SCAN Update - 5/7/25

By WWSCAN Staff • 7 May 2025

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This blog post describes data collected at 8 wastewater treatment plants in the Greater Bay Area of San Francisco, CA, including Sacramento, that are partners in the SCAN project which began in late 2020. The SCAN plants are a subset of the WastewaterSCAN plants.

Map of 8 SCAN sites located in the Greater San Francisco Bay Area, CA

‌All samples picked up by the couriers as of 5/5/25 have been processed and their data are on the site: data.wastewaterscan.org. For site level summaries of the SCAN plants with current Wastewater Categories and concentration plots, see the following links:

COVID-19

SARS-CoV-2 concentration in wastewater and sequencing for variants

SARS-CoV-2 N gene concentrations were between ND - 256,537 copies per gram over the last 3 weeks. The median SARS-CoV-2 N gene RNA concentration across all 8 SCAN sites in past 3 weeks was 38,523 copies/gram. Below are the current SARS-CoV-2 wastewater categories for the SCAN sites (recall the category is determined by both the trend and the level):

Gilroy, Oceanside SF, Palo Alto, Sacramento, San Jose, Southeast SF, SVCW and Sunnyvale are in the LOW Wastewater Category for SARS-CoV-2

Below are all the data from all the SCAN plants for the last two years. You can access the graph here. The population weighted average across the SCAN plants is shown in black. The population weighted average has remained at a low level since early 2025.

Below are plots from Oceanside SF, Sacramento, San Jose, and Southeast SF showing the relative proportions of different variants inferred from sequencing the entire genome of SARS-CoV-2. White and grey striped bars indicate no data is currently available for that week.

Note that the sequencing data are always from samples taken between 1-2 weeks ago (in this case, April 26, 2025). In the most recent samples, LP.8.1 (in brown) made up the largest proportion of lineages detected at Sacramento (56.4%) and KP.1 (in lime green) made up the largest proportion of lineages detected at San Jose (55.6%). Since the week of April 19, 2025, Oceanside SF and Southeast SF have had coverage below the default freyja threshold of 60% to run analysis.

SARS-CoV-2 sequencing data as of April 26, 2025

Other Respiratory Targets

Influenza A & B, RSV, HMPV, and EV-D68

Influenza A (IAV) RNA was detected in ~82% of samples in the past 3 weeks. The median IAV RNA concentration across all 8 SCAN sites in the last 3 weeks was 3,112 copies per gram. Below are all the IAV data from all the SCAN plants for the last two years (you can access the graph here). The population weighted average across the SCAN plants is shown in black.

Below are the current Influenza A wastewater categories for the SCAN sites (recall the category is determined by both the trend and the level):

Gilroy, Sacramento, and SVCW are in the LOW Wastewater Category for Influenza A due to no longer being in seasonal onset
Palo Alto, Oceanside SF, San Jose, Southeast SF, and Sunnyvale are in the MEDIUM Wastewater Category for Influenza A

~64% of samples in the past 3 weeks have tested positive for the H1 marker in Influenza A. The chart below shows H1 marker data from all the SCAN plants since we resumed the H1 assay at the end of 2024. The population weighted average across the SCAN plants is shown in black. Evident in the plot below are decreasing concentrations of the H1 marker across all 8 SCAN sites.

~9% of samples in the past 3 weeks have tested positive for the H3 marker in influenza A. As a reminder, we noted that we looked closely at some of the new sequences submitted to GISAID and NCBI and noticed that there was a primer that needed to be changed to ensure we are picking up all of the H3 that is currently circulating. We implemented the new assay with the updated primer on Friday March 14, 2025 so all data flowing to the website since then reflects this change.

Only 2 samples in the past 3 weeks have tested positive for the H5 marker in influenza A.

Evident in the chart below H5 marker concentrations have come down significantly from the elevated levels we saw during the Nov 2024 - Jan 2025 peak.

Influenza B (IBV) RNA was detected in ~94% of samples in the past 3 weeks. The median IBV RNA concentration across all 8 SCAN sites in past 3 weeks was 6,891 copies/gram. In the chart below (representing data from the past 2 years), the population weighted average across the SCAN plants is shown in black. You can access the graph here. The recent decrease in IBV concentrations across the SCAN sites mirrors what we are seeing at the national level.

Below are the current IBV wastewater categories for the SCAN sites (recall the category is determined by both the trend and the level):

Gilroy is in the LOW Wastewater Category due to not being in seasonal onset for IBV
Oceanside SF, Palo Alto, Sacramento, San Jose, Southeast SF, SVCW, and Sunnyvale are in seasonal onset and in the HIGH Wastewater Category for IBV

RSV RNA was detected in ~67% of samples in the past 3 weeks. The median RSV RNA concentration across all 8 SCAN sites in the last 3 weeks was 1,880 copies per gram. Currently all 8 SCAN sites are in seasonal onset for RSV in wastewater.

In the chart below (representing data from the past 2 years), the population weighted average line across all the SCAN sites is shown in black, and you can see the current concentrations relative to the peak RSV levels from the 2023/2024 respiratory season. The link to the chart below is here if you would like to interact with it.

Below are the current RSV wastewater categories for the SCAN sites (recall the category is determined by both the trend and the level):

Gilroy, Oceanside SF, Palo Alto, Sacramento, SVCW and Sunnyvale are no longer in seasonal onset and the LOW Wastewater Category for RSV
San Jose and Southeast SF are in seasonal onset and in the MEDIUM Wastewater Category for RSV

‌HMPV (Human metapneumovirus) RNA was detected in ~92% of samples in past 3 weeks. The median HMPV RNA concentration across all 8 SCAN sites in the last 3 weeks was 13,203 copies per gram. Across the SCAN sites we have seen an increase in HMPV concentrations since the end of 2024 which mirrors which what we are seeing at the national level.

Below are the current wastewater categories for the SCAN sites (recall the category is determined by both the trend and the level):

Gilroy is in the LOW Wastewater Category due to not being in seasonal onset for HMPV
Oceanside SF, Palo Alto, Sacramento, San Jose, Southeast SF, SVCW, and Sunnyvale are in seasonal onset and in the HIGH Wastewater Category for HMPV

In the chart below, the population weighted average line across all the SCAN plants is shown in black (link here) since we started monitoring HMPV at SCAN sites.

EV-D68 RNA was detected in ~83% of samples collected at all 8 SCAN sites in the last 3 weeks. The median EV-D68 RNA concentration across all 8 SCAN sites in the last 3 weeks was 3,604copies per gram. Across the national WWSCAN network only a handful of sites are still in seasonal onset for EV-D68 with all of these sites being in the Bay Area and Central Valley in California.

Below are the current wastewater categories for the SCAN sites (the category is determined by the frequency of detection):

Gilroy, Oceanside SF, Southeast SF, and SVCW are no longer in seasonal onset and in the LOW Wastewater Category for EV-D68
Palo Alto and Sunnyvale are in seasonal onset and in the MEDIUM Wastewater Category for EV-D68
Sacramento and San Jose are in seasonal onset and in the HIGH Wastewater Category for EV-D68

In the chart below, the population weighted average line across all the SCAN plants is shown in black over the last 12 months. Evident in the chart were increasing EV-D68 concentrations in early August 2024, concentrations plateauing in early November 2024 to mid December 2024 before increasing again late December 2024 to mid January 2025. EV-D68 concentrations at SCAN sites have plateaued in recent months.

Gastrointestinal Targets

Norovirus GII

Norovirus GII RNA was detected in 100% of samples from SCAN sites over the last 3 weeks, which is what we are observing across the national WWSCAN sites as well. In the chart below, the population weighted average line across all the SCAN plants is shown in black (since monitoring began in late 2022). Norovirus concentrations remain elevated across all 8 SCAN sites and are similar to where they were this time last year but are decreasing.

Below are the current Norovirus wastewater categories for the SCAN sites (recall the category is determined by both the trend and the level):

Gilroy, Palo Alto, San Jose, Sacramento, and Sunnyvale are in the LOW Wastewater Category for Norovirus
Oceanside SF, Southeast SF and SVCW are in the MEDIUM Wastewater Category for Norovirus

Other Pathogens of Concern

Mpox clade Ib, Mpox clade II, Candida auris, and Hepatitis A

Mpox clade Ib DNA was not detected in any samples from the last 3 weeks. Currently all SCAN sites are in the LOW category for Mpox clade Ib.

The heat map below shows all the SCAN sites as a row, and each date as a column since late November 2024. The color blue means that Mpox clade Ib DNA was not detected in the sample, and the dark red color means it was detected. White indicates no sample was collected. The chart shows all the data we have collected. You can access the chart here.

Mpox clade II DNA was not detected in any samples from the last 3 weeks. Currently all SCAN sites are in the LOW category for Mpox clade II.

The heat map below shows all the SCAN sites as a row, and each date as a column since June 2022. The color blue means that Mpox clade II DNA was not detected in the sample, and the dark red color means it was detected. White indicates no sample was collected. The chart shows all the data we have collected. You can access the chart here.

Candida auris DNA was detected at 5 SCAN sites in the last 3 weeks (Gilroy, Oceanside SF, San Jose, Southeast SF, and Sunnyvale).

Gilroy, Palo Alto, Sacramento, San Jose, Southeast SF, SVCW, and Sunnyvale are in the LOW Wastewater Category for C. auris
Oceanside SF is in the MEDIUM Wastewater Category for C. auris

The heat map below shows all the SCAN sites as a row, and each date as a column for all data collected since monitoring began in July 2023. The color blue means that Candida auris DNA was not detected in the sample, and the dark red color means it was detected. White indicates no sample was collected. You can access the chart here.

Hepatitis A RNA was detected in ~21% of samples collected at SCAN sites in the last 3 weeks.

Gilroy, Oceanside SF, Palo Alto, Sacramento, SVCW, and Sunnyvale are in the LOW Wastewater Category for Hepatitis A
San Jose and Southeast SF is in the MEDIUM Wastewater Category for Hepatitis A

The heat map below shows all the SCAN sites as a row, and each date as a column for all data collected since monitoring began in July 2023. The color blue means that Hepatitis A RNA was not detected in the sample, and the dark purple color means it was detected. White indicates no sample was collected. You can access the chart here.‌

Join us at the next WWSCAN Partner call at 9am PST this Friday May 9, 2025

Please email Amanda Bidwell (albidwel@stanford.edu) if you do not have the calendar invite for the WWSCAN partner call.