SCAN Update - 11/27/24

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 11/25/24 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:

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

SARS-CoV-2 N gene concentrations were between ND - 767,917 copies per gram 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, 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 come down from the peak observed in this summer (July/August 2024) and has plateaued in the last couple of weeks.

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, KP.3 made up the largest proportion of lineages detected at Oceanside SF (100%) and Southeast SF (61.2%). JN.1 made up the largest proportion of lineages detected at San Jose (49.1%). JN.1.11 made up the largest proportion of lineages detected at Sacramento (72.1%). Note that the sequencing data are always from samples taken between 1-2 weeks ago (in this case, Nov 16, 2024).

Influenza A (IAV) RNA was detected in 89% of samples in the past 3 weeks. 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.

As a reminder we have paused the H1 marker analysis. We are working to design a new H1 assay and confirm that it works with current H1N1 strains. Over the summer, we noted that the RNA sequence in the region of the H1N1 HA gene that the H1 assay targets mutated. There were a large number of influenza A H1N1 sequences added to public databases over the summer that made it possible to observe these changes; sequencing of isolates occurred more often than normal over the summer due to the H5N1 outbreak. These mutations impacted the performance of the H1 assay we were using. The sequences in certain regions of viral genomes can evolve rapidly and influenza A is known to be a virus that does evolve and change over time. As part of our ongoing efforts, WastewaterSCAN actively monitors changing sequences for all of our targets, ensuring the assays continue to be sensitive and specific.

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

All 8 sites in the SCAN network (Gilroy, Oceanside SF, Palo Alto, Sacramento, San Jose, Southeast SF, SVCW, and Sunnyvale) 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 sporadically 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 was detected in ~87% of samples in the past 3 weeks. The median RSV RNA concentration across all SCAN sites in the last 3 weeks was 6,688 copies per gram. 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, and Southeast SF are in the LOW Wastewater Category due to not being in seasonal onset for RSV
• San Jose, SVCW and Sunnyvale are in seasonal onset and in the HIGH Wastewater Category for RSV

‌HMPV (Human metapneumovirus) RNA was detected in ~25% of samples in past 3 weeks. The median HMPV RNA concentration across all SCAN sites in the last 3 weeks was below the limit of detection. 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 not 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 has consistently been detected from samples collected at all SCAN sites in the last 3 weeks. EVD68 RNA was rarely detected in wastewater solids since we began monitoring through August 2024. However, this year we have seen an increase in detection and it is showing characteristics more consistent with a seasonal epidemic pathogen this year. Therefore, we changed its classification for determining the WastewaterSCAN wastewater category from “Not commonly detected (regardless of season)” to “Seasonal detected (rarely detected outside of season/outbreaks)” starting October 15, 2024. It has always been the plan that a “not commonly detected” pathogen could be moved to another category archetype when appropriate, and this change will provide category determinations based on the quantitative measurement of EV-D68 rather than just detections. You can read more about how wastewater categories are calculated here: https://data.wastewaterscan.org/about/#8 

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 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 and concentrations started coming down in early November 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 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. 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):

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

Mpox clade II DNA was not been detected at any SCAN sites in 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 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 2 SCAN sites in the last 3 weeks (Oceanside SF and Gilroy). 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 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 7 of the SCAN sites (expect Oceanside SF) in the last 3 weeks.

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