 on February 02, 2025. For the complete timeseries, see the csv data linked below. For any questions, please contact the author.

This is a plot of estimated reproduction numbers in the Bay Area. The latest estimates are as follows: in Alameda County, from WasteWater Scan, 0.99 on February 04, 2025, from the state, 1.00 on February 04, 2025; in Contra Costa County, from the state, 1.03 on February 03, 2025; in Marin County, from WasteWater Scan, 1.02 on February 05, 2025, from the state, 1.00 on February 04, 2025; in Napa County, from WasteWater Scan, 1.01 on February 05, 2025; in San Francisco County, from WasteWater Scan, 1.02 on February 06, 2025; in San Mateo County, from WasteWater Scan, 1.01 on February 06, 2025, from the state, 1.00 on February 04, 2025; in Santa Clara County, from WasteWater Scan, 1.00 on February 06, 2025; in Solano County, from WasteWater Scan, 1.01 on February 05, 2025, from the state, 0.99 on February 02, 2025; in Sonoma County, from WasteWater Scan, 1.02 on February 02, 2025, from the state, 1.01 on February 02, 2025. For the complete timeseries, see the csv data linked below. For any questions, please contact the author.