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 January 30, 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 Alameda County, from Wastewater Scan, 0.004 as of January 28, 2025, decreasing by about 21 percent per day, from the state, 0.2 as of January 29, 2025, decreasing by about 22 percent per day. In Contra Costa County, from the state, 0.4 as of January 29, 2025, decreasing by about 6 percent per day. In Marin County, from Wastewater Scan, 0.1 as of January 29, 2025, decreasing by about 15 percent per day, from the state, 0.4 as of January 29, 2025, decreasing by about 16 percent per day. In Napa County, from Wastewater Scan, 0.2 as of January 29, 2025, decreasing by about 4 percent per day. In San Francisco County, from Wastewater Scan, 0.2 as of January 30, 2025, decreasing by about 6 percent per day. In San Mateo County, from Wastewater Scan, 0.2 as of January 30, 2025, decreasing by about 6 percent per day, from the state, 0.6 as of January 29, 2025, decreasing by about 8 percent per day. In Santa Clara County, from Wastewater Scan, 0.1 as of January 30, 2025, decreasing by about 6 percent per day. In Solano County, from Wastewater Scan, 0.002 as of January 29, 2025, decreasing by about 21 percent per day, from the state, 0.8 as of January 27, 2025, decreasing by about 4 percent per day. In Sonoma County, from Wastewater Scan, 0.02 as of January 29, 2025, decreasing by about 19 percent per day, from the state, 0.4 as of January 26, 2025, decreasing by about 5 percent per day. 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 Alameda County, from Wastewater Scan, 0.004 as of January 28, 2025, decreasing by about 21 percent per day, from the state, 0.2 as of January 29, 2025, decreasing by about 22 percent per day. In Contra Costa County, from the state, 0.4 as of January 29, 2025, decreasing by about 6 percent per day. In Marin County, from Wastewater Scan, 0.1 as of January 29, 2025, decreasing by about 15 percent per day, from the state, 0.4 as of January 29, 2025, decreasing by about 16 percent per day. In Napa County, from Wastewater Scan, 0.2 as of January 29, 2025, decreasing by about 4 percent per day. In San Francisco County, from Wastewater Scan, 0.2 as of January 30, 2025, decreasing by about 6 percent per day. In San Mateo County, from Wastewater Scan, 0.2 as of January 30, 2025, decreasing by about 6 percent per day, from the state, 0.6 as of January 29, 2025, decreasing by about 8 percent per day. In Santa Clara County, from Wastewater Scan, 0.1 as of January 30, 2025, decreasing by about 6 percent per day. In Solano County, from Wastewater Scan, 0.002 as of January 29, 2025, decreasing by about 21 percent per day, from the state, 0.8 as of January 27, 2025, decreasing by about 4 percent per day. In Sonoma County, from Wastewater Scan, 0.02 as of January 29, 2025, decreasing by about 19 percent per day, from the state, 0.4 as of January 26, 2025, decreasing by about 5 percent per day. 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 El Dorado County, from the state, 0.7 as of January 27, 2025, decreasing by about 8 percent per day. In Los Angeles County, from Wastewater Scan, 0.02 as of January 28, 2025, decreasing by about 11 percent per day, from the state, 0.3 as of January 29, 2025, roughly unchanging. In Merced County, from Wastewater Scan, 0.1 as of January 29, 2025, decreasing by about 5 percent per day. In Mono County, from the state, 0.6 as of January 28, 2025, decreasing by about 2 percent per day. In Monterey County, from Wastewater Scan, 0.03 as of January 29, 2025, decreasing by about 15 percent per day, from the state, 1.5 as of January 29, 2025, decreasing by about 1 percent per day. In Nevada County, from the state, 6.7 as of January 29, 2025, decreasing by about 2 percent per day. In Riverside County, from Wastewater Scan, 0 as of January 29, 2025, decreasing by about 83 percent per day, from the state, 0.02 as of January 29, 2025, decreasing by about 10 percent per day. In Sacramento County, from Wastewater Scan, 0.4 as of January 30, 2025, decreasing by about 4 percent per day. In San Benito County, from the state, 0.2 as of January 27, 2025, decreasing by about 12 percent per day. In San Bernardino County, from Wastewater Scan, 0.01 as of January 29, 2025, decreasing by about 11 percent per day. In San Diego County, from Wastewater Scan, 0 as of January 26, 2025, trend not identifiable. In San Joaquin County, from the state, 0.6 as of January 29, 2025, decreasing by about 6 percent per day. In San Luis Obispo County, from Wastewater Scan, 0.1 as of January 30, 2025, decreasing by about 11 percent per day, from the state, 0.6 as of January 29, 2025, decreasing by about 7 percent per day. In Santa Barbara County, from Wastewater Scan, 0.02 as of January 29, 2025, decreasing by about 15 percent per day. In Santa Cruz County, from Wastewater Scan, 0.03 as of January 28, 2025, decreasing by about 17 percent per day, from the state, 0.6 as of January 28, 2025, decreasing by about 9 percent per day. In Stanislaus County, from Wastewater Scan, 2.8 as of January 29, 2025, decreasing by about 8 percent per day, from the state, 2.1 as of January 28, 2025, decreasing by about 11 percent per day. In Ventura County, from the state, 0.2 as of January 29, 2025, decreasing by about 3 percent per day. In Yolo County, from Wastewater Scan, 0.005 as of January 29, 2025, decreasing by about 16 percent per day. 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 El Dorado County, from the state, 0.7 as of January 27, 2025, decreasing by about 8 percent per day. In Los Angeles County, from Wastewater Scan, 0.02 as of January 28, 2025, decreasing by about 11 percent per day, from the state, 0.3 as of January 29, 2025, roughly unchanging. In Merced County, from Wastewater Scan, 0.1 as of January 29, 2025, decreasing by about 5 percent per day. In Mono County, from the state, 0.6 as of January 28, 2025, decreasing by about 2 percent per day. In Monterey County, from Wastewater Scan, 0.03 as of January 29, 2025, decreasing by about 15 percent per day, from the state, 1.5 as of January 29, 2025, decreasing by about 1 percent per day. In Nevada County, from the state, 6.7 as of January 29, 2025, decreasing by about 2 percent per day. In Riverside County, from Wastewater Scan, 0 as of January 29, 2025, decreasing by about 83 percent per day, from the state, 0.02 as of January 29, 2025, decreasing by about 10 percent per day. In Sacramento County, from Wastewater Scan, 0.4 as of January 30, 2025, decreasing by about 4 percent per day. In San Benito County, from the state, 0.2 as of January 27, 2025, decreasing by about 12 percent per day. In San Bernardino County, from Wastewater Scan, 0.01 as of January 29, 2025, decreasing by about 11 percent per day. In San Diego County, from Wastewater Scan, 0 as of January 26, 2025, trend not identifiable. In San Joaquin County, from the state, 0.6 as of January 29, 2025, decreasing by about 6 percent per day. In San Luis Obispo County, from Wastewater Scan, 0.1 as of January 30, 2025, decreasing by about 11 percent per day, from the state, 0.6 as of January 29, 2025, decreasing by about 7 percent per day. In Santa Barbara County, from Wastewater Scan, 0.02 as of January 29, 2025, decreasing by about 15 percent per day. In Santa Cruz County, from Wastewater Scan, 0.03 as of January 28, 2025, decreasing by about 17 percent per day, from the state, 0.6 as of January 28, 2025, decreasing by about 9 percent per day. In Stanislaus County, from Wastewater Scan, 2.8 as of January 29, 2025, decreasing by about 8 percent per day, from the state, 2.1 as of January 28, 2025, decreasing by about 11 percent per day. In Ventura County, from the state, 0.2 as of January 29, 2025, decreasing by about 3 percent per day. In Yolo County, from Wastewater Scan, 0.005 as of January 29, 2025, decreasing by about 16 percent per day. 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 January 25, 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 based on 2 sites, the same as the previous week. In Contra Costa, 0.5 based on 2 sites, down from 1 the previous week. In Marin, 0 based on 4 sites, the same as the previous week. In Napa, 1 based on 1 site, the same as the previous week. In San Francisco, 1 based on 2 sites, the same as the previous week. In San Mateo, 0.8 based on 5 sites, the same as the previous week. In Santa Clara, 0.75 based on 4 sites, down from 1 the previous week. In Solano, 0.5 based on 2 sites, the same as the previous week. In Sonoma, 1 based on 1 site, up from 0 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 based on 2 sites, the same as the previous week. In Contra Costa, 0.5 based on 2 sites, down from 1 the previous week. In Marin, 0 based on 4 sites, the same as the previous week. In Napa, 1 based on 1 site, the same as the previous week. In San Francisco, 1 based on 2 sites, the same as the previous week. In San Mateo, 0.8 based on 5 sites, the same as the previous week. In Santa Clara, 0.75 based on 4 sites, down from 1 the previous week. In Solano, 0.5 based on 2 sites, the same as the previous week. In Sonoma, 1 based on 1 site, up from 0 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 El Dorado, 1 based on 1 site, up from 0 the previous week. In Los Angeles, 0.5 based on 4 sites, the same as the previous week. In Merced, 1 based on 1 site, the same as the previous week. In Mono, 1 based on 1 site, the same as the previous week. In Monterey, 0.67 based on 3 sites, the same as the previous week. In Nevada, 1 based on 1 site, up from 0 the previous week. In Placer, 0 based on 1 site, down from 1 the previous week. In Riverside, 1 based on 2 sites, up from 0 the previous week. In Sacramento, 1 based on 1 site, the same as the previous week. In San Benito, 0 based on 1 site, the same as the previous week. In San Bernardino, 0 based on 1 site, down from 1 the previous week. In San Diego, 0 based on 1 site, the same as the previous week. In San Joaquin, 0.5 based on 2 sites, down from 1 the previous week. In San Luis Obispo, 0.4 based on 5 sites, down from 0.8 the previous week. In Santa Barbara, 0 based on 2 sites, down from 0.5 the previous week. In Santa Cruz, 0.4 based on 5 sites, the same as the previous week. In Shasta, 1 based on 1 site, up from 0 the previous week. In Stanislaus, 1 based on 2 sites, the same as the previous week. In Ventura, 0.33 based on 3 sites, down from 0.67 the previous week. In Yolo, 0 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 El Dorado, 1 based on 1 site, up from 0 the previous week. In Los Angeles, 0.5 based on 4 sites, the same as the previous week. In Merced, 1 based on 1 site, the same as the previous week. In Mono, 1 based on 1 site, the same as the previous week. In Monterey, 0.67 based on 3 sites, the same as the previous week. In Nevada, 1 based on 1 site, up from 0 the previous week. In Placer, 0 based on 1 site, down from 1 the previous week. In Riverside, 1 based on 2 sites, up from 0 the previous week. In Sacramento, 1 based on 1 site, the same as the previous week. In San Benito, 0 based on 1 site, the same as the previous week. In San Bernardino, 0 based on 1 site, down from 1 the previous week. In San Diego, 0 based on 1 site, the same as the previous week. In San Joaquin, 0.5 based on 2 sites, down from 1 the previous week. In San Luis Obispo, 0.4 based on 5 sites, down from 0.8 the previous week. In Santa Barbara, 0 based on 2 sites, down from 0.5 the previous week. In Santa Cruz, 0.4 based on 5 sites, the same as the previous week. In Shasta, 1 based on 1 site, up from 0 the previous week. In Stanislaus, 1 based on 2 sites, the same as the previous week. In Ventura, 0.33 based on 3 sites, down from 0.67 the previous week. In Yolo, 0 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 : 2025-02-02 01:24:02 PST

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