SCAN Weekly Update - 9/27/23

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. The SCAN plants are a subset of the WastewaterSCAN plants.

‌All samples picked up by the couriers as of 9/25/23 have been processed and their data are on the site: data.wastewaterscan.org. Please email Amanda Bidwell at albidwel@stanford.edu if you identify any bugs on the site. ‌

WastewaterSCAN uses a Wastewater Categorization system to communicate important insights from recent wastewater results. Research shows that the measurements we make in wastewater are related to disease in the community. The wastewater categorization helps us quickly understand if the recent measurements for a disease fall into a low, medium, or high category and are determined based on a combination of the following variables:

• Trends indicate whether wastewater concentrations of pathogens have been changing significantly (i.e., increasing or decreasing) for each location over the last 21 days
• Levels indicate whether wastewater concentrations are relatively lower or higher at each location compared to national concentrations of each pathogen (i.e., upper third, middle third, or lower third, as measured over the last year)
• Frequency of detection indicates how often a pathogen is detected in wastewater for each location over a recent time period (e.g., the last 10 days)

The new Wastewater Categorization system can now be accessed on the map view of the data.wastewaterscan.org site!

The Wastewater Categories are applied slightly differently for three archetypes of diseases:

• Pathogens that are commonly detected (regardless of season) - SARS-CoV-2, Norovirus, and ‘peak season’ Respiratory pathogens (IAV, RSV, HMPV)

• Seasonal pathogens (rarely detected outside of season/outbreaks) - IAV, RSV, HMPV

The methodology used to determine seasonal Onset vs Offset using raw target concentrations (not PMMoV Normalized) for individual sites is as follows:

The onset dates of IAV, RSV, and HMPV wastewater events are identified as the first day for which all samples in a 14 day look back period had concentrations higher than or equal to 2,000 copies/g, which is approximately twice the lowest detectable concentration. Once IAV, RSV, or HMPV are onset,  the method for 'commonly detected pathogens' (see above) is used to determine the wastewater categorization.

The offset dates of IAV, RSV, and HMPV wastewater events were identified as the first day after an onset event for which only 50% of samples during a 14-d look back period have concentrations higher than or equal to 2,000 copies/g. When one of these signals is in offset, it is assign a ‘LOW’ categorization.

• Pathogens that are not commonly detected (regardless of season) - Mpox

SARS-CoV-2 N gene concentrations are between 10,000 and ~1,000,000 copies/g. Below is a chart  that highlights the centered, 5-d trimmed average values for Southeast SF (blue) compared to the population weighted average across the SCAN plants (black) since the beginning of June and with the National Levels benchmarks superimposed.

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):

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

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 ratio of the XBB* mutations/N across SCAN plants is shown in the chart below.  This chart comes from data.wastewaterscan.org (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 majority of recent data for the regional average ratio XBB* mutations/N is ~50-95%. However, you can see three recent points that were ~30%, and these were all from Oceanside SF.  These data suggest that the majority of infections across the SCAN communities are caused by XBB*.  Note that these set of mutations are also present in EG.5 sublineage, but they are not present in BA.2.86.‌

Below are plots from Oceanside, Sacramento, and San Jose showing the relative proportions of different variants inferred from sequencing the entire genome of SARS-CoV-2. Samples with low coverage are not being displayed in the plots (this explains some empty columns San Jose). You can see that that all three plants had >25% of the sublineage EG.5 (in orange) in the most recent sample. EG.5 is an Note that the sequencing data are always from samples taken between 1- 2 weeks ago. We have not detected BA.2.86 in any samples yet, but it should be easy to detect if it is present because it has some characteristic deletions and a large insertion. BA.2.86 was detected in a wastewater sample somewhere, as describe in this press release from CDC.‌

Influenza A (IAV) RNA recently has been detected more frequently and at higher concentrations across SCAN sites than in previous weeks. While only two sites have met the benchmark for onset (Sacramento and Palo Alto), all sites are approaching the benchmark. This can be seen below in a chart of the unnormalized IAV concentrations (copies/g) since the beginning of June. As a reminder we are defining a wastewater onset event as the first day for which all samples in a 14 day look back period (the start date is denoted in the chart below with a vertical black line) had concentrations higher than 2,000 copies/g (denoted in the chart below with a horizontal black line), which is approximately twice the lowest detectable concentration.

Below are the current IAV wastewater categories for the SCAN sites:

• Gilroy, Oceanside SF, San Jose, SVCW, Southeast SF and Sunnyvale are in the LOW Wastewater Category (not in onset)
• Sacramento is in the MEDIUM Wastewater Category (in onset)
• Palo Alto is in the HIGH Wastewater Category (in onset)

In the chart below, the population weighted average line across all the SCAN plants is shown in black for the full time series. The link to the chart below is here if you would like to interact with it.‌

Below is a chart showing the National Levels benchmarks superimposed on the IAV data from the SCAN sites since the beginning of 2023 (you can access this chart here). ‌

RSV RNA recently has been detected more frequently and at higher concentrations across SCAN sites. While only three sites have met the benchmark for wastewater onset (Sunnyvale, Southeast SF, and San Jose) most sites are approaching the benchmark, as can be seen below in a chart of the unnormalized RSV concentrations (copies/g) since the beginning of June. In the chart below, the vertical black line denotes 9/13 and the horizontal black line denotes 2,000 copies/g.

Below are the current RSV wastewater categories for the SCAN sites:

• Oceanside SF, Southeast SF, SVCW,  Palo Alto, Gilroy, and Sacramento are in the LOW Wastewater Category (not in onset)
• Sunnyvale is in the MEDIUM Wastewater Category (in onset)
• Southeast SF and San Jose are in the HGIH Wastewater Category (in onset)

In the chart below, the population weighted average line across all the SCAN plants is shown in black since last winter.  The link to the chart below is here if you would like to interact with it.

Below is a chart showing the National Levels benchmarks superimposed on the RSV data from the SCAN sites since the beginning of 2023 (you can access this chart here). ‌Currently all SCAN sites RSV concentrations in the middle third level.

‌HMPV (human metapneumovirus) RNA concentrations are low 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). ‌

Despite seeing more consistent detections of HMPV over the past couple of weeks, we have still not hit wastewater onset. Currently all SCAN sites are in the 'LOW' category for HMPV.

Below is a chart showing the National Levels benchmarks superimposed on the HMPV data from the SCAN sites since the beginning of 2023. (You can access the chart here.) Currently all SCAN sites HMPV concentrations in the lower third level.

EV-D68 RNA was sporadically detected in most samples collected in the last 21 days at SCAN sites. The heat map below shows all the SCAN sites as a row, and each date as a column since monitoring began in July. 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 been detected in most samples collected from SCAN sites. The heat map below shows all the SCAN sites as a row, and each date as a column since monitoring began in September. The color blue means that Parainfluenza RNA was not detected in the sample, and the colors get darker with higher concentrations. White indicates no sample was collected. You can access the chart here.‌ In future weeks, we will start to provide line charts of these data.

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. You can interact with the chart of all the plants at this link.

Below are the current Norovirus wastewater categories for the SCAN sites:

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

Below is a chart that highlights the centered, 5-d trimmed average Norovirus GII concentrations for Gilroy (orange) compared to the population weighted average across the SCAN plants (black) since the beginning of June.

Below is a chart showing the National Levels benchmarks superimposed on the HuNoV GII data from the SCAN sites since the beginning of 2023. (You can access the chart here.) Currently all SCAN sites HuNoV GII concentrations in the lower third level.‌

‌Rotavirus RNA has been detected in most samples collected from SCAN sites in the past 21 days. The heat map shows all the SCAN sites as a row, and each date as a column since monitoring began in July. The color blue means that Rotavirus RNA was not detected in the sample, and the colors get darker with higher concentrations. White indicates no sample was collected. You can access the chart here.‌ In future weeks, once we have more data, we will start to show a line chart for these data points.

Human Adenovirus Group F DNA has been detected in most samples collected from SCAN sites in the past 21 days. The heat map shows all the SCAN sites as a row, and each date as a column since monitoring began in July. The color blue means that Human Adenovirus Group F RNA was not detected in the sample, and the colors get darker with higher concentrations. White indicates no sample was collected. You can access the chart here.‌ In future weeks, once we have more data, we will start to show a line chart for these data points.

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Mpox DNA were mostly non-detects in the last 21 days for all SCAN plants except for Southeast SF. The plot below shows the normalized Mpox DNA as raw data (points) and 5-d trimmed average values (line) for Southeast SF. You can see a recent small uptick.

Below are the current Mpox wastewater categories for the SCAN sites:

• Oceanside SF, SVCW, Palo Alto, Sunnyvale, San Jose, Gilroy, and Sacramento are in the LOW Wastewater Category
• Southeast SF is in the MEDIUM Wastewater Category (50% of samples in the last 10 days were positive for Mpox)

The heat map below shows all the SCAN sites as a row, and each date as a column. The color blue means that MPXV DNA was not detected in the sample, and the colors get darker with higher concentrations. White indicates no sample was collected. The chart shows all the data we have collected, almost a year's worth of data. You can access the chart here.‌

Candida auris DNA was not detected in most samples collected in the last 21 days at SCAN sites. 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 colors get darker with higher concentrations. White indicates no sample was collected. You can access the chart here.‌

Hepatitis A RNA was not detected in most samples collected in the last 21 days at SCAN sites. However, throughout the full monitoring period, San Jose has had mostly detects for Hepatitis A RNA. 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 Hepatitis A RNA was not detected in the sample, and the colors get darker with higher concentrations. White indicates no sample was collected. You can access the chart here.‌