Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data
Abstract Background The spread of SARS-CoV-2 has been studied at unprecedented levels worldwide. In jurisdictions where molecular analysis was performed on large scales, the emergence and competition of numerous SARS-CoV-2lineages have been observed in near real-time. Lineage identification, traditi...
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-01-01
|
| Series: | BMC Infectious Diseases |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12879-024-08997-8 |
| _version_ | 1797275690715840512 |
|---|---|
| author | David Champredon Devan Becker Shelley W. Peterson Edgard Mejia Nikho Hizon Andrea Schertzer Mohamed Djebli Femi F. Oloye Yuwei Xie Mohsen Asadi Jenna Cantin Xia Pu Charles A. Osunla Markus Brinkmann Kerry N. McPhedran Mark R. Servos John P. Giesy Chand Mangat |
| author_facet | David Champredon Devan Becker Shelley W. Peterson Edgard Mejia Nikho Hizon Andrea Schertzer Mohamed Djebli Femi F. Oloye Yuwei Xie Mohsen Asadi Jenna Cantin Xia Pu Charles A. Osunla Markus Brinkmann Kerry N. McPhedran Mark R. Servos John P. Giesy Chand Mangat |
| author_sort | David Champredon |
| collection | DOAJ |
| description | Abstract Background The spread of SARS-CoV-2 has been studied at unprecedented levels worldwide. In jurisdictions where molecular analysis was performed on large scales, the emergence and competition of numerous SARS-CoV-2lineages have been observed in near real-time. Lineage identification, traditionally performed from clinical samples, can also be determined by sampling wastewater from sewersheds serving populations of interest. Variants of concern (VOCs) and SARS-CoV-2 lineages associated with increased transmissibility and/or severity are of particular interest. Method Here, we consider clinical and wastewater data sources to assess the emergence and spread of VOCs in Canada retrospectively. Results We show that, overall, wastewater-based VOC identification provides similar insights to the surveillance based on clinical samples. Based on clinical data, we observed synchrony in VOC introduction as well as similar emergence speeds across most Canadian provinces despite the large geographical size of the country and differences in provincial public health measures. Conclusion In particular, it took approximately four months for VOC Alpha and Delta to contribute to half of the incidence. In contrast, VOC Omicron achieved the same contribution in less than one month. This study provides significant benchmarks to enhance planning for future VOCs, and to some extent for future pandemics caused by other pathogens, by quantifying the rate of SARS-CoV-2 VOCs invasion in Canada. |
| first_indexed | 2024-03-07T15:18:09Z |
| format | Article |
| id | doaj.art-837b36c669de490cb8ba35ec255c03f0 |
| institution | Directory Open Access Journal |
| issn | 1471-2334 |
| language | English |
| last_indexed | 2024-03-07T15:18:09Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Infectious Diseases |
| spelling | doaj.art-837b36c669de490cb8ba35ec255c03f02024-03-05T17:49:14ZengBMCBMC Infectious Diseases1471-23342024-01-0124111110.1186/s12879-024-08997-8Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater dataDavid Champredon0Devan Becker1Shelley W. Peterson2Edgard Mejia3Nikho Hizon4Andrea Schertzer5Mohamed Djebli6Femi F. Oloye7Yuwei Xie8Mohsen Asadi9Jenna Cantin10Xia Pu11Charles A. Osunla12Markus Brinkmann13Kerry N. McPhedran14Mark R. Servos15John P. Giesy16Chand Mangat17Public Health Agency of Canada, National Microbiology Laboratory, Public Health Risk Sciences DivisionPublic Health Agency of Canada, National Microbiology Laboratory, Public Health Risk Sciences DivisionPublic Health Agency of Canada, National Microbiology Laboratory, One Health DivisionPublic Health Agency of Canada, National Microbiology Laboratory, One Health DivisionPublic Health Agency of Canada, National Microbiology Laboratory, One Health DivisionPublic Health Agency of Canada, Centre for Immunization and Respiratory Infectious DiseasesPublic Health Agency of Canada, Centre for Immunization and Respiratory Infectious DiseasesToxicology Program, University of SaskatchewanToxicology Program, University of SaskatchewanDepartment of Civil, Geological and Environmental Engineering, College of Engineering, University of SaskatchewanToxicology Program, University of SaskatchewanToxicology Program, University of SaskatchewanToxicology Program, University of SaskatchewanToxicology Program, University of SaskatchewanDepartment of Civil, Geological and Environmental Engineering, College of Engineering, University of SaskatchewanDepartment of Biology, University of WaterlooToxicology Program, University of SaskatchewanPublic Health Agency of Canada, National Microbiology Laboratory, One Health DivisionAbstract Background The spread of SARS-CoV-2 has been studied at unprecedented levels worldwide. In jurisdictions where molecular analysis was performed on large scales, the emergence and competition of numerous SARS-CoV-2lineages have been observed in near real-time. Lineage identification, traditionally performed from clinical samples, can also be determined by sampling wastewater from sewersheds serving populations of interest. Variants of concern (VOCs) and SARS-CoV-2 lineages associated with increased transmissibility and/or severity are of particular interest. Method Here, we consider clinical and wastewater data sources to assess the emergence and spread of VOCs in Canada retrospectively. Results We show that, overall, wastewater-based VOC identification provides similar insights to the surveillance based on clinical samples. Based on clinical data, we observed synchrony in VOC introduction as well as similar emergence speeds across most Canadian provinces despite the large geographical size of the country and differences in provincial public health measures. Conclusion In particular, it took approximately four months for VOC Alpha and Delta to contribute to half of the incidence. In contrast, VOC Omicron achieved the same contribution in less than one month. This study provides significant benchmarks to enhance planning for future VOCs, and to some extent for future pandemics caused by other pathogens, by quantifying the rate of SARS-CoV-2 VOCs invasion in Canada.https://doi.org/10.1186/s12879-024-08997-8SARS-CoV-2lineagesMolecular analysisLineage identificationVariant of concernClinical samples: OmicronWastewater-based epidemiology |
| spellingShingle | David Champredon Devan Becker Shelley W. Peterson Edgard Mejia Nikho Hizon Andrea Schertzer Mohamed Djebli Femi F. Oloye Yuwei Xie Mohsen Asadi Jenna Cantin Xia Pu Charles A. Osunla Markus Brinkmann Kerry N. McPhedran Mark R. Servos John P. Giesy Chand Mangat Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data BMC Infectious Diseases SARS-CoV-2lineages Molecular analysis Lineage identification Variant of concern Clinical samples: Omicron Wastewater-based epidemiology |
| title | Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data |
| title_full | Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data |
| title_fullStr | Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data |
| title_full_unstemmed | Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data |
| title_short | Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data |
| title_sort | emergence and spread of sars cov 2 variants of concern in canada a retrospective analysis from clinical and wastewater data |
| topic | SARS-CoV-2lineages Molecular analysis Lineage identification Variant of concern Clinical samples: Omicron Wastewater-based epidemiology |
| url | https://doi.org/10.1186/s12879-024-08997-8 |
| work_keys_str_mv | AT davidchampredon emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT devanbecker emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT shelleywpeterson emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT edgardmejia emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT nikhohizon emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT andreaschertzer emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT mohameddjebli emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT femifoloye emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT yuweixie emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT mohsenasadi emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT jennacantin emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT xiapu emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT charlesaosunla emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT markusbrinkmann emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT kerrynmcphedran emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT markrservos emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT johnpgiesy emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata AT chandmangat emergenceandspreadofsarscov2variantsofconcernincanadaaretrospectiveanalysisfromclinicalandwastewaterdata |