Episode 26: SARS-CoV-2 contextual data specification for open genomic epidemiology

The microbinfie podcast explores the Public Health Alliance for Genomic Epidemiology (PHA4GE) and its critical work in developing standardized approaches for SARS-CoV-2 genomic data sharing during the COVID-19 pandemic.

In this conversation, we engage with Dr. Emma Griffiths (UBC), Dr. Ruth Timme (FDA), and Dr. Duncan MacCannell (CDC) concerning the PHA4GE SARS-CoV-2 contextual data specification, designed for open genomic epidemiology.

Resources

• Paper: PHA4GE SARS-CoV-2 Contextual Data Specification
• Specification: GitHub Repository
• Protocols: Protocols.io Workspace

About PHA4GE

The Public Health Alliance for Genomic Epidemiology (PHA4GE) (visit their website) is a global coalition dedicated to:

• Establishing consensus standards
• Documenting and sharing best practices
• Improving the availability of critical bioinformatic tools and resources
• Advocating for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics

Significance of the Specification

With the ongoing pandemic, PHA4GE has recognized an urgent need for a specifically tailored, open-source SARS-CoV-2 contextual data standard. The team has developed an extension to the INSDC pathogen package to provide a SARS-CoV-2 contextual data specification based on harmonizable, publicly available community standards.

Implementation

• The specification is implementable via a collection template.
• It includes various protocols and tools designed to:
  • Support the harmonization and submission of sequence data
  • Facilitate the inclusion of contextual information to public repositories

Benefits of Rich Contextual Data

• Adds Value: Well-structured data increases usefulness and reusability.
• Promotes Reuse: Easier integration of disparate datasets.
• Enhances Interoperability: Improves consistency and utility across datasets and systems.
• Facilitates Discoveries: Enables novel insights in the study of SARS-CoV-2 and COVID-19.

The adoption of this proposed standard will significantly improve data interoperability, ultimately leading to advances in understanding and combating SARS-CoV-2.

Key Points

1. PHA4GE Origins and Mission

• Established to improve bioinformatics infrastructure and interoperability in public health
• Developed eight working groups focusing on data standards, infrastructure, and ethical data sharing
• Modeled after Global Alliance for Genomics and Health (GA4GH)

2. Data Structures and Contextual Information

• Addresses critical challenges in integrating and sharing genomic surveillance data
• Focuses on developing standardized data models and specifications for SARS-CoV-2
• Aims to improve transparency and reproducibility of public health sequencing workflows

3. COVID-19 Genomic Surveillance

• Developed a contextual data specification for SARS-CoV-2 genome submissions
• Supports international collaboration across multiple national genomic surveillance networks
• Enables more comprehensive analysis of viral spread and characteristics

Take-Home Messages

• Standardized data structures are crucial for effective public health response
• Contextual metadata is essential for meaningful genomic research
• International collaboration can overcome bioinformatics infrastructure challenges