SCAN Weekly Update - 1/24/24

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 1/22/24 have been processed and their data are on the site: data.wastewaterscan.org. Please email Ali at aboehm@stanford.edu if you identify any bugs on the site. ‌

For more information about the Wastewater Categorization system (i.e., how LOW, MEDIUM, or HIGH categories are determined for each pathogen), please see "How are wastewater categories determined?" in the About page for wastewaterSCAN.

SARS-CoV-2 N gene concentrations are between 10,000 and 1,000,000 copies/g. In the chart below, the National Levels benchmarks are superimposed on the the SARS-CoV-2 concentrations at all SCAN sites since July.

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, is in the LOW Wastewater Category
• Palo Alto, San Jose, and Sunnyvale are in the MEDIUM Wastewater Category
• Sacramento, Oceanside SF, SVCW, and Southeast SF are 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 population weighted average is still high at most SCAN sites, consistent with information currently being shared in media coverage of COVID infections, nationally. In our case, we have used consistent methods over time so levels can be compared overtime. Levels appear to be decreasing recently.

Below are plots from Oceanside SF, Sacramento, and San Jose showing the relative proportions of different variants inferred from sequencing the entire genome of SARS-CoV-2 (Note: the sequencing variant plots are now available on the website, so the plots that are shown below are linked above if you want to interact with them). In the most recent samples, JN.1 (bright red) made up the largest proportion of the lineages detected at Oceanside SF (66%), San Jose (57%), and Sacramento (36%). These samples are from weeks ago, and we should have new data on the site soon (within days).

Influenza A (IAV) RNA

We will begin sharing results again on IAV in the newsletter next week. We changed the fluorescent molecule that we use on the probe and started running samples using it last week. We have shared more details on this with our stakeholders.

Influenza B (IBV) RNA has been detected the majority of samples from most 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. 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. We briefly stopped monitoring for IBV, which explains gap in data across sites in September. Here is the link to the heat map chart.

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 are high at most SCAN sites, and all SCAN sites have met the benchmark for wastewater onset. 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 since August.

All SCAN sites are in the 'HIGH' Wastewater Category for RSV and are in onset.

In the chart below, the population weighted average line across all the SCAN sites is shown in black. The link to the chart below is here if you would like to interact with it. Although levels are still relatively high, and all sites are in the high category, levels have been decreasing which is a good sign.

Below is a chart showing the National Levels benchmarks superimposed on the RSV data from the SCAN sites (you can access this chart here). ‌Currently, all SCAN sites have RSV concentrations in the upper third level.

‌HMPV (Human metapneumovirus) RNA concentrations have increased at many SCAN sites, and Sunnyvale, San Jose, and, new this week, Sacramento have met the benchmark for onset. In the chart below, the National Levels benchmarks are superimposed on the the HMPV concentrations at San Jose, Sunnyvale, and Sacramento since August.

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

• Palo Alto, Gilroy, Oceanside SF, SVCW, and Southeast SF are in the LOW Wastewater Category (not in onset)
• Sunnyvale is in the MEDIUM Wastewater Category (in onset)
• San Jose and Sacramento are 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 (link here to this chart if you want to interact with it).

Below is a chart showing the National Levels benchmarks superimposed on the HMPV data from the SCAN sites. (You can access the chart here.) Currently, Gilroy has HMPV concentrations in the middle third level, and all other SCAN sites have HMPV concentrations in the upper third level.

EV-D68 RNA was rarely detected in samples collected in the last 21 days at all 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.‌ EV-D68 is believed to occur biennially, and we saw it last year, so it is not surprising perhaps that we are not seeing it this year.

Parainfluenza RNA has 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.‌

Norovirus GII RNA is commonly detected at all sites. In the chart below, the National Levels benchmarks are superimposed on the the Norovirus concentrations at Palo Alto, SVCW, and Oceanside SF since August.

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

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

The plot below shows the Norovirus concentrations at the SCAN sites. The population weighted average line is shown in black. You can interact with the chart of all the plants at this link.

Below is a chart showing the National Levels benchmarks superimposed on the Norovirus concentrations from the SCAN sites. (You can access the chart here.) Currently, Oceanside SF, SVCW, and Palo Alto are in the upper third tier and all other SCAN sites have Norovirus concentrations in the middle third tier.

‌Rotavirus 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 here.‌

Human Adenovirus Group F DNA 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 here.‌‌‌

We had to sunset the adenovirus assay to make room for IAV in a new fluorescent channel, so this is the last week we will be looking at the adenovirus results in the newsletter.

Mpox DNA was not detected in most samples collected in the last 21 days at all SCAN sites. 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.

Currently all SCAN sites are in the 'LOW' category for Mpox

Candida auris DNA was not detected in most samples collected in the last 21 days at all 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 dark purple color means it was detected. White indicates no sample was collected. You can access the chart here.‌

Hepatitis A RNA was rarely detected at Gilroy, Sacramento, and San Jose, and was detected sporadically at all other 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 all data collected since monitoring began in July. 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.‌