Episode 39: Explaining the naming of SARS-CoV-2 new variants

In this episode of the microbinfie podcast, Andrew and guest Niamh Tumelty from the University of Cambridge dive deep into the complex world of SARS-CoV-2 variant naming and classification, exploring the challenges of tracking viral genomic changes during a global pandemic.

Andrew's discussion with Niamh Tumelty from the University of Cambridge revolves around the various names and classifications emerging for the new variants of SARS-CoV-2. As this is a rapidly evolving field, the information you hear might be outdated by the time you listen. Andrew humorously apologizes in advance for any errors that might exist in the podcast.

For those interested in more detailed information, Andrew suggests an article on Nature that provides further insights: Link to the article.

The conversation aims to clear up some confusion surrounding the numerous names and classifications, helping listeners better understand the ongoing developments in the pandemic.

Extra notes

• Genomic Analysis and Variation:

  • Typically, genomic analysis observes a consistent rate of change, about two mutations per month, which is used to track the spread of different lineages globally.
  • These changes help in understanding the spread and dominant lineages, like those observed in the UK after vacation periods.

• Distinction Between Variants and Lineages:

  • There's considerable confusion between terms like lineage, variant, and strain, often used interchangeably even by professionals.
  • A lineage refers to clusters of genomes used in genomic epidemiology, while a variant may denote additional changes of concern.
  • Naming conventions like VUI (Variant Under Investigation) and VOC (Variant of Concern) complicate the discussion further.

• Challenges in Naming Conventions:

  • Multiple naming conventions create confusion: different systems exist, like B.1.1.7 and 501Y.V1, reflecting different focuses such as phylogenetic lineage or specific mutations.
  • Rapid naming during a pandemic results in inconsistent identifiers across different regions and research groups.

• Public Health Implications:

  • New variants, when declared, often cause public concern due to potential changes in transmission rates or immune evasion.
  • There's a high need for standardization, as inconsistent naming can lead to misinformation and public confusion.

• Global Sequencing Efforts:

  • As genome sequencing accelerates, independent occurrences of similar mutations are arising worldwide, indicating evolutionary advantages for the virus.
  • These changes, though detected independently, suggest increased transmissibility or immune evasion capabilities.

• Impact on Public Perception and Media:

  • Media coverage contributes to public anxiety by frequently reporting on "new variants" without clear scientific backing.
  • Naming variants after locations (e.g., "Kent variant") can stigmatize places and is being discouraged.

• Data Sharing and Analysis Issues:

  • The rapid pace of genomic sequencing leads to challenges in timely data deposition and sharing, as exemplified by the delays in making the genetic data of Brazilian variants publicly available on platforms like GISAID.
  • Accurate analysis and verification of mutations are crucial before drawing conclusions for public health responses.

• Future Outlook and Research Needs:

  • Ongoing studies are required to understand the full implications of various mutations, their effect on transmissibility, severity, and potential vaccine impacts.
  • Collaboration among global researchers is essential to manage and analyze the influx of genomic data.

Key Points

1. Genomic Variation and Naming Complexity

• Typical genomic changes occur at about two mutations per month
• Multiple naming conventions exist simultaneously (lineage, variant, strain)
• Naming systems include phylogenetic, location-based, and mutation-focused approaches

2. Challenges in Variant Classification

• Rapid pandemic research leads to inconsistent terminology
• Different research groups use varied identification methods
• Variants are classified based on potential transmission or immune evasion characteristics

3. Public Health Communication

• Media coverage can create confusion and unnecessary panic
• Avoiding location-based names helps prevent stigmatization
• Careful verification of mutations is crucial before public communication

Take-Home Messages

• Viral variant naming is complex and evolving
• Scientific communication requires precision and multiple reference points
• Global collaboration is essential in tracking viral mutations