SCAN Bay Area weekly update 6/28/23

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.

All samples picked up by the couriers as of 6/26/23 have been processed and their data are on the site: The data from the SCAN sites are also on Please email Amanda Bidwell at if you identify any bugs on the site. ‌


SARS-CoV-2 and Variants

SARS-CoV-2 N gene concentrations at SCAN sites are similar to what they were two weeks ago at most sites, but trending upward at 1 site (see below). Concentrations are between 10,000 and 100,000 copies/g. An example chart from Silicon Valley Clean Water is below.

We ran a 2-week look period trend analysis on the plants for the N gene target using methods outlined in this peer-reviewed paper by Chan et al. from our team (link to paper). Silicon Valley Clean Water has significant upward trend, Oceanside SF shows a significant downward trend while the rest of the plants have no trend.

Here 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 plants is shown in black.  

We recently added a new feature on the site called National Levels to provide a visual benchmark where concentrations fall compared to previously recorded measurements for each pathogen target. The national levels are shown as groups (bottom third, middle third and upper third) that are based on looking back at all data from the last 365 days across all WWSCAN sites (across the entire US). This feature can be applied across all current targets in 'Chart View'. Click the eye icon next to "National Levels" to show this feature. More details can be found under the "How are national levels determined?" section here.

Below is a chart showing the National Levels benchmarks superimposed on the SARS-CoV-2 N gene data from the SCAN sites since the beginning of 2023. Currently most SCAN sites SARS-CoV-2 N gene concentrations are in the bottom third level. You can access the graph here.

The ratio of the XBB* mutations/N across SCAN plants is shown in the chart below.  This chart comes from (link here to the chart). As the ratio reaches 100%, it suggests that all the SARS-CoV-2 genomes in wastewater have the XBB* mutations. These data indicate that the regional average ratio XBB* mutations/N is ~80%.  These data suggest that the majority of infections across the SCAN communities are caused by XBB*.  

XBB.1.16 is present in the wastewater from the three SCAN plants we sequence SARS-CoV-2 from. Here is a plot from San Jose showing the relative proportions of different variants inferred from sequencing the S gene. You can see the information on XBB.1.16 in the deep violet color. The proportion of XBB.1.16  in Sacramento samples was at close to 50% the week of June 17, and during the approximate same time, the proportion was 25% at Oceanside and San Jose. The remainder of the sequences from the plants are mostly other XBB*.

Other Respiratory Viruses

Influenza A & B, RSV and Human metapneumovirus

Influenza A (IAV) RNA  concentrations are very low across the SCAN plants. Concentrations are generally non-detects in samples from recent weeks. The link to the chart below is here if you would like to interact with it.‌ The population weighted average line across all the SCAN plants is shown in black.

The 2-week look period trend analysis on IAV RNA at these plants indicates no trend at all the SCAN plants.

‌Influenza B (IBV) RNA is sporadically detected at low concentrations at the SCAN plants. Each plant is represented by a row (y-axis), and dates are shown along the x-axis. Blue indicates a non-detect, and darker orange/red is proportional to concentration with the highest values being darkest.  A white means no sample was collected. Here is the link to the heat map chart - the linked chart will update automatically as more data are added to the site.

RSV RNA has not been detected in most samples in the past week. This plot shows data from all the SCAN sites together since last winter and can be access here. The black line is the population weighted average.

The 2-week look period trend analysis on RSV RNA at these plants indicates no trend at all the SCAN plants. The heat map below shows the recent occasional occurrence of low-level detections for RSV over the last ~30 days.

‌‌HMPV (human metapneumovirus) RNA  concentrations continue to decline at most of plants in SCAN. Below are charts showing data from all the SCAN plants together (link here to this chart if you want to interact with it).

The 2-week look period trend analysis on HMPV RNA at these plants indicates no trend at all the SCAN plants.

Enteric Targets

Norovirus GII

Norovirus GII RNA concentrations are shown in the chart below; all the SCAN plants are shown together. The population weighted average line is shown in black, and that line shows a slow decrease over the last couple weeks.  You can interact with the chart of all the plants at this link.

The 2-week look period trend analysis on HuNoV GII RNA at SCAN plants indicates a significant downward trend at Oceanside SF, and significant upward trends at Southeast SF and Silicon Valley Clean Water. There is no trend at the other plants.

Other Pathogens of Concern


We've observed non-detects in the last 12 weeks for MPXV DNA at the SCAN plants, with the exception of one sample on 5/7/23 (Silicon Valley Clean Water) and one sample on 6/18/23 (Southeast SF) (shown in orange below). The heat map show all the SCAN sites as a row, and each date as a column. The color blue means the sample was non-detect for MPXV DNA and the colors get darker with higher concentrations. White indicates no sample was collected. The charts shows all the data we have collected, almost a year's worth of data.  You can access the chart here.

There was recently a national warning that we might see a resurgence in Mpox cases. The data from wastewater suggests that is not the case presently at the SCAN plants.

The next SCAN Bay Area meeting will be Thursday July 6th, 2023

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Jamie Larson