Episode 42: Overcoming barriers to SARS-CoV-2 data analysis

In this episode of the microbinfie podcast, panelists from the ARTIC Network and CLIMB-BIG-DATA workshop discuss COVID-19 genomics challenges, data analysis strategies, and collaborative bioinformatics efforts during the pandemic.

Presented by: ARTIC Network & CLIMB-BIG-DATA

Panelists:

• Nick Loman and Will Rowe - University of Birmingham
• Áine O'Toole - University of Edinburgh
• Andrew Page - Quadram Institute
• Anna Price - MRC CLIMB and Cardiff University

This panel discussion was part of a comprehensive workshop focused on COVID-19 data analysis. Below is a summary of the topics covered and the resources shared during the event.

Topics Covered

• Collecting Sample Metadata
• Intrapatient Variability
• Building Bridges with Policy Makers to Initiate Sequencing
• Data Sharing
• Improving Bioinformatics Skills
• Pipeline and Software Validation
• Bioinformatics Reproducibility and Quality

Papers

• The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology
  Read the preprint here

• MAJORA: Continuous Integration Supporting Decentralized Sequencing for SARS-CoV-2 Genomic Surveillance
  Read the preprint here

• Genomic Sequencing of SARS-CoV-2: A Guide to Implementation for Maximum Impact on Public Health
  Read the guide here

Resources

• ARTIC and CLIMB-BIG-DATA Joint Workshop
• Majora on GitHub
• Majora on SoundCloud
• PHA4GE SARS-CoV-2 Contextual Data Specification on GitHub
• PHA4GE Website

Software

• Pangolin on GitHub
• Civet on GitHub
• Grapevine on GitHub
• pangoLEARN on GitHub

This panel discussion and the accompanying resources aim to facilitate better understanding and collaboration in SARS-CoV-2 data analysis, providing valuable insights into overcoming current challenges in the field.

Key Points

1. COVID-19 Genomic Sequencing Challenges

• Rapid development of bioinformatics tools under intense time pressure
• Importance of direct collaboration between sequencing teams and public health organizations
• Challenges in collecting and managing complex metadata from healthcare institutions

2. Intra-host Viral Variation

• Limited intra-patient variation observed in typical short SARS-CoV-2 infections
• Potential for significant mutation in immunocompromised patients with prolonged infections
• Speculation about chronic infections potentially generating novel viral variants

3. Collaborative Software Development

• Open-source development of tools like Pangolin, Civet, and ARTIC pipeline
• Collaborative approach allowing rapid feature implementation and community feedback
• Emphasis on making bioinformatics tools accessible and user-friendly

Take-Home Messages

• Minimal metadata collection is crucial for effective data sharing
• Collaborative, open-source development accelerates scientific progress
• Flexibility and adaptability are key in pandemic-era bioinformatics