NWSS Data Dictionary

Attachment-12_Component-1_ref-NWSS Data Dictionary_v5.0.0.xlsx

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

NWSS Data Dictionary

OMB: 0920-1422

Document [xlsx]
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Overview

Read Me
Metadata
Value Sets
Change Log


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














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

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'.
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