Episode 41: SARS-CoV-2 Phylogenomics questions answered

This panel served as an informative session shedding light on the nuances of SARS-CoV-2 phylogenomics, including methodological insights and tools for genome analysis.

Presented by: ARTICnetwork & CLIMB-BIG-DATA

Panelists:

• Nick Loman - University of Birmingham
• Verity Hill - University of Edinburgh
• Andrew Page - Quadram Institute
• Anna Price - MRC CLIMB and Cardiff University

This discussion was part of a broader workshop focused on COVID-19 data analysis.

Topics Covered:

• More about Polecat: Understanding its utility in the analysis of SARS-CoV-2.
• COG-UK Phylotypes vs. Pangolin Lineages: Exploring the differences between these classifications.
• Civet and Llama: Differentiating these tools and their use case scenarios.
• Using BLAST for SARS-CoV-2: Can it identify similar genomes?
• Finding Similar Sequences: Techniques for placing sample sequences in context using public repositories.
• Manual Curation for PangoLEARN: Understanding the process and its importance.
• Subtree Selection in Civet: Criteria and methods used in defining subtrees.
• Adaptation of Civet for Other Viruses: Exploring broader applications beyond SARS-CoV-2.
• Vaccine Sequences Availability: Where and how these sequences can be accessed.
• Databases Reporting Variation: An overview of resources tracking genomic variations.
• Quality of Variant Calls: Discussing the reliability and accuracy of variant assessments.

Groups and Resources:

• ARTIC and CLIMB-BIG-DATA Joint Workshop
• CLIMB
• ARTIC Network
• COG-UK Consortium

Software Tools:

• Polecat
• Pangolin
• Llama
• Civet
• PangoLEARN
• FigTree

Analysis Websites:

• Cov-Lineages
• Nextstrain Clades
• Pangolin COG-UK
• Cov-Glue

This panel served as an informative session shedding light on the nuances of SARS-CoV-2 phylogenomics, including methodological insights and tools for genome analysis.

Key Points

1. Phylogenomic Tools and Techniques

• Discussed advanced software like Polecat for detecting genomic clusters and potential outbreaks
• Explored differences between COG-UK phylotypes and Pangolin lineages for sequence classification
• Compared computational tools like Civet and Llama for genomic sequence analysis

2. Sequence Classification and Curation

• Explained manual curation process for PangoLEARN's machine learning lineage assignments
• Highlighted the importance of high-resolution genomic tracking for understanding viral spread
• Discussed challenges in identifying closely related genomic sequences

3. Collaborative Genomic Research

• Emphasized open and collaborative approaches to viral genome classification
• Showcased international efforts in tracking SARS-CoV-2 genomic variations
• Demonstrated interdisciplinary collaboration in pandemic response

Take-Home Messages

• Phylogenomic tools are crucial for understanding viral evolution and transmission
• Manual curation remains essential in accurately classifying viral lineages
• Collaborative, open-source approaches accelerate scientific understanding during pandemics