Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratories
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...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-09-01
|
| Series: | BMC Public Health |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12889-022-14210-9 |
| _version_ | 1811265199506718720 |
|---|---|
| author | C. Nadon M. Croxen N. Knox J. Tanner A. Zetner C. Yoshida G. Van Domselaar |
| author_facet | C. Nadon M. Croxen N. Knox J. Tanner A. Zetner C. Yoshida G. Van Domselaar |
| author_sort | C. Nadon |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T20:19:19Z |
| format | Article |
| id | doaj.art-7a87d1db5eb449b1b3093ef5f81f77f8 |
| institution | Directory Open Access Journal |
| issn | 1471-2458 |
| language | English |
| last_indexed | 2024-04-12T20:19:19Z |
| publishDate | 2022-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Public Health |
| spelling | doaj.art-7a87d1db5eb449b1b3093ef5f81f77f82022-12-22T03:18:02ZengBMCBMC Public Health1471-24582022-09-0122111310.1186/s12889-022-14210-9Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratoriesC. Nadon0M. Croxen1N. Knox2J. Tanner3A. Zetner4C. Yoshida5G. Van Domselaar6Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of CanadaAlberta Precision Laboratories, Public Health LaboratoryDepartment of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of ManitobaDivision of Science and Technology Cores and Services, Bioinformatics Section, National Microbiology Laboratory, Public Health Agency of CanadaDivision of Science and Technology Cores and Services, Bioinformatics Section, National Microbiology Laboratory, Public Health Agency of CanadaCanadian Public Health Laboratory Network COVID Genomics Program, National Microbiology Laboratory, Public Health Agency of CanadaDepartment of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of ManitobaAbstract 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.https://doi.org/10.1186/s12889-022-14210-9GenomicsCapacity buildingSurveillanceSARS-CoV-2Public health laboratory |
| spellingShingle | C. Nadon M. Croxen N. Knox J. Tanner A. Zetner C. Yoshida G. Van Domselaar Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratories BMC Public Health Genomics Capacity building Surveillance SARS-CoV-2 Public health laboratory |
| title | Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratories |
| title_full | Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratories |
| title_fullStr | Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratories |
| title_full_unstemmed | Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratories |
| title_short | Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada’s public health laboratories |
| title_sort | public health genomics capacity assessment readiness for large scale pathogen genomic surveillance in canada s public health laboratories |
| topic | Genomics Capacity building Surveillance SARS-CoV-2 Public health laboratory |
| url | https://doi.org/10.1186/s12889-022-14210-9 |
| work_keys_str_mv | AT cnadon publichealthgenomicscapacityassessmentreadinessforlargescalepathogengenomicsurveillanceincanadaspublichealthlaboratories AT mcroxen publichealthgenomicscapacityassessmentreadinessforlargescalepathogengenomicsurveillanceincanadaspublichealthlaboratories AT nknox publichealthgenomicscapacityassessmentreadinessforlargescalepathogengenomicsurveillanceincanadaspublichealthlaboratories AT jtanner publichealthgenomicscapacityassessmentreadinessforlargescalepathogengenomicsurveillanceincanadaspublichealthlaboratories AT azetner publichealthgenomicscapacityassessmentreadinessforlargescalepathogengenomicsurveillanceincanadaspublichealthlaboratories AT cyoshida publichealthgenomicscapacityassessmentreadinessforlargescalepathogengenomicsurveillanceincanadaspublichealthlaboratories AT gvandomselaar publichealthgenomicscapacityassessmentreadinessforlargescalepathogengenomicsurveillanceincanadaspublichealthlaboratories |