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, 0.97 on March 13, 2025; in Marin County, from WasteWater Scan, 1.01 on March 17, 2025; in Napa County, from WasteWater Scan, 0.98 on March 17, 2025; in San Francisco County, from WasteWater Scan, 0.98 on March 19, 2025; in San Mateo County, from WasteWater Scan, 0.98 on March 19, 2025; in Santa Clara County, from WasteWater Scan, 1.00 on March 19, 2025; in Solano County, from WasteWater Scan, 0.96 on March 18, 2025; in Sonoma County, from WasteWater Scan, 0.96 on March 16, 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, 0.97 on March 13, 2025; in Marin County, from WasteWater Scan, 1.01 on March 17, 2025; in Napa County, from WasteWater Scan, 0.98 on March 17, 2025; in San Francisco County, from WasteWater Scan, 0.98 on March 19, 2025; in San Mateo County, from WasteWater Scan, 0.98 on March 19, 2025; in Santa Clara County, from WasteWater Scan, 1.00 on March 19, 2025; in Solano County, from WasteWater Scan, 0.96 on March 18, 2025; in Sonoma County, from WasteWater Scan, 0.96 on March 16, 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 California outside the Bay Area. The latest estimates are as follows: in Los Angeles County, from WasteWater Scan, 1.01 on March 17, 2025; in Merced County, from WasteWater Scan, 0.98 on March 17, 2025; in Monterey County, from WasteWater Scan, 1.02 on March 17, 2025; in Riverside County, from WasteWater Scan, 0.98 on March 17, 2025; in Sacramento County, from WasteWater Scan, 0.99 on March 19, 2025; in San Bernardino County, from WasteWater Scan, 1.03 on March 19, 2025; in San Diego County, from WasteWater Scan, 1.00 on March 17, 2025; in San Luis Obispo County, from WasteWater Scan, 0.98 on March 18, 2025; in Santa Barbara County, from WasteWater Scan, 0.96 on March 17, 2025; in Santa Cruz County, from WasteWater Scan, 0.95 on March 16, 2025; in Stanislaus County, from WasteWater Scan, 1.02 on March 17, 2025; in Yolo County, from WasteWater Scan, 1.05 on March 19, 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 California outside the Bay Area. The latest estimates are as follows: in Los Angeles County, from WasteWater Scan, 1.01 on March 17, 2025; in Merced County, from WasteWater Scan, 0.98 on March 17, 2025; in Monterey County, from WasteWater Scan, 1.02 on March 17, 2025; in Riverside County, from WasteWater Scan, 0.98 on March 17, 2025; in Sacramento County, from WasteWater Scan, 0.99 on March 19, 2025; in San Bernardino County, from WasteWater Scan, 1.03 on March 19, 2025; in San Diego County, from WasteWater Scan, 1.00 on March 17, 2025; in San Luis Obispo County, from WasteWater Scan, 0.98 on March 18, 2025; in Santa Barbara County, from WasteWater Scan, 0.96 on March 17, 2025; in Santa Cruz County, from WasteWater Scan, 0.95 on March 16, 2025; in Stanislaus County, from WasteWater Scan, 1.02 on March 17, 2025; in Yolo County, from WasteWater Scan, 1.05 on March 19, 2025. For the complete timeseries, see the csv data linked below. For any questions, please contact the author.

Wastewater

This is a plot of individual and smoothed wastewater readings in the Bay Area. The latest smoothed readings are as follows: in Alameda County, from Wastewater Scan, 7.3 as of March 13, 2025; in Marin County, from Wastewater Scan, 9.8 as of March 17, 2025; in Napa County, from Wastewater Scan, 3.6 as of March 17, 2025; in San Francisco County, from Wastewater Scan, 9.6 as of March 19, 2025; in San Mateo County, from Wastewater Scan, 8.5 as of March 19, 2025; in Santa Clara County, from Wastewater Scan, 4.6 as of March 19, 2025; in Solano County, from Wastewater Scan, 2.8 as of March 18, 2025; in Sonoma County, from Wastewater Scan, 2.7 as of March 16, 2025. All values are gene copies detected per hundred thousand copies of the pepper moth virus control. For the complete timeseries, please download the CSV data linked below. For any questions, please contact the author.

This is a plot of individual and smoothed wastewater readings in the Bay Area. The latest smoothed readings are as follows: in Alameda County, from Wastewater Scan, 7.3 as of March 13, 2025; in Marin County, from Wastewater Scan, 9.8 as of March 17, 2025; in Napa County, from Wastewater Scan, 3.6 as of March 17, 2025; in San Francisco County, from Wastewater Scan, 9.6 as of March 19, 2025; in San Mateo County, from Wastewater Scan, 8.5 as of March 19, 2025; in Santa Clara County, from Wastewater Scan, 4.6 as of March 19, 2025; in Solano County, from Wastewater Scan, 2.8 as of March 18, 2025; in Sonoma County, from Wastewater Scan, 2.7 as of March 16, 2025. All values are gene copies detected per hundred thousand copies of the pepper moth virus control. For the complete timeseries, please download the CSV data linked below. For any questions, please contact the author.

This is a plot of individual and smoothed wastewater readings in California outside the Bay Area. The latest smoothed readings are as follows: in Los Angeles County, from Wastewater Scan, 4.8 as of March 17, 2025; in Merced County, from Wastewater Scan, 0.5 as of March 17, 2025; in Monterey County, from Wastewater Scan, 4.8 as of March 17, 2025; in Riverside County, from Wastewater Scan, 2.7 as of March 17, 2025; in Sacramento County, from Wastewater Scan, 5 as of March 19, 2025; in San Bernardino County, from Wastewater Scan, 5.4 as of March 19, 2025; in San Diego County, from Wastewater Scan, 5.6 as of March 17, 2025; in San Luis Obispo County, from Wastewater Scan, 1.3 as of March 18, 2025; in Santa Barbara County, from Wastewater Scan, 3.6 as of March 17, 2025; in Santa Cruz County, from Wastewater Scan, 3 as of March 16, 2025; in Stanislaus County, from Wastewater Scan, 7 as of March 17, 2025; in Yolo County, from Wastewater Scan, 4.3 as of March 19, 2025. All values are gene copies detected per hundred thousand copies of the pepper moth virus control. For the complete timeseries, please download the CSV data linked below. For any questions, please contact the author.

This is a plot of individual and smoothed wastewater readings in California outside the Bay Area. The latest smoothed readings are as follows: in Los Angeles County, from Wastewater Scan, 4.8 as of March 17, 2025; in Merced County, from Wastewater Scan, 0.5 as of March 17, 2025; in Monterey County, from Wastewater Scan, 4.8 as of March 17, 2025; in Riverside County, from Wastewater Scan, 2.7 as of March 17, 2025; in Sacramento County, from Wastewater Scan, 5 as of March 19, 2025; in San Bernardino County, from Wastewater Scan, 5.4 as of March 19, 2025; in San Diego County, from Wastewater Scan, 5.6 as of March 17, 2025; in San Luis Obispo County, from Wastewater Scan, 1.3 as of March 18, 2025; in Santa Barbara County, from Wastewater Scan, 3.6 as of March 17, 2025; in Santa Cruz County, from Wastewater Scan, 3 as of March 16, 2025; in Stanislaus County, from Wastewater Scan, 7 as of March 17, 2025; in Yolo County, from Wastewater Scan, 4.3 as of March 19, 2025. All values are gene copies detected per hundred thousand copies of the pepper moth virus control. For the complete timeseries, please download the CSV data linked below. For any questions, please contact the author.

Historical

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, 0.97 on March 13, 2025; in Marin County, from WasteWater Scan, 1.01 on March 17, 2025; in Napa County, from WasteWater Scan, 0.98 on March 17, 2025; in San Francisco County, from WasteWater Scan, 0.98 on March 19, 2025; in San Mateo County, from WasteWater Scan, 0.98 on March 19, 2025; in Santa Clara County, from WasteWater Scan, 1.00 on March 19, 2025; in Solano County, from WasteWater Scan, 0.96 on March 18, 2025; in Sonoma County, from WasteWater Scan, 0.96 on March 16, 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, 0.97 on March 13, 2025; in Marin County, from WasteWater Scan, 1.01 on March 17, 2025; in Napa County, from WasteWater Scan, 0.98 on March 17, 2025; in San Francisco County, from WasteWater Scan, 0.98 on March 19, 2025; in San Mateo County, from WasteWater Scan, 0.98 on March 19, 2025; in Santa Clara County, from WasteWater Scan, 1.00 on March 19, 2025; in Solano County, from WasteWater Scan, 0.96 on March 18, 2025; in Sonoma County, from WasteWater Scan, 0.96 on March 16, 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 California outside the Bay Area. The latest estimates are as follows: in Los Angeles County, from WasteWater Scan, 1.01 on March 17, 2025; in Merced County, from WasteWater Scan, 0.98 on March 17, 2025; in Monterey County, from WasteWater Scan, 1.02 on March 17, 2025; in Riverside County, from WasteWater Scan, 0.98 on March 17, 2025; in Sacramento County, from WasteWater Scan, 0.99 on March 19, 2025; in San Bernardino County, from WasteWater Scan, 1.03 on March 19, 2025; in San Diego County, from WasteWater Scan, 1.00 on March 17, 2025; in San Luis Obispo County, from WasteWater Scan, 0.98 on March 18, 2025; in Santa Barbara County, from WasteWater Scan, 0.96 on March 17, 2025; in Santa Cruz County, from WasteWater Scan, 0.95 on March 16, 2025; in Stanislaus County, from WasteWater Scan, 1.02 on March 17, 2025; in Yolo County, from WasteWater Scan, 1.05 on March 19, 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 California outside the Bay Area. The latest estimates are as follows: in Los Angeles County, from WasteWater Scan, 1.01 on March 17, 2025; in Merced County, from WasteWater Scan, 0.98 on March 17, 2025; in Monterey County, from WasteWater Scan, 1.02 on March 17, 2025; in Riverside County, from WasteWater Scan, 0.98 on March 17, 2025; in Sacramento County, from WasteWater Scan, 0.99 on March 19, 2025; in San Bernardino County, from WasteWater Scan, 1.03 on March 19, 2025; in San Diego County, from WasteWater Scan, 1.00 on March 17, 2025; in San Luis Obispo County, from WasteWater Scan, 0.98 on March 18, 2025; in Santa Barbara County, from WasteWater Scan, 0.96 on March 17, 2025; in Santa Cruz County, from WasteWater Scan, 0.95 on March 16, 2025; in Stanislaus County, from WasteWater Scan, 1.02 on March 17, 2025; in Yolo County, from WasteWater Scan, 1.05 on March 19, 2025. For the complete timeseries, see the csv data linked below. For any questions, please contact the author.

Case counts

This is a plot of daily and smoothed counts of new cases per ten thousand population per day in the Bay Area. Case counts are no longer being provided by the health departments. The last data recorded here was on December 18, 2023.

This is a plot of daily and smoothed counts of new cases per ten thousand population per day in the Bay Area. Case counts are no longer being provided by the health departments. The last data recorded here was on December 18, 2023.

This is a plot of daily and smoothed counts of new cases per ten thousand population per day in California outside the Bay Area. Case counts are no longer being provided by the health departments. The last data recorded here was on December 18, 2023.

This is a plot of daily and smoothed counts of new cases per ten thousand population per day in California outside the Bay Area. Case counts are no longer being provided by the health departments. The last data recorded here was on December 18, 2023.

Wastewater