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Nationwide WWSCAN Update 5/24/24

Hi everyone,

This newsletter contains updates on the WastewaterSCAN program with wastewater samples analyzed by the lab through May 23, 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

Participating Plants

191 plants from 40 states and Washington DC are sampling, which represents ~13.5% of the US population

WastewaterSCAN Participant Stats:

  • 191 plants sampling
  • 45,350,248 people covered through sampling efforts
  • 40 states and Washington DC represented
WastewaterSCAN site coverage map

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.

Program Publications

New papers, fact sheets, and more!

New WastewaterSCAN Published Body of Work document:

New Peer-Reviewed Scientific Publications:

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.

COVID-19

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

SARS-CoV-2 N gene RNA median concentration across all sites over the last 21 days is 41,824 copies/gram. For reference, the median concentration in April 2024 was 38,787 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 "High" category with aggregated measurements showing medium concentrations and an upward 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 is in the "High" category due to medium concentrations and an upward trend in the last 21 days. The Northeast is in the "Low" category due to low concentrations and no trend in the last 21 days. The Southern is in the "Medium" category is due to low concentrations and an upward trend in the last 21 days. The Western region is the "Medium" category due to medium 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, WV and Washington DC. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

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):

  • 78 are in the LOW Wastewater Category
  • 57 are in the MEDIUM Wastewater Category
  • 32 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

IAV Wastewater Categories. This map includes sample collection data through May 23, 2024. 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, WV and Washington DC. 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 JN.1 (shown in purple) is the still most abundant variant across all sites (51.2%).

Data from the week of May 11th 2024 illustrates that JN.1 (purple) made up the largest proportion of the lineages detected at detected at Lincoln, NE (86.2%) and Central Salt Lake City (58.7%). Whereas KP.2 (slate blue) made up the largest proportion of the lineages detected at detected at Portland, ME (26.7%) and College Park, GA (65.6%)

Plots show 1 site from the Midwest US (top left panel), West US (top right panel), Northeast US (bottom left panel) and South US (bottom right panel)

Other Respiratory Pathogens

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

Influenza A (IAV) RNA median concentration across all sites over the last 21 days is 5,807 copies/gram. For reference, the median concentration in April 2024 was 7,298 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 "Medium" category with aggregated measurements showing medium 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.

All regions are currently in the "Medium" category due to medium concentrations. The Northeast, Southern and Western regions have a downward trend over the last 21 days, whereas the Midwest has no significant trend upwards or downwards.

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, WV and Washington DC. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

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):

  • 90 are in the LOW Wastewater Category
  • 57 are in the MEDIUM Wastewater Category
  • 20 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

IAV Wastewater Categories. This map includes sample collection data through May 23, 2024. 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, WV and Washington DC. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

Influenza B (IBV) RNA has been detected ~37% samples in the last 21 days. IBV RNA median concentration across all sites over the last 21 days is below the limit of detection. For reference, the median concentration in April 2024 was 3,346 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 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):

  • 146 are in the LOW Wastewater Category
  • 6 are in the MEDIUM Wastewater Category
  • 14 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

IBV Wastewater Categories. This map includes sample collection data through May 23, 2024. 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, WV and Washington DC. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

Respiratory syncytial virus (RSV) RSV RNA median concentration across all sites over the last 21 days is below the limit of detection. 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 current RSV wastewater categories for all WWSCAN sites (recall the category is determined by both the trend and the level when in seasonal onset):

  • 165 are in the LOW Wastewater Category
  • 1 are in the MEDIUM Wastewater Category
  • 1 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

RSV Wastewater Categories. This map includes sample collection data through May 23, 2024. 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, WV and Washington DC. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

HMPV (human metapneumovirus) RNA median concentrations across all sites over the last 21 days is 6,923 copies/gram. There have been detected in ~73% of samples over the last 21 days. 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.

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, WV and Washington DC. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

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

  • 69 are in the LOW Wastewater Category
  • 7 are in the MEDIUM Wastewater Category
  • 91 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

HMPV Wastewater Categories. This map includes sample collection data through May 23, 2024. 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, WV and Washington DC. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

Enterovirus D68 (EV-D68) RNA was rarely detected (~19%) 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 Texas 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):

  • 140 are in the LOW Wastewater Category
  • 27 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

EV-D68 Wastewater Categories. This map includes sample collection data through May 23, 2024. 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, WV and Washington DC. Western Region includes: AK, CA, CO, HI, ID, NV, UT, WA.

Gastrointestinal Pathogens

Norovirus GII and Rotavirus

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 11,289,671 copies/gram (for reference median concentration in April 2024 was 13,212,511 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.

Norovirus is in the "High" category nationally with aggregated measurements showing high concentrations and no significant trend up or down 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).

All regions are in the "High" category. The aggregated measurements in the Midwest show an upward trend while there is no significant upward or downward trend in the remaining regions.

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, WV and Washington DC. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

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

  • 11 are in the LOW Wastewater Category
  • 41 are in the MEDIUM Wastewater Category
  • 115 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

Norovirus Wastewater Categories. This map includes sample collection data through May 23, 2024. Each dot represents a single site and the four US Census regions are outlined in gray. 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, WV and Washington DC. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

Rotavirus RNA median concentrations across all sites over the last 21 days is 234,327 copies/gram. For reference, the median concentration in April 2024 was 347,466 copies/gram. Below are the Rotavirus RNA concentrations (normalized by PMMoV) from all participating WWSCAN sites across the country. The population-weighted average is shown.

Nationally, Rotavirus is in "High" category with aggregated measurements showing high concentrations with a downward trend in the 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 have high concentrations in the "High" Wastewater Category for Rotavirus. South have had a downward trend over the last 21 days while the Midwest, Northeast and Western regions have no trend upward or downward.

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

  • 16 are in the LOW Wastewater Category
  • 57 are in the MEDIUM Wastewater Category
  • 94 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

Rotavirus Wastewater Categories. This map includes sample collection data through May 23, 2024. Each dot represents a single site and the four US Census regions are outlined in gray. 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, WV and Washington DC. Western States: AK, CA, CO, HI, ID, NV, UT, WA.

Other Pathogens of Concern

Mpox, Candida auris, and Hepatitis A

Mpox DNA We have only detected mpox DNA in 1 sample 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 2 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):

  • 167 are in the LOW Wastewater Category
  • 0 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

Candida auris (C.auris) DNA - We have detected C. auris DNA in 1.6% 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 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.

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

  • 165 are in the LOW Wastewater Category
  • 2 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

Hepatitis A (Hep A) RNA - We have detected Hep A RNA in ~16% 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 9 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.

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

  • 145 are in the LOW Wastewater Category
  • 22 are in the MEDIUM Wastewater Category
  • 0 are in the HIGH Wastewater Category
  • 24 do not have enough data to calculate (Anchorage, AK; Fremont, CA; Newark, CA; Pacifica, CA; Petaluma, CA; San Rafael, CA; Sausalito, CA; South San Diego, CA; Union City, CA; Woodland, CA; South Miami, FL; College Park, GA; RM Clayton, Atlanta, GA; South River, Atlanta, GA; Utoy Creek, Atlanta, GA; Hilo, HI; P20, Kansas City, KS; Louisville, KY; York, ME; Traverse City, MI; Gautier, MS; Pascagoula Moss Point, MS; Ithaca, NY; Sunnyvale, TX)

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 June 14th, 2024

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

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Jamie Larson
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