Nationwide WastewaterSCAN June 2026 Update

Hi Everyone,

This newsletter contains updates on the WastewaterSCAN program with wastewater samples analyzed by the lab through June 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.

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.

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 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 West Nile Virus in Wastewater Solids

WWSCAN Factsheets and Guidance Documents 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, or Adenovirus Group F.

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

SARS-CoV-2 N gene RNA was detected in ~60% of samples in June 2026. The median SARS-CoV-2 concentration across all sites in June 2026 was 3,960 copies/gram. The median SARS-CoV-2 concentration in June 2026 was down ~23% compared to May 2026. SARS-CoV-2 concentrations are low across all regions. Currently levels of SARS-CoV-2 across all regions are lower than they were this time last year and some of the lowest we've observed since monitoring began.

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 24 months. Evident in this is plot are the very low SARS-CoV-2 levels measures across all regions. In past years we have seen the summer SARS-CoV-2 peak start around mid June/early July so we will continue to monitor as we move through the summer months. Nationally, SARS-CoV-2 is in the 'LOW' category with aggregated measurements showing low concentrations and no trend over the last 3 weeks.

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.

It is important to note that concentrations of SARS-CoV2 RNA in samples have been low, and with low concentrations it is hard to obtain high quality, high confidence sequences.

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 45.7% followed by OTHER (shown in gray) at 29.6% and JN.1 (shown in purple) at 24.8%. The hashed lines indicate weeks with lower confidence sequencing results.

Influenza A (IAV) RNA was detected in 13% of samples in June 2026. The median IAV RNA concentration across all sites in June 2026 was below the limit of detection. IAV concentrations have been trending down over since February (with most sites seeing consistent non-detects) and only a handful of sites are still in seasonal wastewater onset for IAV.

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 no longer being in seasonal onset.

H1 Marker in Influenza A (IAV) The H1 marker in Influenza A was detected in ~3% of samples in June 2026. The H1 median concentration across all sites in June 2026 was below the limit of detection. You can find a heat map of positive H1 detections here. This flu season we saw very low detections of the H1 influenza marker compared to the H3 influenza marker.

H3 Marker in Influenza A (IAV) In June 2026, the H3 marker in influenza A was detected in ~3% of samples. The H3 median concentration across all sites in June 2026 was below the limit of detection. During the 2025-2026 influenza season, the H3 marker appeared to increasingly drive the higher influenza A concentrations. You can find a heat map of positive H3 detections here.

H5 Marker in Influenza A (IAV) As of June 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, 1,100/50,448 samples have tested positive (~2.2% detection rate). In June 2026, there were 5 positive H5 marker detection (all in NJ). 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 now assigned to the 'Pathogens that are not commonly detected ' category logic. Nationally, the H5 influenza marker is in the 'LOW' category due to limited detections.

Influenza B (IBV) RNA was detected in ~17% of samples in June 2026. The median IBV RNA concentration across all sites in June 2026 was below the limit of detection. Concentrations of IBV have been trending down since early March 2026.

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 no longer being in seasonal onset.

Respiratory syncytial virus (RSV) RNA was detected in ~18% of samples in June 2026. The RSV RNA median concentration across all sites in June 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 year (2025-2026) compared to last year (2024-2025). Concentrations of RSV have been trending down since early April 2026.

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 no longer being in seasonal onset.

HMPV (human metapneumovirus) RNA was detected in ~33% of samples in June 2026. The median HMPV RNA concentrations across all sites in June 2026 was below the limit of detection. HMPV concentrations began decreasing mid April 2026.

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 24 months. Evident in the plot HMPV concentrations over the last 2 respiratory virus seasons began decreasing around the same time, mid April - early May. Nationally, HMPV is in the 'LOW' Wastewater Category due to no longer being in seasonal onset.

Enterovirus D68 (EV-D68) RNA was detected in ~1% of samples collected in June 2026. The median concentration across all sites in June 2026 was below the limit of detection. Nationally, EV-D68 is in the 'LOW' Wastewater Category and not in onset.

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. We will continue to monitor EV-D68 levels as we move through the summer season to see if detections start to take off or not.

Parvovirus (Parvo) DNA - We detected Parvo DNA in ~18% of samples from all WWSCAN sites in June 2026. In March 2026 WWSCAN started calculating a wastewater category for Parvo. Parvo is now assigned to the 'Pathogens that are not commonly detected ' category logic. Nationally, Parvo is in the 'LOW' category due to limited detections.

The chart below shows each WWSCAN plant in the San Francisco Bay Area, CA 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 and frequent detections at other sites.

Norovirus GII (HuNoV GII) RNA was detected in 99% of samples analyzed in June 2026. The median Norovirus concentration in June 2026 was down ~37% compared to May 2026. Last year, we saw Norovirus concentrations start to increase in early October 2024 and peak early February 2025. While we saw a slower start to the winter Norovirus wave this year (2025-2026), the pattern is similar to what we observed during the 2023-2024 winter Norovirus wave.

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 24 months. Nationally, Norovirus is in the 'MEDIUM' Wastewater Category with aggregated measurements showing medium concentrations and a downward trend in the last 21 days.

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

HAdV-F RNA was detected in 100% of samples from all WWSCAN sites in June 2026. The median concentrations across all sites in June 2026 was 3,878,897 copies/gram.

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. In March 2026 WWSCAN started calculating a wastewater category for Rota. Rota is now assigned to the 'Commonly detected' category logic.

Rota RNA was detected in ~94% of samples from all WWSCAN sites in June 2026. The median concentrations across all sites in June 2026 was 53,470 copies/gram, down ~74% from May 2026.

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 24 months. The dashed black lines indicate the period of time the Rota assay was paused (~6 months). Evident in the plot is rotavirus concentrations decreasing across all regions. Nationally, Rotavirus is in the 'MEDIUM' Wastewater Category with aggregated measurements showing medium concentrations and a downward trend in the last 21 days.

Candidozyma auris (C.auris) DNA - We detected C. auris DNA in ~3.8% of samples from all WWSCAN sites in June 2026. Nationally, C. auris is in the 'LOW' category due to limited detections.

The chart below shows plants in Kansas 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.

Hepatitis A (Hep A) RNA - We detected Hep A RNA in ~7% of samples from all WWSCAN sites in June 2026. Nationally, HepA is in 'LOW' category due to limited detections.

The chart below shows each WWSCAN plant in New Jersey 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 consistent detections while others have few to no detections of HepA.

Measles (MeV) RNA - In mid-May 2025, WWSCAN began prospectively monitoring for MeV. Since prospective monitoring began, 214/26,664 samples have tested positive (~0.8% detection rate). In June 2026, there were 9 positive detections of MeV in wastewater samples (1 in CA, 1 in FL, 1 in IN, 2 in PA, and 1 in TX). Nationally, MeV is in the 'LOW' category due to limited detections.

Since monitoring began, 49 sites across 23 states (AK, CA, CO, CT, FL, GA, IA, ID, IL, IN, KS, MD, 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 June 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 - There were 4 positive detections of Mpox clade II in June 2026. Nationally, Mpox clade II is in the 'LOW' category due to limited detections.

West Nile Virus RNA - In mid October 2025, WWSCAN began prospective monitoring for West Nile Virus (WNV). Nationally, WNV in the 'NOT-DETECTED' category due to no recent detections. There were no positive detections of WNV in June 2026.

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

Pre-prints and 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