Nationwide WastewaterSCAN October 2026 Update

Hi Everyone,

This newsletter contains updates on the WastewaterSCAN program with wastewater samples analyzed by the lab through October 31, 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 October 2026 include:

• SARS-CoV-2 (SC2): Wastewater levels remain elevated from the late SC2 summer wastewater wave but appear to slowly be trending down across all regions.
• Enterovirus D68 levels in wastewater are elevated: Enterovirus D68 (EV-D68) was detected in 82% of samples in October (for comparison it was only detected in ~74% of samples in September). Typically EV-D68 circulates in the late summer and early fall with major outbreaks occurring biennially (every other year) in the U.S. For reference in 2024 we observed an EV-D68 wastewater wave across all 4 U.S. regions.
• Respiratory virus season is upon us: We are starting to see more positive detections of Influenza A, RSV and HMPV in samples across the network. Influenza A was detected in ~71% of samples in October (IAV was only detected in ~40% of in September). Below is a plot that shows the national aggregate for the 6 core respiratory pathogens WWSCAN monitors over the last 2 years. The orange line indicates where wastewater levels were 365 days ago for reference.

Best,

WastewaterSCAN Team

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

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:

• Frequently Asked Questions on WWSCAN Measurements of bla_NDM nucleic acids in Wastewater Solids
• Frequently Asked Questions on Measurements of Candida auris (C. auris) in Wastewater Solids
• Frequently Asked Questions on WWSCAN Measurements of H5 Marker in Wastewater Solids
• Frequently Asked Questions on WWSCAN Measurements of Hepatitis A Virus (HAV) RNA in Wastewater Solids
• Frequently Asked Questions on WWSCAN Measurements of Measles RNA in Wastewater Solids
  • WWSCAN Measles Protocol -High throughput wild type measles quantification in settled solids using digital RT-PCR
• Frequently Asked Questions on WWSCAN Measurements of Mpox clade Ib in Wastewater Solids
  • WWSCAN Mpox Clade Ib Testing Methods
• Frequently Asked Questions on WWSCAN Measurements of Mycobacterium tuberculosis (TB) nucleic acids in Wastewater Solids
• Frequently Asked Questions on WWSCAN Measurements of West Nile Virus in Wastewater Solids

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

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, bla_NDM, or Mycobacterium tuberculosis.

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

SARS-CoV-2 (SC2) RNA was detected in ~95% of samples in October 2026 (for reference the detection rate in September 2026 was 95%). The median SC2 concentration in October 2026 was down ~19% compared to September 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 July 2026, which started later than we have seen compared to past summer SC2 wastewater waves. SC2 concentrations appear to have peaked in September 2026 in the Midwest, South and West regions and in October 2026 in the Northeast region. 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 a downward trend over the last 3 weeks. As a reminder WWSCAN uses a 365 day look-back period to determine wastewater categories.

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 52.3% followed by LF.7 (shown in yellow) at 17% and JN.1.16 (in pink) at 12.6%. The hashed lines indicate weeks with lower confidence sequencing results.

Influenza A (IAV) RNA was detected in ~71% of samples in October 2026 (for reference the detection rate in September 2026 was ~40%). The median IAV RNA concentration across all sites in October 2026 was 6,782 copies/gram (for reference the median IAV RNA concentration in September 2026 was below the limit of detection).

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 slowly increasing across all regions since late September 2026. Currently IAV wastewater concentrations slightly higher than where they were this time last year. Nationally, Influenza A is in seasonal onset and in the 'HIGH' Wastewater Category due high concentrations.

Below is a year-over-year look at the IAV national aggregate for sites in WWSCAN since monitoring began. Evident in the plot is an earlier start to IAV seasonal onset in wastewater this respiratory virus season (2026-27, shown in red) compared to previous respiratory virus seasons (shown in various shades of gray). This season (2026-26) are elevated concentrations compared to this time last year (2025-26 season in dark gray). During last year's respiratory virus season (2025-26), we did not observed the current IAV wastewater levels we are measuring until early December 2025.

H1 Marker in Influenza A (IAV) The H1 marker in Influenza A was detected in ~58% of samples in October 2026 (for reference the detection rate in September 2026 was ~30%). The H1 median concentration across all sites in October 2026 was 3,512 copies/gram (for reference the median H1 concentration in September 2026 was below the limit of detection). You can find a heat map of positive H1 detections here. Evident in the plot below are higher H1 influenza marker concentrations this year (2026-27) compared to last respiratory virus season (2025-26).

H3 Marker in Influenza A (IAV) In October 2026, the H3 marker in influenza A was detected in ~3% of samples (for reference the detection rate in September 2026 was ~3%). The H3 median concentration across all sites in October 2026 was below the limit of detection. During the 2025-26 respiratory virus season, the H3 marker appeared to increasingly drive the higher IAV concentrations, but this year (2026-27) we are seeing the H1 marker drive higher IAV concentrations. You can find a heat map of positive H3 detections here.

H5 Marker in Influenza A (IAV) As of October 31, 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, 1,110/58,328 samples have tested positive (~1.9% detection rate). In October 2026, there was 1 positive H5 marker detection (in TX). You can find a heat map of positive detections here.

In January 2026 WWSCAN started calculating a wastewater category for the H5 influenza marker. The H5 marker is 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.

Influenza B (IBV) RNA was detected in ~6% of samples in October 2026 (for reference the detection rate in September 2026 was ~3%) . The median IBV RNA concentration across all sites in October 2026 was below the limit of detection. Currently, most sites are seeing consistent non-detects for IBV, which is what we would expect this time of year.

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.

Respiratory syncytial virus (RSV) RNA was detected in ~18% of samples in October 2026 (for reference the detection rate in September 2026 was ~9%). The RSV RNA median concentration across all sites in October 2026 was below the limit of detection. As a reminder, we saw a slower start to the RSV wastewater wave this past respiratory virus season (2025-26) compared to the previous season (2024-25), but it remains to be seen what will happen this season (2026-27). 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, but RSV concentrations and detections are starting to pick up at sites across the South.

HMPV (human metapneumovirus) RNA was detected in ~11% of samples in October 2026 (for reference the detection rate in September 2026 was ~9%). The median HMPV RNA concentrations across all sites in October 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.

Enterovirus D68 (EV-D68) RNA was detected in ~82% of samples collected in October 2026 (for reference the detection rate in September 2026 was ~74%). The median concentration across all sites in October 2026 was 11,700 copies per gram (for reference the median concentration in September 2026 was 10,282 copies/gram) up ~14% from 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 EV-D68 concentrations in the Midwest (shown in red) rose 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 all regions. In early October 2026, we observed 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 and a downward trend in the last 3 weeks. It appears EV-D68 wastewater concentrations may have peaked early October 2026 and are steadily decreasing across all regions.

Parvovirus (Parvo) DNA was detected in ~4% of samples from all WWSCAN sites in October 2026. Nationally, Parvo is in the 'LOW' category due to limited detections.

The chart below shows each WWSCAN plant in Iowa 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 sporadic detections at some sites and no detections are other sites.

Norovirus GII (HuNoV GII) RNA was detected in 100% of samples analyzed in October 2026. The median Norovirus concentration in October 2026 were up ~28% compared to September 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. Current Norovirus wastewater concentrations are slightly below where they were this time last year (Oct 2025).

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

Human Adenovirus Group F (HAdV-F) RNA was detected in ~99% of samples from all WWSCAN sites in October 2026. The median HAdV-F concentration in October 2026 was up ~34% compared to September 2026.

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 ~68% of samples from all WWSCAN sites in October 2026. Earlier this year Rotavirus concentrations peaked in April 2026 and have been remained though the summer months.

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. Rota concentrations are slowly starting to increase in the South.

blaNDM RNA/DNA- New Delhi metallo-beta lactamase (bla_NDM) data went live to the WWSCAN dashboard in early July 2026. bla_NDM 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 bla_NDM 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 bla_NDM. 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 bla_NDM please see: Frequently Asked Questions on WWSCAN Measurements of bla_NDM nucleic acids in Wastewater Solids.

Candidozyma auris (C. auris) DNA was detected C. auris DNA in ~5.4% of samples from all WWSCAN sites in October 2026. Nationally, C. auris is in the 'LOW' category due to limited detections.

The chart below shows plants in Michigan 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 one site have consistent detections.

Hepatitis A (HepA) RNA was detected Hep A RNA in ~4.5% of samples from all WWSCAN sites in October 2026. Nationally, HepA is in 'LOW' category due to limited detections.

The chart below shows each WWSCAN plant in Florida 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 most sites have few to no detections of HepA, but one site have consistent detections.

Measles (MeV) RNA - In mid-May 2025, WWSCAN began prospectively monitoring for MeV. Since prospective monitoring began, 265/34,544 samples have tested positive (0.76% detection rate). In October 2026, there were 16 positive detections of MeV in wastewater samples (1 in CA, 8 in CT, 1 in IN, 3 in IA, 1 in NY and 2 in UT). Nationally, MeV is in the 'LOW' category due to limited detections.

Since monitoring began, 56 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.

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 October 2026, there was 1 positive detections of Mpox clade Ib.

Mpox clade II DNA - In October 2026, there was 1 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, 23/25,552 samples have tested positive (0.09% detection rate) for WNV. There was 1 positive detections of WNV in October 2026 (1 in KY). 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.

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
• High Throughput wild type measles quantification in settled solids using digital RT-PCR
• WWSCAN Probe-based hybridization of wastewater for metagenomic analysis of viruses

Peer-reviewed publications provided WWSCAN methods: 

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

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