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Updated: Sep 20, 2025
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Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
Published on: June 30, 2023
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Development of a Framework for Establishing 'Gold Standard' Outbreak Data from Submitted SARS-CoV-2 Genome Samples.
Yannan Shen1, Russell Steele2, Philip Abdelmalik3
1Department of Epidemiology, Biostatistics and Occupation Health, McGill University, Montreal, Quebec, Canada.
Summary
Genomic surveillance data can establish outbreak onset dates for new respiratory virus variants. A Bayesian online change point detection algorithm (BOCP) framework using genomic submission data provides reliable
Area of Science:
- * Genomic epidemiology and infectious disease surveillance.
- * Computational biology and statistical modeling for public health.
Background:
- * Genomic data submission for respiratory viruses tracks variant emergence and spread.
- * Delays in genomic data submission hinder prospective surveillance but can aid in evaluating other surveillance systems.
- * Limited research exists on utilizing genomic submission data for aberration detection in surveillance.
Purpose of the Study:
- * To develop a framework for establishing 'gold standard' outbreak onset dates using global genomic submission data.
- * To evaluate the utility of a Bayesian online change point detection algorithm (BOCP) for this purpose.
- * To assess the impact of data transformations and parameter settings on change point detection.
Main Methods:
- * Application of a Bayesian online change point detection algorithm (BOCP) to detect increases in submitted genome samples.
- * Utilized genomic submission data from multiple countries to establish outbreak onset dates.
- * Compared different data transformation techniques and algorithm parameter values for BOCP.
Main Results:
- * BOCP successfully identified a significant number of change points indicative of outbreak onsets.
- * Change point detection results were robust and not highly sensitive to parameter value variations.
- * Data transformations were found to be crucial for effective change point detection.
Conclusions:
- * A framework using global genomic submission data and BOCP can establish reliable 'gold standard' outbreak onset dates.
- * This approach enhances the evaluation of genomic surveillance data for tracking new variants.
- * The findings support the use of genomic data for retrospective analysis and validation of surveillance systems.
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