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Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation.
Thakali, Ocean; Mercier, Élisabeth; Eid, Walaa; Wellman, Martin; Brasset-Gorny, Julia; Overton, Alyssa K; Knapp, Jennifer J; Manuel, Douglas; Charles, Trevor C; Goodridge, Lawrence; Arts, Eric J; Poon, Art F Y; Brown, R Stephen; Graber, Tyson E; Delatolla, Robert; DeGroot, Christopher T.
Afiliación
  • Thakali O; Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
  • Mercier É; Department of Civil Engineering, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
  • Eid W; Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada.
  • Wellman M; The Ottawa Hospital Research Institute, 1053 Carling Ave, Ottawa, ON, K1Y 4E9, Canada.
  • Brasset-Gorny J; Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada.
  • Overton AK; Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
  • Knapp JJ; Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
  • Manuel D; Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada.
  • Charles TC; Department of Family Medicine, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON, K1N 6N5, Canada.
  • Goodridge L; School of Epidemiology and Public Health, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON, K1N 6N5, Canada.
  • Arts EJ; Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
  • Poon AFY; Department of Food Science, Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, N1G 2W1, Canada.
  • Brown RS; Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada.
  • Graber TE; Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada.
  • Delatolla R; School of Environmental Studies and Department of Chemistry, Queen's University, Kingston, ON, Canada.
  • DeGroot CT; Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada.
Sci Rep ; 14(1): 3728, 2024 02 14.
Article en En | MEDLINE | ID: mdl-38355869
ABSTRACT
Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity of RT-qPCR has been achieved, in part, by monitoring two or more genomic loci of SARS-CoV-2. In Ontario, Canada, the provincial Wastewater Surveillance Initiative reports the average copies of the CDC N1 and N2 loci normalized to the fecal biomarker pepper mild mottle virus. In November 2021, the emergence of the Omicron variant of concern, harboring a C28311T mutation within the CDC N1 probe region, challenged the accuracy of the consensus between the RT-qPCR measurements of the N1 and N2 loci of SARS-CoV-2. In this study, we developed and applied a novel real-time dual loci quality assurance and control framework based on the relative difference between the loci measurements to the City of Ottawa dataset to identify a loss of sensitivity of the N1 assay in the period from July 10, 2022 to January 31, 2023. Further analysis via sequencing and allele-specific RT-qPCR revealed a high proportion of mutations C28312T and A28330G during the study period, both in the City of Ottawa and across the province. It is hypothesized that nucleotide mutations in the probe region, especially A28330G, led to inefficient annealing, resulting in reduction in sensitivity and accuracy of the N1 assay. This study highlights the importance of implementing quality assurance and control criteria to continually evaluate, in near real-time, the accuracy of the signal produced in wastewater surveillance applications that rely on detection of pathogens whose genomes undergo high rates of mutation.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Aguas Residuales / Monitoreo Epidemiológico Basado en Aguas Residuales Tipo de estudio: Prognostic_studies / Screening_studies País/Región como asunto: America do norte Idioma: En Revista: Sci Rep Año: 2024 Tipo del documento: Article País de afiliación: Canadá Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
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XML
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Aguas Residuales / Monitoreo Epidemiológico Basado en Aguas Residuales Tipo de estudio: Prognostic_studies / Screening_studies País/Región como asunto: America do norte Idioma: En Revista: Sci Rep Año: 2024 Tipo del documento: Article País de afiliación: Canadá Pais de publicación: Reino Unido