This repository is under review for potential modification in compliance with Administration directives.
Study Information

dbGaP Study Accession: phs002525

NIH Institute/Center: NIDA

RADx Data Program: RADx-rad

DOI: 10.60773/tca1-nb16

Release Date: 01/26/2022

Study Description: The University of Miami (UM), with three primary campuses in Miami, Florida, was geographically spread within one of the worst COVID-19 hotbeds at the time of study. UM deployed an elaborate human surveillance testing, tracking, and tracing (3T) system to monitor the student body, faculty, and staff. The 3T system included a major hospital that is part of UM and that treats COVID-19 patients. To augment the COVID-19 monitoring system, UM deployed a pilot wastewater surveillance program for detecting SARS-CoV-2 from clusters of buildings on campus. Weill Cornell Medicine (WCM) is located in New York City, NY, an area that (at the time of study) had one of the worst outbreaks of COVID-19. WCM established an international consortium for SARS-CoV-2 environmental surveillance, including in NYC and globally with the MetaSUB Consortium, which created metagenomic and metatranscriptomic maps of the world's sewage. Based on this work at both UM and WCM, the aim of the project was to develop, implement, and demonstrate effective and predictive wastewater surveillance by optimizing sampling, concentration, and detection strategies. Working closely with the RADx-rad Data Coordination Center (DCC), work under application SF-RAD included the development and implementation of data standards and informatics infrastructure and performing integrative analyses that made all data, results, and models available to the community, thus providing a critical contribution to the national SARS-COV-2 RADx-rad Wastewater Detection Consortium. The objectives were addressed through three aims. Aim 1: Data Standardization, focused on developing and implementing data standards and quality metrics, and establishing the operational infrastructure to manage SARS-CoV-2 wastewater-based surveillance datasets and metadata. Aim 2: Wastewater Characterization, focused on optimizing wastewater surveillance protocols and parameters for wastewater sampling, sample concentration, and viral detection technologies. Aim 3: Integration with Human Health Surveillance, focused on metatranscriptomic analyses and on the integration of wastewater quantification data with community and hospital COVID-19 prevalence, to develop predictive models to detect local and community level spread of COVID-19. The results from this project developed and deployed experimental and informatics infrastructure and operations as part of the national RADx-rad SARS-CoV-2 wastewater surveillance network and provided a proof-of-concept implementation to use wastewater for infectious disease surveillance for early detection of localized COVID-19 outbreaks.

Updated Date: 10/30/2023

Principal Investigator: Solo-Gabriele, Helena

Has Data Files: Yes

Study Domain: Community Outreach Programs; Wastewater Surveillance

Data Collection Method: Wastewater Sampling

Keywords: Cluster/Outbreaks; Data Standardization; Fecal Coliform; Pepper Mild Mottle Virus (PMMoV); Predictive Modeling; Transcription; Virological Detection Technology; Volcano Second Generation (V2G)-qPCR; Water Quality; β-2 Microglobulin (B2M)

Study Design: Longitudinal Cohort

Multi-Center Study: No

Data Types: Clinical; Electronic Medical Records; Environmental; Genomic; Genotyping; Immunological; Metagenomic; Questionnaire or Survey; Sequencing; Supporting Documents

Study Start Date: 01/01/2021

Study End Date: 12/31/2022

Species: Human; Non-Human

Sample Size: 47269

Study Population Focus: Adults

Publication URL: https://pubmed.ncbi.nlm.nih.gov/33795001/; https://pubmed.ncbi.nlm.nih.gov/34039416/; https://pubmed.ncbi.nlm.nih.gov/34043940/; https://pubmed.ncbi.nlm.nih.gov/34375259/; https://pubmed.ncbi.nlm.nih.gov/34504351/; https://pubmed.ncbi.nlm.nih.gov/35132260/; https://pubmed.ncbi.nlm.nih.gov/35136383/; https://pubmed.ncbi.nlm.nih.gov/35136384/; https://pubmed.ncbi.nlm.nih.gov/35233546/; https://pubmed.ncbi.nlm.nih.gov/35313580/; https://pubmed.ncbi.nlm.nih.gov/35864089/; https://pubmed.ncbi.nlm.nih.gov/35999570/; https://pubmed.ncbi.nlm.nih.gov/35999570/; https://pubmed.ncbi.nlm.nih.gov/36202365/; https://pubmed.ncbi.nlm.nih.gov/36202365/; https://pubmed.ncbi.nlm.nih.gov/36292799/; https://pubmed.ncbi.nlm.nih.gov/36292799/; https://pubmed.ncbi.nlm.nih.gov/36398131/; https://pubmed.ncbi.nlm.nih.gov/36398131/; https://pubmed.ncbi.nlm.nih.gov/36623667/; https://pubmed.ncbi.nlm.nih.gov/36623667/; https://pubmed.ncbi.nlm.nih.gov/37160974/; https://pubmed.ncbi.nlm.nih.gov/37160974/`; https://pubmed.ncbi.nlm.nih.gov/37216988/; https://pubmed.ncbi.nlm.nih.gov/37216988/; https://pubmed.ncbi.nlm.nih.gov/37406055/; https://pubmed.ncbi.nlm.nih.gov/37502918/; https://pubmed.ncbi.nlm.nih.gov/37502918/; https://pubmed.ncbi.nlm.nih.gov/37601294/; https://pubmed.ncbi.nlm.nih.gov/37601294/; https://pubmed.ncbi.nlm.nih.gov/37622131/

Acknowledgement Statement: This study was supported through funding, 4U01DA053941-02, for the National Institute on Drug Abuse (NIDA) as part of the RADx-rad program. Approved users should acknowledge the provision of data access by dbGaP for accession phs002525.v1.p1, and the NIH RADx Data Hub. Approved users should also acknowledge the specific version(s) of the dataset(s) obtained from the NIH RADx Data Hub.

Funding Opportunity Announcement (FOA) Number: RFA-OD-20-015

NIH Grant or Contract Number(s): 4U01DA053941-02

Consent/Data Use Limitations: General Research Use

Variable Information
Total Variables: 363
Study Variables Information Table
Variable Name
Label
Date_of_flu_vac_3-
input_amount_ul-
incubation_time_beads_on_magnet-
rna_libprep_primer_version-
institution_type-
manual_bead_concentrate_id_um_sharkey-
chronic_kidney_diseaseChronic kidney disease
analysis_software_name-
filter_weight_initial_1-
rna_libprep_industry-
bead_manufacturer-
filter_3a_volume-
patient_remdesivir_use-
split_pre_treatment_purpose_2-
Comments_for_flu_vac_2-
sample_collection_method-
bead_beating-
splits_pre_treatment-
tot_conc_vol-
stud_sun_gable_rsmas_na_neg-
inhibition_method-
Comments_for_flu_vac_5-
pcr_target_organism_taxonomy_id-
nih_hypertensionHypertension
epaid-
pcr_standard_type-
rec_eff_notes-
rnaquant_date_of_quant-
patient_ventilator-
rna_seq_pf_prct_reads_per_library-
concentrate_id-
rna_seq_protocol-
filter_1b_volume-
alcohol_useAlcohol Use
nih_asthmaAsthma
no_aliquot_post_rec_addition_ni_EN-
pcr_protocol_name-
water_salinity-
Num_Test-
pcr_instrument-
nih_ageWhat is your age?
composite_start_time-
concentration_protocol-
calculated_total_pos-
Result-
patient_icu-
capacity_mgd-
sodium_thiosulfate_added-
nih_zipWhat is your zip code?
staff_faculty_gable_rsmas_neg-
Date_of_Covid_19_vac_3-
influent_equilibrated-
h_cl_added-
patient_stay_length-
stormwater_input-
volume_manual_bead_concentrate_um_sharkey-
nih_diabetesDiabetes
sample_collect_time-
nih_vaping_ynVaping use (Yes or No)
rna_seq_raw_reads-
covid_test_result-
aliquot_id_um_sharkey_en-
stud_sun_gable_rsmas_on_neg-
height_feetHeight Feet
Date_of_flu_vac_5-
staff_faculty_gable_rsmas_pos-
filter_1a_volume-
pcr_run_id-
composite_freq-
split_pre_treatment_aliquot_vol_1-
split_pre_treatment_purpose_3-
collection_storage_time-
hypertensionHypertension
nih_sexWhat is your biological sex assigned at birth?
concentration_method-
Date_of_Covid_19_vac_5-
hum_frac_mic_unit-
pcr_target_organism_pango_lineage-
sars_cov2_units-
elution_buffer-
volume_manual_bead_concentrate_um_williams-
stud_sun_gable_rsmas_off_neg-
equiv_sewage_amt-
sample_collect_date-
exp_eff_target_name-
post_treatment_ID-
spikein_1_type-
shield_volume-
Comments_for_Covid_19_vac_3-
instrument_software_version-
file_name-
commercially_performed-
user-
location_air_temp-
recovery_cntl_added_manual_bead-
sample_turbidity-
elution_volume_1-
wwtp_name-
cardiovascular_diseaseCardiovascular disease
exp_eff_source-
rnaquant_sample_ul-
sample_matrix-
nih_chronic_kidney_diseaseChronic kidney disease
sample_location-
filter_weight_final_2-
order_date-
rnaquant_concentration-
primer_source-
pregnancy_statusPregnancy status
solids_separation-
pcr_target_chromosome-
patient_mortality-
Comments_for_flu_vac_4-
State-
assay_date-
gps_longitude_minutes-
covid_test_type-
water_flow_unit-
stud_epic_gable_rsmas_off_pos-
diabetesDiabetes
Date_of_flu_vac_4-
spikein_1_conc_cp_ul-
Date_of_flu_vac_2-
sexWhat is your biological sex assigned at birth?
ph-
surface_area_wiped-
nih_immunosuppressive_conditionImmunosuppressive condition
composite_start_date-
aliquot_id_cornell_en-
Date_of_Covid_19_vac_4-
pre_ext_storage_temp-
other_norm_name-
mg_cl_added-
pcr_target_refseq-
collection_storage_temp-
stud_sun_gable_rsmas_na_pos-
aliquot_id_um_williams_en-
hum_frac_mic_conc-
split_pre_treatment_aliquot_vol_3-
stud_sun_gable_rsmas_on_pos-
volume_in_qPCR_wells-
flow_rate-
time_zone-
manual_bead_concentrate_id_um_williams-
nih_sickle_cell_diseaseSickle cell disease
lab_name_to_receive_extra_sample_1-
format-
Comments_for_Covid_19_vac_6-
initial_ww_sample_volume_before_split-
parent_split_before_pre_treatment-
pcr_target-
vol_wastewater_receiving_control-
inhibition_detect-
ww_volume_manual_bead-
country-
patient_data_date-
Date_of_Covid_19_vac_1-
separation_on_magnet_time-
vol_wastewater_receiving_exp_control-
well_id-
nih_serious_mental_illnessSerious mental illness
split_pre_treatment_purpose_1-
pcr_type-
sop_name-
other_norm_unit-
composite_end_date-
pcr_multipexed-
rec_eff_spike_matrix-
concentration_of_sodium_thiosulfate-
start_sampling_time-
passive_reference-
cancerCancer
gps_latitude_degrees-
rna_libprep_input_volume-
composite_aliqots_volume-
wwtp_jurisdiction-
filter_2b_volume-
target_cq-
pcr_target_organism_gisaid_clade-
nih_chronic_lung_diseaseChronic lung disease
Comments_for_Covid_19_vac_4-
manual_bead_concentrate_id_cornell-
gps_latitude_seconds-
pre_conc_storage_time-
spiked_matrix_aliquot-
rna_libprep_elution_volume-
other_norm_conc-
notes_surface_area_wiped-
test_result_date-
end_sampling_date-
sample_class-
volume_input_apex-
rec_eff_target_name-
pasteurized-
approach-
sickle_cell_diseaseSickle cell disease
filter_2a_volume-
filter_weight_initial_2-
zipZip or Postal Code: (De-Identified zip code)
rnaquant_yn-
study_id-
instrument_software_name-
nih_raceWhat is your race?
pcr_gene_target-
incubation_time_ww_on_beads-
particulate_amount-
height_inchesHeight Inches
standard_type-
dorm_location-
split_pre_treatment_ID_3-
population_served-
filter_type-
nih_ethnicityAre you of Hispanic or Latino origin? May include Spanish origin.
state_names-
immunosuppressive_conditioImmunosuppressive condition
ph_final-
rnaquant_assay_kit-
staff_faculty_med_neg-
composite_end_time-
rna_seq_date-
exp_eff_spike_conc-
air_vacuum_flow_rate-
lab_id-
pcr_target_gene_name-
weight_lbsWhat is your weight? (Weight in pounds)
ww_split_id_manual_bead-
chronic_lung_diseaseChronic lung disease
positive_students-
rec_eff_spike_conc-
exp_eff_volume-
split_pre_treatment_ID_2-
spiked_matrix_ID-
Order_Name-
gps_longitude_seconds-
extraction_run_id-
forward_primer_sequence-
sars_cov2_avg_conc-
nicotineNicotine Use
volume_shield_manual_bead-
stud_epic_gable_rsmas_off_neg-
recovery_addition-
zipcode-
nih_heightWhat is your height in inches?
initial_ww_volume_manual_bead-
no_aliquot_post_exp_addition_ni_EN-
sewage_turbidity-
rna_seq_machine_model-
experimental_addition-
spiked_exp_matrix_aliquot-
pcr_target_organism_who_label-
collection_water_temp-
plate_format-
volume_of_sodium_thiosulfate-
asthmaAsthma
split_pre_treatment_ID_1-
nih_insuranceWhat kind of health insurance do you have?
gps_longitude_degrees-
nih_alcohol_ynAlcohol use (Yes or No)
ph_meter-
ww_split_id_apex-
filter_3b_volume-
Collection_date-
sample_location_specify-
raceWhat is your race? Mark one or more boxes.
reverse_primer_sequence-
insuranceWhat kind of health insurance do you have?
gps_latitude_minutes-
rna_libprep_rRNA_depletion-
filter_weight_final_1-
extractant_id-
filter_insertion-
nih_weightWhat is your weight in pounds?
ageWhat is your age? (Age in years. For babies less than 1 year old, write 0 as the age)
pcr_target_organism_subtype-
rna_seq_flowcell-
stud_epic_gable_rsmas_na_neg-
rna_libprep_protocol_version-
Date_of_Covid_19_vac_7-
location_air_humidity-
Comments_for_Covid_19_vac_2-
nih_pregnancyPregnancy status
probe_serial_number-
rna_libprep_index_2-
pcr_target_gene_region-
calculated_total_neg-
nih_nicotine_ynNicotine use (Yes or No)
Comments_for_flu_vac_3-
tube_volume_um_williams-
lab_extra_sample_volume_1-
start_sampling_date-
volume_PBS_manual_bead_wash-
rna_libprep_kit-
instrument_serial_number-
chemical_principle-
sewage_travel_time-
standard_vendor-
pcr_target_organism_name-
extraction_method-
pcr_target_gisaid_id-
rna_libprep_index_1-
patient_covid_test_complete-
rec_eff_source-
analysis_software_version-
pcr_count-
stud_epic_gable_rsmas_na_pos-
Comments_for_flu_vac_1-
split_pre_treatment_aliquot_vol_2-
Comments_for_Covid_19_vac_7-
manual_protocol_name-
ethnicityAre you of Hispanic or Latino origin?
composite_type-
date-
stud_epic_gable_rsmas_on_pos-
Date_of_flu_vac_1-
rna_seq_pf_reads-
volume_used_for_reaction-
volume_concentrate_output_apex-
conductivity-
lod_ref-
rna_libprep_date_of_prep-
Comments_for_Covid_19_vac_5-
exp_eff_notes-
exp_eff_spike_matrix-
sewage_color-
staff_faculty_med_pos-
composite_aliqots_attempted-
spikein_1_amount_ul-
sample_id-
Date_of_Covid_19_vac_6-
county_names-
rec_eff_volume-
tests_performed-
stud_sun_gable_rsmas_off_pos-
serious_mental_illnessSerious mental illness
rna_seq_yield_mbases-
rna_libprep_rRNA_depletion_kit-
pre_ext_storage_time-
rna_seq_machine_serial_number-
nih_record_idUser ID
hum_frac_target_mic-
probe_sequence-
output_sample_type-
specimen_id-
tube_volume_cornell-
Comments_for_Covid_19_vac_1-
vapingVaping Use
exp_spiked_matrix_ID-
rna_seq_lane-
extract_label-
pcr_target_gene_id-
nih_cardiovascular_diseaseCardiovascular disease
rna_seq_runid-
ph_calibration-
sample_dissolved_oxygen-
end_samping_time-
Date_of_Covid_19_vac_2-
rna_seq_industry-
particulate_color-
nih_cancerCancer
ww_appearance_notes-
tube_volume_um_sharkey-
stud_epic_gable_rsmas_on_neg-
pre_conc_storage_temp-
Study Documents
Study Documents Table
Document
Document Name
File Size
Download
Study Protocolphs002525_Protocol.pdf654.88 KB
Data Files
Total Files: 48
Data Files: 16
Metadata Files: 16
Dictionary Files: 16
Study Datasets Table
File Name
File Type
File Format(s)
# of Records
# of Variables
Metadata
Dictionary
rad_015_941-01_deidentified_clinicaldata_DATA_origcopy.csvTabular Data - Non-harmonizedcsv8123
rad_015_941-01_qPCR_RawData_DATA_origcopy.csvTabular Data - Non-harmonizedcsv21483
rad_015_941-01_qPCRData_DATA_origcopy.csvTabular Data - Non-harmonizedcsv775
rad_015_941-01_RNA_seq_Results_DATA_origcopy.csvTabular Data - Non-harmonizedcsv1253
rad_015_941-01_deidentified_clinicaldata_DATA_transformcopy.csvTabular Data - Harmonizedcsv8123
rad_015_941-01_covid_campus_counts_DATA_origcopy.csvTabular Data - Non-harmonizedcsv850
rad_015_941-01_deidentified_student_individual_Testing_DATA_transformcopy.csvTabular Data - Harmonizedcsv261497
rad_015_941-01_deidentified_student_individual_Testing_DATA_origcopy.csvTabular Data - Non-harmonizedcsv261497
rad_015_941-01_deidentified_student_individual_vaccine_DATA_transformcopy.csvTabular Data - Harmonizedcsv47277
rad_015_941-01_deidentified_student_individual_vaccine_DATA_origcopy.csvTabular Data - Non-harmonizedcsv47277
rad_015_941-01_extraction_DATA_origcopy.csvTabular Data - Non-harmonizedcsv3314
rad_015_941-01_FieldData_DATA_origcopy.csvTabular Data - Non-harmonizedcsv3055
rad_015_941-01_pretreatment_DATA_origcopy.csvTabular Data - Non-harmonizedcsv2069
rad_015_941-01_qPCR_ProcessedData_DATA_origcopy.csvTabular Data - Non-harmonizedcsv2351
rad_015_941-01_aggregated_student_DATA_origcopy.csvTabular Data - Non-harmonizedcsv4990
rad_015_941-01_concentration_DATA_origcopy.csvTabular Data - Non-harmonizedcsv3023