Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada's public health laboratories.

COVID-19 / diagnosis Genomics Humans Laboratories Public Health SARS-CoV-2 / genetics
Capacity building Genomics Public health laboratory SARS-CoV-2 Surveillance

Journal

BMC public health
ISSN: 1471-2458
Titre abrégé: BMC Public Health
Pays: England
ID NLM: 100968562

Informations de publication

Date de publication:
24 09 2022
Historique:
received: 24 03 2022
accepted: 13 09 2022
entrez: 24 9 2022
pubmed: 25 9 2022
medline: 28 9 2022
Statut: epublish

Résumé

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.

Sections du résumé

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.

Identifiants

DOI: 10.1186/s12889-022-14210-9 PMID: 36153510 PMC: PMC9508744
pubmed: 36153510
doi: 10.1186/s12889-022-14210-9
pii: 10.1186/s12889-022-14210-9
pmc: PMC9508744
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1817

Informations de copyright

© 2022. The Author(s).

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Auteurs

C Nadon (C)

Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.
Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada.

M Croxen (M)

Alberta Precision Laboratories, Public Health Laboratory, Edmonton, Canada.
Department of Laboratory Medicine, University of Alberta, Edmonton, Canada.
Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada.

N Knox (N)

Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada.
Division of Science and Technology Cores and Services, Bioinformatics Section, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.

J Tanner (J)

Division of Science and Technology Cores and Services, Bioinformatics Section, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.

A Zetner (A)

Division of Science and Technology Cores and Services, Bioinformatics Section, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.

C Yoshida (C)

Canadian Public Health Laboratory Network COVID Genomics Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.

G Van Domselaar (G)

Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada. gary.vandomselaar@phac-aspc.gc.ca.
Division of Science and Technology Cores and Services, Bioinformatics Section, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada. gary.vandomselaar@phac-aspc.gc.ca.

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Classifications MeSH

questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › Public health genomics capacity assessment:...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Public health genomics capacity assessment:...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Public health genomics capacity assessment:...
questionsmedicales.fr › Établissements, main d'oeuvre et services de soins de santé › Établissements de santé › Laboratoires › Public health genomics capacity assessment:...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Public health genomics capacity assessment:...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › Public health genomics capacity assessment:...