Episode 51: SARSCOV2 Round-up 3 and updates from Denmark

The microbinfie podcast explores the latest developments in SARS-CoV-2 genomics, focusing on variant tracking, genomic surveillance, and emerging research tools during the COVID-19 pandemic in March 2021.

In the past two weeks, there have been significant developments in SARS-CoV-2 genomics, as discussed with Mads Albertsen, particularly in Denmark. For the latest COVID statistics in Denmark, visit their statistics page.

Guests

• Mads Albertsen
  • Twitter

Tools and Resources

• Outbreak Info: A resource for gathering data about outbreaks.
• Outbreak Info: SARS-CoV-2 Mutation Situation Reports: Detailed reports on the mutation landscape.
• GitLab Repository by Johan Bernal Morales: Tools related to SARS-CoV-2 research.

Publications

• A Comparison of Performance for Different SARS-CoV-2 Sequencing Protocols examines the efficiency of various sequencing protocols.
• Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report provides insight into the early presence of the virus in NYC.
• SARS-CoV-2 Within-host Diversity and Transmission: An article examining the genetic diversity of the virus within hosts and its implications for transmission.

Additional Information

• For issues related to SARS-CoV-2 sequencing data, see this discussion.
• You can find masking information for SARS-CoV-2 sites in this GitHub repository.

These resources and studies are crucial for understanding the genomic evolution of the virus and strategizing public health responses.

Extra notes

Variants of Concern

• Terminology Confusion: Different terms used globally (e.g., VOC - Variant of Concern, VUI - Variant Under Investigation, VOI - Variant of Interest) cause confusion.
• Example Variants: Discussion about specific variants such as B.1.1.7 (UK), B.1351 (South Africa), P.1 (Brazil), and others.
• Data Sharing Issues: Variants being claimed by countries without data release leads to confusion and miscommunication.

Genomic Surveillance

• Sequencing Rates: Denmark sequences over 90% of cases, while the U.S. has lower rates, highlighting a lag in genomic surveillance.
• Current Trends: B.1.1.7 variant dominates in Denmark, while other variants are also present but at lower rates.

Tools and Resources

• Dashboards: Emergence of various dashboards to track genomic data globally (e.g., covid19genomics.dk).
• Tools: Introduction of Galaxy public health community and new resources like outbreak.info for data compilation.
• Nextflow Pipeline: A new pipeline for SARS-CoV-2 that integrates variant visualization, providing a one-stop workflow.

Publications and Research Insights

• Cautionary Tales: Critique of poor research practices, including incorrect assembly methods leading to misleading results.
• WHO Terminology Proposal: Efforts to standardize definitions for variants of interest and concern to reduce confusion in the field.
• Pooling Samples Issue: Concerns over pooling samples for sequencing and the potential for misleading results without proper labeling.

Key Points

1. COVID-19 Variants and Terminology

• Confusion exists around variant classification terms (VOC, VUI, VOI)
• Multiple variants identified, including B.1.1.7 (UK), B.1351 (South Africa), P.1 (Brazil)
• Countries competing to claim and name new variants

2. Genomic Surveillance

• Denmark sequences over 90% of COVID-19 cases
• B.1.1.7 variant dominates in Denmark (80% of cases)
• US significantly lagging in sequencing compared to European countries

3. Tools and Resources

• Emergence of COVID-19 genomic dashboards (outbreak.info, country-specific platforms)
• Galaxy developing public health bioinformatics community
• New Nextflow pipelines for SARS-CoV-2 analysis

Take-Home Messages

• Genomic surveillance is crucial for tracking COVID-19 variants
• Standardized terminology and data sharing remain challenging
• Technological tools are rapidly evolving to support pandemic research