ABSTRACT
Background The timely sharing of public health information is critical during a pandemic and is an obstacle that Canada has yet to fully address. During the current Coronavirus Disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome sequencing has provided a deeper understanding of transmission patterns, enabled the identification of variants of concern, and facilitated diagnostic tests and vaccine development and evaluation. The Canadian national response faces challenges in aggregating genomic contextual data and carrying out integrated analysis across regions partly due to disparities in the case report forms used to capture epidemiological and clinical data. Such variations delay data integration and make consistent analysis difficult or impossible. The objective of this work is to understand what information is being collected from severe acute respiratory syndrome coronavirus 2 case report forms used across Canada and identify potential genome sequence data harmonization issues and solutions.Methods Provincial/territorial/national Canadian COVID-19 case report forms were subjected to field-by-field comparisons to identify variations in data categorization, structures, formats, types, granularity, ambiguity, and questions asked. Federal epidemiologists were consulted to substantiate the results.Results Data harmonization issues and common data elements were identified. We make recommendations for better national coordination, integrated databases, and data harmonization tools.Conclusion This report compares data elements of the various case report forms used across Canada to identify overlaps and differences in the collection method of COVID-19 case information, while also highlighting data harmonization complications and potential solutions. Knowing which data elements are available to researchers and health officials will better inform the development of Coronavirus Disease 2019 surveillance and research questions.
Subject(s)
COVID-19ABSTRACT
The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatic tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a clear and present need for a fit-for-purpose, open source SARS-CoV-2 contextual data standard. As such, we have developed an extension to the INSDC pathogen package, providing a SARS-CoV-2 contextual data specification based on harmonisable, publicly available, community standards. The specification is implementable via a collection template, as well as an array of protocols and tools to support the harmonisation and submission of sequence data and contextual information to public repositories. Well-structured, rich contextual data adds value, promotes reuse, and enables aggregation and integration of disparate data sets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19.