SCAN Weekly Update - 6/19/24

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.

In mid-May we began testing SCAN samples for the H5 marker in influenza A prospectively; all samples to date measured prospectively have been negative for the H5 marker. A peer reviewed paper describing our work on the marker and its application to biobanked samples from TX, NC, and Hawai'i can be found here.

‌All samples picked up by the couriers as of 6/17/24 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

We are excited to share a document that provides an overview of the program’s peer-reviewed scientific literature, organized by topics and themes. Click here to access the WastewaterSCAN published body of work.

SARS-CoV-2 N gene concentrations are between 21,520 to 1,111,000 copies/g over the last 21 days. 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, Sunnyvale and SVCW are in the MEDIUM Wastewater Category for SARS-CoV-2
• Oceanside SF, Palo Alto, and Southeast SF are in the HIGH 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 shows a recent increase compared to the lower concentrations we measured in early spring 2024. This mirrors what we have seen across other Bay Area sites in the WastewaterSCAN project (see more info here).

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 starting to see greater portions of KP.1 (light green), 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, June 8, 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. Most SCAN sites are still in onset for IAV (Palo Alto, Oceanside SF, Sacramento, San Jose, Southeast SF, Sunnyvale) and are continuing to come down from the peak seen at the end of 2023/beginning of 2024.

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

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

No sites in the SCAN network have tested positive for the H5 marker in influenza A since we began testing for the marker prospectively about a month ago. There has been one positive detection in the Greater Bay Area at West Contra Costa County, CA on 6/10/24 but all subsequent samples have been non-detect.

Influenza B (IBV) RNA has been detected in most samples collected from SCAN sites in the last 21 days. 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, Southeast SF, SVCW and Sunnyvale are in the LOW Wastewater Category due to no longer being in seasonal onset for IBV
• Sacramento and San Jose are in the MEDIUM Wastewater Category for IBV

RSV RNA concentrations have decreased to low levels. 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 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 no longer being in in seasonal onset for RSV

‌HMPV (Human metapneumovirus) RNA concentrations remain elevated across all SCAN sites (expect at Gilroy and SVCW). Below are the current wastewater categories for the SCAN sites (recall the category is determined by both the trend and the level):

• Gilroy and SVCW are in the LOW Wastewater Category due to no longer being in seasonal onset for HMPV
• Palo Alto, Sacramento, San Jose, and Sunnyvale are in the MEDIUM Wastewater Category for HMPV
• Oceanside SF, and Southeast SF are 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 to this chart if you want to interact with it) since December 2022. Evident in the chart is the recent decrease in HMPV concentrations across all SCAN sites, but most sites are still experiencing elevated concentrations of HMPV.

EV-D68 RNA was detected at all SCAN sites from samples collected in the last 10 days (expect Gilroy). Below are the current wastewater categories for the SCAN sites (the category is determined by the frequency of detection):

• Gilroy, Palo Alto, Oceanside SF, and SVCW are in the LOW Wastewater Category for EV-D68
• Sacramento, San Jose, Southeast SF, and Sunnyvale are in the MEDIUM Wastewater Category for EV-D68

The heat map below shows all the SCAN sites as a row, and each date as a column since monitoring began in July 2023. The color blue means the sample was non-detect for EV-D68 RNA and the colors get darker with higher concentrations. White indicates no sample was collected. You can access the chart here.‌

Parainfluenza RNA- As a reminder we are temporarily pausing 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. We've seen an uptick in Norovirus concentrations across all SCAN sites since early spring and concentrations are on average 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):

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

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

Mpox DNA was not detected at any SCAN sites recently. Currently all SCAN sites are in the 'LOW' category for Mpox.

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 MPXV DNA was not detected in the sample, and the dark purple 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 rarely detected in the last 10 days at most SCAN sites (1 positive detection from Sacramento on 6/14/24). Currently all SCAN sites are in the 'LOW' 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. The color blue means that Candida auris DNA 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.‌

Hepatitis A RNA has been frequently detected at all SCAN sites in the last 10 days except for Southeast SF and SVCW. Below are the current wastewater categories for the SCAN sites (the category is determined by the frequency of detection):

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

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