SCAN Weekly Update - 4/24/24

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 4/22/24 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 7,990 to 519,200 copies/g over the last 10 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, Palo Alto, Sacramento, San Jose, Southeast SF, Sunnyvale, and SVCW are in the LOW Wastewater Category for SARS-CoV-2
• Oceanside SF is 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 decreased from the last peak we saw at the end of 2023/beginning of 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, JN.1 (dark purple) made up the largest proportion of the lineages detected at Oceanside SF (90.9%), Sacramento (67.7%), San Jose (52%), and Southeast SF (67%). Note that the sequencing data are always from samples taken between 1-2 weeks ago (in this case, April 13, 2024). As concentrations of SARS-CoV-2 continue to fall, it is becoming more difficult to sequence the samples, so if concentrations continue to fall, we may need to pause sequencing.

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. All SCAN sites are still in onset for IAV but have 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):

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

Influenza B (IBV) RNA has been detected in most samples collected from SCAN sites in the last 21 days. The heat map below shows all the SCAN sites as a row and each date as a column for the last year. The color blue means the sample was non-detect for IBV RNA and the colors get darker with higher concentrations. White indicates no sample was collected. Here is the link to the heat map chart.

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

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

In the chart below, the population weighted average line across all the SCAN plants is shown in black and raw IBV data for the SCAN sites are shown as points. Here is the link to the chart if you want to interact with it.

RSV RNA concentrations have decreased to low levels. In the chart below, the population weighted average line across all the SCAN plants (black) is compared to the RSV concentrations at individual SCAN plants over the last 6 months. The National Levels benchmarks superimposed on the RSV data from the SCAN sites (you can access this chart here). ‌

Below are the current RSV 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, Sunnyvale, and SVCW are in the LOW Wastewater Category due to no longer being in in seasonal onset
• Southeast SF is in the MEDIUM Wastewater Category for RSV

In the chart below (representing data from Sept 2022-present), 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.

‌HMPV (Human metapneumovirus) RNA concentrations are elevated across all SCAN sites. 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 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 all sites are still experiencing high concentrations of HMPV.

EV-D68 RNA was detected at all SCAN sites from samples collected in the last 10 days (expect Oceanside SF). 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 in the LOW Wastewater Category for EV-D68
• Palo Alto, Sacramento, San Jose, 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 has consistently been detected in most samples collected from SCAN sites. The population weighted average across SCAN sites is shown in black. You can access the chart here.‌

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

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

Norovirus GII RNA was commonly detected at all SCAN sites, which is what we are observing across the national WWSCAN sites as well. Below is a plot with Oceanside SF and Southeast SF showing relatively high levels being measured in daily samples.

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

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

Mpox DNA was not detected in the last 10 days at any SCAN sites. 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 not detected in the last 10 days at most SCAN sites (2 positive detection from Palo Alto on 4/19/24 and 4/20/24, and 2 positive detection from Southeast SF on 4/15/24 and 4/16/24). 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 was detected sporadically at all SCAN sites in the last 10 days (minus Gilroy and Sacramento). 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 Sacramento are in the LOW Wastewater Category for Hepatitis A
• San Jose, Southeast SF, SVCW, 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.