This is a daily updated website tracking information related to avian influenza, in California, based on public data from genetic sequencing of material in wastewater samples. Avian influenza, or “bird flu”, may be any of several subtypes of influenza A, including subtype H5N1. It can infect cows, pigs, and other mammals as well as birds, and can cause disease in humans, though to date it is not known to be transmissible from one human to another.

H5 Influenza in Wastewater

These plots summarize H5 influenza wastewater readings from the Cal-SuWers network, and H5 influenza wastewater readings from WastewaterScan. Individual readings are combined into a smoothed curve. These readings are likely mainly bovine influenza, together with maybe some avian cases (as of December 2024).

Data through June 20, 2025

This is a plot of individual and smoothed wastewater readings by county in the Bay Area. The latest smoothed readings are as follows: In Marin County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Napa County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In San Francisco County, from Wastewater Scan, 0 as of June 06, 2025, trend not identifiable. In San Mateo County, from Wastewater Scan, 0 as of June 06, 2025, trend not identifiable. In Santa Clara County, from Wastewater Scan, 0 as of June 06, 2025, trend not identifiable. In Solano County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Sonoma County, from Wastewater Scan, 0 as of June 01, 2025, trend not identifiable. All values are gene copies detected per hundred thousand copies of the pepper moth virus control. For the complete timeseries, see the CSV data linked below. For any questions, please feel free to contact the author.

This is a plot of individual and smoothed wastewater readings by county in the Bay Area. The latest smoothed readings are as follows: In Marin County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Napa County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In San Francisco County, from Wastewater Scan, 0 as of June 06, 2025, trend not identifiable. In San Mateo County, from Wastewater Scan, 0 as of June 06, 2025, trend not identifiable. In Santa Clara County, from Wastewater Scan, 0 as of June 06, 2025, trend not identifiable. In Solano County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Sonoma County, from Wastewater Scan, 0 as of June 01, 2025, trend not identifiable. All values are gene copies detected per hundred thousand copies of the pepper moth virus control. For the complete timeseries, see the CSV data linked below. For any questions, please feel free to contact the author.

This is a plot of individual and smoothed wastewater readings by county in California outside the Bay Area. The latest smoothed readings are as follows: In Los Angeles County, from Wastewater Scan, 0 as of June 02, 2025, trend not identifiable. In Merced County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Monterey County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Riverside County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Sacramento County, from Wastewater Scan, 0 as of June 06, 2025, trend not identifiable. In San Bernardino County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In San Diego County, from Wastewater Scan, 0 as of June 02, 2025, trend not identifiable. In San Luis Obispo County, from Wastewater Scan, 0 as of June 05, 2025, trend not identifiable. In Santa Barbara County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Santa Cruz County, from Wastewater Scan, 0 as of June 03, 2025, trend not identifiable. In Stanislaus County, from Wastewater Scan, 0 as of June 02, 2025, trend not identifiable. In Yolo County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. All values are gene copies detected per hundred thousand copies of the pepper moth virus control. For the complete timeseries, see the CSV data linked below. For any questions, please feel free to contact the author.

This is a plot of individual and smoothed wastewater readings by county in California outside the Bay Area. The latest smoothed readings are as follows: In Los Angeles County, from Wastewater Scan, 0 as of June 02, 2025, trend not identifiable. In Merced County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Monterey County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Riverside County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Sacramento County, from Wastewater Scan, 0 as of June 06, 2025, trend not identifiable. In San Bernardino County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In San Diego County, from Wastewater Scan, 0 as of June 02, 2025, trend not identifiable. In San Luis Obispo County, from Wastewater Scan, 0 as of June 05, 2025, trend not identifiable. In Santa Barbara County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. In Santa Cruz County, from Wastewater Scan, 0 as of June 03, 2025, trend not identifiable. In Stanislaus County, from Wastewater Scan, 0 as of June 02, 2025, trend not identifiable. In Yolo County, from Wastewater Scan, 0 as of June 04, 2025, trend not identifiable. All values are gene copies detected per hundred thousand copies of the pepper moth virus control. For the complete timeseries, see the CSV data linked below. For any questions, please feel free to contact the author.

H5 Detection

[Note: the new administration may be halting CDC data releases. We are monitoring the situation.]

CDC is providing a weekly dataset of which wastewater sites have detectable H5-type influenza A, a classification that includes H5N1. Here we display the current and past fraction of sites detecting H5, by county.

Data through June 14, 2025

This is a plot of the fraction of sites detecting H5 type influenza in wastewater in the Bay Area. The latest fractions are as follows: In Alameda, 0 percent based on 2 sites, the same as the previous week. In Contra Costa, 0 percent based on 2 sites, the same as the previous week. In Marin, 0 percent based on 4 sites, the same as the previous week. In Napa, 0 percent based on 1 site, the same as the previous week. In San Francisco, 0 percent based on 2 sites, the same as the previous week. In San Mateo, 0 percent based on 5 sites, the same as the previous week. In Santa Clara, 0 percent based on 4 sites, the same as the previous week. In Solano, 0 percent based on 2 sites, the same as the previous week. In Sonoma, 0 percent based on 2 sites, the same as the previous week. For the complete timeseries, see the CSV data linked below. For any questions, please feel free to contact the author.

This is a plot of the fraction of sites detecting H5 type influenza in wastewater in the Bay Area. The latest fractions are as follows: In Alameda, 0 percent based on 2 sites, the same as the previous week. In Contra Costa, 0 percent based on 2 sites, the same as the previous week. In Marin, 0 percent based on 4 sites, the same as the previous week. In Napa, 0 percent based on 1 site, the same as the previous week. In San Francisco, 0 percent based on 2 sites, the same as the previous week. In San Mateo, 0 percent based on 5 sites, the same as the previous week. In Santa Clara, 0 percent based on 4 sites, the same as the previous week. In Solano, 0 percent based on 2 sites, the same as the previous week. In Sonoma, 0 percent based on 2 sites, the same as the previous week. For the complete timeseries, see the CSV data linked below. For any questions, please feel free to contact the author.

This is a plot of the fraction of sites detecting H5 type influenza in wastewater in California outside the Bay Area. The latest fractions are as follows: In Butte, 0 percent based on 2 sites, the same as the previous week. In Del Norte, 0 percent based on 1 site, the same as the previous week. In El Dorado, 0 percent based on 1 site, the same as the previous week. In Kings, 0 percent based on 1 site, the same as the previous week. In Lake, 0 percent based on 1 site, the same as the previous week. In Los Angeles, 0 percent based on 4 sites, the same as the previous week. In Madera, 0 percent based on 1 site, the same as the previous week. In Merced, 0 percent based on 1 site, the same as the previous week. In Mono, 0 percent based on 1 site, the same as the previous week. In Monterey, 0 percent based on 3 sites, the same as the previous week. In Nevada, 0 percent based on 1 site, the same as the previous week. In Placer, 0 percent based on 1 site, the same as the previous week. In Plumas, 0 percent based on 1 site, the same as the previous week. In Riverside, 0 percent based on 2 sites, the same as the previous week. In Sacramento, 0 percent based on 1 site, the same as the previous week. In San Benito, 0 percent based on 1 site, the same as the previous week. In San Bernardino, 0 percent based on 1 site, the same as the previous week. In San Diego, 0 percent based on 1 site, the same as the previous week. In San Joaquin, 0 percent based on 3 sites, the same as the previous week. In San Luis Obispo, 0 percent based on 5 sites, the same as the previous week. In Santa Barbara, 0 percent based on 2 sites, the same as the previous week. In Santa Cruz, 0 percent based on 4 sites, the same as the previous week. In Shasta, 0 percent based on 2 sites, the same as the previous week. In Stanislaus, 0 percent based on 2 sites, the same as the previous week. In Sutter, 0 percent based on 1 site, the same as the previous week. In Ventura, 0 percent based on 3 sites, the same as the previous week. In Yolo, 0 percent based on 2 sites, the same as the previous week. For the complete timeseries, see the CSV data linked below. For any questions, please feel free to contact the author.

This is a plot of the fraction of sites detecting H5 type influenza in wastewater in California outside the Bay Area. The latest fractions are as follows: In Butte, 0 percent based on 2 sites, the same as the previous week. In Del Norte, 0 percent based on 1 site, the same as the previous week. In El Dorado, 0 percent based on 1 site, the same as the previous week. In Kings, 0 percent based on 1 site, the same as the previous week. In Lake, 0 percent based on 1 site, the same as the previous week. In Los Angeles, 0 percent based on 4 sites, the same as the previous week. In Madera, 0 percent based on 1 site, the same as the previous week. In Merced, 0 percent based on 1 site, the same as the previous week. In Mono, 0 percent based on 1 site, the same as the previous week. In Monterey, 0 percent based on 3 sites, the same as the previous week. In Nevada, 0 percent based on 1 site, the same as the previous week. In Placer, 0 percent based on 1 site, the same as the previous week. In Plumas, 0 percent based on 1 site, the same as the previous week. In Riverside, 0 percent based on 2 sites, the same as the previous week. In Sacramento, 0 percent based on 1 site, the same as the previous week. In San Benito, 0 percent based on 1 site, the same as the previous week. In San Bernardino, 0 percent based on 1 site, the same as the previous week. In San Diego, 0 percent based on 1 site, the same as the previous week. In San Joaquin, 0 percent based on 3 sites, the same as the previous week. In San Luis Obispo, 0 percent based on 5 sites, the same as the previous week. In Santa Barbara, 0 percent based on 2 sites, the same as the previous week. In Santa Cruz, 0 percent based on 4 sites, the same as the previous week. In Shasta, 0 percent based on 2 sites, the same as the previous week. In Stanislaus, 0 percent based on 2 sites, the same as the previous week. In Sutter, 0 percent based on 1 site, the same as the previous week. In Ventura, 0 percent based on 3 sites, the same as the previous week. In Yolo, 0 percent based on 2 sites, the same as the previous week. For the complete timeseries, see the CSV data linked below. For any questions, please feel free to contact the author.

Downloads

Smoothed and scaled wastewater readings.

Archived H5 detection data.

Methods

Wastewater readings are downloaded from the CalHHS Open Data Portal and from WastewaterScan each day. From each wastewater sample, the number of copies of an influenza gene detected in the sample is reported. Copies of a gene of the Pepper Moth Mottle Virus (PPMoV) are also counted, which is a widespread and relatively benign virus used as an indicator of the amount of human waste in the sample. The ratio of flu virus counts to PPMoV counts is used as a measure of disease prevalence. Counts for which the PPMoV control is not present are excluded. Each count is used in all counties included in its wastewater collection region. Exceptionally high wastewater counts are indicated by ^ signs at the top of each plot.

Since the individual wastewater readings can be widely variable, we construct a smoothed curve through them to de-emphasize short-term variation and make longer-term trends visible. This smoothing is implemented using kernel density smoothing with a Gaussian kernel with bandwidth of 28 days.

The most recent week’s H5 presence/absence data is updated weekly. We[1] download the data from the CDC website daily and combine current data with past data that we have archived.

Credits

Lee Worden,

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 : 2025-06-23 01:16:33 PDT

[1] The royal we