SCAN Update - 10/2/24

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.

‌All samples picked up by the couriers as of 9/30/24 have been processed and their data are on the site: data.wastewaterscan.org. Please email Amanda at albidwel@stanford.edu if you identify any bugs on the site. ‌

For site level summaries of the SCAN plants with current Wastewater Categories and concentration plots, see the following links:

• Gilroy
• Oceanside SF
• Palo Alto
• Sacramento
• San Jose
• Southeast SF
• Sunnyvale
• SVCW

SARS-CoV-2 N gene concentrations are between 6,163 - 541,100 copies/g over the last 3 weeks. 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, Sacramento, San Jose, SVCW, and Sunnyvale are in the LOW Wastewater Category for SARS-CoV-2
• Palo Alto, Oceanside SF, and Southeast SF are in the MEDIUM 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 come down from the peak observed in July/August 2024.

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. In the most recent samples, we are continuing to see greater portions of KP.2 (slate blue), and KP.3 (light blue). Note that the sequencing data are always from samples taken between 1-2 weeks ago (in this case, Sept 21, 2024).

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

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

3 sites in the SCAN network (Oceanside SF, Southeast SF, and San Jose) have tested positive for the H3 marker in influenza A since we began testing for the marker prospectively in mid July 2024.

2 sites in the SCAN network (Palo Alto and Southeast SF) have tested positive for the H5 marker in influenza A since we began testing for the marker prospectively in May 2024.

Influenza B (IBV) RNA has rarely been detected in samples collected from SCAN sites in the last 3 weeks. In the chart below (representing data from the past 1 year), the population weighted average across the SCAN plants is shown in black. You can access the graph here.

Below are the current IBV 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 due to no longer being in seasonal onset for IBV

RSV RNA has sporadically been detected in samples collected from SCAN sites in the last 3 weeks. 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 late last year. 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, San Jose, Southeast SF, Sunnyvale, and SVCW are in the LOW Wastewater Category due to not being in seasonal onset for RSV

‌HMPV (Human metapneumovirus) RNA has rarely been detected in samples collected from SCAN sites in the last 3 weeks. Below are the current 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, Sunnyvale, and SVCW are in the LOW Wastewater Category due to no longer being in seasonal onset for HMPV

In the chart below, the population weighted average line across all the SCAN plants is shown in black (link here to this chart if you want to interact with it) since we started monitoring HMPV at SCAN sites. Evident in the chart are the very low HMPV concentrations across all SCAN sites.

EV-D68 RNA was detected at all SCAN sites from samples collected in the last 3 weeks. Below are the current wastewater categories for the SCAN sites (the category is determined by the frequency of detection):

• Gilroy, Oceanside SF, Palo Alto, Sacramento, San Jose, Southeast SF, SVCW and Sunnyvale are in the MEDIUM 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 are increasing EV-D68 concentrations since early August 2024. This mirrors what were are seeing across the national WWSCAN sites.

Parainfluenza RNA- As a reminder we paused Parainfluenza RNA measurements while we run the H5 specific influenza assay. Below is the population weighted average across SCAN sites is shown in black with data through May 19, 2024. You can access the chart here.‌

Norovirus GII RNA was commonly detected at all SCAN sites, 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. Norovirus concentrations remain elevated across all SCAN sites and are still higher than they were this time last year.

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

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

The plot below shows the Norovirus concentrations at the SCAN sites since we began monitoring in late 2022. The population weighted average line is shown in black. You can interact with the chart of all the plants at this link.

‌Rotavirus RNA concentrations are shown in the chart below (all the SCAN plants are shown together) since mid Oct 2023. The population weighted average line is shown in black. You can interact with the chart of all the plants here.‌

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

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

Mpox clade II DNA was not been detected at most SCAN sites in the last 3 weeks (expect 1 positive detection at Southeast SF on 9/25/24). 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 July 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 three of the SCAN sites in the last 3 weeks (Gilroy, Oceanside SF, and San Jose).

• Gilroy, Oceanside SF, Palo Alto, Sacramento, San Jose, Southeast SF, SVCW and Sunnyvale are in the LOW 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 at five of the SCAN sites in the last 3 weeks (Oceanside SF, Palo Alto, Sacramento, San Jose, and Sunnyvale). Below are the current wastewater categories for the SCAN sites (the category is determined by the frequency of detection):

• Gilroy, Oceanside SF, Palo Alto, San Jose Sacramento, Southeast SF, SVCW, and Sunnyvale are in the LOW 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.‌

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