Wastewater-Based Epidemiology Surveillance for Early Detection SARS-CoV-2: Method Development

Details

• Personal Author:
  Wright-Foulkes D
• Description:
  Evaluation of RT-qPCR assay for the detection of SARS-CoV-2 quantitatively measured in standard calibration curves using gene targets that yield precise, sensitive, specific, and efficient results. Two gene targets were used to detect two regions in the SARS-COV-2 nucleocapsid N1 and N2 loci of the nucleocapsid (N) gene, specific to SARS-CoV-2, bovine coronavirus (BCoV) to determine virus recovery, and Pepper mild mottle virus (PPMoV), a marker of human stool. Evaluation required standard calibration curves for each of the two targets using primers and probes. The purpose of these standard calibration curves was to evaluate whether the RT-qPCR assay and instruments give consistent data with low to no variability from run to run. Thus, the curves can be used to estimate the RNA viral concentrations in wastewater samples. Six standard calibration curves for two gene markers were performed. Data analysis included examining the linearity of the calibration curves, residual analysis to determine the consistency of slope with repeated calibrations and determining the lower limit of quantification (LLOQ) for the four targets of interest. Indicate that the calibration curves of log-transformed concentration versus cycle threshold (Ct) are linear over 5 orders of magnitude for N1 and N2, 6 orders of magnitude for BCoV, and seven orders of magnitude for PMMoV. Average slopes (standard deviation) are - 3.19 (0.06), -3.38 (0.12), -3.55 (0.09), and -3.32 (0.05) for N1, N2, BCoV, and PMMoV, respectively. Residual analysis of the slopes for each experiment showed average residuals equal to zero for each of the four gene targets with a small upward but low correlation trend for N1 and small downward trends, with low correlations for N2, BCoV, and PMMoV. The LLOQ values are 0.018 , 0.018, 0.017, 0.017 for N1, N2, BCoV, and PMMoV, respectively. This analysis reveals the methodology and instruments are giving consistent data with low variability over time allowing for confidence in the detection of SARS-CoV-2. The consistency gives confidence that the four targets (N1, N2, BCoV, PMMoV) can be used to detect and quantify SARS-CoV-2 in wastewater. Our laboratory will use this method to test for SARS-CoV-2 in environmental wastewater samples. [Description provided by NIOSH]
• Subjects:
  Communicable Diseases Epidemiology Genetics Occupational Health Safety Viral Diseases
• Keywords:
  Coronavirus Genes SARS-CoV-2 Surveillance Viral Diseases Water Sampling
• Publisher:
  University of Illinois at Chicago
• Document Type:
  Text
• Funding:
  Grant
• Genre:
  Thesis
• Place as Subject:
  Illinois ; OSHA Region 5
• CIO:
  National Institute for Occupational Safety and Health (NIOSH)
• Topic:
  Workplace Safety & Health
• Location:
  North America
• Pages in Document:
  1-38
• NIOSHTIC Number:
  nn:20068713
• Citation:
  Chicago, IL: University of Illinois at Chicago, 2022 Nov; :1-38
• Federal Fiscal Year:
  2023
• Performing Organization:
  University of Illinois at Chicago
• Peer Reviewed:
  False
• Start Date:
  20050701
• Source Full Name:
  Wastewater-based epidemiology surveillance for early detection SARS-CoV-2: method development
• End Date:
  20290630
• Collection(s):
  National Institute for Occupational Safety and Health
• Main Document Checksum:
  urn:sha-512:0802513015f232411acd1999780460d46e38e4c4e97123480d74c1165a872d0b3d308e3dec248fedca043805b1bf6462789d2e4882f9fa763362cc6af71440cf
• Download URL:
  https://stacks.cdc.gov/view/cdc/207299/cdc_207299_DS1.pdf
• File Type:
  [PDF - 512.44 KB ]