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, 1.00 on April 15, 2025; in Marin County, from WasteWater Scan, 0.99 on April 21, 2025; in Napa County, from WasteWater Scan, 1.02 on April 21, 2025; in San Francisco County, from WasteWater Scan, 1.00 on April 22, 2025; in San Mateo County, from WasteWater Scan, 1.00 on April 22, 2025; in Santa Clara County, from WasteWater Scan, 1.00 on April 22, 2025; in Solano County, from WasteWater Scan, 1.01 on April 17, 2025; in Sonoma County, from WasteWater Scan, 1.01 on April 20, 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, 1.00 on April 15, 2025; in Marin County, from WasteWater Scan, 0.99 on April 21, 2025; in Napa County, from WasteWater Scan, 1.02 on April 21, 2025; in San Francisco County, from WasteWater Scan, 1.00 on April 22, 2025; in San Mateo County, from WasteWater Scan, 1.00 on April 22, 2025; in Santa Clara County, from WasteWater Scan, 1.00 on April 22, 2025; in Solano County, from WasteWater Scan, 1.01 on April 17, 2025; in Sonoma County, from WasteWater Scan, 1.01 on April 20, 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, 1.00 on April 20, 2025; in Merced County, from WasteWater Scan, 0.96 on April 18, 2025; in Monterey County, from WasteWater Scan, 1.00 on April 21, 2025; in Riverside County, from WasteWater Scan, 0.98 on April 21, 2025; in Sacramento County, from WasteWater Scan, 0.99 on April 22, 2025; in San Bernardino County, from WasteWater Scan, 1.02 on April 21, 2025; in San Diego County, from WasteWater Scan, 1.01 on April 16, 2025; in San Luis Obispo County, from WasteWater Scan, 0.98 on April 21, 2025; in Santa Barbara County, from WasteWater Scan, 0.99 on April 18, 2025; in Santa Cruz County, from WasteWater Scan, 0.99 on April 20, 2025; in Stanislaus County, from WasteWater Scan, 0.94 on April 18, 2025; in Yolo County, from WasteWater Scan, 1.00 on April 21, 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, 1.00 on April 20, 2025; in Merced County, from WasteWater Scan, 0.96 on April 18, 2025; in Monterey County, from WasteWater Scan, 1.00 on April 21, 2025; in Riverside County, from WasteWater Scan, 0.98 on April 21, 2025; in Sacramento County, from WasteWater Scan, 0.99 on April 22, 2025; in San Bernardino County, from WasteWater Scan, 1.02 on April 21, 2025; in San Diego County, from WasteWater Scan, 1.01 on April 16, 2025; in San Luis Obispo County, from WasteWater Scan, 0.98 on April 21, 2025; in Santa Barbara County, from WasteWater Scan, 0.99 on April 18, 2025; in Santa Cruz County, from WasteWater Scan, 0.99 on April 20, 2025; in Stanislaus County, from WasteWater Scan, 0.94 on April 18, 2025; in Yolo County, from WasteWater Scan, 1.00 on April 21, 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, 5.6 as of April 15, 2025; in Marin County, from Wastewater Scan, 19.5 as of April 21, 2025; in Napa County, from Wastewater Scan, 4.8 as of April 21, 2025; in San Francisco County, from Wastewater Scan, 10.9 as of April 22, 2025; in San Mateo County, from Wastewater Scan, 9.4 as of April 22, 2025; in Santa Clara County, from Wastewater Scan, 6.4 as of April 22, 2025; in Solano County, from Wastewater Scan, 5.2 as of April 17, 2025; in Sonoma County, from Wastewater Scan, 3.4 as of April 20, 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, 5.6 as of April 15, 2025; in Marin County, from Wastewater Scan, 19.5 as of April 21, 2025; in Napa County, from Wastewater Scan, 4.8 as of April 21, 2025; in San Francisco County, from Wastewater Scan, 10.9 as of April 22, 2025; in San Mateo County, from Wastewater Scan, 9.4 as of April 22, 2025; in Santa Clara County, from Wastewater Scan, 6.4 as of April 22, 2025; in Solano County, from Wastewater Scan, 5.2 as of April 17, 2025; in Sonoma County, from Wastewater Scan, 3.4 as of April 20, 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, 3.7 as of April 20, 2025; in Merced County, from Wastewater Scan, 0.7 as of April 18, 2025; in Monterey County, from Wastewater Scan, 4.8 as of April 21, 2025; in Riverside County, from Wastewater Scan, 2.5 as of April 21, 2025; in Sacramento County, from Wastewater Scan, 7 as of April 22, 2025; in San Bernardino County, from Wastewater Scan, 1.9 as of April 21, 2025; in San Diego County, from Wastewater Scan, 7.2 as of April 16, 2025; in San Luis Obispo County, from Wastewater Scan, 3 as of April 21, 2025; in Santa Barbara County, from Wastewater Scan, 4.5 as of April 18, 2025; in Santa Cruz County, from Wastewater Scan, 10.3 as of April 20, 2025; in Stanislaus County, from Wastewater Scan, 2.7 as of April 18, 2025; in Yolo County, from Wastewater Scan, 7.8 as of April 21, 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, 3.7 as of April 20, 2025; in Merced County, from Wastewater Scan, 0.7 as of April 18, 2025; in Monterey County, from Wastewater Scan, 4.8 as of April 21, 2025; in Riverside County, from Wastewater Scan, 2.5 as of April 21, 2025; in Sacramento County, from Wastewater Scan, 7 as of April 22, 2025; in San Bernardino County, from Wastewater Scan, 1.9 as of April 21, 2025; in San Diego County, from Wastewater Scan, 7.2 as of April 16, 2025; in San Luis Obispo County, from Wastewater Scan, 3 as of April 21, 2025; in Santa Barbara County, from Wastewater Scan, 4.5 as of April 18, 2025; in Santa Cruz County, from Wastewater Scan, 10.3 as of April 20, 2025; in Stanislaus County, from Wastewater Scan, 2.7 as of April 18, 2025; in Yolo County, from Wastewater Scan, 7.8 as of April 21, 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, 1.00 on April 15, 2025; in Marin County, from WasteWater Scan, 0.99 on April 21, 2025; in Napa County, from WasteWater Scan, 1.02 on April 21, 2025; in San Francisco County, from WasteWater Scan, 1.00 on April 22, 2025; in San Mateo County, from WasteWater Scan, 1.00 on April 22, 2025; in Santa Clara County, from WasteWater Scan, 1.00 on April 22, 2025; in Solano County, from WasteWater Scan, 1.01 on April 17, 2025; in Sonoma County, from WasteWater Scan, 1.01 on April 20, 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, 1.00 on April 15, 2025; in Marin County, from WasteWater Scan, 0.99 on April 21, 2025; in Napa County, from WasteWater Scan, 1.02 on April 21, 2025; in San Francisco County, from WasteWater Scan, 1.00 on April 22, 2025; in San Mateo County, from WasteWater Scan, 1.00 on April 22, 2025; in Santa Clara County, from WasteWater Scan, 1.00 on April 22, 2025; in Solano County, from WasteWater Scan, 1.01 on April 17, 2025; in Sonoma County, from WasteWater Scan, 1.01 on April 20, 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, 1.00 on April 20, 2025; in Merced County, from WasteWater Scan, 0.96 on April 18, 2025; in Monterey County, from WasteWater Scan, 1.00 on April 21, 2025; in Riverside County, from WasteWater Scan, 0.98 on April 21, 2025; in Sacramento County, from WasteWater Scan, 0.99 on April 22, 2025; in San Bernardino County, from WasteWater Scan, 1.02 on April 21, 2025; in San Diego County, from WasteWater Scan, 1.01 on April 16, 2025; in San Luis Obispo County, from WasteWater Scan, 0.98 on April 21, 2025; in Santa Barbara County, from WasteWater Scan, 0.99 on April 18, 2025; in Santa Cruz County, from WasteWater Scan, 0.99 on April 20, 2025; in Stanislaus County, from WasteWater Scan, 0.94 on April 18, 2025; in Yolo County, from WasteWater Scan, 1.00 on April 21, 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, 1.00 on April 20, 2025; in Merced County, from WasteWater Scan, 0.96 on April 18, 2025; in Monterey County, from WasteWater Scan, 1.00 on April 21, 2025; in Riverside County, from WasteWater Scan, 0.98 on April 21, 2025; in Sacramento County, from WasteWater Scan, 0.99 on April 22, 2025; in San Bernardino County, from WasteWater Scan, 1.02 on April 21, 2025; in San Diego County, from WasteWater Scan, 1.01 on April 16, 2025; in San Luis Obispo County, from WasteWater Scan, 0.98 on April 21, 2025; in Santa Barbara County, from WasteWater Scan, 0.99 on April 18, 2025; in Santa Cruz County, from WasteWater Scan, 0.99 on April 20, 2025; in Stanislaus County, from WasteWater Scan, 0.94 on April 18, 2025; in Yolo County, from WasteWater Scan, 1.00 on April 21, 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

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, 5.6 as of April 15, 2025; in Marin County, from Wastewater Scan, 19.5 as of April 21, 2025; in Napa County, from Wastewater Scan, 4.8 as of April 21, 2025; in San Francisco County, from Wastewater Scan, 10.9 as of April 22, 2025; in San Mateo County, from Wastewater Scan, 9.4 as of April 22, 2025; in Santa Clara County, from Wastewater Scan, 6.4 as of April 22, 2025; in Solano County, from Wastewater Scan, 5.2 as of April 17, 2025; in Sonoma County, from Wastewater Scan, 3.4 as of April 20, 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, 5.6 as of April 15, 2025; in Marin County, from Wastewater Scan, 19.5 as of April 21, 2025; in Napa County, from Wastewater Scan, 4.8 as of April 21, 2025; in San Francisco County, from Wastewater Scan, 10.9 as of April 22, 2025; in San Mateo County, from Wastewater Scan, 9.4 as of April 22, 2025; in Santa Clara County, from Wastewater Scan, 6.4 as of April 22, 2025; in Solano County, from Wastewater Scan, 5.2 as of April 17, 2025; in Sonoma County, from Wastewater Scan, 3.4 as of April 20, 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, 3.7 as of April 20, 2025; in Merced County, from Wastewater Scan, 0.7 as of April 18, 2025; in Monterey County, from Wastewater Scan, 4.8 as of April 21, 2025; in Riverside County, from Wastewater Scan, 2.5 as of April 21, 2025; in Sacramento County, from Wastewater Scan, 7 as of April 22, 2025; in San Bernardino County, from Wastewater Scan, 1.9 as of April 21, 2025; in San Diego County, from Wastewater Scan, 7.2 as of April 16, 2025; in San Luis Obispo County, from Wastewater Scan, 3 as of April 21, 2025; in Santa Barbara County, from Wastewater Scan, 4.5 as of April 18, 2025; in Santa Cruz County, from Wastewater Scan, 10.3 as of April 20, 2025; in Stanislaus County, from Wastewater Scan, 2.7 as of April 18, 2025; in Yolo County, from Wastewater Scan, 7.8 as of April 21, 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, 3.7 as of April 20, 2025; in Merced County, from Wastewater Scan, 0.7 as of April 18, 2025; in Monterey County, from Wastewater Scan, 4.8 as of April 21, 2025; in Riverside County, from Wastewater Scan, 2.5 as of April 21, 2025; in Sacramento County, from Wastewater Scan, 7 as of April 22, 2025; in San Bernardino County, from Wastewater Scan, 1.9 as of April 21, 2025; in San Diego County, from Wastewater Scan, 7.2 as of April 16, 2025; in San Luis Obispo County, from Wastewater Scan, 3 as of April 21, 2025; in Santa Barbara County, from Wastewater Scan, 4.5 as of April 18, 2025; in Santa Cruz County, from Wastewater Scan, 10.3 as of April 20, 2025; in Stanislaus County, from Wastewater Scan, 2.7 as of April 18, 2025; in Yolo County, from Wastewater Scan, 7.8 as of April 21, 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.

Downloads

R estimates and smoothed case counts and wastewater readings.

Methods

Daily new cases by county are downloaded from the California Health and Human Services Open Data Portal. This data source is no longer updating.

Wastewater readings are downloaded from the data.ca.gov Open Data Portal and from WastewaterScan each day. Counts of the n and s gene targets are used, normalized to counts of the pepper mottle virus. Counts for which the PPMoV control is not present are excluded. Each count is used in all counties included in its wastewater collection region. The wastewater estimates published by BioBot Analytics are included as well, because they include some additional locations. Exceptionally high wastewater counts are indicated by ^ signs at the top of each plot.

We apply kernel density smoothing with a Gaussian kernel with bandwidth of 28 days to both wastewater and case counts, to de-emphasize day-to-day fluctuations and pick out longer-term changes.

The Wallinga-Teunis technique is used to estimate reproduction numbers, corrected for right censoring of the case detection data, and a small number of the earliest days are trimmed from the estimates to avoid artifacts due to left censoring. Periods when case numbers are less than 2 per day in a county are excluded from estimation from case numbers. The generation interval distribution used for estimation is that estimated here. The generation time estimate for the Delta variant is used for dates before Dec. 24, 2021, and for Omicron is used thereafter. Thus the estimates may have a small bias in the case of variants with other transmission intervals.

Contact

Lee Worden,

Original group:

Lee Worden, F.I. Proctor Foundation Alex Y. Ge, UCSF School of Medicine
Micaela Neus, Woodlamp Technology
Jennifer C. Kwan, Woodlamp Technology
Nathan Murthy, Tesla
Jianda Monique
Eugene T. Richardson, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, Department of Global Health and Social Medicine, Harvard University, Boston, MA
Rae Wannier, F.I. Proctor Foundation, UCSF Dept. of Epidemiology and Biostatistics
Travis Porco, F.I. Proctor Foundation, UCSF Dept. of Epidemiology and Biostatistics

This is not an official UCSF website. The opinions or statements expressed herein should not be taken as a position of or endorsement by the University of California, San Francisco.

Last updated : 2025-04-25 01:30:25 PDT