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Nationwide WastewaterSCAN September 2025 Update

Hi everyone,

This newsletter contains updates on the WastewaterSCAN program with wastewater samples analyzed by the lab through September 30, 2025. Below you will find information on the program in terms of participating partners, review of targets being measured, as well as current wastewater categories (low, medium, high) of the infectious disease targets.

Best,

WastewaterSCAN Team

Participating Plants

147 WWTPs plants across 40 states

WWSCAN Participant Stats:

  • 147 plants sampling
  • >37 million people covered through sampling efforts
  • 40 states
WWSCAN site coverage map as of September 2025

Infectious Disease Target Review

Currently monitoring a suite of Respiratory, Gastrointestinal and Outbreak Pathogens of Concern

The methods for our assays are in the public domain and links for these are provided at the end of the newsletter. As a reminder, in mid-May 2025 WWSCAN resumed measurements of Rotavirus and Adenovirus group F, and added Measles and Parvovirus to the list of pathogens monitored.

Program Publications

Recent publications, factsheets, FAQs, and more!

WWSCAN Published Body of Work document:

WWSCAN FAQs:

WWSCAN Factsheets and Guidance Documents can be found here.

Wastewater Category Logic

As a reminder, WWSCAN's categorize sites based on Levels + Trends + Frequency of detection. We adopted this methodology back in 2023 as a way to clearly communicate what wastewater is telling us about community disease circulation. 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 tell us how concentrations are changing  (↑, ↓, -) over the last 21 days
  • Levels tell us whether concentrations are relatively lower or higher (based on national tertiles over last 365 days)
  • Frequency of detection indicates how often a pathogen is detected in wastewater (important for pathogens that are not commonly detected)

There are 3 Archetypes for WWSCAN Pathogens:

  • Pathogens that are commonly detected (regardless of season - includes SARS-CoV-2, Norovirus)
  • Seasonal pathogens (rarely detected outside of season/outbreaks - includes Influenza A + B, RSV, HMPV, EV-D68)
  • Pathogens that are not commonly detected (regardless of season - includes C. auris, HepA, Measles, Mpox clade Ib, Mpox clade II)

*Categories are not being calculated for H1/H3/H5 Influenza markers, Parvovirus, Rotavirus or Adenovirus Group F.

To learn more about WWSCAN's categorization logic, please see: https://data.wastewaterscan.org/about/#8

COVID-19

SARS-CoV-2 concentration in wastewater and sequencing for variants

SARS-CoV-2 N gene RNA median concentration across all sites in September 2025 was 67,496 copies/gram. SARS-CoV-2 was detected in 98% of samples in September. The median SARS-CoV-2 concentration in September 2025 was down ~12% compared to August 2025. It appears we may have seen the peak of the summer wave in early September, but we will continue to monitor as we move through fall.

Below is the population weighted average SARS-CoV-2 N gene concentrations (normalized by PMMoV) is shown in black from all participating WWSCAN sites across the country over the last 365 days. All regions have seen decreasing concentrations over the last month.

Midwest states: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast states: CT, MA, ME, NH, NJ, NY, PA, VT. Southern states: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

Nationally, SARS-CoV-2 is in the 'MEDIUM' category with aggregated measurements showing medium concentrations and a downward trend over the last 3 weeks.

Below are the current SARS-CoV-2 wastewater categories for all WWSCAN sites (recall the category is determined by both the trend and the level):

  • 53 are in the LOW Wastewater Category
  • 48 are in the MEDIUM Wastewater Category
  • 33 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

SARS-CoV-2 Wastewater Categories. This map includes sample collection data through September 30, 2025. Each dot represents a single site and the four US Census regions are outlined in gray. Midwest Region includes: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast Region includes: CT, MA, ME, NH, NJ, NY, PA, VT. Southern Region includes: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

Sequencing of SARS-CoV-2 from wastewater is available for a select number of individual sites. The sequencing 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. Results are based on sequencing of 2 samples per week, combined to provide a weekly value.

Sequencing data is also available in aggregate across all sites in WWSCAN with sequencing data. That plot is shown below and also suggests that XFG (shown in orange) is the most abundant variant across all sites at 93.2%, followed by NB.1.8.1 (shown in mauve) is at 2.4%.

SARS-CoV-2 sequencing data through the week of September 27, 2025

Other Respiratory Pathogens

Influenza A & B, Respiratory Syncytial Virus, Human metapneumovirus, EV-D68 & Parvovirus

Influenza A (IAV) RNA was detected in ~16% of samples in September 2025. IAV RNA median concentration across all sites in the past 3 weeks was below the limit of detection. Recently we've seen elevated IAV concentrations at a handful of sites in the network (mainly in AK, CA, FL, IA, KS, ME & MI). We will continue to monitor as we move into respiratory virus season this fall/winter.

Below is the population weighted average IAV concentrations (normalized by PMMoV) is shown in black from all participating WWSCAN sites across the country over the last 365 days.

Midwest states: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast states: CT, MA, ME, NH, NJ, NY, PA, VT. Southern states: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

Nationally, Influenza A is in the 'LOW' Wastewater Category with >50% of sites in seasonal offset of IAV in wastewater.

Below are the current Influenza A wastewater categories for all WWSCAN sites (recall the category is determined by both the trend and the level when in seasonal onset):

  • 130 are in the LOW Wastewater Category
  • 2 are in the MEDIUM Wastewater Category
  • 2 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

Influenza A Wastewater Categories. This map includes sample collection data through September 30, 2025. Each dot represents a single site and the four US Census regions are outlined in gray. Midwest Region includes: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast Region includes: CT, MA, ME, NH, NJ, NY, PA, VT. Southern Region includes: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

H1 Marker in Influenza A (IAV) The H1 marker in influenza A has been detected in ~3.8% of samples in September 2025. The H1 median concentration across all sites in the past 3 weeks was below the limit of detection. You can find a heat map of positive detections here.

H3 Marker in Influenza A (IAV) In September 2025, the H3 marker in influenza A was detected in ~3.8% of samples. You can find a heat map of positive detections here.

H5 Marker in Influenza A (IAV) As of September 30, 2025, WWSCAN sites across 28 states (AK, AR, CA, CO, CT, DE, FL, IA, ID, IL, KS, KY, MA, ME, MD, MI, MN, NC, NE, NH, NJ, NV, SD, TN, TX, UT, VA and VT) have seen positive detections for the H5 marker in influenza A. Since prospective monitoring began, 1,028/32,022 samples have tested positive (~3.2% detection rate). In September 2025, there were only 5 positive H5 marker detections (1 detection in AK, 2 detections in CA, 1 detection in KS, and 1 detection in MN). You can find a heat map of positive detections here.

Map showing the location of WWSCAN sites that have had positive detection(s) of the H5 marker in Influenza A as of September 2025

Influenza B (IBV) RNA was detected in ~2.7% of samples in September 2025. IBV RNA median concentration across all sites in the past 3 weeks was below the limit of detection. Below the population-weighted average IBV RNA concentrations (normalized by PMMoV) is shown in black from all participating WWSCAN sites across the country over the last 365 days.

Midwest states: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast states: CT, MA, ME, NH, NJ, NY, PA, VT. Southern states: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

Nationally, Influenza B is in the 'LOW' Wastewater Category with with all sites in seasonal offset for IBV in wastewater.

Below are the current Influenza B wastewater categories for all WWSCAN sites (recall the category is determined by both the trend and the level when in seasonal onset):

  • 134 are in the LOW Wastewater Category
  • 0 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

IBV Wastewater Categories. This map includes sample collection data through September 30, 2025. Each dot represents a single site and the four US Census regions are outlined in gray. Midwest Region includes: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast Region includes: CT, MA, ME, NH, NJ, NY, PA, VT. Southern Region includes: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

Respiratory syncytial virus (RSV) RNA was detected in ~9.2% of samples in September 2025 (with most positive detections in CA, FL, GA, and TX). RSV RNA median concentration across all sites in the last 3 weeks was below the limit of detection. Below the population-weighted average RSV RNA concentrations (normalized by PMMoV) is shown in black from all participating WWSCAN sites across the country over the last 365 days. In this plot you can see a slow increase in RSV concentrations in the South (shown in chartreuse).

Midwest states: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast states: CT, MA, ME, NH, NJ, NY, PA, VT. Southern states: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

Nationally, RSV is in the 'LOW' Wastewater Category with all sites in seasonal offset for RSV in wastewater.

Below are the current RSV wastewater categories for all WWSCAN sites (recall the category is determined by both the trend and the level when in seasonal onset):

  • 134 are in the LOW Wastewater Category
  • 0 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

RSV Wastewater Categories. This map includes sample collection data through September 30, 2025. Each dot represents a single site and the four US Census regions are outlined in gray. Midwest Region includes: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast Region includes: CT, MA, ME, NH, NJ, NY, PA, VT. Southern Region includes: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

HMPV (human metapneumovirus) RNA was detected in ~7.7% of samples in September 2025. The median HMPV RNA concentrations across all sites in the last 3 weeks was below the limit of detection. Below is the population weighted average HMPV RNA concentrations (normalized by PMMoV) shown in black from all participating WWSCAN sites across the country over the last 365 days.

Midwest states: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast states: CT, MA, ME, NH, NJ, NY, PA, VT. Southern states: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

Nationally, HMPV is in the 'LOW' Wastewater Category with all sites in seasonal offset for HMPV in wastewater.

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

  • 134 are in the LOW Wastewater Category
  • 0 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

HMPV Wastewater Categories. This map includes sample collection data through September 30, 2025. Each dot represents a single site and the four US Census regions are outlined in gray. Midwest Region includes: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast Region includes: CT, MA, ME, NH, NJ, NY, PA, VT. Southern Region includes: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

Enterovirus D68 (EV-D68) RNA was detected in ~21% of samples collected in September 2025 (with most positive detections in the Midwest and a handful of sites in CA). The median concentration across all sites was below the limit of detection in the last 3 weeks. Below is the population-weighted average EV-D68 RNA(normalized by PMMoV) shown in black from all participating WWSCAN sites across the country over the last 365 days. In this plot you can see increasing EV-D68 concentrations in the Midwest (shown in red) which began in mid August 2025.

Midwest states: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast states: CT, MA, ME, NH, NJ, NY, PA, VT. Southern states: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

Nationally, EV-D68 is in the 'LOW' Wastewater Category with >50% of sites in seasonal offset of HMPV in wastewater.

Below are the current EV-D68 wastewater categories for all WWSCAN sites (recall the category is determined by both the trend and the level):

  • 126 are in the LOW Wastewater Category
  • 0 are in the MEDIUM Wastewater Category
  • 8 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

EV-D68 Wastewater Categories. This map includes sample collection data through September 30, 2025. Each dot represents a single site and the four US Census regions are outlined in gray. Midwest Region includes: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast Region includes: CT, MA, ME, NH, NJ, NY, PA, VT. Southern Region includes: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

Parvovirus (Parvo) DNA - In mid May 2025, we began prospectively monitoring for Parvovirus. Parvovirus B19 DNA was detected in ~8.8% of samples collected in September 2025 across WWSCAN sites.

The chart below shows each WWSCAN plant in Georgia as rows, and days as columns (labeled at the bottom axis). White indicates no samples, blue is a non-detect for Parvo DNA and red is a detection for Parvo DNA.

Heat map of positive Parvovirus detections (in red) across sites in Georgia participating in WWSCAN. Blue indicates non-detect.

As a reminder, we are not currently calculating wastewater categories for Parvovirus. In order to calculate wastewater categories we need a longer time series of data to examine trends and levels.

We recently published a paper on 'Community Infections Linked with Parvovirus B19 Genomic DNA in Wastewater, Texas, USA, 2023–2024'. This paper covers retrospective analysis conducted at two WWTPs in Texas prior to WWSCAN rolling out the assay to all participating WWSCAN sites. You can find the paper linked here.

Gastrointestinal Pathogens

Norovirus GII, Human Adenovirus Group F, & Rotavirus

Norovirus GII (HuNoV GII) RNA was detected in 99% of samples analyzed in September 2025. The median concentrations across all sites in September 2025 was is 2,596,812 copies per gram, up ~16% from August 2025. Below is the population weighted average HuNoV GII RNA concentrations (normalized by PMMoV) shown in black from all participating WWSCAN sites across the country over the last 365 days.

Midwest states: IA, IL, IN, KS, MI, MN, NE, OH, SD, WI. Northeast states: CT, MA, ME, NH, NJ, NY, PA, VT. Southern states: AL, AR, DE, FL, GA, KY, LA, MD, MS, NC, TN, TX, VA, and WV. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

Nationally, Norovirus is in the 'LOW' Wastewater Category with aggregated measurements showing low concentrations and no trend over the last 3 weeks.

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

  • 88 are in the LOW Wastewater Category
  • 31 are in the MEDIUM Wastewater Category
  • 15 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

Human Adenovirus Group F (HAdV-F) RNA - In mid May 2025, we began prospectively monitoring for HAdV-F.

We have detected HAdV-F RNA in 100% of samples from all WWSCAN sites in September 2025. The median concentrations across all sites in September 2025 was is 3,894,059 copies per gram, up ~31% from August 2025.

As a reminder, we are not currently calculating wastewater categories for HAdV-F. In order to calculate wastewater categories we need a longer time series of data to examine trends and levels.

Rotavirus (Rota) RNA- In mid May 2025, we started measuring Rotavirus again. We previously paused measurements of Rota in December 2024 in order to being measuring Mpox clade Ib.

We have detected Rota RNA in ~84% of samples from all WWSCAN sites in September 2025. The median concentrations across all sites in September 2025 was 13,573 copies per gram, down ~23% from August 2025.

Below is the is the population weighted average Rota RNA concentrations (normalized by PMMoV) shown in black from all participating WWSCAN sites across the country over the last 365 days. Note measurements of Rota RNA were paused for a 6 month period (indicated by the dashed red lines in the chart).

As a reminder, we are not currently calculating wastewater categories for Rota. In order to calculate wastewater categories we need a longer time series of data to examine trends and levels.

Other Pathogens of Concern

Candida auris, Hepatitis A, Measles, Mpox clade Ib & Mpox clade II

Candida auris (C.auris) DNA - We have detected C. auris DNA in ~6% of samples from all WWSCAN sites in September 2025. Nationally, C. auris is in the 'LOW' category due to limited detections.

The chart below shows plants in HHS Region 5 as rows, and 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.

Heat map of positive C. auris detections (in red) across HHS Region 5 sites participating in WWSCAN. Blue indicates non-detect.

Below are the C. auris wastewater categories for all WWSCAN sites (recall the category is determined by the frequency of detection):

  • 121 are in the NOT-DETECTED Wastewater Category
  • 9 are in the LOW Wastewater Category
  • 4 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

Hepatitis A (Hep A) RNA - We have detected Hep A RNA in ~8% of samples from all WWSCAN sites in September 2025. Nationally, HepA is in 'LOW' category due to limited detections.

The chart below shows each WWSCAN plant in California as rows, and 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 detection for Hep A RNA.

Heat map of positive HepA detections (in red) across sites from California participating in WWSCAN. Blue indicates non-detect.

Below are the current HepA wastewater categories for all WWSCAN sites (the category is determined by the frequency of detection):

  • 119 are in the NOT-DETECTED Wastewater Category
  • 10 are in the LOW Wastewater Category
  • 5 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

Measles (MeV) RNA - In mid-May 2025, we began prospectively monitoring for MeV. In September 2025, there were 4 positive detections of MeV in wastewater samples (1 in CA, 2 in GA, and 1 in NY). Nationally, MeV is in the 'LOW' category due to limited detections.

Since monitoring began, 19 sites across 14 (CA, CO, CT, FL, GA, IA, ID, IN, KS, MD, MI, NV, NY, UT) states have had at least 1 positive detection of MeV in wastewater samples collected. Below is a map of sites with MeV detections in wastewater since prospective monitoring began.

The WWSCAN program began monitoring for measles in wastewater start mid May 2025. This map only shows data from the sites/states that are covered by the WWSCAN program.

Below are the current MeV wastewater categories for all WWSCAN sites (the category is determined by the frequency of detection):

  • 132 are in the NOT-DETECTED Wastewater Category
  • 2 are in the LOW Wastewater Category
  • 0 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

Mpox clade Ib DNA - In mid December 2024 we began prospective monitoring for Mpox clade Ib. You can find a heat map of the Mpox clade Ib data here. In September 2025, there were no positive detections of Mpox clade Ib. Nationally, Mpox clade Ib is in the 'NOT-DETECTED' category due to no detections.

Below are the Mpox clade Ib wastewater categories for all WWSCAN sites (recall the category is determined by the frequency of detection):

  • 134 are in the NOT-DETECTED Wastewater Category
  • 0 are in the LOW Wastewater Category
  • 0 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

Mpox clade II DNA - There were 7 positive detection of Mpox clade II in September 2025. Nationally, Mpox clade Ib is in the 'LOW' category due to limited detections.

Below are the Mpox clade II wastewater categories for all WWSCAN sites (recall the category is determined by the frequency of detection):

  • 132 are in the NOT-DETECTED Wastewater Category
  • 2 are in the LOW Wastewater Category
  • 0 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 13 do not have enough data to calculate

WWSCAN protocols and methods

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

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

Join us at the next WWSCAN Stakeholder call on October 10, 2025

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

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