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

post grit removal

composite

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)

cycles (Ct value)

Ginkgo Bioworks clinical laboratory

4119.D

PRJNA839090

wastewater metagenome

9/20/2022

USA: Vermont

Wastewater

GenomeTrakr

Biobot Analytics

public health surveillance community-level

wastewater treatment plant

36 liters per day

3500

raw wastewater

grab

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

Ginkgo Bioworks clinical laboratory

3990.C

PRJNA839090

wastewater metagenome

9/21/2022

USA: Arkansas

Wastewater

GenomeTrakr; LFFM ww project

Biobot Analytics

public health surveillance community-level

wastewater treatment plant

12000000

5500

raw wastewater

composite

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

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

detection of target by RT PCR or ddPCR

USA: Alaska

Clinical

public health surveillance institution-level

GenomeTrakr; LFFM ww project

composite

long-term care facility

sewer pipeline sediments

Not Applicable

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

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

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

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

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

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

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

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

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

USA: Florida

airport

Not Provided

nsp1

membrane filtration with no amendment

phenol chloroform

Pennsylvania State University - University Park

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

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

USA: Hawaii

wastewater treatment plant

Nsp4

membrane filtration with sample acidification, membrane recombined with separated solids

promega manual tna kit

South Dakota State University

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

USA: Illinois

sewer pipeline

nsp6

peg precipitation

qiagen allprep dna/rna kit

Nevada State Public Health Laboratory

USA: Indiana

food or meat processing plant

nsp7

peg precipitation + ultracentrifugation

qiagen allprep powerfecal dna/rna kit

Virginia Division of Consolidated Laboratory Services

USA: Iowa

other: define

nsp8

promega wastewater large volume tna capture kit

qiagen powerwater kit

Washington State Department of Agriculture

USA: Kansas

Not Applicable

nsp9

skimmed milk flocculation

qiagen qiaamp buffers with epoch columns

Washington State Department of Health

USA: Kentucky

Not Collected

nsp10

ultracentrifugation

qiagen qiaamp viral rna mini kit

West Virginia Department of Agriculture

USA: Louisiana

Not Provided

RdRp gene (nsp12)

zymo environ water rna kit

qiagen rneasy kit

FDA Center for Food Safety and Applied Nutrition

USA: Maine

Missing

hel gene (nsp13)

zymo water concentration buffer

qiagen rneasy powermicrobiome kit

Not Applicable

USA: Maryland

Restricted Access

exoN gene (nsp14)

Not Applicable

thermofisher magmax microbiome ultra nucleic acid isolation kit

Not Collected

USA: Massachusetts

nsp15

Not Collected

thermofisher magmax viral/pathogen nucleic acid isolation kit

Not Provided

USA: Michigan

nsp16

Not Provided

trizol, zymo mag beads w/ zymo clean and concentrator

Missing

USA: Minnesota

orf3a

Missing

zymo quick-rna fungal/bacterial miniprep #r2014

Restricted Access

USA: Mississippi

orf3b

Restricted Access

zymo quick-rna viral kit

USA: Missouri

orf6 (ns6)

Not Applicable

USA: Montana

orf7a

Not Collected

USA: Nebraska

orf7b (ns7b)

Not Provided

USA: Nevada

orf8 (ns8)

Missing

USA: New Hampshire

orf9b

Restricted Access

USA: New Jersey

orf9c

USA: New Mexico

orf10

USA: New York

orf14

USA: North Carolina

SARS-COV-2 5' UTR

USA: North Dakota

Not Applicable

USA: Ohio

Not Collected

USA: Oklahoma

Not Provided

USA: Oregon

Missing

USA: Pennsylvania

Restricted Access

USA: Puerto Rico

USA: Rhode Island

USA: South Carolina

USA: South Dakota

USA: Tennessee

USA: Texas

USA: Utah

USA: Vermont

USA: Virgin Islands

USA: Virginia

USA: Washington

USA: West Virginia

USA: Wisconsin

USA: Wyoming

Afghanistan

Albania

Algeria

American Samoa

Andorra

Angola

Anguilla

Antarctica

Antigua and Barbuda

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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