Nationwide WWSCAN Update 4/26/24

Hi everyone,

This newsletter contains updates on the WastewaterSCAN program with wastewater samples analyzed by the lab through April 24, 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.

WastewaterSCAN current funding is ending on June 30, 2024. Good news, funding has been secured to continue monitoring for another year!

New WastewaterSCAN Published Body of Work document:

• We are excited to share a new 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.

Public Health Factsheets:

• Influenza A Fact Sheet: Provides a summary of a November 2023 paper exploring how to analyze wastewater data to extract relevant public health insights on Influenza A. Click here to access the IAV fact sheet.
• RSV Fact Sheet: Provides a summary of a March 2024 paper exploring how to analyze wastewater data to extract relevant public health insights on RSV. Click here to access the RSV fact sheet.

SARS-CoV-2 N gene RNA median concentration across all sites over the last 21 days is 39,921 copies/gram. For reference, the median concentration in March 2024 was 55,508 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 "Low" category with aggregated measurements showing low concentrations and 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.

The Midwest and Northeast regions are currently in the "Medium" category (due to medium concentrations and downward trends in the last 21 days), whereas the Southern and Western regions are in the "Low" category (due to low concentrations).

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):

• 108 are in the LOW Wastewater Category
• 56 are in the MEDIUM Wastewater Category
• 11 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad - San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

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 JN.1 (shown in purple) is the most abundant variant across all sites (73.3%).

The plots show one site each from the Midwest (top left panel), Northeast (top right panel), South (bottom left panel) and West (bottom right panel). Data from the week of April 13th 2024 illustrates that JN.1 (purple) made up the largest proportion of the lineages detected at detected at Ann Arbor (43.5%), Portland, ME (100%), Washington DC (70%) and Central Salt Lake City (92.1%).

Influenza A (IAV) RNA median concentration across all sites over the last 21 days is 7,484 copies/gram. For reference, the median concentration in March 2024 was 8,700 copies/gram. Below is the population weighted average IAV concentrations (normalized by PMMoV) from all participating WWSCAN sites across the country over the last 365 days.

Nationally, IAV is in the "High" category with aggregated measurements showing high concentrations and a downward trend over the past 21 days.

Below are the population-weighted average IAV 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 Midwest, Northeast, and Southern regions are currently in the "High" category (due to high concentrations and downward trends in the last 21 days), whereas the Western region are in the "Medium" category (due to medium concentrations but no trend in the last 21 days).

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):

• 47 are in the LOW Wastewater Category
• 56 are in the MEDIUM Wastewater Category
• 72 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

Influenza B (IBV) RNA has been detected in 798 out of 1,394 samples during the past 21 days (~57% detection rate). IBV RNA median concentration across all sites over the last 21 days is 3,110 copies/gram. For reference, the median concentration in March 2024 was 9,344 copies/gram. 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 <50% of sites showing onset of IBV in wastewater.

Below are the population-weighted average IBV 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.

In the plots below, the Midwest and Northeast region show high concentrations but downward trends over the last 21 days, and the Southern and Western regions are in the Low category due to <50% of sites no longer being in wastewater onset for IBV.

Below are the current Influenza B wastewater categories for all WWSCAN sites, with 35% of sites showing wastewater onset for IBV (recall the category is determined by both the trend and the level when in seasonal onset):

• 109 are in the LOW Wastewater Category
• 13 are in the MEDIUM Wastewater Category
• 53 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

Respiratory syncytial virus (RSV) RSV RNA median concentration across all sites over the last 21 days is below the limit of detection. For reference, the median concentration in March 2024 was 2,716 copies/gram. 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.

Nationally, RSV is in the "Low" category, with <50% of sites showing onset of RSV in wastewater.

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 all regions are no longer in seasonal onset for RSV.

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):

• 163 are in the LOW Wastewater Category
• 7 are in the MEDIUM Wastewater Category
• 5 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

HMPV (human metapneumovirus) RNA median concentrations across all sites over the last 21 days is 11,422 copies/gram. There have been 1,150 positive samples out of 1,394 samples during the past 21 days (82% 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 "High" category with >50% of sites showing onset of HMPV in wastewater and aggregated measurements showing high concentrations but no over the last 21 days.

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) over the last 365 days.

The plots below show relatively high concentrations across all US regions.

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

• 50 are in the LOW Wastewater Category
• 2 are in the MEDIUM Wastewater Category
• 123 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

Human Parainfluenza (HPIV) RNA has been detected in ~81% of samples collected from WWSCAN sites. The HPIV median concentration across all sites over the last 21 days is 8,400 copies/gram. Below is the population weighted average HPIV RNA concentrations (normalized by PMMoV) from all participating WWSCAN sites across the country since we started monitoring in fall 2023.

Nationally, HPIV is in the "Medium" category with aggregated measurements showing medium concentrations and a downward trend over the last 21 days.

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

• 50 are in the LOW Wastewater Category
• 60 are in the MEDIUM Wastewater Category
• 65 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

Enterovirus D68 (EV-D68) RNA was rarely detected (~17%) 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 chart below plants in Florida as rows, and the days as columns (labeled at the bottom axis). White indicates no samples, blue is non-detect for EV-D68 DNA and red is detect for EV-D68 RNA.

Below are the current EV-D68 wastewater categories for all WWSCAN sites (recall the category is determined by the frequency of detection):

• 149 are in the LOW Wastewater Category
• 26 are in the MEDIUM Wastewater Category
• 0 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

Norovirus GII (HuNoV GII) RNA was detected in all samples analyzed in the last three weeks. The median concentration across all sites over the last 21 days is 12,812,428 copies/gram (for reference median concentration in March 2024 was 11,226,796 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 the "High" category with aggregated measurements showing high concentrations and a downward 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).

Most regions are in the "High" category except the West, which is in the "Medium" category. The aggregated measurements in the Midwest & Northeast show a downward trend but is no significant upward or downward trend in the South & West.

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

• 15 are in the LOW Wastewater Category
• 42 are in the MEDIUM Wastewater Category
• 118 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

Rotavirus RNA median concentrations across all sites over the last 21 days is 311,682 copies/gram. For reference, the median concentration in February 2024 was 278,820 copies/gram. Below are the Rotavirus RNA concentrations (normalized by PMMoV) from all participating WWSCAN sites across the country over about the last 6 months. The population-weighted average is shown.

Nationally, Rotavirus is in "High" category with aggregated measurements showing high concentrations with a downward trend in last 21 days.

Below are the population-weighted average Rotavirus 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" Wastewater Category for Rotavirus with high concentrations and a downward trend over the last 21 days.

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

• 12 are in the LOW Wastewater Category
• 57 are in the MEDIUM Wastewater Category
• 106 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

Mpox DNA We have only detected mpox DNA in 8 samples from all sites in the past 21 days. Nationally, Mpox is in the "Low" category due to limited detections.

The chart below plants in HHS region 1 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.

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

• 175 are in the LOW Wastewater Category
• 0 are in the MEDIUM Wastewater Category
• 0 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

Candida auris (C.auris) DNA - We have detected C. auris DNA in 2.6% of samples from all WWSCAN sites over the past three weeks. Nationally, C. auris is in the "Low" category due to limited detections.

The chart below shows each WWSCAN plant in HHS Region 6 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.

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

• 172 are in the LOW Wastewater Category
• 3 is in the MEDIUM Wastewater Category
• 0 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

Hepatitis A (Hep A) RNA - We have detected Hep A RNA in 17.2% of samples from all WWSCAN sites over the past three weeks. Nationally, HepA is in "Low" category due to limited detections.

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.

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

• 143 are in the LOW Wastewater Category
• 32 are in the MEDIUM Wastewater Category
• 0 are in the HIGH Wastewater Category
• 16 do not have enough data to calculate (Fremont, CA; Pacifica, CA; Petaluma, CA; Sausalito, CA; South San Diego, CA; West Railroad, San Rafael, CA; Blue Plains, Washington, DC; South Miami, FL; College Park, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; Gautier, MS; Pascagoula Moss Point, MS; Provo, UT; South Burlington, VT)

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

To see find a complete list of peer-reviewed publications utilizing the WWSCAN data here.

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