Nationwide WWSCAN Update 1/26/24

Hi everyone,

This newsletter contains updates on the WastewaterSCAN program with wastewater samples analyzed by the lab through January 25, 2024. Below you will find information on the program in terms of participating partners, review of targets being measured, as well as current categories (low, medium, high) of the infectious disease targets.

Ali & Marlene

WastewaterSCAN Participant Stats:

• 191 plants sampling
• 45,350,248 people covered through sampling efforts
• 40 states and Washington DC represented

The methods for our assays are in the public domain and links for these are provided at the end of the newsletter. Please note that due to performance issues with the Influenza A assay, we have stopped testing for Adenovirus group F in early January to accommodate the necessary changes for Influenza A.

WastewaterSCAN currently has funding to continue monitoring approximately until May 2024. We anticipate to be able to provide an update on this within the next four weeks.

SARS-CoV-2 N gene RNA median concentration across all sites over the last 21 days is 227,748 copies/gram. For reference, the median concentration in December 2023 was 186,016 copies/gram. Below is the population weighted average SARS-CoV-2 N gene concentrations (normalized by PMMoV) from all participating WWSCAN sites across the country over the last 365 days. Nationally, SARS-CoV-2 is in the "High" category with aggregated measurements showing high concentrations but a downward trend over the past 21 days.

Below are the population-weighted average SARS-CoV-2 N gene concentrations (normalized by PMMoV) from sites in the Midwest US (top left panel), Northeast US (top right panel), Southern US (bottom left panel) and Western US (bottom right panel) over the last 365 days. Raw data have been omitted from the plots for clarity of presentation but are still available in the chart settings on dashboard.

All regions are currently in the "High" category. Concentration levels remain high across all US regions with significant decreasing trends occurring in the Northeast and the Southern regions based on the last 21 days.

Below are the current SARS-CoV-2 wastewater categories for all WWSCAN sites:

• 12 are in the LOW Wastewater Category
• 32 are in the MEDIUM Wastewater Category
• 125 are in the HIGH Wastewater Category
• 21 do not have enough data to calculate (Fremont, CA; Mammoth, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Diego, CA; Santa Rosa, CA; Sausalito, CA; South San Diego, CA; Sunnyvale, CA; Union City, CA; Vallejo, CA; North Miami, FL; South Miami, FL; Hilo, HI; Wolcott, Kansas City, KS; Louisville, KY; Brunswick, ME; Lewiston, ME; Traverse City, MI; Pascagoula Moss Point, MS; Newark, NJ)

Sequencing of SARS-CoV-2 from wastewater is now available for a select number of individual sites and nationally aggregated data will be available soon. A protocol is available on protocol.io. The plots below show the relative proportions of different variants inferred from sequencing the entire genome of SARS-CoV-2. There is a site shown from the Midwest US (top left panel), Northeast US (top right panel), Southern US (bottom left panel) and Western US (bottom right panel). (Note: the sequencing variant plots are now available on the website, so the plots shown below are linked above if you want to interact with them)

In each plot, data from the week of December 30th illustrates that JN.1 (bright red) made up the largest proportion of the lineages detected at detected at Rochester (48.7%), Chester (45.3%), Garland (56.2%) and Central Salt Lake Valley (53.9%). Note these are samples from about 4 weeks ago. New sequencing will be available soon and is usually posted weekly. We also anticipate being able to share nationally aggregated sequencing data soon.

Influenza A (IAV) RNA A couple of weeks ago, we identified a technical issue with the IAV assay. In brief, the fluorescent molecule on the IAV assay probe impacted the performance of the assay. All of the impacted data (1 Oct 2023 to approximately 11 Jan 2024) were removed from the website. We are now analyzing samples for IAV RNA using a probe containing a different, better performing fluorescent molecule. These data are now available on the website, and recent trends will become clearer as more samples are processed. We will be retrospectively rerunning a subset of samples between 1 Oct 2023 and early Jan 2024 and adding those results to the site as they become available. We will share our schedule for completing those reruns on the next stakeholder call.

Influenza B (IBV) RNA has been detected in 816 out of 1,353 samples during the past 21 days (~60.3% detection rate). Below is the population-weighted average IBV RNA concentrations (normalized by PMMoV) from all participating WWSCAN sites across the country over the last 365 days.

Nationally, influenza B is in the "Low" category with onset in <50% of sites. The South is the only region in the "High" category.

Below are the current Influenza B wastewater categories for all WWSCAN sites, with at least 70 sites showing wastewater onset for IBV:

• 100 are in the LOW Wastewater Category
• 0 are in the MEDIUM Wastewater Category
• 69 are in the HIGH Wastewater Category
• 22 do not have enough data to calculate (Fremont, CA; Mammoth, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Diego, CA; Santa Rosa, CA; Sausalito, CA; South San Diego, CA; Sunnyvale, CA; Union City, CA; Vallejo, CA; North Miami, FL; South Miami, FL; Hilo, HI; Wolcott, Kansas City, KS; Louisville, KY; Brunswick, ME; Lewiston, ME; Traverse City, MI; Pascagoula Moss Point, MS; Newark, NJ)

Respiratory syncytial virus (RSV) RSV RNA median concentration across all sites over the last 21 days is 20,438 copies/gram. For reference, the median concentration in December 2023 was 24,905 copies/gram. There have been 1,225 positive samples out of 1,353 samples during the past 21 days (~90.5% detection rate). Below are the RSV RNA concentrations (normalized by PMMoV) from all participating WWSCAN sites across the country over the last 365 days shown as the population-weighted average.

Below are the population-weighted average RSV RNA concentrations (normalized by PMMoV) from sites in the Midwest US (top left panel), Northeast US (top right panel), Southern US (bottom left panel) and Western US (bottom right panel) over the last 365 days.

The plots below show relatively high concentrations across all US regions, with decreasing trends. Nationally, RSV is in the "High" category, with >50% of sites showing onset of RSV in wastewater and aggregated measurements showing high concentrations. The Midwest, Northeast, and West have had a downward trend over the past 21 days.

Below are the current RSV wastewater categories for all WWSCAN sites, with at least 155 sites showing wastewater onset for RSV:

• 19 are in the LOW Wastewater Category
• 11 are in the MEDIUM Wastewater Category
• 138 are in the HIGH Wastewater Category
• 22 do not have enough data to calculate (Fremont, CA; Mammoth, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Diego, CA; Santa Rosa, CA; Sausalito, CA; South San Diego, CA; Sunnyvale, CA; Union City, CA; Vallejo, CA; North Miami, FL; South Miami, FL; Hilo, HI; Wolcott, Kansas City, KS; Louisville, KY; Brunswick, ME; Lewiston, ME; Traverse City, MI; Pascagoula Moss Point, MS; Newark, NJ)

HMPV (human metapneumovirus) RNA median concentrations across all sites over the last 21 days are below the lower detection limit of the assay. There have been 563 positive samples out of 1,353 samples during the past 21 days (~41.6% detection rate). Below is the population weighted average HMPV RNA concentrations (normalized by PMMoV) from all participating WWSCAN sites across the country over the last 365 days.

Nationally, HMPV is in the "Low" category. Levels are lower compared to around this time last year.

Below are the population-weighted average HMPV RNA concentrations (normalized by PMMoV) from sites in the Midwest US (top left panel), Northeast US (top right panel), Southern US (bottom left panel) and Western US (bottom right panel) since we started monitoring HMPV late December 2022.

All regions are in the "Low" category.

Below are the current HMPV wastewater categories for all WWSCAN sites, with at least 23 sites showing wastewater onset for HMPV:

• 16 are in the LOW Wastewater Category
• 3 is in the MEDIUM Wastewater Category
• 149 are in the HIGH Wastewater Category
• 22 do not have enough data to calculate (Fremont, CA; Mammoth, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Diego, CA; Santa Rosa, CA; Sausalito, CA; South San Diego, CA; Sunnyvale, CA; Union City, CA; Vallejo, CA; North Miami, FL; South Miami, FL; Hilo, HI; Wolcott, Kansas City, KS; Louisville, KY; Brunswick, ME; Lewiston, ME; Traverse City, MI; Pascagoula Moss Point, MS; Newark, NJ)

Human Parainfluenza (HPIV) RNA has been detected in ~62% of samples collected from WWSCAN sites. The HPIV median concentration across all sites over the last 21 days is 3,232 copies/gram. The population-weighted average line is shown below. You can interact with the chart of all the plants here. These data will become easier to interpret as we collect more data; we do not have enough data currently to start assessing trends or levels.

Enterovirus D68 (EV-D68) RNA was rarely detected (0.9%) in samples collected in the last 21 days at most WWSCAN sites and the median concentration across all sites over the last 21 days is below the level of detection. The heat map below shows all WWSCAN sites in HHS Region 1 as a row, and each date as a column since monitoring began in September 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.

Norovirus GII (HuNoV GII) RNA has been consistently detected at the sites. The median concentration across all sites over the last 21 days is 9,087,577 copies/gram (for reference median concentration in December 2023 was 7,885,724 copies/gram). Below are the HuNoV GII RNA concentrations (normalized by PMMoV) from all participating WWSCAN sites across the country over the last 365 days. The population-weighted average is shown. Nationally, Norovirus is in "High" category with aggregated measurements showing high concentrations and no significant trend over the past 21 days.

Below are the population-weighted average HuNoV GII RNA concentrations (normalized by PMMoV) from sites in the Midwest US (top left panel), Northeast US (top right panel), Southern US (bottom left panel) and Western US (bottom right panel).

All regions are in the "High" category. Concentrations in Northeast and West regions are showing an upward trend in the last 21 days while the South is seeing a downward trend.

Below are the current Norovirus wastewater categories for ALL WWSCAN sites:

• 18 are in the LOW Wastewater Category
• 46 are in the MEDIUM Wastewater Category
• 104 are in the HIGH Wastewater Category
• 22 do not have enough data to calculate (Fremont, CA; Mammoth, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Diego, CA; Santa Rosa, CA; Sausalito, CA; South San Diego, CA; Sunnyvale, CA; Union City, CA; Vallejo, CA; North Miami, FL; South Miami, FL; Hilo, HI; Wolcott, Kansas City, KS; Louisville, KY; Brunswick, ME; Lewiston, ME; Traverse City, MI; Pascagoula Moss Point, MS; Newark, NJ)

Rotavirus RNA concentrations are shown in the chart below; all the WWSCAN plants are shown together as a population-weighted average line. Rotavirus median concentrations across all sites over the last 21 days is 111,354 copies/gram. For reference, the median concentration in December 2023 was 75,775 copies/gram. You can interact with the chart of all the plants here. Levels recently peaked at the beginning of the year. As we collect more data, we will be better able to interpret trends and levels of this pathogen.

Human Adenovirus Group F DNA has been detected in ~40.2 % of samples collected from WWSCAN sites in the past 21 days. (Note: We stopped testing for Adenovirus in early January to accommodate the necessary changes for Influenza A.) Concentrations from sample collected September 5th, 2023 to January 11th, 2024 are shown in the chart below; all WWSCAN plants are shown together as a population-weighted average line. Based on samples analyzed through 1/25/24, the human Adenovirus Group F median concentration across all sites over the last 21 days is 7,075,016 copies/gram (for reference median concentration in December 2023 was 7,170,533 copies/gram). You can interact with the chart of all the plants here. This is the last newsletter that will feature a section on Adenovirus group F.

Mpox DNA We have only detected mpox DNA in 4 samples from all sites in the past 21 days. The chart below plants in HHS region 5 as rows, and the last 21 days as columns (labeled at the bottom axis). White indicates no samples, blue is non-detect for mpox DNA and red is detect for mpox DNA.

The wastewater categorization for Mpox at 168 sites is LOW. 23 sites did not have enough data to calculate a category.

Candida auris (C.auris) DNA - We have detected C. auris DNA in 1.0% of samples from all WWSCAN sites over the past three weeks. The chart below shows each WWSCAN plant in HHS Region 4 as rows, and the last 21 days as columns (labeled at the bottom axis). White indicates no samples, blue is non-detect for C. auris DNA and red is detect for C. auris DNA.

Hepatitis A (Hep A) RNA - We have detected Hep A RNA in 9.2% of samples from all WWSCAN sites over the past three weeks. The chart below shows each WWSCAN plant in HHS Region 7 as rows, and the last 21 days as columns (labeled at the bottom axis). White indicates no samples, blue is a non-detect for Hep A RNA and red is a detect for Hep A RNA.

Protocols (Pre-analytical methods and SARS-CoV-2 analytical methods including controls):

• High Throughput RNA Extraction and PCR Inhibitor Removal of Settled Solids for Wastewater Surveillance of SARS-CoV-2 RNA
• High Throughput pre-analytical processing of wastewater settled solids for SARS-CoV-2 RNA analyses
• Quantification of SARS-CoV-2 variant mutations (HV69-70, E484K/N501Y, del156-157/R158G, del143-145, LPPA24S, S:477-505, and ORF1a Del 141-143) in settled solids using digital RT-PCR
• High Throughput SARS-COV-2, PMMoV, and BCoV quantification in settled solids using digital RT-PCR

Pre-prints and peer-reviewed publications provided WWSCAN methods: 

• SARS-CoV-2 
• Influenza, Human metapneumovirus, Respiratory syncytial virus, Human parainfluenza
• Mpox
• Norovirus GII
• Adenovirus group F, Rotavirus, Candida auris, Hepatitis A
• Enterovirus D68

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If you have questions about the website or anything else, please email: wwscan_stanford_emory@lists.stanford.edu.