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Nationwide WastewaterSCAN September 2026 Update

Hi Everyone,

This newsletter contains updates on the WastewaterSCAN program with wastewater samples analyzed by the lab through September 30, 2026. 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. Some key summaries from September 2026 include:

  • SARS-CoV-2 (SC2): Wastewater levels are still elevated but appear to have peaked in the Midwest, South and West. As of September 30, SC2 concentrations are slowly leveling off at sites in the Northeast.
  • Enterovirus D68 levels in wastewater are on the rise: Enterovirus D68 (EV-D68) was detected in 72% of samples in September (for comparison it was only detected in ~20% of samples in August). Typically EV-D68 circulates in the late summer and early fall with major outbreaks usually biennially (every other year) in the U.S. For reference in 2024 we observed a EV-D68 wastewater wave of across all 4 U.S. regions.
  • Wild-type Measles: In September, there were 11 positive measles samples across 4 states ( 2 in CA, 1 in GA, 6 in IA, and 2 in PA).
  • Respiratory virus season is upon us: We are starting to see more positive detections of Influenza A, RSV and HMPV samples across the network. Influenza A was detected in ~38% of samples in September (IAV was only detected in ~17% of in August).

Best,

WastewaterSCAN Team

Participating Plants

>38 million people covered across 40 states

WWSCAN site coverage map as of September 2026

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.

In mid-July 2026, blaNDM (an antibiotic-resistance gene) and Mycobacterium tuberculosis (TB) were added to the pathogen panel WWSCAN monitors for in early July 2026.

Program Publications

Recent publications, factsheets, FAQs, and more!

WWSCAN Published Body of Work document:

We are excited to share a document that provides an overview of the program’s peer-reviewed scientific literature, organized by topics and themes. Click here to access the WastewaterSCAN published body of work.

WWSCAN FAQs:

WWSCAN Factsheets, Guidance Documents, and Protocols can be found here.

Wastewater Category Logic

As a reminder, WWSCAN categorizes 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 infectious 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  (⬆up,⬇down, ━ no change) 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, Rotavirus)
  • Seasonal pathogens (rarely detected outside of season/outbreaks - includes Influenza A + B, RSV, HMPV, EV-D68)
  • Pathogens that are not commonly detected (rare regardless of season - includes C. auris, HepA, H5 influenza marker, Measles, Mpox clade Ib, Mpox clade II, Parvovirus, West Nile Virus)

*Categories are not currently being calculated for H1 and H3 Influenza markers, Adenovirus Group F, blaNDM, or Mycobacterium tuberculosis.

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 (SC2) RNA was detected in ~95% of samples in September 2026 (for reference the detection rate in August 2026 was 90%). The median SC2 concentration in September 2026 was up ~ 43% compared to August 2026.

SARS-CoV-2 (SC2) detection rate plot over the last 24 months for the WastewaterSCAN network. Positive detection rates are shown in red and non-detection rates are shown in light blue. Note SC2 detection rates have been increasing since July 2026.

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. Evident in this is plot is increasing in SC2 concentrations starting mid-June 2026, which started later than we have seen compared to past summer SC2 wastewater waves. SC2 concentrations appear to have peaked in the Midwest, South and West regions. In this years late summer SC2 wave, both the South and Midwest surpassed concentrations observed during the 2025-2026 winter peak. It is important to note that for sites in the Midwest and Northeast we have typically seen larger SC2 waves during the winter months compared to summer months, whereas at sites in the South and West we've typically see larger SC2 waves during the summer months compared to winter months.

Nationally, SARS-CoV-2 is in the 'HIGH' category with aggregated measurements showing high concentrations and no trend over the last 3 weeks. As a reminder WWSCAN uses a 365 day look-back period to determine wastewater categories.

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. In the top right corner is a zoomed in plot of SARS-CoV-2 contractions over the last 3 months, which shows an increase across all regions starting in July 2026.

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 65.7% followed by LF.7 (shown in yellow) at 8.1%. The hashed lines indicate weeks with lower confidence sequencing results.

SARS-CoV-2 sequencing data from the last 12 months. This plot includes data through the week of September 26, 2026. The hashed lines indicate lower confidence sequencing results.

Other Respiratory Pathogens

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

Influenza A (IAV) RNA was detected in ~38% of samples in September 2026 (for reference the detection rate in August 2026 was ~17%). The median IAV RNA concentration across all sites in September 2026 was below the limit of detection, but we are starting to see increasing IAV sites in the west (AK, CA, HI, NV, UT) and a handful of sites across the Midwest and South.

Influenza A(IAV) detection rate plot over the last 24 months for the WastewaterSCAN network. Positive detection rates are shown in red and Non-detection rates are shown in light blue.

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. Evident in the plot are IAV wastewater concentrations peaking in early January 2026 across all regions. Nationally, Influenza A is in the 'LOW' Wastewater Category due to not being in seasonal onset.

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.

H1 Marker in Influenza A (IAV) The H1 marker in Influenza A was detected in ~28% of samples in September 2026 (for reference the detection rate in August 2026 was ~7%). The H1 median concentration across all sites in September 2026 was below the limit of detection. You can find a heat map of positive H1 detections here. This past flu season (2025-2026) we saw very low detections of the H1 influenza marker compared to the H3 influenza marker.

Plot shows last 12 months of data for the WWSCAN national aggregate of the H1 marker. Note the y-axis scale shows normalized wastewater concentrations for the H1 influenza marker.

H3 Marker in Influenza A (IAV) In September 2026, the H3 marker in influenza A was detected in ~3.4% of samples (for reference the detection rate in August 2026 was ~2%). The H3 median concentration across all sites in September 2026 was below the limit of detection. During the 2025-2026 respiratory virus season, the H3 marker appeared to increasingly drive the higher influenza A concentrations. You can find a heat map of positive H3 detections here.

Plot shows last 12 months of data for the WWSCAN national aggregate. Note the y-axis scale shows normalized wastewater concentrations for the H3 influenza marker.

H5 Marker in Influenza A (IAV) As of September 30, 2026, 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, 1,109/56,292 samples have tested positive (~1.9% detection rate). In September 2026, there were 2 positive H5 marker detection (1 in SD and 1 in TX). You can find a heat map of positive detections here.

Map shows the location of all WWSCAN sites that have had at least 1 positive detection(s) of the H5 marker in Influenza A since prospective monitoring began in May 2024. Map shows data through September 2026.

In January 2026 WWSCAN started calculating a wastewater category for the H5 influenza marker. The H5 marker is now assigned to the 'Pathogens that are not commonly detected ' category logic. Nationally, the H5 influenza marker is in the 'NOT DETECTED' category due no recent detections.

Below is a plot of positive H5 influenza marker sample counts (by week) since monitoring began in May 2024. Evident in the plot are minimal positive detections of the H5 influenza marker since the wave observed Oct 2024 - May 2025.

Plot shows the weekly count of positive wastewater H5 influenza marker detections since WWSCAN began monitoring for H5. Evident in the plot is minimal detections (<10 detections/week) since May 2025.

Influenza B (IBV) RNA was detected in ~2.8% of samples in September 2026 (for reference the detection rate in August 2026 was ~2.8%) . The median IBV RNA concentration across all sites in September 2026 was below the limit of detection. Currently, most sites are seeing consistent non-detects for IBV.

Below is 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. Nationally, Influenza B is in the 'LOW' Wastewater Category due to not being in seasonal onset. For reference in past respiratory virus seasons we typically start to see IBV positive detections increase in December and January.

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.

Respiratory syncytial virus (RSV) RNA was detected in ~8% of samples in September 2026 (for reference the detection rate in August 2026 was ~8%). The RSV RNA median concentration across all sites in September 2026 was below the limit of detection. As a reminder, during last years respiratory virus season the WWSCAN network hit seasonal onset for RSV in early December 2024 and peaked in late January/early February 2025. We saw a slower start to the RSV wastewater wave this past respiratory virus season (2025-2026) compared to last year (2024-2025). Currently, most sites are seeing consistent non-detects for RSV.

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. Nationally, RSV is in the 'LOW' Wastewater Category due to not being in seasonal onset.

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.

HMPV (human metapneumovirus) RNA was detected in ~9% of samples in September 2026 (for reference the detection rate in August 2026 was ~9%). The median HMPV RNA concentrations across all sites in September 2026 was below the limit of detection. During this past years wave HMPV concentrations began decreasing mid April 2026. Currently most sites are seeing consistent non-detects for HMPV.

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. Evident in the plot HMPV concentrations over the 2025-2026 respiratory virus seasons began decreasing mid-April. Nationally, HMPV is in the 'LOW' Wastewater Category due to not being in seasonal onset.

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.

Enterovirus D68 (EV-D68) RNA was detected in ~72% of samples collected in September 2026 (for reference the detection rate in August 2026 was ~20%). The median concentration across all sites in September 2026 was 8,864 copies per gram (for reference the median concentration in August 2026 was below the limit of detection).

EV-D68 detection rate plot since WastewaterSCAN began monitoring in Sept 2023. Positive detection rates are shown in red and non-detect rates are shown in light blue. Note EV-D68 detection rates showed a significant increase in September 2026.

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 24 months. In this plot you can see elevated EV-D68 concentrations across all regions during the 2024-2025 season. EV-D68 concentrations in the Midwest (shown in red) rose again in mid August 2025 before coming down in November 2025, and concentrations in the West (shown in blue) rose in late September 2025 and have come down since the beginning of January 2026. Recently we have seen more positive detections of EV-D68 in samples across the Midwest, Northeast and South. Since mid-September 2026, we are seeing some of the highest concentrations of EV-D68 we've measured since monitoring began back in September 2023.

Nationally, EV-D68 is in the 'HIGH' Wastewater Category due to high concentrations.

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.

Parvovirus (Parvo) DNA was detected in ~3.3% of samples from all WWSCAN sites in September 2026. Nationally, Parvo is in the 'LOW' category due to limited detections.

The chart below shows each WWSCAN plant in Kansas 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. Evident in the plot is limited detections at some sites.

Heat map of positive Parvovirus detections (in red) across sites in Kansas participating in WWSCAN over the last 12 months. Blue indicates non-detect.

Gastrointestinal Pathogens

Norovirus GII, Human Adenovirus Group F, & Rotavirus

Norovirus GII (HuNoV GII) RNA was detected in 99% of samples analyzed in September 2026. The median Norovirus concentration in September 2026 was down <1% compared to August 2026.

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. Nationally, Norovirus is in the 'LOW' Wastewater Category with aggregated measurements showing low concentrations and no trend in the last 21 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.

Human Adenovirus Group F (HAdV-F) RNA was detected in 100% of samples from all WWSCAN sites in September 2026. The median HAdV-F concentration in September 2026 was down ~2% compared to August 2026.

Plot shows last 12 months of HAdV-F for the WWSCAN national aggregate since monitoring resumed. Note the y-axis scale shows normalized wastewater concentrations for HAdV-F.

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 was detected in ~73% of samples from all WWSCAN sites in September 2026. Earlier this year Rotavirus concentrations peaked in April 2026 and have been remained low ever since. Currently we are measuring lower levels of Rotavirus at sites across the network which is what we would typically expect to see this time of year.

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. Nationally, Rotavirus is in the 'LOW' Wastewater Category with aggregated measurements showing low concentrations and no trend in the last 21 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.

Other Pathogens of Concern

blaNDM, Candidozyma auris, Hepatitis A, Measles, Mpox clade Ib + II, Mycobacterium tuberculosis, and West Nile Virus

blaNDM RNA/DNA- New Delhi metallo-beta lactamase (blaNDM) data went live to the WWSCAN dashboard in early July 2026. blaNDM is an antibiotic-resistance gene that makes bacteria resistant to nearly all beta-lactam antibiotics by producing NDM, an enzyme that inactivates these antibiotics. It is extremely versatile in inactivating a broad class of antibiotics and its high genetic mobility. The assay we run will detect blaNDM variants 1-15, 17-31, and 33-47 (Chavda et al., 2016).

As we just started measuring this new pathogen, we are not currently calculating wastewater categories for blaNDM. In order to calculate wastewater categories we need a longer time series of data to examine trends, levels and differences in prevalence across regions. For now, this data can only be viewed in chart mode on the data dashboard. For more information on blaNDM please see: Frequently Asked Questions on WWSCAN Measurements of blaNDM nucleic acids in Wastewater Solids.

Candidozyma auris (C. auris) DNA was detected C. auris DNA in ~4.5% of samples from all WWSCAN sites in September 2026. 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. Evident in the plot below is most sites have few to no detections of C. auris, but several sites have consistent detections.

Heat map shows last 6 months of C. auris wastewater data from WWSCAN sites in HHS Region 5. Blue indicates non-detect.

Hepatitis A (HepA) RNA was detected Hep A RNA in ~3.4% of samples from all WWSCAN sites in September 2026. Nationally, HepA is in 'LOW' category due to limited detections.

The chart below shows each WWSCAN plant in Souther 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. Evident in the plot below is some sites have sporadic detections while others have few to no detections of HepA.

Heat map shows last 6 months of Hepatitis A wastewater data from WWSCAN sites in Southern California. Blue indicates non-detect.

Measles (MeV) RNA - In mid-May 2025, WWSCAN began prospectively monitoring for MeV. Since prospective monitoring began, 248/32,508 samples have tested positive (0.76% detection rate). In September 2026, there were 11 positive detections of MeV in wastewater samples ( 2 in CA, 1 in GA, 6 in IA, and 2 in PA). Nationally, MeV is in the 'LOW' category due to limited detections.

MeV positive sample count by month since WastewaterSCAN began monitoring in May 2025.

Since monitoring began, 53 sites across 25 states (AK, CA, CO, CT, FL, GA, IA, ID, IL, IN, KS, KY, MD, ME, MI, MN, NE, NJ, NV, NY, PA, TX, UT, VA, and VT) 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.

Mpox clade Ib DNA - In mid December 2024, WWSCAN began prospective monitoring for Mpox clade Ib. You can find a heat map of the Mpox clade Ib data here. In September 2026, there were no positive detections of Mpox clade Ib. Nationally, Mpox clade Ib is in the 'NOT-DETECTED' category due to no recent detections.

Mpox clade II DNA - In September 2026, there were no positive detections of Mpox clade II. Nationally, Mpox clade II is in the 'NOT-DETECTED' category due to no recent detections.

Mycobacterium tuberculosis (TB) RNA/DNA - Mycobacterium tuberculosis (TB) data went live to the WWSCAN dashboard in early July 2026. Globally, TB cases have increased in recent years after having previously fallen. There were more than 1 million deaths from TB in 2024. Monitoring TB nucleic-acids in wastewater can help shed light on TB infections across sewersheds in the WWSCAN network.

As we just started measuring this new pathogen, we are not currently calculating wastewater categories for TB. In order to calculate wastewater categories we need a longer time series of data to examine trends, levels, and frequency of detection. For now, this data can only be viewed in chart mode on the data dashboard. For more information on TB please see: Frequently Asked Questions on WWSCAN Measurements of Mycobacterium tuberculosis (TB) nucleic acids in Wastewater Solids

West Nile Virus RNA - Since prospective monitoring began, 21/23,516 samples have tested positive (0.08% detection rate) for WNV. There were 7 positive detections of WNV in September 2026 (1 in IA, 1 in KS, 3 in MI, 1 in NY, and 1 in OH). Nationally, WNV in the 'LOW' category due to limited detections.

Since monitoring began, 14 sites across 11 states (AL, CA, CO, CT, IA, KS, KY, MI, NY, OH and UT) have had at least 1 positive detection of WNV in wastewater samples collected. Below is a map of sites with WNV detections in wastewater since prospective monitoring began.

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

WWSCAN protocols and methods

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

Peer-reviewed publications provided WWSCAN methods: 

Questions about WastewaterSCAN?

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

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