Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratories
Background Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomi...
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| Vydáno v: | BMC public health Ročník 22; číslo 1; s. 1 - 13 |
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| Hlavní autoři: | , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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London
BioMed Central
24.09.2022
BioMed Central Ltd Springer Nature B.V BMC |
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| ISSN: | 1471-2458, 1471-2458 |
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| Abstract | Background
Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada’s public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic.
Methods
We used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada.
Results
We found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel.
Conclusions
These findings enable the strategic prioritization and deployment of resources to increase Canada’s ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building. |
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| AbstractList | Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada's public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic. We used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada. We found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel. These findings enable the strategic prioritization and deployment of resources to increase Canada's ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building. Abstract Background Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada’s public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic. Methods We used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada. Results We found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel. Conclusions These findings enable the strategic prioritization and deployment of resources to increase Canada’s ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building. Background Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada’s public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic. Methods We used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada. Results We found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel. Conclusions These findings enable the strategic prioritization and deployment of resources to increase Canada’s ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building. Background Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada's public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic. Methods We used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada. Results We found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel. Conclusions These findings enable the strategic prioritization and deployment of resources to increase Canada's ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building. Keywords: Genomics, Capacity building, Surveillance, SARS-CoV-2, Public health laboratory Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada's public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic.BACKGROUNDAlong with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada's public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic.We used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada.METHODSWe used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada.We found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel.RESULTSWe found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel.These findings enable the strategic prioritization and deployment of resources to increase Canada's ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building.CONCLUSIONSThese findings enable the strategic prioritization and deployment of resources to increase Canada's ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building. Background Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada’s public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic. Methods We used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada. Results We found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel. Conclusions These findings enable the strategic prioritization and deployment of resources to increase Canada’s ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building. |
| ArticleNumber | 1817 |
| Audience | Academic |
| Author | Nadon, C. Tanner, J. Zetner, A. Croxen, M. Yoshida, C. Van Domselaar, G. Knox, N. |
| Author_xml | – sequence: 1 givenname: C. surname: Nadon fullname: Nadon, C. organization: Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba – sequence: 2 givenname: M. surname: Croxen fullname: Croxen, M. organization: Alberta Precision Laboratories, Public Health Laboratory, Department of Laboratory Medicine, University of Alberta, Li Ka Shing Institute of Virology, University of Alberta – sequence: 3 givenname: N. surname: Knox fullname: Knox, N. organization: Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Division of Science and Technology Cores and Services, Bioinformatics Section, National Microbiology Laboratory, Public Health Agency of Canada – sequence: 4 givenname: J. surname: Tanner fullname: Tanner, J. organization: Division of Science and Technology Cores and Services, Bioinformatics Section, National Microbiology Laboratory, Public Health Agency of Canada – sequence: 5 givenname: A. surname: Zetner fullname: Zetner, A. organization: Division of Science and Technology Cores and Services, Bioinformatics Section, National Microbiology Laboratory, Public Health Agency of Canada – sequence: 6 givenname: C. surname: Yoshida fullname: Yoshida, C. organization: Canadian Public Health Laboratory Network COVID Genomics Program, National Microbiology Laboratory, Public Health Agency of Canada – sequence: 7 givenname: G. surname: Van Domselaar fullname: Van Domselaar, G. email: gary.vandomselaar@phac-aspc.gc.ca organization: Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Division of Science and Technology Cores and Services, Bioinformatics Section, National Microbiology Laboratory, Public Health Agency of Canada |
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| CitedBy_id | crossref_primary_10_1016_j_lanmic_2024_100969 crossref_primary_10_1057_s41292_024_00326_1 crossref_primary_10_3389_fpubh_2025_1587112 crossref_primary_10_3389_fsci_2024_1298248 |
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| Keywords | SARS-CoV-2 Capacity building Public health laboratory Surveillance Genomics |
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| Snippet | Background
Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based... Background Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based... Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance.... Abstract Background Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates... |
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| SubjectTerms | Bioinformatics Biostatistics Capacity Capacity building Capacity development Contact tracing Coronaviruses COVID-19 Environmental Health Epidemiology Evaluation Gene sequencing Genomics Infectious diseases Laboratories Leadership Medicine Medicine & Public Health Pandemics Pathogens Preparedness Public Health Public health laboratories Public health laboratory Qualitative research SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Surveillance Vaccine Whole genome sequencing |
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| Title | Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratories |
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