Component 1 - STLT Health Depts

[NCEZID] National Wastewater Surveillance System for COVID-19 and other Infectious Disease Targets of Public Health Concern

Attachment-04_Component-1_BioSample_ww_template_v1.9_NWSS.xlsx

Component 1 - STLT Health Depts

OMB: 0920-1422

Document [xlsx]
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Overview

ww template
GUIDANCE
vocabulary


Sheet 1: ww template

# This is a submission template for batch deposit of 'SARS-CoV-2: wastewater surveillance; version 1.0' samples to the NCBI BioSample database (https://www.ncbi.nlm.nih.gov/biosample/).

























































# GREEN fields are mandatory for NCBI. Your submission will fail if any mandatory fields are not completed. If information is unavailable for any mandatory field, please enter 'not collected', 'not applicable' or 'missing' as appropriate.

























































# YELLOW fields are optional. Leave optional fields empty (or delete them) if no information is available.

























































# Purple fields are highly recommended for US submitters

























































# Hover over field name to view definition, or see https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/.

























































# CAUTION: Be aware that Excel may automatically apply formatting to your data. In particular, take care with dates, incrementing autofills and special characters like / or -. Doublecheck that your text file is accurate before uploading to BioSample.

























































# TO MAKE A SUBMISSION:

























































# 1. Complete this template table.

























































# 2. Upload the file on the 'Attributes' tab of the BioSample Submission Portal at https://submit.ncbi.nlm.nih.gov/subs/biosample/.

























































# If you have any questions, please contact us at [email protected].

























































#

























































Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. *sample_name Title of the sample. sample_title The accession number of the BioProject(s) to which the BioSample belongs. If the BioSample belongs to more than one BioProject, enter multiple bioproject_accession columns. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345. bioproject_accession The most descriptive organism name for this sample (to the species, if possible). It is OK to submit an organism name that is not in our database. In the case of a new species, provide the desired organism name, and our taxonomists may assign a provisional taxID. In the case of unidentified species, choose the appropriate Genus and include 'sp.', e.g., "Escherichia sp.". When sequencing a genome from a non-metagenomic source, include a strain or isolate name too, e.g., "Pseudomonas sp. UK4". For more information about providing a valid organism, including new species, metagenomes (microbiomes) and metagenome-assembled genomes, see https://www.ncbi.nlm.nih.gov/biosample/docs/organism/. *organism the date on which the sample was collected; date/time ranges are supported by providing two dates from among the supported value formats, delimited by a forward-slash character; collection times are supported by adding "T", then the hour and minute after the date, and must be in Coordinated Universal Time (UTC), otherwise known as "Zulu Time" (Z); supported formats include "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY" or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm", "YYYY-mm-ddThh:mm:ss"; e.g., 30-Oct-1990, Oct-1990, 1990, 1990-10-30, 1990-10, 21-Oct-1952/15-Feb-1953, 2015-10-11T17:53:03Z; valid non-ISO dates will be automatically transformed to ISO format *collection_date For grab samples: the time of day the sample was collected in your timezone. 1-12 AM - 1-12 PM. collection_time Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps" *geo_loc_name Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. *isolation_source collection_site_id project_name Name of persons or institute who collected the sample collected_by The reason the sample was collected purpose_of_ww_sampling The type of site where the wastewater sample was collected Allowed values: correctional facility, long-term care facility, hospital, child day care, school, college or university, social services shelter, other residential building, ship, airplane, septic tank, other holding tank, wastewater treatment plant, wastewater lagoon, sewer pipeline, other, restricted access, not applicable, not collected, not provided, missing ww_sample_site Daily volumetric flow through collection site, in units of liters per day, e.g., 110000000. ww_flow instantaneous_flow Number of persons contributing wastewater to this sample collection site; if unknown, estimate to the nearest order of magnitude, e.g., 10000. If no estimate is available, input NA. *ww_population A jurisdiction identifer that can be used to support linking the sample to a public health surveillance system, e.g., va ww_surv_jurisdiction Source of value specified in 'ww_population', e.g., wastewater utility billing records, population of jurisdiction encompassing the wastewater service area, census blocks clipped to wastewater service area polygon ww_population_source The wastewater matrix that was sampled *ww_sample_matrix Type of wastewater sample collected *ww_sample_type collection_volume Duration of composite sample collected, in units of hours, e.g., 24. Specify integer values. If the sample is not a composite sample, use 0. *ww_sample_duration Temperature of the wastewater sample at the time of sampling in Celsius, e.g., 25. ww_temperature pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid, e.g., 7.2 ww_ph Percentage of industrial effluents received by wastewater treatment plant, e.g., 10 ww_industrial_effluent_percent Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample or derived from the conductivity measurement (practical salinity) in milligrams per liter, e.g., 100. ww_sample_salinity Total concentration of solids in raw wastewater influent sample including a wide variety of material, such as silt, decaying plant and animal matter in milligrams per liter, e.g., 500. ww_total_suspended_solids The sample ID used for submission to a public health surveillance system (e.g., CDC's National Wastewater Surveillance System), e.g., s123456 ww_surv_system_sample_id Describe any process of pre-treatment that removes materials that can be easily collected from the raw wastewater, e.g., flow equilibration basin promotes settling of some solids ww_pre_treatment The time primary sludge remains in tank, in hours, e.g., 4. ww_primary_sludge_retention_time Any laboratory processing applied to the sample from the point of collection through RNA extraction. specimen_processing Identifer used to distinguish specimen processing treatments specimen_processing_id Detailed description of the speciman processing steps employed (free text). specimen_processing_details The protocol used to process the wastewater sample. Processing includes laboratory procedures prior to and including nucleic acid purification (e.g., pasteurization, concentration, extraction, etc). Specify a reference, website, or brief description. ww_processing_protocol concentration_method extraction_method extraction_control The name of an organism, gene, or compound used as an endogenous wastewater control, e.g., pepper mild mottle virus ww_endog_control_1 The concentration of the endogenous control specified in 'ww_endog_control_1' on a per wastewater unit basis, e.g., 700000000 ww_endog_control_1_conc The protocol used to quantify 'ww_endog_control_1'. Specify a reference, website, or brief description. ww_endog_control_1_protocol The units of the value specified in 'ww_endog_control_1_conc', e.g., copies/L wastewater ww_endog_control_1_units The name of an organism, gene, or compound used as an endogenous wastewater control, e.g., crassphage ww_endog_control_2 The concentration of the endogenous control specified in 'ww_endog_control_2' on a per wastewater unit basis, e.g., 140000000 ww_endog_control_2_conc The protocol used to quantify 'ww_endog_control_2'. Specify a reference, website, or brief description. ww_endog_control_2_protocol The units of the value specified in 'ww_endog_control_2_conc', e.g., copies/L wastewater ww_endog_control_2_units Taxonomic name of the surveillance target. For the COVID-19 response, use 'SARS-CoV-2'. *ww_surv_target_1 Is genetic material of the surveillance target(s) known to the submitter to be present in this wastewater sample? Presence defined as microbiological evidence of the target organism in the wastewater sample, such as genetic- or culture-based detection. *ww_surv_target_1_known_present The protocol used to quantify 'ww_surv_target_1'. Specify a reference, website, or brief description. ww_surv_target_1_protocol The concentration of the wastewater surveillance target specified in 'ww_surv_target_1' on a per wastewater unit basis, e.g., 200000 ww_surv_target_1_conc The units of the value specified in 'ww_surv_target_1_conc', e.g., copies/L wastewater ww_surv_target_1_conc_unit The name of the gene quantified for the the surveillance target specified in 'ww_surv_target_1', e.g., N gene ww_surv_target_1_gene ww_surv_target_2 ww_surv_target_2_conc ww_surv_target_2_conc_unit ww_surv_target_2_gene ww_surv_target_2_known_present The reason the sample was sequenced, e.g., identification of mutations within a specific region, presence of clinically known mutations, or diversity of mutations across entire genome purpose_of_ww_sequencing The name of the agency that generated the sequence, e.g., Centers for Disease Control and Prevention sequenced_by free text - include any extra useful information here. description
6493.P   PRJNA839090 wastewater metagenome 9/21/2022
USA: New Jersey Wastewater 8675 GenomeTrakr Biobot Analytics public health surveillance community-level wastewater treatment plant 110000000
40000 nj   post grit removal composite
24           6493.P           Pasteurized; virus captured with Ceres NanoTrap particles; nucleic acid extracted with MagMAX DNA/RNA binding beads ceres nanotrap thermo magmax microbiome ultra nucleic acid isolation kit BRSV



        SARS-CoV-2 yes RT-qPCR Detection of SARS-CoV-2 from Wastewater Using the AB 7500 (protocols.io) 35 cycles (Ct value) N1             Ginkgo Bioworks clinical laboratory
4119.D   PRJNA839090 wastewater metagenome 9/20/2022
USA: Vermont Wastewater 30 GenomeTrakr Biobot Analytics public health surveillance community-level wastewater treatment plant
36 liters per day 3500 vt   raw wastewater grab
0           4119.D           Pasteurized; virus captured with Ceres NanoTrap particles; nucleic acid extracted with MagMAX DNA/RNA binding beads ceres nanotrap thermo magmax microbiome ultra nucleic acid isolation kit BRSV



        SARS-CoV-2 yes ddPCR detection of SARS-CoV-2 using the BioRad PREvalence Kit on the BioRad QXOne 20000 copies/L N1             Ginkgo Bioworks clinical laboratory
3990.C   PRJNA839090 wastewater metagenome 9/21/2022   USA: Arkansas Wastewater 9 GenomeTrakr; LFFM ww project Biobot Analytics public health surveillance community-level wastewater treatment plant 12000000
5500 ar   raw wastewater composite   24           3990.C           Pasteurized; virus captured with Ceres NanoTrap particles; nucleic acid extracted with MagMAX DNA/RNA binding beads ceres nanotrap thermo magmax microbiome ultra nucleic acid isolation kit BRSV



        SARS-CoV-2 yes GT-Digital SARS-CoV-2 Wastewater Surveillance Assay For QIAcuity dPCR 50000 copies/L N2             Ginkgo Bioworks clinical laboratory

Sheet 2: GUIDANCE

Field Name Definition NWSS Requirement GenomeTrakr requirement US FDA guidance for LFFM-funded laboratories US CDC guidance for ELC-funded laboratories Example Data US NWSS Data Dictionary NCBI validation (value format) Field Source Notes/Questions PHA4GE synonym
sample_name Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. mandatory mandatory Biosamples are created at the extraction level (each RNA extraction will get a unique BioSample ID). Create a base ID for each sample collection (for example, LABID_001), then add an index to represent each extraction (e.g. LABID_001.01). Every Sample Name from a single Submitter must be unique. wwtp12_raw_20210609 [none] NA
SARS-CoV-2: clinical or host-associated

sample_title Title of the sample. If no value is specified, this will be imputed as “SARS-CoV-2: wastewater surveillance sample from Wastewater metagenome”. optional optional Enter the following "SARS-CoV-2: wastewater surveillance sample from Wastewater metagenome" SARS-CoV-2: wastewater surveillance sample from Wastewater metagenome [none] NA
SARS-CoV-2: clinical or host-associated

isolation_source Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. mandatory mandatory Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. Select "Wastewater" from the pick list. Wastewater [none] NA {text} PHA4GE

collection_date The date on which the sample was collected; date/time ranges are supported by providing two dates from among the supported value formats, delimited by a forward-slash character; collection times are supported by adding "T", then the hour and minute after the date, and must be in Coordinated Universal Time (UTC), otherwise known as "Zulu Time" (Z); supported formats include "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY" or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm", "YYYY-mm-ddThh:mm:ss"; e.g., 30-Oct-1990, Oct-1990, 1990, 1990-10-30, 1990-10, 21-Oct-1952/15-Feb-1953, 2015-10-11T17:53:03Z; valid non-ISO dates will be automatically transformed to ISO format. mandatory mandatory The date on which the sample was collected; date/time ranges are supported by providing two dates from among the supported value formats, delimited by a forward-slash character. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". Sample pooling guidance: enter the latest collection date within the pooled samples. 5/1/2021 sample_collect_date sample_collect_date {timestamp} SARS-CoV-2: clinical or host-associated

collection_time For grab samples: the time of day the sample was collected in your timezone. 1-12 AM - 1-12 PM. optional optional For grab samples: the time of day the sample was collected in your timezone. 1:00 AM - 12:00 PM
8:00 AM sample_collect_time custom attribute


geo_loc_name Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps". mandatory mandatory Geographical origin of the sample. Use the appropriate country names from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location. Note that US state should be spelled out directly following the colon. USA:Virginia [none] wwtp_jurisdiction {term}:{term}:{text} SARS-CoV-2: clinical or host-associated

organism The most descriptive organism name for this sample (to the species, if possible). It is OK to submit an organism name that is not in our database. In the case of a new species, provide the desired organism name, and our taxonomists may assign a provisional taxID. In the case of unidentified species, choose the appropriate Genus and include 'sp.', e.g., "Escherichia sp.". When sequencing a genome from a non-metagenomic source, include a strain or isolate name too, e.g., "Pseudomonas sp. UK4". For more information about providing a valid organism, including new species, metagenomes (microbiomes) and metagenome-assembled genomes, see https://www.ncbi.nlm.nih.gov/biosample/docs/organism/. mandatory mandatory For all wastewater surveillance samples using this attribute package, use "wastewater metagenome", even if metagenomic sequencing was not applied to this sample. wastewater metagenome [none] Enter the following "SARS-CoV-2: wastewater surveillance sample from Wastewater metagenome
SARS-CoV-2: clinical or host-associated

specimen_processing Any laboraotry processing applied to the sample from the point of collection through RNA extraction. optional optional Critical for interpreting data. If the sample is a replicate, specify the type of replicate using the options in the dropdown.
technical replicate, biological replicate NA custom attribute
biological replicate: when processing occurs prior to concentration (e.g. multiple grabs taken at the same time or multiple aliquots from the same grab); technical replicate: when different concentration, extraction, storage, etc. protocols have occurred on the same grab or composite sample specimen processing
specimen_processing_id Identifer used to distinguish specimen processing treatments optional optional Identifer used to distinguish specimen processing treatments, for example IDs used to indentify replicates.
replicate_1, rep_1 NA custom attribute


specimen_processing_details Detailed description of the speciman processing steps employed. optional optional Detailed description of the speciman processing steps employed.
Grabbed sample was separated into two, 50mL aliquots NA custom attribute

speciman processing details
ww_surv_target_1 Taxonomic name of the surveillance target. For the COVID-19 response, use 'SARS-CoV-2'. mandatory mandatory If a target for wastewater surveillance activity known, please list all. If looking for emerging pathogens, use "unknown". If no target specified, put "NA". For the COVID-19 response, use "SARS-CoV-2". For corresponding SRA, also include a custom variable with this field name (i.e., "ww_surv_target_1") and value (e.g., "SARS-CoV-2") to link the SRA to BioSample in the event multiple SRA's and targets correspond to the same BioSample. SARS-CoV-2 [none] pcr_target {text} Wastewater surveillance-specific

ww_surv_target_1_known_present Is genetic material of the surveillance target(s) known to the submitter to be present in this wastewater sample? Presence defined as microbiological evidence of the target organism in the wastewater sample, such as genetic- or culture-based detection. mandatory mandatory Select from "yes" or "no" picklist. Presence defined as microbiological evidence of the target organism in the wastewater sample, such as genetic- or culture-based detection. yes [none] NA no | yes Wastewater surveillance-specific

ww_sample_matrix The wastewater matrix that was sampled. mandatory mandatory Select a value from the pick list.
raw wastewater sample_matrix raw wastewater | sewer pipeline sediments | post grit removal | primary sludge | primary effluent | secondary sludge | secondary effluent | other | restricted access | not applicable | not collected | not provided | missing Wastewater surveillance-specific

ww_sample_duration Duration of composite sample collected, in units of hours, e.g., 24. Specify integer values. If the sample is not a composite sample, use 0. mandatory mandatory Specify integer values. If the sample is not a composite sample, use 0.
24 composite_freq {integer}{text} Wastewater surveillance-specific

ww_sample_type Type of wastewater sample collected mandatory mandatory Select a value from the pick list.
composite sample_type grab | composite | swab-grab | swab-composite | restricted access | not applicable | not collected | not provided | missing Wastewater surveillance-specific

ww_population Number of persons contributing wastewater to this sample collection site; if unknown, estimate to the nearest order of magnitude, e.g., 10000. If no estimate is available, input NA. mandatory mandatory Specify a numeric value. If unknown, estimate to the nearest order of magnitude. If no estimate is available, input "NA". US CDC NWSS recommendation: if population is less than 3,000 people, input 3000. 93000 population_served population_served {integer} Wastewater surveillance-specific

collection_site_id ID that uniquely identifies the sample collection site among other sample collection sites in this BioProject. It must be unique at the level of the submitter's data BioProject. optional mandatory ID that uniquely identifies the sample collection site among other sample collection sites in this BioProject. It must be unique at the level of the submitter's data BioProject. Where possible, and with agreement from the facility, include the full name of the wastewater treatment plant. If annonymity is requested, create a masking ID to use for all samples collected at this site (e.g. AL-plant-1). Use an anonymized ID that does not identify the wastewater utility unless you have obtained written permission from the utility to publish the utility's name. Use only numbers, English alphabetic characters, underscores, and hyphens (white space is not allowed). C.C. Williams Wastewater Treatment Plant, or ALplant.1 NA custom attribute Wastewater surveillance-specific

project_name A concise name that describes the overall project, for example "Analysis of sequences collected from Antarctic soil" optional mandatory Name of the coordinated sequencing efforts or project within which the sequencing was organized. For FDA LFFM-funded laboratories, specify which funding year (FY) for which the isolate was collected. FY1, FY2, etc. GenomeTrakr; LFFM ww project
NA custom attribute


bioproject_accession The accession number of the BioProject(s) to which the BioSample belongs. If the BioSample belongs to more than one BioProject, enter multiple bioproject_accession columns. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345. mandatory mandatory Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. PRJNA99999 [none] NWSS Umbrella linked local BioProject
SARS-CoV-2: clinical or host-associated

collected_by Name of persons or institute who collected the sample optional mandatory Name of person, lab, organization, or jurisdiction that led the program or study for which the wastewater sample was collected. virginia department of health [none] NA {text} SARS-CoV-2: clinical or host-associated

description Description of the sample. optional optional Opportunity to add additional free text metadata (was the sample a replicate?)
[Any useful descriptive metadata.] NA {text} SARS-CoV-2: clinical or host-associated

sequenced_by The name of the agency that generated the sequence, e.g., Centers for Disease Control and Prevention. optional mandatory Name of the laboratory that generated the sequence data
virginia division of consolidated laboratory services NA {text} SARS-CoV-2: clinical or host-associated

ww_sample_site The type of site where the wastewater sample was collected. optional mandatory Select a value from the pick list.
wastewater treatment plant institution_type correctional facilility | long-term care facility | hospital | child day care | school | college or university | social services shelter | other residential building | ship | airplane | airport | septic tank | other holding tank | wastewater treatment plant | wastewater lagoon | sewer pipeline | food or meat processing plant | other: define Wastewater surveillance-specific
environmental site
ww_surv_jurisdiction A jurisdiction identifer that can be used to support linking the sample to a public health surveillance system, e.g., va. optional optional A jurisdiction identifer that can be used to support linking the sample to a public health surveillance system. For GenomeTrakr labs: this information should be captured in geo_loc_name, leave this field empty. va reporting_jurisdiction reporting_jurisdiction  {text} Wastewater surveillance-specific

ww_surv_system_sample_id The sample ID used for submission to a public health surveillance system (e.g., CDC's National Wastewater Surveillance System), e.g., s123456. mandatory optional Not relevant for GenomeTrakr labs, unless a laboratory is also reporting results of this sample to NWSS. s123456 sample_id sample_id {text} Wastewater surveillance-specific

ww_population_source Source of value specified in 'ww_population', e.g., wastewater utility billing records, population of jurisdiction encompassing the wastewater service area, census blocks clipped to wastewater service area polygon. optional optional Provide a brief description. The purpose of this field is to provide a sense of the accuracy of the value specified in 'population_served'. Examples include: wastewater utility billing records, population of jurisdiction encompassing the wastewater service area, census block approximation of service area polygon. Also, if 'ww_population' is suppressed (e.g., specified as 3000 to suppress a true value less than 3000), use the term "suppressed" (e.g., "wastewater utility billing records; suppressed"). census block approximation of service area polygon [none] NA {text} Wastewater surveillance-specific

purpose_of_ww_sampling The reason the sample was collected. optional mandatory The reason the sample was collected. For GenomeTrakr labs, this is likely "public health surveillance community-level" public health surveillance community-level [none] NA public health surveillance community-level | public health surveillance institution-level | public health surveillance building-level | research | other | restricted access | not applicable | not collected | not provided | missing Wastewater surveillance-specific

purpose_of_ww_sequencing The reason the sample was sequenced, e.g., identification of mutations within a specific region, presence of clinically known mutations, or diversity of mutations across entire genome. optional optional Describe the reason(s) for sequencing the wastewater sample, which will be dependent on the methods used. For example, identification of mutations within a specific region, presence of clinically known mutations, or diversity of mutations across entire genome. detection of target organism by RT PCR or ddPCR [none] NA {text} Wastewater surveillance-specific

ww_processing_protocol The protocol used to process the wastewater sample. Processing includes laboratory procedures prior to and including nucleic acid purification (e.g., pasteurization, concentration, extraction, etc). Specify a reference, website, or brief description. optional optional Populate the individual protocol attributes instead of summarizing here.

pretreatment_specify {text} Wastewater surveillance-specific

collection_volume
optional optional Enter the volume of the sample collected
1L NA custom attribute


concentration_method The method used to concentrate a target organism, nucleic acid, organelle, etc within a sample. optional mandatory The method used to concentrate a target organism, nucleic acid, organelle, etc within a sample. peg precipitation + ultracentrifugation [none] concentration_method  custom attribute Wastewater surveillance-specific

extraction_method The protocol used to extract nucleic acids (DNA or RNA) from a sample optional mandatory The protocol used to extract nucleic acids (DNA or RNA) from a sample
qiagen rneasy kit extraction_method  custom attribute Wastewater surveillance-specific

extraction_control Organism (or nucleic acid) used in the extraction protocol to determine successful extraction. mandatory mandatory The extraction control used to spike samples prior to processing and used to determine success of extraction, or extraction efficiency. murine norovirus [none] NA (e.g. murine norovirus, OC43 Recovery Control, none, etc.)  custom attribute


ww_surv_target_1_conc The concentration of the wastewater surveillance target specified in 'ww_surv_target_1' on a per wastewater unit basis, e.g., 200000. optional mandatory Submitters should report Ct values for RT qPCR and concentration values for ddPCR. 200000 sars_cov2_avg_conc pcr_target_avg_conc {integer} Wastewater surveillance-specific

ww_surv_target_1_conc_unit The units of the value specified in 'ww_surv_target_1_conc', e.g., copies/L wastewater. optional mandatory Suggested units for liquid wastewater samples are "Ct values", "copies per liter wastewater", for sludge samples: "copies per gram sludge", "mg per gram sludge", or "micrograms per gram sludge" copies/L wastewater sars_cov2_units pcr_target_units {text} Wastewater surveillance-specific

ww_surv_target_1_gene The name of the gene quantified for the the surveillance target specified in 'ww_surv_target_1', e.g., N gene. optional mandatory For example, "N gene" for quantification of SARS-CoV-2 RNA using the US CDC N1 or N2 assay.
N gene pcr_gene_target {text} Wastewater surveillance-specific

ww_surv_target_1_protocol The protocol used to quantify 'ww_surv_target_1'. Specify a reference, website, or brief description. optional mandatory Specify a reference, website, or brief description.
author et al, title, journal, year pcr_target_ref {text} Wastewater surveillance-specific

ww_surv_target_2 Taxonomic name of the second surveillance target, if any optional optional If a target for wastewater surveillance activity known, please list all. If looking for emerging pathogens, use "unknown". If no target specified, put "NA". For the COVID-19 response, use "SARS-CoV-2". For corresponding SRA, also include a custom variable with this field name (i.e., "ww_surv_target_1") and value (e.g., "SARS-CoV-2") to link the SRA to BioSample in the event multiple SRA's and targets correspond to the same BioSample.
[none] NA {text} Wastewater surveillance-specific

ww_surv_target_2_conc The concentration of the wastewater surveillance target specified in 'ww_surv_target_2' on a per wastewater unit basis, e.g., 24000. optional optional For example, SARS-CoV-2 concentrations measured by RT-qPCR would be provided units of "copies per liter" wastewater or "copies per gram" of sludge. For example, SARS-CoV-2 concentrations measured by RT-qPCR would be provided units of "copies per liter" wastewater or "copies per gram" of sludge. 24000 NA {integer} Wastewater surveillance-specific

ww_surv_target_2_conc_unit The units of the value specified in 'ww_surv_target_2_conc', e.g., copies/L wastewater. optional optional Units should be on a per unit of wastewater basis. Suggested units for liquid wastewater samples are "copies per liter wastewater", suggested units for sludge samples are "copies per gram sludge", "mg per gram sludge", or "micrograms per gram sludge". Units should be on a per unit of wastewater basis. Suggested units for liquid wastewater samples are "copies per liter wastewater", suggested units for sludge samples are "copies per gram sludge", "mg per gram sludge", or "micrograms per gram sludge". copies/L wastewater NA {text} Wastewater surveillance-specific

ww_surv_target_2_gene The name of the gene quantified for the the surveillance target specified in 'ww_surv_target_2', e.g., ORF1-ORF2 junction. optional mandatory For example, "N gene" for quantification of SARS-CoV-2 RNA using the US CDC N1 or N2 assay. For example, "N gene" for quantification of SARS-CoV-2 RNA using the US CDC N1 or N2 assay. ORF1-ORF2 junction NA {text} Wastewater surveillance-specific

ww_surv_target_2_known_present Is genetic material of the surveillance target(s) known to the submitter to be present in this wastewater sample? Presence defined as microbiological evidence of the target organism in the wastewater sample, such as genetic- or culture-based detection. optional mandatory Select from "yes" or "no" picklist. Presence defined as microbiological evidence of the target organism in the wastewater sample, such as genetic- or culture-based detection. Select from "yes" or "no" picklist. Presence defined as microbiological evidence of the target organism in the wastewater sample, such as genetic- or culture-based detection. yes NA no | yes Wastewater surveillance-specific

ww_endog_control_1 The name of an organism, gene, or compound used as an endogenous wastewater control, e.g., pepper mild mottle virus. optional mandatory Provide the name of the organism, gene, or compound used as an endogenous wastewater control. Common endogenous controls may serve as a proxy for human excretory content and as laboratory processing controls. pepper mild mottle virus hum_frac_target_mic, hum_frac_target_chem, other_norm_name hum_frac_target_mic {text} Wastewater surveillance-specific

ww_endog_control_1_conc The concentration of the endogenous control specified in 'ww_endog_control_1' on a per wastewater unit basis, e.g., 700000000. optional optional Specify the concentration in units per liter wastewater or gram of sludge; the same units specified in 'ww_endog_control_1_units'. 700000000 hum_frac_mic_conc, hum_frac_chem_conc, other_norm_con hum_frac_mic_conc {integer} Wastewater surveillance-specific

ww_endog_control_1_protocol The protocol used to quantify 'ww_endog_control_1'. Specify a reference, website, or brief description. optional optional Specify a reference, website, or brief description.
author et al, title, journal, year hum_frac_target_mic_ref {text} Wastewater surveillance-specific

ww_endog_control_1_units The units of the value specified in 'ww_endog_control_1_conc', e.g., copies/L wastewater. optional optional Units should be on a per unit of wastewater basis. Suggested units for liquid wastewater samples are "copies/L wastewater", "mg/L wastewater", or "micrograms/L wastewater"; suggested units for sludge samples are "copies/g sludge", "mg/g sludge", or "micrograms/g sludge". copies/L wastewater hum_frac_mic_unit, hum_frac_chem_unit, other_norm_unit hum_frac_mic_unit {text} Wastewater surveillance-specific

ww_endog_control_2 The name of an organism, gene, or compound used as an endogenous wastewater control, e.g., crassphage. optional optional Provide the name of the organism, gene, or compound used as an endogenous wastewater control. Common endogenous controls may serve as a proxy for human excretory content and as laboratory processing controls. crassphage hum_frac_target_mic, hum_frac_target_chem, other_norm_name NA {text} Wastewater surveillance-specific

ww_endog_control_2_conc The concentration of the endogenous control specified in 'ww_endog_control_2' on a per wastewater unit basis, e.g., 140000000. optional optional Specify the concentration in units per liter wastewater or gram of sludge and specify the units in 'ww_endog_control_2_units'. 140000000 hum_frac_mic_conc, hum_frac_chem_conc, other_norm_con NA {integer} Wastewater surveillance-specific

ww_endog_control_2_protocol The protocol used to quantify 'ww_endog_control_2'. Specify a reference, website, or brief description. optional optional Specify a reference, website, or brief description.
author et al, title, journal, year NA {text} Wastewater surveillance-specific

ww_endog_control_2_units The units of the value specified in 'ww_endog_control_2_conc', e.g., copies/L wastewater. optional optional Units should be on a per unit of wastewater basis. Suggested units for liquid wastewater samples are "copies/L wastewater", "mg/L wastewater", or "micrograms/L wastewater"; suggested units for sludge samples are "copies/g sludge", "mg/g sludge", or "micrograms/g sludge". copies/L wastewater hum_frac_mic_unit, hum_frac_chem_unit, other_norm_unit NA {text} Wastewater surveillance-specific

ww_flow Daily volumetric flow through collection site, in units of liters per day, e.g., 110000000. optional mandatory Daily volumetric flow through collection site, in units of liters per day, e.g., 110000000. Numeric value in units of liters per day. If only an instantaneous flow measurement is available, report it in units of liters per day. 110000000 flow_rate {integer} Wastewater surveillance-specific

instantaneous_flow For grab samples: enter the an instantaneous volumetric flow measurement. The time of this measurement should correspond to when the grab sample was taken, and should be reported in UNITS per LITER per day. optional optional For grab samples: enter the an instantaneous volumetric flow measurement. The time of this measurement should correspond to when the grab sample was taken, and should be reported in units of liters per day.

NA custom attribute


ww_temperature Temperature of the wastewater sample at the time of sampling in Celsius, e.g., 25. optional mandatory Temperature of the wastewater sample at the time of sampling in Celsius, e.g., 25.
25 collection_water_temp {integer} Wastewater surveillance-specific

ww_total_suspended_solids Total concentration of solids in raw wastewater influent sample including a wide variety of material, such as silt, decaying plant and animal matter in milligrams per liter, e.g., 500. optional optional [none]
500 tss {integer} Wastewater surveillance-specific

ww_industrial_effluent_percent Percentage of industrial effluents received by wastewater treatment plant, e.g., 10. optional optional [none]
10 industrial_input {integer} Wastewater surveillance-specific

ww_ph pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid, e.g., 7.2. optional optional [none]
7.2 ph {integer} Wastewater surveillance-specific

ww_sample_salinity Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample or derived from the conductivity measurement (practical salinity) in milligram per liter, e.g., 100. optional optional [none]
100 conductivity {integer} Wastewater surveillance-specific

ww_pre_treatment Describe any process of pre-treatment that removes materials that can be easily collected from the raw wastewater, e.g., flow equilibration basin promotes settling of some solids. optional optional Processes within the sewer distribution system or wastewater treatment plant that remove solids or chemically treat prior to wastewater surveillance sample collection. flow equilibration basin promotes settling of some solids [none] pretreatment {text} Wastewater surveillance-specific

ww_primary_sludge_retention_time The time primary sludge remains in tank in hours, e.g., 4. optional optional [none]
4 NA {integer} Wastewater surveillance-specific


Sheet 3: vocabulary

organism
geo_loc_name
isolation_source
purpose_of_ww_sampling
project_name
ww_sample_type
ww_sample_site
ww_sample_matrix
ww_surv_target_1
ww_surv_target_1_known_present
ww_surv_target_1_gene
ww_surv_target_1_protocol
ww_surv_target_1_conc_unit
specimen_processing
concentration_method
extraction_method
collected_by
sequenced_by
purpose_of_sequencing
reporting_jurisdiction
wastewater metagenome
USA: Alabama
Wastewater
public health surveillance community-level
GenomeTrakr
grab
correctional facilility
raw wastewater
SARS-CoV-2
Yes
E gene (orf4)
RT-qPCR Detection of SARS-CoV-2 from Wastewater Using the AB 7500 (protocols.io)
cycles (Ct value)
technical replicate
membrane filtration with addition of mgcl2
qiagen allprep powerviral dna/rna kit
Arizona State Department of Health Services
Arizona State Department of Health Services
detection of target by RT PCR or ddPCR
AL


USA: Alaska
Clinical
public health surveillance institution-level
GenomeTrakr; LFFM ww project
composite
long-term care facility
sewer pipeline sediments
Not Applicable
No
M gene (orf5)
RT-qPCR Detection of SARS-CoV-2 using Luna Probe One-Step RT-qPCR 4X Mix with UDG kit
copies/L
biological replicate
amicon ultrafiltration
4s method (https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-bpdfmi3n)
California Department of Public Health
California Department of Public Health


AK


USA: Arizona
Animal
public health surveillance building-level
CDC NWSS
swab - grab
hospital
post grit removal
Not Collected


N gene (orf9)
RTqPCR of SARS-CoV-2 N1 Target on ABI 7500 Fast Using Promega GoTaq Enviro Wastewater SARS-CoV-2 System
copies/uL
specimans pooled
beef extract flocculation
ceres magnetic beads
Indiana State Department of Health
Indiana State Department of Health


AS


USA: Arkansas
Missing
research


swab - composite
child day care
primary sludge
Not Provided


N gene (N1)
ddPCR detection of SARS-CoV-2 using the BioRad PREvalence Kit on the BioRad QXOne


Not Applicable
centricon ultrafiltration
chemagic viral dna/rna 300 kit
Kentucky State Cabinet for Health and Family Services
Kentucky State Cabinet for Health and Family Services


AZ


USA: California
Restricted Access
other: define


Not Applicable
school
primary effluent
Missing


N gene (N2)
GT-Digital SARS-CoV-2 Wastewater Surveillance Assay For QIAcuity dPCR


Not Collected
ceres nanotrap
macherey-nagel nucleomag dna/rna water kit
Massachusetts State Department of Public Health
Massachusetts State Department of Public Health


AR


USA: Canal Zone


Not Applicable


Not Collected
college or university
secondary sludge
Restricted Access


Spike gene (orf2)
Not Applicable


Not Provided
hollow fiber dead end ultrafiltration
neb monarch total rna miniprep kit
New Jersey State Department of Agriculture
New Jersey State Department of Agriculture


CA


USA: Colorado


Not Collected


Not Provided
social services shelter
secondary effluent




S gene
Not Collected


Missing
innovaprep ultrafiltration
neb monarch total rna miniprep kit + zymo onestep pcr inhibitor removal kit
New Jersey State Department of Health and Senior Servces
New Jersey State Department of Health and Senior Servces


CI


USA: Connecticut


Not Provided


Missing
other residential building
other: define




orf1ab (rep)
Not Provided


Restricted Access
membrane filtration with acidification and mgcl2
nuclisens automated magnetic bead extraction kit
New Mexico State University - Las Cruces
New Mexico State University - Las Cruces


CO


USA: Delaware


Missing


Restricted Access
ship
Not Applicable




   orf1a (pp1a)
Missing




membrane filtration with acidification and mgcl2, membrane recombined with separated solids
nuclisens manual magnetic bead extraction kit
North Carolina State University - Raleigh
North Carolina State University - Raleigh


MP


USA: District of Columbia


Restricted Access




airplane
Not Collected




      nsp11
Restricted Access




membrane filtration with addition of mgcl2, membrane recombined with separated solids
omega-biotek on the hamilton robot
Ohio State Department of Agriculture
Ohio State Department of Agriculture


CT


USA: Florida








airport
Not Provided




   nsp1 






membrane filtration with no amendment
phenol chloroform
Pennsylvania State University - University Park
Pennsylvania State University - University Park


DE


USA: Georgia








septic tank
Missing




   nsp2






membrane filtration with no amendment, membrane recombined with separated solids
promega automated tna kit
Rhode Island Department of Health
Rhode Island Department of Health


DC


USA: Guam








other holding tank
Restricted Access




   nsp3






membrane filtration with sample acidification
promega ht tna kit
South Carolina Department of Health and Environmental Control
South Carolina Department of Health and Environmental Control


FM


USA: Hawaii








wastewater treatment plant






   Nsp4






membrane filtration with sample acidification, membrane recombined with separated solids
promega manual tna kit
South Dakota State University
South Dakota State University


FL


USA: Idaho








wastewater lagoon






   nsp5






no liquid concentration, liquid recombined with separated solids
promega wastewater large volume tna capture kit
Texas Department of State Health Services
Texas Department of State Health Services


GA


USA: Illinois








sewer pipeline






   nsp6






peg precipitation
qiagen allprep dna/rna kit
Nevada State Public Health Laboratory
Nevada State Public Health Laboratory


GU


USA: Indiana








food or meat processing plant






   nsp7






peg precipitation + ultracentrifugation
qiagen allprep powerfecal dna/rna kit
Virginia Division of Consolidated Laboratory Services
Virginia Division of Consolidated Laboratory Services


HI


USA: Iowa








other: define






   nsp8






promega wastewater large volume tna capture kit
qiagen powerwater kit
Washington State Department of Agriculture
Washington State Department of Agriculture


HO


USA: Kansas








Not Applicable






   nsp9






skimmed milk flocculation
qiagen qiaamp buffers with epoch columns
Washington State Department of Health
Washington State Department of Health


ID


USA: Kentucky








Not Collected






   nsp10






ultracentrifugation
qiagen qiaamp viral rna mini kit
West Virginia Department of Agriculture
West Virginia Department of Agriculture


IL


USA: Louisiana








Not Provided






   RdRp gene (nsp12)






zymo environ water rna kit
qiagen rneasy kit
FDA Center for Food Safety and Applied Nutrition
FDA Center for Food Safety and Applied Nutrition


IN


USA: Maine








Missing






   hel gene (nsp13)






zymo water concentration buffer
qiagen rneasy powermicrobiome kit
Not Applicable
Not Applicable


IA


USA: Maryland








Restricted Access






   exoN gene (nsp14)






Not Applicable
thermofisher magmax microbiome ultra nucleic acid isolation kit
Not Collected
Not Collected


KS


USA: Massachusetts
















   nsp15






Not Collected
thermofisher magmax viral/pathogen nucleic acid isolation kit
Not Provided
Not Provided


KY


USA: Michigan
















   nsp16






Not Provided
trizol, zymo mag beads w/ zymo clean and concentrator
Missing
Missing


LC


USA: Minnesota
















orf3a






Missing
zymo quick-rna fungal/bacterial miniprep #r2014
Restricted Access
Restricted Access


LA


USA: Mississippi
















orf3b






Restricted Access
zymo quick-rna viral kit






ME


USA: Missouri
















orf6 (ns6)








Not Applicable






MD


USA: Montana
















orf7a








Not Collected






MA


USA: Nebraska
















orf7b (ns7b)








Not Provided






MI


USA: Nevada
















orf8 (ns8)








Missing






MN


USA: New Hampshire
















orf9b








Restricted Access






MS


USA: New Jersey
















orf9c
















MO


USA: New Mexico
















orf10
















MT


USA: New York
















orf14
















NE


USA: North Carolina
















SARS-COV-2 5' UTR
















NV


USA: North Dakota
















Not Applicable
















NH


USA: Ohio
















Not Collected
















NJ


USA: Oklahoma
















Not Provided
















NM


USA: Oregon
















Missing
















NY


USA: Pennsylvania
















Restricted Access
















NZ


USA: Puerto Rico


































NC


USA: Rhode Island


































ND


USA: South Carolina


































OH


USA: South Dakota


































OK


USA: Tennessee


































OR


USA: Texas


































PA


USA: Utah


































PH


USA: Vermont


































PR


USA: Virgin Islands


































MH


USA: Virginia


































PW


USA: Washington


































RI


USA: West Virginia


































SC


USA: Wisconsin


































SD


USA: Wyoming


































TN


Afghanistan


































TX


Albania


































VI


Algeria


































UT


American Samoa


































VT


Andorra


































VA


Angola


































WA


Anguilla


































WV


Antarctica


































WI


Antigua and Barbuda


































WY


Argentina


































Not Applicable


Armenia


































Not Collected


Aruba


































Not Provided


Ashmore and Cartier Islands


































Missing


Australia


































Restricted Access


Austria





































Azerbaijan





































Bahamas





































Bahrain





































Baker Island





































Bangladesh





































Barbados





































Bassas da India





































Belarus





































Belgium





































Belize





































Benin





































Bermuda





































Bhutan





































Bolivia





































Borneo





































Bosnia and Herzegovina





































Botswana





































Bouvet Island





































Brazil





































British Virgin Islands





































Brunei





































Bulgaria





































Burkina Faso





































Burundi





































Cambodia





































Cameroon





































Canada





































Cape Verde





































Cayman Islands





































Central African Republic





































Chad





































Chile





































China





































Christmas Island





































Clipperton Island





































Cocos Islands





































Colombia





































Comoros





































Cook Islands





































Coral Sea Islands





































Costa Rica





































Cote d'Ivoire





































Croatia





































Cuba





































Curacao





































Cyprus





































Czech Republic





































Democratic Republic of the Congo





































Denmark





































Djibouti





































Dominica





































Dominican Republic





































Ecuador





































Egypt





































El Salvador





































Equatorial Guinea





































Eritrea





































Estonia





































Eswatini





































Ethiopia





































Europa Island





































Falkland Islands (Islas Malvinas)





































Faroe Islands





































Fiji





































Finland





































France





































French Guiana





































French Polynesia





































French Southern and Antarctic Lands





































Gabon





































Gambia





































Gaza Strip





































Georgia





































Germany





































Ghana





































Gibraltar





































Glorioso Islands





































Greece





































Greenland





































Grenada





































Guadeloupe





































Guam





































Guatemala





































Guernsey





































Guinea





































Guinea-Bissau





































Guyana





































Haiti





































Heard Island and McDonald Islands





































Honduras





































Hong Kong





































Howland Island





































Hungary





































Iceland





































India





































Indonesia





































Iran





































Iraq





































Ireland





































Isle of Man





































Israel





































Italy





































Jamaica





































Jan Mayen





































Japan





































Jarvis Island





































Jersey





































Johnston Atoll





































Jordan





































Juan de Nova Island





































Kazakhstan





































Kenya





































Kerguelen Archipelago





































Kingman Reef





































Kiribati





































Kosovo





































Kuwait





































Kyrgyzstan





































Laos





































Latvia





































Lebanon





































Lesotho





































Liberia





































Libya





































Liechtenstein





































Line Islands





































Lithuania





































Luxembourg





































Macau





































Madagascar





































Malawi





































Malaysia





































Maldives





































Mali





































Malta





































Marshall Islands





































Martinique





































Mauritania





































Mauritius





































Mayotte





































Mexico





































Micronesia





































Midway Islands





































Moldova





































Monaco





































Mongolia





































Montenegro





































Montserrat





































Morocco





































Mozambique





































Myanmar





































Namibia





































Nauru





































Navassa Island





































Nepal





































Netherlands





































New Caledonia





































New Zealand





































Nicaragua





































Niger





































Nigeria





































Niue





































Norfolk Island





































North Korea





































North Macedonia





































North Sea





































Northern Mariana Islands





































Norway





































Oman





































Pakistan





































Palau





































Panama





































Papua New Guinea





































Paracel Islands





































Paraguay





































Peru





































Philippines





































Pitcairn Islands





































Poland





































Portugal





































Puerto Rico





































Qatar





































Republic of the Congo





































Reunion





































Romania





































Ross Sea





































Russia





































Rwanda





































Saint Helena





































Saint Kitts and Nevis





































Saint Lucia





































Saint Pierre and Miquelon





































Saint Vincent and the Grenadines





































Samoa





































San Marino





































Sao Tome and Principe





































Saudi Arabia





































Senegal





































Serbia





































Seychelles





































Sierra Leone





































Singapore





































Sint Maarten





































Slovakia





































Slovenia





































Solomon Islands





































Somalia





































South Africa





































South Georgia and the South Sandwich Islands





































South Korea





































South Sudan





































Spain





































Spratly Islands





































Sri Lanka





































State of Palestine





































Sudan





































Suriname





































Svalbard





































Swaziland





































Sweden





































Switzerland





































Syria





































Taiwan





































Tajikistan





































Tanzania





































Thailand





































Timor-Leste





































Togo





































Tokelau





































Tonga





































Trinidad and Tobago





































Tromelin Island





































Tunisia





































Turkey





































Turkmenistan





































Turks and Caicos Islands





































Tuvalu





































USA





































Uganda





































Ukraine





































United Arab Emirates





































United Kingdom





































Uruguay





































Uzbekistan





































Vanuatu





































Venezuela





































Viet Nam





































Virgin Islands





































Wake Island





































Wallis and Futuna





































West Bank





































Western Sahara





































Yemen





































Zambia





































Zimbabwe





































Not Applicable





































Not Collected





































Not Provided





































Missing





































Restricted Access



































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