NWSS Data Dictionary

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Overview

Read Me
Metadata
Value Sets
Change Log

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Sheet 1: Read Me

General Notes

The level of measure for NWSS DCIPHER SARS-CoV-2 reporting:

Each SARS-CoV-2 PCR target ('pcr_target') that is measured should be specified on a separate row in the CSV file. For example, if N1 and N2 are both measured for the same sample, they should each be reported on a separate row. Other fields that correspond to this sample, including 'sample_id', should be repeated across those rows. In general, this format can be thought of as being "wide" with respect to most measurements made on a given sample, but "long" with respect to SARS-CoV-2 PCR targets.

Data types:

Fields are read in as strings; data type casting happens after file read in.

Submission Requirements

Required fields:

These fields must be included in the data file; if they are omitted, file upload will be prohibited. For required fields that allow [empty] values, the field column header must be included in the data file even if all row values are [empty].

Non-required but non-empty fields:

Some fields are "not required" but also must have non-empty values, conditional on the completion of another field. Omission of these fields will not interfere with upload of the data file, but will cause them to be flagged for quality control issues once uploaded.

Value Sets

Missing values:

Missing values should be left blank, denoted as [empty] in the Value Sets. Do not use other strings, such as "NA" or "[empty]", to denote missing values."

Requesting additional values for categorical fields:

For categorical fields, restrict values to those listed in the Value Sets. To request that values be added to the vocabulary, please contact NWSS staff.

Case sensitivity:

Fields are not case sensitive.

Data Type Definitions

string

ASCII-encoded characters; do not use line breaks within a value

float

Floating-point (i.e., decimal) number

integer

Integer number

ZIP code

5-digit US ZIP code (#####)

date

yyyy-mm-dd

time

hh:mm (24-hr format in the local time zone)

list

Comma-separated strings

category

Categorical variable with a defined value set of strings

NPDES permit number

National Pollutant Discharge Elimination System (NPDES) permit number (<2-letter abbreviation><#######>). Search engine to locate this identifier is available here: https://echo.epa.gov/facilities/facility-search?mediaSelected=cwa

EPA registry ID number

EPA Registry ID or Facility Registry Service (FRS) identifier (<############>). Search engine to locate this identifier is availble here: https://echo.epa.gov/facilities/facility-search?mediaSelected=cwa

time zone

Time zone, represented as a UTC time offset (UTC-[hh]:[mm], e.g., UTC-06:00); offsets can be found at https://www.timeanddate.com/time/zone/usa

jurisdiction id

String 20 characters or less, containing only numbers, English alphabetic characters, underscores, and hyphens (white space is not allowed); not case sensitive

Field Name Groups

Reporter

Collection Site

WWTP

Collection Method

Processing Method

SARSCoV2 Quantification Method

Sample

SARSCoV2 Quantification Results

Terminology

PCR:

Throughout this data dictionary, the term "PCR" (polymerase chain reaction) is used as a shorthand for "PCR-based quantification methods", even when the method is an RT-PCR (reverse transcriptase PCR)-based method for RNA targets, such as SARS-CoV-2. In addition, the term PCR does not refer to end-point PCR methods, but rather quantitative PCR methods, such as quantitative (real time) PCR or digital PCR.

Field Name Color Key

Data that may be generated by the reporting jurisdiction public health agency, possibly in collaboration with either wastewater utilities or testing laboratories

Data likely generated by testing laboratories

Data likely generated by wastewater utilities

New fields or changes to existing fields

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Sheet 2: Metadata

Field Name	Data Type	Description	Value Set	Units	Submission Requirement	Dependent Fields
Reporter
reporting_jurisdiction	category	The CDC Epidemiology and Laboratory Capacity (ELC) jurisdiction, most frequently a state, reporting these data (2-letter abbreviation)	[See Value Sets: vs_reporting_jurisdiction]	[none]	Required	None
Collection Site
site_id	<#####-###-##-##-##>	Nationally unique sampling site identifier assigned following NWSS format. <5 digit county FIPS code for WWTP address>-<3 digit facility code>-<2 digit interceptor and sewershed code>-<2 digit subsewershed code>-<2 digit site code>			Required	None
county_names	list (comma-separated integers)	5-digit numeric FIPS codes of all counties and county equivalents served by this sampling site (i.e., served by this wastewater treatment plant or, if 'sample_location' is "upstream", then by this upstream location). Note that most jurisdictions are covered by counties, but some are covered by county equivalents, such as independent cities, parishes, or census areas.	[5-digit integers]	[none]	Required	None
zipcode	ZIP code (#####)	Zip code in which this sampling site is physically located (one 5-digit zip code)	[5-digit integers]	[none]	Required	None
population_served	integer	Estimated number of persons served by this sampling site (i.e., served by this wastewater treatment plant or, if 'sample_location' is "upstream", then by this upstream location)	[greater than or equal to 0]	[none]	Required	None
sewage_travel_time	float	What is the approximate sewage travel time, on average, from sewage source to this sampling site (i.e., this wastewater treatment plant or, if 'sample_location' is "upstream", then this upstream location)? This should be specified as a duration in hours, not a time of day.	[greater than or equal to 0]; [empty]	Hours	Not required	None
sample_location	category	Sample collection location in the wastewater system, whether at a wastewater treatment plant (or other community level treatment infrastructure such as community-scale septic) or upstream in the wastewater system	[See Value Sets: vs_sample_location]	[none]	Required	If 'sample_location' is "upstream", specify in 'sample_location_specify'
sample_location_specify	string	If 'sample_location' is "upstream", specify the collection location in the wastewater system; an arbitrary name may be used if you do not wish to disclose the real name.	[string, length less than or equal to 40 characters]; [empty]	[none]	Required	If sample_location is "upstream", then this must have a non-empty value
institution_type	category	If this sample represents wastewater from a single institution, facility, or building, specify the institution type; otherwise, specify "not institution specific"	[See Value Sets: vs_institution_type]	[none]	Required	None
WWTP
epaid	NPDES permit number (<2-letter abbreviation><#######>)	NPDES permit number for the wastewater treatment plant specified in 'wwtp_name'. If 'upstream location' use the NPDES permit number for the wastewater treatment plant in which the water flows. If facility does not have an NPDES permit number, enter -1.	[NPDES permit number]; -1 if not permitted	[none]	Required	None
epa_registry_id	EPA Registry ID (<############>)	EPA registry ID for the wastewater treatment plant specified in 'wwtp_name'. If 'upstream location' use the registry ID number for the wastewater treatment plant in which the water flows. If the water does not flow to a treatment plant, enter -1.	[EPA Registry ID]; -1 if not registered with EPA	[none]	Not required	None
wwtp_name	string	The name of the Wastewater Treatment Plant (WWTP) to which this wastewater flows. If this wastewater does not flow to a WWTP, specify an identifiable name for the septic or other treatment system to which this wastewater flows. An arbitrary name may be used if you do not wish to disclose the real name.	[string, length less than or equal to 40 characters]	[none]	Required	None
wwtp_jurisdiction	category	State, DC, US territory, or Freely Associated State jurisdiction name (2-letter abbreviation) in which the wastewater treatment plant provided in 'wwtp_name' is located	[See Value Sets: vs_wwtp_jurisdiction]	[none]	Required	None
capacity_mgd	float	Wastewater treatment plant design capacity. This should be the capacity for which the plant is permitted. If 'upstream location', use the design capacity for the wastewater treatment plant to which the water flows.	[greater than or equal to 0]	Million gallons per day (MGD)	Required	None
industrial_input	float	Approximate average percentage of wastewater from industrial sources that is received by the wastewater treatment plant specified in 'wwtp_name'	[0-100]; [empty]	percent	Not required	None
stormwater_input	category	Does the wastewater treatment plant specified in 'wwtp_name' treat water from a combined sewer system (i.e., a sewer system that collects both sewage and stormwater)?	[See Value Sets: vs_yne]	[none]	Not required	None
influent_equilibrated	category	Is influent to the wastewater treatment plant specified in 'wwtp_name' ever stored prior to treatment to equilibrate or modulate the influent flow rate?	[See Value Sets: vs_yne]	[none]	Not required	None
Collection Method
sample_type	category	Type of sample collected, whether grab or composite. If composite, also provide the duration of sampling and type of composite, as listed in the Value Set (e.g., "24-hr flow-weighted composite"). A grab sample is defined as an individual sample collected without compositing or adding other samples, regardless of whether the sample matrix is liquid wastewater or sludge.	[See Value Sets: vs_sample_type]	[none]	Required	None
composite_freq	float	Frequency of sub-sample collection (for composite samples only): for flow-weighted, the number of sub-samples collected per million gallons of flow; for time-weighted, the number of sub-samples per hour. Flow-weighted example: a value of 5 would indicate 5 sub-samples per million gallons, or 1 sub-sample per 200,000 gallons	[greater than or equal to 0]; [empty]	If flow-weighted composite: number per million gallons; if time-weighted or manual composite: number per hour	Not required	None
sample_matrix	category	Wastewater matrix from which the sample was collected	[See Value Sets: vs_sample_matrix]	[none]	Required	None
collection_storage_time	float	Duration of time from sample collection start time to time sample reached the lab.	[greater than or equal to 0]; [empty]	Hours	Not required	None
collection_storage_temp	float	Temperature at which the sample was stored after collection and prior to reaching the lab	[float]; [empty]	Celsius	Not required	None
pretreatment	category	Was the sample treated with any chemicals prior to reaching the lab? These could include chemicals, such as stabilizers, added to the sample or chemicals, such as chlorine, added to the wastewater treatment train upstream of the sample collection point. Do not be specify pasteurization here; it should be specified in the 'pasteurized' field.	[See Value Sets: vs_yn]	[none]	Required	if 'pretreatment' is "yes", then specify in 'pretreatment_specify'
pretreatment_specify	string	If 'pretreatment' is "yes", then specify the chemicals used	[string]; [empty]	[none]	Not required	if 'pretreatment' is "yes", then 'pretreatment_specify' must have a non-empty field
Processing Method
solids_separation	category	Process used to separate solid and liquid phases of the sample, either prior to or in the absence of the concentration method specified in 'concentration_method'	[See Value Sets: vs_solids_separation]	[none]	Not required	None
concentration_method	category	Method used to concentrate the sample prior to analysis of the concentrate	[See Value Sets: vs_concentration_method]	[none]	Required	None
extraction_method	category	Method used for nucleic acid extraction from the sample	[See Value Sets: vs_extraction_method]	[none]	Required	None
pre_conc_storage_time	float	The approximate average duration of time between when samples reach the lab and when they are concentrated (if concentrated)	[greater than or equal to 0]; [empty]	Hours	Not required	None
pre_conc_storage_temp	float	The storage temperature of samples after reaching the lab and prior to concentration (if concentrated)	[float]; [empty]	Celsius	Not required	None
pre_ext_storage_time	float	The approximate average duration of time between when samples are concentrated (if concentrated) and when they are extracted	[greater than or equal to 0]; [empty]	Hours	Not required	None
pre_ext_storage_temp	float	The storage temperature of samples after concentration (if concentrated) and prior to extraction	[float]; [empty]	Celsius	Not required	None
tot_conc_vol	float	Total volume of sample concentrated (if concentrated); this total volume is not necessarily assayed and is not necessarily equal to the value specified in 'equiv_sewage_amt'	[greater than or equal to 0]; [empty]	mL	Not required	None
ext_blank	category	Are extraction blanks included in the extraction process?	[See Value Sets: vs_yne]	[none]	Not required	None
rec_eff_target_name	category	Name of the recovery efficiency control target that is spiked in	[See Value Sets: vs_rec_eff_target_name]	[none]	Required	If 'rec_eff_percent' is equal to a value other than "-1", then this must have a non-empty value
rec_eff_spike_matrix	category	Matrix into which the recovery efficiency control target is spiked	[See Value Sets: vs_rec_eff_spike_matrix]	[none]	Required	If 'rec_eff_target_name' has a non-empty value, then this must have a non-empty value
rec_eff_spike_conc	float	Spike concentration, on average, of the recovery control on a per sample volume basis	[float]; [empty]	log10 copies/mL	Required	If 'rec_eff_target_name' has a non-empty value, then this must have a non-empty value
pasteurized	category	Was the sample pasteurized?	[See Value Sets: vs_yn]	[none]	Required	None
SARSCoV2 Quantification Method
pcr_target	category	The target of the PCR quantification	[See Value Sets: vs_pcr_target]	[none]	Required	None
pcr_gene_target	category	The PCR gene used to quantify PCR target	[See Value Sets: vs_pcr_gene_target]	[none]	Required	The value selected for pcr_gene_target should align with the value selected for pcr_target
pcr_gene_target_ref	string	A publication, website, or brief description of the PCR gene target used	[string]	[none]	Required	None
pcr_type	category	The type of PCR used to quantify the PCR target	[See Value Sets: vs_pcr_type]	[none]	Required	If 'pcr_target' is not "sars-cov-2", "delta", "omicron", "hMPXV", "hMPXV Clade I", or "hMPXV Clade II" then this must be a type of digital PCR, i.e. "ddpcr", "qiagen dpcr", "fluidigm dpcr", "life technologies dpcr", "raindance dpcr", or "dpcr"
lod_ref	string	A publication, website, or brief description of the method used to calculate the limit of detection	[string]	[none]	Required	None
hum_frac_target_mic	category	Name of microbial target used to estimate human fecal content	[See Value Sets: vs_hum_frac_target_mic]	[none]	Not required	If 'hum_frac_mic_conc' has a non-empty value, then this must have a non-empty value
hum_frac_target_mic_ref	string	A publication, website, or brief description of the microbial target specified in 'hum_frac_target_mic'	[string]; [empty]	[none]	Not required	If 'hum_frac_mic_conc' has a non-empty value, then this must have a non-empty value
hum_frac_target_chem	category	Name of chemical compound used to estimate human fecal content	[See Value Sets: vs_hum_frac_target_chem]	[none]	Not required	If 'hum_frac_chem_conc' has a non-empty value, then this must have a non-empty value
hum_frac_target_chem_ref	string	A publication, website, or brief description of the chemical compound specified in 'hum_frac_target_chem'	[string]; [empty]	[none]	Not required	If 'hum_frac_chem_conc' has a non-empty value, then this must have a non-empty value
other_norm_name	category	Name of a target or compound not specified in 'hum_frac_target_mic' or 'hum_frac_target_chem' used to estimate human fecal content	[See Value Sets: vs_other_norm_name]	[none]	Not required	If 'other_norm_conc' has a non-empty value, then this must have a non-empty value
other_norm_ref	string	A publication, website, or brief description of the target or compound specified in 'other_norm_name'	[string]; [empty]	[none]	Not required	If 'other_norm_conc' has a non-empty value, then this must have a non-empty value
quant_stan_type	category	The type of nucleic acid used as a standard for the PCR target quantification	[See Value Sets: vs_quant_stan_type]	[none]	Required	None
stan_ref	string	A publication, website, or brief description of the quantitative standard material used	[string]	[none]	Required	None
inhibition_method	string	A publication, website, or brief description of the method used to evaluate molecular inhibition	[string]; none (if inhibition not tested)	[none]	Required	None
num_no_target_control	category	Number of no-template controls (NTC) per instrument run	[See Value Sets: vs_num_no_target_control]	[none]	Required	None
Sample
sample_collect_date	date ([yyyy]-[mm]-[dd])	The date of sample collection; for composite samples, specify the date on which sample collection began	[date not after tomorrow's date]	[none]	Required	None
sample_collect_time	time, 24-hr ([hh]:[mm])	The local time of sample collection; for composite samples, specify the time at which sample collection began	[time]	[none]	Required	None
time_zone	time zone (UTC-[hh]:[mm])	Current local time zone corresponding to the time specified in 'sample_collect_time', represented as a UTC time offset (e.g., UTC-06:00)	[time zone]	[none]	Not required	None
flow_rate	float	Wastewater volumetric flow rate at the sample collection location over the 24-hr period during which the sample was collected. If only an instantaneous flow measurement is available, it may be reported in units of million gallons per day.	[greater than or equal to 0]; [empty]	Million gallons per day (MGD)	Required.	If 'sars_cov2_units' is on a per volume wastewater basis (e.g., copies/l wastewater), then this must have a non-empty value (i.e., measurements of wastewater solids are permitted empty values for 'flow_rate'). If 'hum_frac_mic_conc' has a non-empty value and it is not possible to measure flow rate at all, then this may have an empty value.
ph	float	pH of wastewater sample (if sludge, pH of influent at time of collection)	[float]; [empty]	pH units	Not required	None
conductivity	float	Specific conductivity of wastewater sample (if sludge, conductivity of influent at time of collection)	[greater than or equal to 0]; [empty]	microsiemens/cm	Not required	None
tss	float	Total suspended solids of raw (or, if unavailable, post-grit removal) wastewater	[greater than or equal to 0]; [empty]	mg/L	Not required	None
collection_water_temp	float	Sample temperature at time of collection	[greater than or equal to 0]; [empty]	Celsius	Not required	None
equiv_sewage_amt	float	Equivalent unconcentrated volume of wastewater or mass of sludge in PCR reaction	[greater than or equal to 0]; [empty]	mL wastewater or g sludge	Not required	None
sample_id	jurisdiction id (a string 20 characters or less, containing only numbers, English alphabetic characters, underscores, and hyphens; white space is not allowed; not case sensitive)	An ID assigned to a wastewater sample. It must be unique for this NWSS reporting jurisdiction. Wastewater samples that are split and measured by different labs should have the same sample ID but different lab IDs. Wastewater samples for which multiple PCR targets are measured should also have the same sample ID. Note: do not include PII in this field.	[sample id]	[none]	Required	None
lab_id	jurisdiction id (a string 20 characters or less, containing only numbers, English alphabetic characters, underscores, and hyphens; white space is not allowed; not case sensitive)	An ID assigned to a testing lab. It must be unique across labs used for this NWSS reporting jurisdiction's testing. If the same lab is used across multiple NWSS reporting jurisdictions, each NWSS reporting jurisdiction may assign that lab a different lab ID. Note: including PII in this field is discouraged.	[lab id]	[none]	Required	None
qc_ignore	category	Should the DCIPHER QC report ignore this sample? The purpose of this field is to allow for removal of samples from the QC report so that samples with unresolvable QC issues do not clutter the report. This field only affects whether samples are shown in the QC report, not how they are otherwise processed or analyzed. If the value is "yes", then this sample will be excluded from the QC report. If the value is "no" or [empty], then this sample will be included in the QC report for up to 90 days. Samples will only be included in the QC report for up to 90 days, regardless of the value specified in ‘qc_ignore’.	[See Value Sets: vs_yne]	[none]	Not required	None
dashboard_ignore	category	Should the DCIPHER dashboard ignore this sample? If the value is "yes", then this sample will be excluded from the dashboard. If the value is "no" or [empty], then this sample will be included in the dashboard. In addition to excluding the sample from the DCIPHER dashboard, this field will also prevent the sample from public data release.	[See Value Sets: vs_yne]	[none]	Not required	None
analysis_ignore	category	Should DCIPHER data analysis ignore this sample? If the value is "yes", then this sample will be excluded from DCIPHER data analysis, which will also cause it to be excluded from the dashboard. If the value is "no" or [empty], then this sample will be included in DCIPHER data analysis.	[See Value Sets: vs_yne]	[none]	Not required	None
SARSCoV2 Quantification Results
test_result_date	date ([yyyy]-[mm]-[dd])	The date on which this PCR target measurement was made	[date greater than sample collect date and less than DCIPHER upload date]	[none]	Required	None
pcr_target_units	category	Units of PCR target sample concentration	[See Value Sets: vs_mic_chem_units]	[none]	Required	The units should relate to the PCR target indicated in pcr_target
pcr_target_avg_conc	float	Concentration of the PCR target back-calculated to unconcentrated sample basis; enter "0" if no amplification occurred, using the definition of amplification described in 'ntc_amplify'; otherwise, enter the estimated concentration; do not adjust for matrix recovery efficiency. Only the technical or biological replicate concentrations for the same pcr_gene_target should be averaged. For example, if there are three replicates of a given PCR target, average those concentrations and report the average value only. Do not include the three individual concentrations. Different pcr_gene_target concentrations should not be averaged for this field (e.g., do not average concentrations for N1 and N2).	[any float other than 0]; 0 (if no amplification observed)	[units specified in 'pcr_target_units']	Required	The concentration should relate to the PCR target indicated in pcr_target
pcr_target_std_error	float	Standard error (SE) of the PCR target in wastewater sample, or best estimate that is consistently available. If sample replicates are always performed, use SE of sample replicates; else, if processing replicates are always performed, use SE of processing replicates; else, if qPCR is performed, use SE of PCR replicates; else, if digital PCR is performed, use error from multiple replicates if available, and Poisson error if not	[greater than or equal to 0]; -1 (if cannot be calculated, such as when no amplification observed)	[units specified in 'pcr_target_units']	Not required	The standard error should relate to the PCR target indicated in pcr_target
pcr_target_cl_95_lo	float	Lower bound of 95% confidence interval of the PCR target in wastewater sample, or best estimate that is consistently available. Follow the same hierarchy as described for standard error. (Note: 'cl' stands for confidence limit)	[any float other than -1]; -1 (if cannot be calculated, such as when no amplification observed)	[units specified in 'pcr_target_units']	Not required	The lower bound of the 95% confidence interval should relate to the PCR target indicated in pcr_target
pcr_target_cl_95_up	float	Upper bound of 95% confidence interval of the PCR target in wastewater sample, or best estimate that is consistently available. Follow the same hierarchy as described for standard error. (Note: 'cl' stands for confidence limit)	[any float other than -1]; -1 (if cannot be calculated, such as when no amplification observed)	[units specified in 'pcr_target_units']	Not required	The upper bound of the 95% confidence interval should relate to the PCR target indicated in pcr_target
pcr_target_below_lod	category	Was the concentration of the PCR target below the limit of detection?	[See Value Sets: vs_yne]	[none]	Not required	Whether the concentration was below the LOD should be based on the LOD of the PCR target indicated in lod_sewage
lod_sewage	float	PCR target limit of detection back-calculated to unconcentrated sample basis	[float]	[units specified in 'pcr_target_units']	Required	The LOD should relate to the PCR target indicated in pcr_target
ntc_amplify	category	For qPCR, did any no-template controls on this instrument run have a Ct value less than 40? For ddPCR, did any no-template controls on this instrument run have 3 or more positive droplets?	[See Value Sets: vs_yn]	[none]	Required	None
rec_eff_percent	float	Percent of spiked recovery control, specified in 'rec_eff_target_name', that was recovered	[greater than or equal to 0.0]; -1 (if not tested)	percent	Required	None
inhibition_detect	category	Was molecular inhibition detected?	[See Value Sets: vs_ynn]	[none]	Required	None
inhibition_adjust	category	Was inhibition incorporated into the PCR target concentration calculation?	[See Value Sets: vs_yne]	[none]	Required	If 'inhibition_detect' is "yes", then this must have a non-empty value
hum_frac_mic_conc	float	Concentration of microbial target specified in 'hum_frac_target_mic'; follow the same guidelines outlined for 'pcr_target_avg_conc'	[float]; [empty]	[units specified in 'hum_frac_mic_unit']	Not required	If 'hum_frac_mic_unit' has a non-empty value, then this must have a non-empty value
hum_frac_mic_unit	category	Concentration units of microbial target specified in 'hum_frac_target_mic'	[See Value Sets: vs_mic_chem_units_e]	[none]	Not required	If 'hum_frac_mic_conc' has a non-empty value, then this must have a non-empty value
hum_frac_chem_conc	float	Concentration of chemical target specified in 'hum_frac_target_chem'	[float]; [empty]	[units specified in 'hum_frac_chem_unit']	Not required	If 'hum_frac_chem_unit' has a non-empty value, then this must have a non-empty value
hum_frac_chem_unit	category	Concentration units of chemical target specified in 'hum_frac_target_chem'	[See Value Sets: vs_mic_chem_units_e]	[none]	Not required	If 'hum_frac_chem_conc' has a non-empty value, then this must have a non-empty value
other_norm_conc	float	Concentration of target spcified in 'other_norm_name'	[float]; [empty]	[units specified in 'other_norm_conc']	Not required	If 'other_norm_unit' has a non-empty value, then this must have a non-empty value
other_norm_unit	category	Concentration units of target spcified in 'other_norm_name'	[See Value Sets: vs_mic_chem_units_e]	[none]	Not required	If 'other_norm_conc' has a non-empty value, then this must have a non-empty value
quality_flag	category	Does this observation have quality control issues?	[See Value Sets: vs_yne]	[none]	Not required	None
major_lab_method	integer	A number used to distinguish major lab methods at the reporting jurisdiction level. Differences in lab methods may limit the comparability of PCR target concentrations. Reporting jurisdictions should use this field to indicate that lab methods are sufficiently different that caution should be used when comparing PCR target concentrations across them. These differences may result from any lab processing or quantification steps, including different PCR gene targets. Note that 'major_lab_method' may be the same for different laboratories if the reporting jurisdiction believes concentrations measured by those laboratories are comparable; conversely, 'major_lab_method' may be different for the same laboratory if changes made to the laboratory protocol rendered concentrations not comparable.	[greater than or equal to 0]; [empty]	[none]	Required	None
major_lab_method_desc	string	Brief description of the basis for assigning a ‘major_lab_method’, e.g., "this lab uses a lab method distinct from other labs in this reporting jurisdiction", "this lab changed lab methods - new concentration method" or "lab method is same as other labs in this reporting jurisdiction but performance differs"	[string]; [empty]	[none]	Required	None

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Sheet 3: Value Sets

Field

Value Set Name

Value Set Name:

vs_concentration_method

vs_extraction_method

vs_hum_frac_target_chem

vs_hum_frac_target_mic

vs_institution_type

vs_mic_chem_units

vs_mic_chem_units_e

vs_num_no_target_control

vs_other_norm_name

vs_pcr_target

vs_pcr_gene_target

vs_pcr_type

vs_quant_stan_type

vs_rec_eff_spike_matrix

vs_rec_eff_target_name

vs_reporting_jurisdiction

vs_sample_location

vs_sample_matrix

vs_sample_type

vs_solids_separation

vs_wwtp_jurisdiction

vs_yn

vs_yne

vs_ynn

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

Value Set

Description

concentration_method

vs_concentration_method

membrane filtration with addition of mgcl2

qiagen allprep powerviral dna/rna kit

caffeine

pepper mild mottle virus

not institution specific

This sample does not represent wastewater from a single institution, facility, or building

copies/L wastewater

copies/L wastewater

0

pepper mild mottle virus

sars-cov-2

n1

sars-cov-2 gene target

qpcr

Real-time PCR, also called 'quantitative' PCR

dna

raw sample

bcov vaccine

AL

Alabama

wwtp

A sampling location at a wastewater treatment plant or other community-scale treatment infrastructure specified in 'wwtp_name'

raw wastewater

Wastewater without any form of treatment applied to it

grab

An individual sample collected without compositing or adding other samples

filtration

Filtration to remove solids from a wastewater sample prior to further concentration or analysis of the liquid filtrate

AL

Alabama

yes

yes

yes

extraction_method

vs_extraction_method

membrane filtration with sample acidification

qiagen allprep powerfecal dna/rna kit

creatinine

crassphage

correctional

A prison, penitentiary, penal facility, jail, detention unit, or other facility in which persons are incarcerated by government officials

log10 copies/L wastewater

log10 copies/L wastewater

1

crassphage

delta

n2

sars-cov-2 gene target

ddpcr

Used to refer specifically to BioRad digital droplet emulsification technology

rna

raw sample post pasteurization

bcov culture

AK

Alaska

upstream

A sampling location other than "wwtp"

post grit removal

Wastewater after removal of large solids at a treatment plant but prior to a primary clarifier

48-hr flow-weighted composite

centrifugation

Centrifugation prior to or in the absence of a concentration step; centrifugation as part of a flocculation or precipitation process, or part of a filtration-based concentration process, is considered part of a concentration method; centrifugation to dewater sludge samples is considered a solids separation process, not a concentration process

AK

Alaska

no

no

no

hum_frac_target_chem

vs_hum_frac_target_chem

membrane filtration with acidification and mgcl2

qiagen allprep dna/rna kit

sucralose

hf183

long term care - nursing home

A residential healthcare facility that provides 24-medical care. These are also called skilled nursing facilities. Generally licensed by CMS.

copies/g wet sludge

Wet sludge mass is based on the mass of sludge without drying the solids in a drying oven

copies/g wet sludge

Wet sludge mass is based on the mass of sludge without drying the solids in a drying oven

2

hf183

omicron

n3

sars-cov-2 gene target

qiagen dpcr

clarified sample

brsv vaccine

AS

American Samoa

primary sludge

Sludge from the primary clarifier

47-hr flow-weighted composite

gravity settling

Solids separated from liquid by allowing solids to settle by gravity

AS

American Samoa

[empty]

not tested

hum_frac_target_mic

vs_hum_frac_target_mic

membrane filtration with no amendment

qiagen rneasy powermicrobiome kit

ibuprofen

f+ rna coliphage

long term care - assisted living

A residential facility that provides assistance with daily care but generally does not provide skilled nursing care. May be licensed as healthcare facility based on state regulations.

log10 copies/g wet sludge

Wet sludge mass is based on the mass of sludge without drying the solids in a drying oven

log10 copies/g wet sludge

Wet sludge mass is based on the mass of sludge without drying the solids in a drying oven

3

f+ rna coliphage

hMPXV

e_sarbeco

sars-cov-2 gene target

fluidigm dpcr

sample concentrate

brsv culture

AZ

Arizona

primary effluent

Effluent from the primary clarifier

46-hr flow-weighted composite

none

AZ

Arizona

institution_type

vs_institution_type

membrane filtration with addition of mgcl2, membrane recombined with separated solids

qiagen powerwater kit

[empty]

f+ dna coliphage

other long term care

Other residential facilities that provide daily and/or medical care, but are not defined as nursing home/skilled nursing facilities or assisted living facilities. An example of this is a state-licensed intermediate care facility.

copies/g dry sludge

Dry sludge mass is based on the mass of solids after drying in a drying oven

copies/g dry sludge

Dry sludge mass is based on the mass of solids after drying in a drying oven

more than 3

f+ dna coliphage

hMPXV Clade I

n_sarbeco

sars-cov-2 gene target

life technologies dpcr

lysis buffer

murine coronavirus

AR

Arkansas

secondary sludge

Sludge from the secondary clarifier

45-hr flow-weighted composite

[empty]

AR

Arkansas

sars_cov2_units

vs_mic_chem_units

membrane filtration with sample acidification, membrane recombined with separated solids

qiagen rneasy kit

PMMoV (GT-Digital)

short stay acute care hospital

log10 copies/g dry sludge

Dry sludge mass is based on the mass of solids after drying in a drying oven

log10 copies/g dry sludge

Dry sludge mass is based on the mass of solids after drying in a drying oven

caffeine

hMPXV Clade II

rdrp_sarsr

sars-cov-2 gene target

raindance dpcr

dewatered solids

oc43

CA

California

secondary effluent

Efluent from the secondary clarifier

44-hr flow-weighted composite

CA

California

hum_frac_chem_unit

vs_mic_chem_units_e

membrane filtration with acidification and mgcl2, membrane recombined with separated solids

qiagen ez1 virus mini kit v2.0

[empty]

long term acute care hospital

Acute care hospitals that provide care for patients with average length of stay longer than 25 days. LTACH patients are often transferred from intensive care units of ACH.

micrograms/L wastewater

micrograms/L wastewater

creatinine

caur

Candida auris. Source: KEGG

niid_2019-ncov_n

sars-cov-2 gene target

dpcr

Generic digital PCR

[empty]

phi6

CI

Chicago, IL

septage

Wastewater sampled from within a septic tank

43-hr flow-weighted composite

CO

Colorado

other_norm_units

vs_mic_chem_units_e

membrane filtration with no amendment, membrane recombined with separated solids

promega ht tna kit

child day care

log10 micrograms/L wastewater

log10 micrograms/L wastewater

sucralose

NoV GI

Norovirus GI. Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446575/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446575/

rdrp gene / ncov_ip2

sars-cov-2 gene target

puro

CO

Colorado

holding tank

Wastewater sampled from a holding tank, such as from an airplane or ship

42-hr flow-weighted composite

MP

Commonwealth of Northern Mariana Islands

hum_frac_mic_unit

vs_mic_chem_units_e

peg precipitation

promega automated tna kit

k12

A school serving students in the kindergarten to 12th grade range

micrograms/g wet sludge

Wet sludge mass is based on the mass of sludge without drying the solids in a drying oven

micrograms/g wet sludge

Wet sludge mass is based on the mass of sludge without drying the solids in a drying oven

ibuprofen

NoV GII

Norovirus GII. Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446575/

rdrp gene / ncov_ip4

sars-cov-2 gene target

ms2 coliphage

MP

Commonwealth of Northern Mariana Islands

41-hr flow-weighted composite

CT

Connecticut

num_no_target_control

vs_num_no_target_control

aloh3 precipitation

promega manual tna kit

higher ed dorm

Solely higher education dormitory buildings

log10 micrograms/g wet sludge

Wet sludge mass is based on the mass of sludge without drying the solids in a drying oven

log10 micrograms/g wet sludge

Wet sludge mass is based on the mass of sludge without drying the solids in a drying oven

rnase p

FLUAV

Influenza A. Source: Bacterial and Viral Bioinformatics Resource Center (BV-BRC)

taqpath n

sars-cov-2 gene target

hep g armored rna

CT

Connecticut

40-hr flow-weighted composite

DE

Delaware

other_norm_name

vs_other_norm_name

ultracentrifugation

promega wastewater large volume tna capture kit

higher ed other

Higher education buildings or facilities that do not include dorms or that include dorms and other buildings

micrograms/g dry sludge

Dry sludge mass is based on the mass of solids after drying in a drying oven

micrograms/g dry sludge

Dry sludge mass is based on the mass of solids after drying in a drying oven

[empty]

FLUBV

Influenza B. Source: Bacterial and Viral Bioinformatics Resource Center (BV-BRC)

taqpath s

sars-cov-2 gene target

heat inactivated sars-cov-2 virus

DE

Delaware

39-hr flow-weighted composite

DC

District of Columbia

pcr_target

vs_pcr_target

skimmed milk flocculation

nuclisens automated magnetic bead extraction kit

social services shelter

Other type of social services shelter

log10 micrograms/g dry sludge

Dry sludge mass is based on the mass of solids after drying in a drying oven

log10 micrograms/g dry sludge

Dry sludge mass is based on the mass of solids after drying in a drying oven

NVO

Non-Variolla Orthopoxvirus. Source: CDC https://www.cdc.gov/mmwr/volumes/71/wr/mm7128e1.htm

orf1b

sars-cov-2 gene target

murine hepatitis virus

DC

District of Columbia

38-hr flow-weighted composite

FM

Federated States of Micronesia

pcr_gene_target

vs_pcr_gene_target

beef extract flocculation

nuclisens manual magnetic bead extraction kit

other residential building

Individual residential buildings or institutions not captured in other categories

[empty]

Cjejuni

Campylobacter jejuni. Source: KEGG

orf1ab

sars-cov-2 gene target

MHV (PREvalence)

FM

Federated States of Micronesia

37-hr flow-weighted composite

FL

Florida

pcr_type

vs_pcr_type

promega wastewater large volume tna capture kit

phenol chloroform

ship

HAdV-F

Adenovirus Group F41. Source: PubChem Taxonomy

n1 and n2 combined

sars-cov-2 gene target; Detection of N1 and N2 targets was performed on a single fluorescence channel, such that distinct measurements for N1 and N2 do not exist

BCoV (GT-Digital)

FL

Florida

36-hr flow-weighted composite

GA

Georgia

quant_stan_type

vs_quant_stan_type

centricon ultrafiltration

chemagic viral dna/rna 300 kit

airplane

Col

Colistin AMR

n

sars-cov-2 gene target

[empty]

GA

Georgia

35-hr flow-weighted composite

GU

Guam

rec_eff_spike_matrix

vs_rec_eff_spike_matrix

amicon ultrafiltration

trizol, zymo mag beads w/ zymo clean and concentrator

other worksite

Any commercial facility not captured in other commercial facility categories

Gly

Vancomycin AMR

s

sars-cov-2 gene target

parapoxvirus

GU

Guam

34-hr flow-weighted composite

HI

Hawaii

rec_eff_target_name

vs_rec_eff_target_name

hollow fiber dead end ultrafiltration

4s method (https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-bpdfmi3n)

Bla

Beta-Lactamase AMR

orf1a

sars-cov-2 gene target

HI

Hawaii

33-hr flow-weighted composite

ID

Idaho

reporting_jurisdiction

vs_reporting_jurisdiction

innovaprep ultrafiltration

qiagen qiaamp buffers with epoch columns

Integrase

Integrase AMR

ddcov_n

sars-cov-2 gene target

HO

Houston, TX

32-hr flow-weighted composite

IL

Illinois

sample_location

vs_sample_location

no liquid concentration, liquid recombined with separated solids

zymo quick-rna fungal/bacterial miniprep #r2014

Tet

Tetracycline AMR

ddcov_e

sars-cov-2 gene target

ID

Idaho

31-hr flow-weighted composite

IN

Indiana

sample_matrix

vs_sample_matrix

ceres nanotrap

thermo magmax microbiome ultra nucleic acid isolation kit

RSV

Respiratory Syncytial Virus

ip2 and ip4 combined

sars-cov-2 gene target

IL

Illinois

30-hr flow-weighted composite

IA

Iowa

sample_type

vs_sample_type

zymo environ water rna kit/ zymo environ water rna kit (cat. r2042)

zymo environ water rna kit/ zymo environ water rna kit (cat. r2042)

Fluor

Fluoroquinolone AMR

CDC N1 (GT-Digital)

sars-cov-2 gene target

IN

Indiana

29-hr flow-weighted composite

KS

Kansas

solids_separation

vs_solids_separation

membrane filtration with addition of mgcl3

luminultra wastewater extraction kit

Macro

Macrolide AMR

CDC N2 (GT-Digital)

sars-cov-2 gene target

IA

Iowa

28-hr flow-weighted composite

KY

Kentucky

wwtp_jurisdiction

vs_wwtp_jurisdiction

water concentrating buffer (R2042-1)

qiaamp viral rna kit

Shigella

Shigella spp.

N2 (PREvalence)

sars-cov-2 gene target

KS

Kansas

27-hr flow-weighted composite

LA

Louisiana

sars_cov2_below_lod

vs_yn

none

trizol and RNA purification kit

STEC

Shiga-toxin producing or intimin-producing E. coli or other bacteria

E (PREvalence)

sars-cov-2 gene target

KY

Kentucky

26-hr flow-weighted composite

ME

Maine

ntc_amplify

vs_yn

trizol, garnet bead beating, alcohol precipitation

cycloc

Cyclospora cayetanensis

a1306s

delta gene target

LC

Los Angeles County, CA

25-hr flow-weighted composite

MD

Maryland

stormwater_input

vs_yne

zymo quick-rna viral 96 kit #r1041

Other Bacteria

Other bacteria not listed

p2046l

delta gene target

LA

Louisiana

24-hr flow-weighted composite

MA

Massachusetts

influent_equilibrated

vs_yne

zymo quick-rna viral kit #r1035

Other Virus

Other virus not listed

p2287s

delta gene target

ME

Maine

23-hr flow-weighted composite

MI

Michigan

pretreatment

vs_yne

qiagen qiaamp dsp viral rna mini kit

Other Parasite

Other parasite not listed

t3646a

delta gene target

MD

Maryland

22-hr flow-weighted composite

MN

Minnesota

ext_blank

vs_yne

monarch total RNA miniprep kit (new england biolabs) + onestep PCR inhibitor removal kit (zymo)

Other Fungus or Yeast

Other fungus or yeast not listed

v2930l

delta gene target

MA

Massachusetts

21-hr flow-weighted composite

MS

Mississippi

pasteurized

vs_yne

exclusions based sample preparation (ESP)

Other Eukaryote

Other eukaryote not listed

g662s

delta gene target

MI

Michigan

20-hr flow-weighted composite

MO

Missouri

inhibition_adjust

vs_yne

sciencell viral rna isolation kit

Other Archaea

Other archaea not listed

p100l

delta gene target

MN

Minnesota

19-hr flow-weighted composite

MT

Montana

quality_flag

vs_yne

thermo magmax viral/pathogen nucleic acid isolation kit

a1918v

delta gene target

MS

Mississippi

18-hr flow-weighted composite

NE

Nebraska

inhibition_detect

vs_ynn

t19r

delta gene target

MO

Missouri

17-hr flow-weighted composite

NV

Nevada

e156g

delta gene target

MT

Montana

16-hr flow-weighted composite

NH

New Hampshire

del 157/158

delta gene target

NE

Nebraska

15-hr flow-weighted composite

NJ

New Jersey

l452r

delta gene target

NV

Nevada

14-hr flow-weighted composite

NM

New Mexico

p681r

delta gene target

NH

New Hampshire

13-hr flow-weighted composite

NY

New York

d950n

delta gene target

NJ

New Jersey

12-hr flow-weighted composite

NC

North Carolina

i82t

delta gene target

NM

New Mexico

11-hr flow-weighted composite

ND

North Dakota

d63g

delta gene target

NY

New York

10-hr flow-weighted composite

OH

Ohio

r203m

delta gene target

NZ

New York City, NY

9-hr flow-weighted composite

OK

Oklahoma

g215c

delta gene target

NC

North Carolina

8-hr flow-weighted composite

OR

Oregon

d377y

delta gene target

ND

North Dakota

7-hr flow-weighted composite

PA

Pennsylvania

wt214

delta gene target

OH

Ohio

6-hr flow-weighted composite

PR

Puerto Rico

del156-157

delta gene target

OK

Oklahoma

5-hr flow-weighted composite

MH

Republic of the Marshall Islands

k856r

omicron gene target

OR

Oregon

4-hr flow-weighted composite

PW

Republic of Palau

s2083i

omicron gene target

PA

Pennsylvania

3-hr flow-weighted composite

RI

Rhode Island

del2084/2084

omicron gene target

PH

Philadelphia, PA

2-hr flow-weighted composite

SC

South Carolina

a2710t

omicron gene target

PR

Puerto Rico

1-hr flow-weighted composite

SD

South Dakota

p3395h

omicron gene target

MH

Republic of the Marshall Islands

72-hr time-weighted composite

TN

Tennessee

del3674/3676

omicron gene target

PW

Republic of Palau

48-hr time-weighted composite

TX

Texas

i3758v

omicron gene target

RI

Rhode Island

47-hr time-weighted composite

VI

U.S. Virgin Islands

i1566v

omicron gene target

SC

South Carolina

46-hr time-weighted composite

UT

Utah

a67v

omicron gene target

SD

South Dakota

45-hr time-weighted composite

VT

Vermont

del69/70

omicron gene target

TN

Tennessee

44-hr time-weighted composite

VA

Virginia

a67v/del69/del70

omicron gene target

TX

Texas

43-hr time-weighted composite

WA

Washington

del143/145

omicron gene target

VI

U.S. Virgin Islands

42-hr time-weighted composite

WV

West Virginia

n211i

omicron gene target

UT

Utah

41-hr time-weighted composite

WI

Wisconsin

del212/212

omicron gene target

VT

Vermont

40-hr time-weighted composite

WY

Wyoming

g339d

omicron gene target

VA

Virginia

39-hr time-weighted composite

s371l

omicron gene target

WA

Washington

38-hr time-weighted composite

s373p

omicron gene target

WV

West Virginia

37-hr time-weighted composite

s375f

omicron gene target

WI

Wisconsin

36-hr time-weighted composite

s477n

omicron gene target

WY

Wyoming

35-hr time-weighted composite

e484a

omicron gene target

AP

Acoma Pueblo

34-hr time-weighted composite

q493r

omicron gene target

CN

Catawba Nation

33-hr time-weighted composite

g496s

omicron gene target

CVBPI

Coyote Valley Band of Pomo Indians

32-hr time-weighted composite

q498r

omicron gene target

EBCI

Eastern Band of Cherokee Indians

31-hr time-weighted composite

y505h

omicron gene target

GTBI

Grand Traverse Band of Ottawa and Chippewa Indians

30-hr time-weighted composite

t547k

omicron gene target

MAT

Mescalero Apache Tribe

29-hr time-weighted composite

n679k

omicron gene target

NPT

Nez Perce Tribe

28-hr time-weighted composite

d796y

omicron gene target

OMT

Otoe-Missouria Tribe

27-hr time-weighted composite

n856k

omicron gene target

SBT

The Shoshone Bannock Tribes

26-hr time-weighted composite

q954h

omicron gene target

TRIT

Tule River Indian Tribe

25-hr time-weighted composite

n969k

omicron gene target

ZP

Zuni Pueblo

24-hr time-weighted composite

l981f

omicron gene target

PBCI

Poarch Band of Creek Indians

23-hr time-weighted composite

t9i

omicron gene target

22-hr time-weighted composite

d3g

omicron gene target

21-hr time-weighted composite

q19e

omicron gene target

20-hr time-weighted composite

a63t

omicron gene target

19-hr time-weighted composite

ins214epe

omicron gene target

18-hr time-weighted composite

del142-144

omicron gene target

17-hr time-weighted composite

del31-33

omicron gene target

16-hr time-weighted composite

l24s

omicron gene target

15-hr time-weighted composite

lppa24s

omicron gene target

14-hr time-weighted composite

p13L

omicron gene target

13-hr time-weighted composite

E9L​-NVAR

hMPXV gene target. orthopoxvirus DNA polymerase. CDC Assay all hMPXV​ and non-variola Orthopoxvirus. https://doi.org/10.1016/j.jcv.2006.03.012

12-hr time-weighted composite

G2R_G​

hMPXV gene target. G2R_G primers and probe: detects all MPXV strains ​. https://doi.org/10.1016/j.jviromet.2010.07.012​

11-hr time-weighted composite

G2R_WA​

hMPXV Clade II gene target. hMPXV G2R_WA primers and probe: detects Clade II viruses.CDC https://doi:10.1016/j.jviromet.2010.07.012​

10-hr time-weighted composite

C3L​

hMPXV Clade I gene target. hMPXV C3L primers and probe: detects Clade I viruses ​. CDC https://doi:10.1016/j.jviromet.2010.07.012​

9-hr time-weighted composite

E9L-OPX​3

hMPXV gene target. CDC ​https://doi.org/10.4269/ajtmh.2010.09-0716

8-hr time-weighted composite

B6R

hMPXV gene target. Envelope protien gene CDC Assay; selective for MPXV. CDC https://doi.org/10.1016/j.jcv.2006.03.012

7-hr time-weighted composite

gtmol_hMPXV

hMPXV gene target. hMPXV gene target proprietary GT Molecular

6-hr time-weighted composite

MCR-1.1

Colistin AMR gene target. Source: ARG-ANNOT

5-hr time-weighted composite

VanA-A

Vancomycin AMR gene target. Source: ARG-ANNOT

4-hr time-weighted composite

blaNDM

New-Delhi Metallo- (NDM) Beta-Lactamase AMR gene target. Source: ARG-ANNOT

3-hr time-weighted composite

blaKPC

Klebsiella pneumoniae Carbapenam (KPC) Beta-Lactamase AMR gene target. Source: ARG-ANNOT

2-hr time-weighted composite

blaOXA-48

OXA-type Beta-Lactamase AMR gene target. Source: ARG-ANNOT

1-hr time-weighted composite

blaVIM

Verone Integron-Encoded Metallo- (VIM) Beta-Lactamase AMR gene target. Source: ARG-ANNOT

48-hr manual composite

blaCTX-M-1

CTX-M Beta-Lactamase AMR gene target. Source: ARG-ANNOT

47-hr manual composite

blaCMY

Cephamycin Beta-Lactamase AMR gene target. Source: ARG-ANNOT

46-hr manual composite

blaTEM

Beta-Lactamase AMR gene target. Source: ARG-ANNOT

45-hr manual composite

Class I Integrase

Integrase AMR gene target.

blaSHV

Beta-Lactamase AMR gene target. Source: ARG-ANNOT

44-hr manual composite

TetW

Tetracycline AMR gene target. Source: ARG-ANNOT

43-hr manual composite

blaIMP

Impenemase (IMP) Beta-Lactamase AMR gene target. Source: ARG-ANNOT

42-hr manual composite

caur

Candida auris gene target. Source: https://www.cdc.gov/fungal/candida-auris/pdf/Real-time-PCR-based-Id-C-auris-508.pdf

41-hr manual composite

NoV GI

Norovirus GI ORF1-ORF2 junction gene target. Source: https://wwwnc.cdc.gov/eid/article/17/8/10-1837-t2#r27

40-hr manual composite

NoV GII

Norovirus GII ORF1-ORF2 junction gene target. Source: https://wwwnc.cdc.gov/eid/article/17/8/10-1837-t2#r27

39-hr manual composite

InfA1

Influenza A 1 gene target. Source: https://www.cdc.gov/coronavirus/2019-ncov/lab/multiplex.html?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-ncov%2Flab%2Fmultiplex-primer-probes.html

InfA2

Influenza A 2 gene target. Source: https://www.cdc.gov/coronavirus/2019-ncov/lab/multiplex.html?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-ncov%2Flab%2Fmultiplex-primer-probes.html

38-hr manual composite

InfA1 and InfA2 combined

Influenza A gene target; Detection of InfA1 and InfA2 targets was performed on a single fluorescence channel, such that distinct measurements for InfA1 and InfA2 do not exist. An example is the GT-Digital Influenza and SARS-CoV-2 Wastewater Surveillance Multiplex Assay Kits.

37-hr manual composite

InfB

Influenza B gene target. Source: https://www.cdc.gov/coronavirus/2019-ncov/lab/multiplex.html?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-ncov%2Flab%2Fmultiplex-primer-probes.html

36-hr manual composite

Cjejuni

Campylobacter jejuni gene target. Source: https://www.sciencedirect.com/science/article/pii/S0882401017303728?via%3Dihub

35-hr manual composite

HAdV-F

Adenovirus Group F41 Fiber gene target. Source: https://www.sciencedirect.com/science/article/pii/S0022347608006744?via%3Dihub

34-hr manual composite

RSVL1

RSV-A and RSV-B gene tartget. Primer sets are reactive to both viruses. Two separate probes for RSV-A and RSV-B. https://cdn.who.int/media/docs/default-source/influenza/rsv-surveillance/who-rsv-surveillance-strategy-phase-26mar2021.-final.pdf?sfvrsn=d8b1c36a_9;%20https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015098

33-hr manual composite

ipaH

Shigella gene target

32-hr manual composite

18S rRNA

Eukaryotic gene target (e.g., Cyclospora)

31-hr manual composite

mph(A)

Macrolide resistance target

30-hr manual composite

stx1

STEC gene target

29-hr manual composite

stx2

STEC gene target

28-hr manual composite

eae

STEC gene target

27-hr manual composite

RSV

RSV gene target

26-hr manual composite

fluor

Fluoroquinolone gene target

25-hr manual composite

Other

Please contact NWSS staff to submit data using the "Other" category, or to request that values be added to the vocabulary.

24-hr manual composite

23-hr manual composite

22-hr manual composite

21-hr manual composite

20-hr manual composite

19-hr manual composite

18-hr manual composite

17-hr manual composite

16-hr manual composite

15-hr manual composite

14-hr manual composite

13-hr manual composite

12-hr manual composite

11-hr manual composite

10-hr manual composite

9-hr manual composite

8-hr manual composite

7-hr manual composite

6-hr manual composite

5-hr manual composite

4-hr manual composite

3-hr manual composite

2-hr manual composite

1-hr manual composite

72-hr passive sample

E.g., Moore swabs

48-hr passive sample

E.g., Moore swabs

47-hr passive sample

E.g., Moore swabs

46-hr passive sample

E.g., Moore swabs

45-hr passive sample

E.g., Moore swabs

44-hr passive sample

E.g., Moore swabs

43-hr passive sample

E.g., Moore swabs

42-hr passive sample

E.g., Moore swabs

41-hr passive sample

E.g., Moore swabs

40-hr passive sample

E.g., Moore swabs

39-hr passive sample

E.g., Moore swabs

38-hr passive sample

E.g., Moore swabs

37-hr passive sample

E.g., Moore swabs

36-hr passive sample

E.g., Moore swabs

35-hr passive sample

E.g., Moore swabs

34-hr passive sample

E.g., Moore swabs

33-hr passive sample

E.g., Moore swabs

32-hr passive sample

E.g., Moore swabs

31-hr passive sample

E.g., Moore swabs

30-hr passive sample

E.g., Moore swabs

29-hr passive sample

E.g., Moore swabs

28-hr passive sample

E.g., Moore swabs

27-hr passive sample

E.g., Moore swabs

26-hr passive sample

E.g., Moore swabs

25-hr passive sample

E.g., Moore swabs

24-hr passive sample

E.g., Moore swabs

23-hr passive sample

E.g., Moore swabs

22-hr passive sample

E.g., Moore swabs

21-hr passive sample

E.g., Moore swabs

20-hr passive sample

E.g., Moore swabs

19-hr passive sample

E.g., Moore swabs

18-hr passive sample

E.g., Moore swabs

17-hr passive sample

E.g., Moore swabs

16-hr passive sample

E.g., Moore swabs

15-hr passive sample

E.g., Moore swabs

14-hr passive sample

E.g., Moore swabs

13-hr passive sample

E.g., Moore swabs

12-hr passive sample

E.g., Moore swabs

11-hr passive sample

E.g., Moore swabs

10-hr passive sample

E.g., Moore swabs

9-hr passive sample

E.g., Moore swabs

8-hr passive sample

E.g., Moore swabs

7-hr passive sample

E.g., Moore swabs

6-hr passive sample

E.g., Moore swabs

5-hr passive sample

E.g., Moore swabs

4-hr passive sample

E.g., Moore swabs

3-hr passive sample

E.g., Moore swabs

2-hr passive sample

E.g., Moore swabs

1-hr passive sample

E.g., Moore swabs

120-hr passive sample

E.g., Moore swabs

---

Sheet 4: Change Log

Use of semantic versioning began with v2.0.0. A description follows; see https://semver.org/ for further details.
Major changes (indicated by X in version X.Y.Z): not backwards compatible. In the context of NWSS DCIPHER data submission, these are changes that would cause submission (see note on Submission Requirements) of a data file, if unaltered, to fail upload. These may include addition of required fields or name changes to required fields.
Minor changes (indicated by Y in version X.Y.Z): backwards compatible functionality added. In the context of NWSS DCIPHER data submission, these may be additions of non-required fields, name changes to non-required fields, or changes to value sets, which will not prohibit upload but will be flagged in on-platform QC checks.
Patches (indicated by Z in version X.Y.Z): backwards compatible bug fixes. In the context of NWSS DCIPHER data submission, these may be clarifications of field descriptions, additions to value sets, or reorganization of the metadata.
Date of change	New file name	Version	Major changes	Minor changes	Patches
20200923	NWSS_DCIPHERForm_DataDictionary_Sent-to-states_9.23.20	0.1.0	NA	NA	NA
20201020	NWSS_DCIPHERForm_DataDictionary_20201020	0.2.0	None	1. Changed to allow for sampling location not associated with treatment plant; 2. EPAID no longer required	Description of treatment plant changed to be 'identifiable name'
20201021	NWSS_DCIPHERForm_DataDictionary_20201021	0.3.0	Replaced Pascal Case variable names with snake case variable names to align with bulk upload template variables	None	Added red to data source color scheme to denote DCIPHER generated variables.
20201103	NWSS_DCIPHERForm_DataDictionary_20201103	0.3.1	None	None	Clarified that state variable response for WWTP should be 2-letter abbreviation.
20201105	NWSS_DCIPHERForm_DataDictionary_20201104	0.4.0	None	A number of changes were made to reflect the shift from form-based data submission, which had built-in validation prior to submission, to CSV file submission to DCIPHER: 1. Recharacterized "Pre-populated value set" values as "Allowed values"; 2. Added variable type column	A number of changes were made to reflect the shift from form-based data submission, which had built-in validation prior to submission, to CSV file submission: 1. Changed "Forced column" to "Required Field"; 2. Changed possible responses for "Required Field" to "Not required" and "Required"; 3. Changed "DCIPHER Form Format", "DCIPHER Form Pre-populated Value Set", and "DCIPHER Form Data Validation" column names to denote Internal-Use only; 4. Made all values lower case (not a major change because all values are cast to lower during file parsing);
20201201	NWSS_DCIPHERForm_DataDictionary_20201201	0.5.0	Changed "Required Field" value for the 'state' variable in the "Wastewater Treatment Plant" table from blank to "Required"
20201204	NWSS_DCIPHERForm_DataDictionary_20201204	1.0.0	None	Changed 'composite_freq' from "Required" (if composite) to "Not required"
20201215	NWSS_DCIPHERForm_DataDictionary_20201215	1.0.1	None	None	Changed 'pcr_target_ref' description to "A publication, website, or description of the PCR gene target used"
20201218	NWSS_DCIPHERForm_DataDictionary_20201218	1.0.2	None	None	Changed "Allowed values" from "[any]" to "0-100" for 'industrial_input' to clarify percentage units
20210111	NWSS_DCIPHERForm_DataDictionary_20210111	1.0.3	None	None	Changed "Tooltip / descriptive text" for standard error and confidence interval fields so that '-1' is only entered when these values cannot be calculated
202101222	NWSS_DCIPHERForm_DataDictionary_20210122	1.0.4	None	None	Changed "Tooltip / descriptive text" for 'ntc_amplify' field to be more specific: "For qPCR, did any no-template controls on this instrument run have a Ct value less than 40? For ddPCR, did any no-template controls on this instrument run have 3 or more positive droplets?" This definition aligns with the definition of positivity given on the NWSS webpage for Data Reporting and Analytics, and aligns with guidance provided by a ddPCR instrument manufacturer.
202101225	NWSS_DCIPHERForm_DataDictionary_20210125	1.0.5	None	None	Added clarification to "Tooltip / descriptive text" for 'population_served' field to consider population estimates for upstream sampling locations: "if the sampling location is upstream of a treatment plant (i.e., sample_location = "upstream"), please use the estimated population served by the corresponding service area"
20210127	NWSS_DCIPHERForm_DataDictionary_20210127	1.0.6	None	None	Added additional text and example to "Tooltip / descriptive text" for 'composite_freq' to clarify definition
202102110	NWSS_DCIPHERForm_DataDictionary_20210210	1.0.7	None	None	1. Removed "Internal Use" columns; 2. Updated "Allowed values" column to make 'suggested' values more explicit (e.g., for fields that do not have a finite value set but have values that are commonly used) and to indicate where '-1' should be used to indicate unavailable data for required numeric fields; 3. Added "Notes" column to provide additional guidance, such as where appropriate to leave blank; 4. Clarified "Tooltip / descriptive text" for 'sars_cov2_std_error' and 'tss'; 5. Changed "Display Variable Name" for 'population_served' for clarity
20210319	NWSS_DCIPHER_Data_Dictionary_v2.0.0_20210323	2.0.0	1. New required fields (3): 'institution_type', 'sample_id', 'lab_id'; 2. Name changes to required fields (2): 'state' changed to 'wwtp_jurisdiction', 'reporting_state' changed to 'reporting_jurisdiction';	1. Important description change relevant for upstream sites for 3 fields: 'county_names', 'other_jurisdiction', and 'sewage_travel_time' (these previously pertained to the treatment plant but have been changed to pertain to the sampling site, which is more relevant); 2. Removal and addition of values in value sets (>2 fields): 'sample_location' ("primary influent" and "primary sludge" changed to "wwtp"), 'rec_eff_target_name' ("bovine coronavirus" changed to "bcov vaccine"), other fields where similar values with the same meaning were submitted have been consolidated into one value, and will be indicated in QC checks; 3. Addition of non-required fields (3): 'pasteurized', 'time_zone', 'solids_separation' 4. Name changes to non-required fields (4): 'hum_frac_target_phys' changed to 'other_norm_name', 'hum_frac_target_phys_ref' changed to 'other_norm_ref', 'hum_frac_phys_conc' changed to 'other_norm_conc', 'hum_frac_phys_unit' changed to 'other_norm_unit'
20210416	NWSS_DCIPHER_Data_Dictionary_v2.0.1_20210416	2.0.1	None	None	1. Additions to Value Sets: 'sample_type' now allows composite sample values for any integer duration from 1 to 30 hrs; 'flow_rate' now allows empty values to accommodate a 'sample_matrix' that is not a flowing liquid, such as "primary sludge" or "holding tank"; 'concentration_method' now allows values that capture when solids and liquid are separated but both are tested, e.g., "membrane filtration with addition of mgcl2, membrane recombined with separated solids"; 'pcr_target' now allows these additional values: "n", "s," "orf1a"; 'rec_eff_spike_matrix' now allows [empty] values; 'hum_frac_target_chem' now allows [empty] values; 'hum_frac_target_mic' now allows [empty] values; 'other_norm_name' now allows [empty] values; 'hum_frac_mic_unit' now allows [empty] values; 'hum_frac_chem_unit' now allows [empty] values; 'other_norm_unit' now allows [empty] values; 2. Description clarification: 'other_jurisdiction' has been further clarified to indicate that this refers to locations that exist outside of county boundaries; 'sample_id' has been clarified to indicate that PII must not be included in this field; 'lab_id' has been clarified to indicate that PII is discouraged from being included in this field; the 'jurisdiction id' data type description has been modified to explicitly state that is is not case sensitive, which was previously and is still described in the note on all data types in the Read Me tab
20210512	NWSS_DCIPHER_Data_Dictionary_v2.0.2_20210512	2.0.2	None	None	1. Additions to Value Sets: 'extraction_method' now allows "chemagic viral dna/rna 300 kit", "trizol, zymo mag beads w/ zymo clean and concentrator", "4s method (https://www.protocols.io/view/v-4-direct-wastewater-rna-capture-and-purification-bpdfmi3n)"; 'pcr_target' now allows "ddcov_n" and "ddcov_e"
20210621	NWSS_DCIPHER_Data_Dictionary_v2.0.3_20210621	2.0.3	None	None	1. Additions to Value Sets: 'rec_eff_spike_matrix' now allows "dewatered solids"; 'flow_rate' now allows empty values when SARS-CoV-2 units are provided on a per mass sludge basis; 'concentration_method' now allows "innovaprep ultrafiltration"; 'extraction_method' now allows "qiagen qiaamp buffers with epoch columns"; 'hum_frac_target_mic' and 'other_norm_name' both now allow "f+ rna coliphage" and "f+ dna coliphage"; 2. Description clarification: 'pretreatment' has been clarified to indicate that this field pertains to both chemicals added to the sample and chemicals added as part of the treatment train upstream of the sample collection point, but that pasteurization should be specified in the 'pasteurized' field
20210818	NWSS_DCIPHER_Data_Dictionary_v2.1.0_20210818	2.1.0	None	1. Addition of non-required fields: 'qc_ignore' has been added to allow samples to be intentionally excluded from the DCIPHER QC report; 'analysis_ignore' has been added to allow samples to be intentionally excluded from DCIPHER data analysis; 'dashboard_ignore' has been added to allow samples to be intentionally excluded from the DCIPHER dashboard; 'major_lab_method' has been added to allow reporting jurisdictions to identify major lab methods in their data, which may be useful for determining groups of SARS-CoV-2 results that can be reasonably compared; 'major_lab_method_desc' has been added to allow a brief description of the rationale for assigning a 'major_lab_method'.	1. Additions to Value Sets: 'extraction_method' now allows "zymo quick-rna fungal/bacterial miniprep #r2014"; 'pcr_target' now allows "ip2 and ip4 combined"; 'sars_cov2_below_lod' now allows [empty] values; 'concentration_method' now allows "ceres nanotrap"; 2. Corrections to Value Sets (value yet to be used): 'reporting_jurisdiction' value for Arkansas has been corrected to "AR"; 'extraction_method' value "qiange allprep dna/rna kit" has been corrected to "qiagen allprep dna/rna kit"; 3. Dependent Fields clarification: Dependent Fields for 'flow_rate' has been clarified to indicate that 'flow_rate' can have an [empty] value when SARS-CoV-2 RNA is measured on a per unit wastewater solids basis, rather than a per volume wastewater basis; 4. Dependent Fields change: All uncertainty fields now allow [empty] values, regardless of the values submitted for the other uncertainty fields. In other words, the three fields 'sars_cov2_std_error', 'sars_cov2_cl_95_lo', and 'sars_cov2_cl_95_up' are now all allowed to be [empty]; 5. Requirement dropped: 'sars_cov2_std_error', 'sars_cov2_cl_95_lo', 'sars_cov2_cl_95_up', and 'sars_cov2_below_lod' are no longer required.
20211028	NWSS_DCIPHER_Data_Dictionary_v2.1.1_20211028	2.1.1	None	None	1. Additions to Value Sets: 'concentration_method' now allows "aloh3 precipitation"; 'rec_eff_target_name' now allows "heat inactivated sars-cov-2 virus"; 'extraction_method' now allows "qiagen ez1 virus mini kit v2.0" and "thermo magmax microbiome ultra nucleic acid isolation kit"; 'sample_type' now allows composite sample values for any integer duration from 1 to 48 hrs; 'vs_rec_eff_target_name' now allows "bcov culture" and "brsv culture"; 'extraction_method' now allows "zymo environ water rna kit/ zymo environ water rna kit (cat. r2042)"; 'concentration_method' now allows "zymo environ water rna kit/ zymo environ water rna kit (cat. r2042)"; 2. Description clarification: 'capacity_mgd' has been clarified to indicate that this should be the capacity for which the plant is permitted; 3. Description change: 'county_names' has been changed to ask for FIPS codes rather than names; it also now takes values for both counties and county equivalents; 'other_jurisdiction' has been deprecated, since all jurisdictions previously specified in this field should now be specified in the 'county_names' field. Submitting this field will not interfere with data upload, but this field will no longer be used; 4. Requirement dropped: 'other_jurisdiction' is no longer required;
2021202	NWSS_DCIPHER_Data_Dictionary_v3.0.0_2021202	3.0.0	1. Addition of a new required field 'pcr_gene_target' which should contain the information previously captured in 'pcr_target'. 2. Renaming of fields: 'sars_cov2_units' renamed to 'pcr_target_units' 'sars_cov2_avg_conc' renamed to 'pcr_target_avg_conc' 'sars_cov2_std_error' renamed to 'pcr_target_std_error' 'sars_cov2_cl_95_lo' renamed to 'pcr_target_cl_95_lo' 'sars_cov2_cl_95_up' renamed to 'pcr_target_cl_95_up' 'sars_cov2_below_lod' renamed to 'pcr_target_below_lod'	1. Repurposing of existing fields: 'pcr_target' will be repurposed from the field where PCR gene target information is submitted to now capturing what the overall PCR target was. For example, 'n1' was previously submitted to indicate the target gene for total SARS-CoV-2 was n1. Now that information will be captured in 'pcr_gene_target' and 'pcr_target' will be 'sars-cov-2'. For variants, you would put the variant target gene in 'pcr_gene_target' and 'pcr_target' would be the variant name (currently 'delta' or 'omicron').	1. Additions to Value Sets: 'vs_other_norm_name' now allows "rnase p"; 'vs_institution_type' now allows 'other_worksite' 'vs_pcr_gene_target' now allows 'delta' and 'omicron' genes targets. See 'vs_pcr_gene_target' for the updated valueset options 'vs_pcr_target' now only allows 'sars-cov-2', 'delta', and 'omicron' 2. Field description modifications: Many PCR fields have been modified to reflect the new PCR targets now able to be submitted using the dynamic 'pcr_target' fields as opposed to the total SARS-CoV-2 specific descriptions.
20211208	NWSS_DCIPHER_Data_Dictionary_v3.1.0_20211208	3.1.0	1. Renaming of fields: 'pcr_target_ref' renamed to 'pcr_gene_target_ref'	None	None
20220524	NWSS_DCIPHER_Data_Dictionary_v3.1.1_20220524	3.1.1	None	None	1.Additions to Value Sets: 'vs_concentration_method' now allows 'membrane filtration with addition of mgcl3' 'vs_extraction_method' now allows 'luminultra wastewater extraction kit', 'qiaamp viral rna kit', 'trizol and RNA purificaton kit', 'trizol, garnet bead beating, alcohol precipitation', 'zymo quick-rna viral 96 kit #r1041', 'zymo quick-rna viral kit #r1035', 'qiagen qiaamp dsp viral rna mini kit' 'vs_pcr_gene_target' now allows 'wt214', 'ins214epe', 'del142-144', 'del156-157', 'del31-33' 'vs_pcr_type' now allows 'qiagen dpcr', 'fluidigm dpcr', 'life technologies dpcr', 'raindance dpcr', 'dpcr' 'vs_rec_eff_target_name' now allows 'murine hepatitis virus' 'vs_reporting_jurisdiction' now allows 'AP', 'CN', 'CVBPI', 'EBCI', 'GTBI', 'MAT', 'NPT', 'OMT', 'SBT', 'TRIT', 'ZP' 'vs_sample_type' now allows '120-hr passive sample', from '48-hr passive sample' to '1-hr passive sample' in one hour increments 2. Field description modified: 'pcr_gene_target' description modified to clarify different gene target concentrations should not be averaged
		3.1.2	none	none	1. Additons to Value Sets: 'pcr_gene_target' now allows 'CDC N1 (GT-Digital)', 'CDC N2 (GT-Digital)', 'N2 (PREvalence)', 'E (PREvalence)'. 'rec_eff_target_name' now allows: 'MHV (PREvalence)', 'BCoV (GT-Digital)'. 'hum_frac_target_mic' now allows: 'PMMoV (GT-Digital)'
20220906	NWSS Data Dictionary_v3_1_3_20220906	3.1.3	none	none	1. Additions to Value Sets: 'pcr_target' now allows: 'hMPXV', 'hMPXV Clade I', and 'hMPXV Clade II'. 'rec_eff_target_name' now allows: parapoxvirus'. 'pcr_gene_target' now allows: 'E9L​-NVAR', 'G2R_G'​, 'G2R_WA', 'C3L​', 'E9L-OPX​3', 'B6R', 'B2R', and 'gtmol_hMPXV'
20221018	NWSS Data Dictionary_v3_1_4_20221018	3.1.4	none	none	1. Additions to Value Sets: 'pcr_gene_target' now allows 'a67v/del69/del70'. Reporting_jurisdiction now allows: 'PBCI'.
20221122	NWSS Data Dictionary_v3_1_5_20221122	3.1.5	none	none	1. Addition to Value Sets:'concentration_methods' now allows: 'water concentrating buffer (R2042-1)'; 'extraction_method' now allows 'monarch total RNA miniprep kit (new england biolabs) + onestep PCR inhibitor removal kit (zymo)'; 'pcr_gene_target' now includes 'p13L'; 'sample_type' now includes '72-hr time-weighted composite'.
20230322	NWSS Data Dictionary_v4.0.0_20230322	4.0.0	1. Changing existing fields to required (5): 'epaid', 'pretreatment', 'pasteurized', 'major_lab_method', 'major_lab_method_desc'	1. Changes to value sets: 'pcr_target' now allows 'caur', 'NoV GI', 'NoVGII', 'FLUAV', 'FLUBV', 'NVO', 'Cjejuni', 'HAdV-F', 'Col', 'Gly', 'Bla', 'Integrase', 'Tet'. 'pcr_gene_target' now allows 'MCR-1.1', 'VanA-A', 'blaNDM', 'blaKPC', 'blaOXA-48', 'blaVIM', 'blaCTX-M-1', 'blaCMY', 'blaTEM', 'Class I Integrase', 'blaSHV', 'TetW', 'blaIMP', 'caur', 'NoV GI', 'NoV GII', 'InfA1', 'InfA2', 'InfB', 'Cjejuni', 'HAdv-F'. 'sample_type' now allows '72-hr time-weighted composite'. 'pasteurized' no longer allows [empty]. 'pretreatment' no longer allows [empty]. 'extraction_method' now allows 'exclusions based sample preparation (ESP)' 2. Changes to dependencies of existing field: 'pcr_type' must be a type of dpcr if 'pcr_target' is not 'sars-covs-2', 'delta', 'omicron', ' 3. Added 'epa_registry_id' field	1. Clarifications of field or value set descriptions (2): 'zipcode', 'capacity_mdg', 'test_result_date', 'pcr_target_avg_conc', 'pcr_target_std_error', 'pcr_target_cl_95_lo', 'pcr_target_cl_95_up' 2. Added website to look-up NPDES ID and EPA Registry ID to 'Read Me' and to description in 'Metadata' tabs. 3. Removed space from "other long term care" value for 'institution type'
20230606	NWSS Data Dictionary_v5.0.0_20230606	5.0.0	1. Add new required field: 'site_id'	1. Changes to value sets: 'extraction method' now allows 'sciencell viral rna isolation kit', 'thermo magmax viral/pathogen nucleic acid isolation kit'.