Episode 55: SARS-CoV-2 And Sequencing Spike With Sanger Sequencing - Welcome To 1995

The microbinfie podcast explores an innovative method for rapid COVID-19 variant identification using Sanger sequencing, developed at the Technical University of Denmark to quickly detect and report variants of concern.

Resources

• Preprint: Link to preprint on medRxiv
• Protocol: Sanger sequencing of a part of the SARS-CoV-2 spike
• Software: GitHub repository for COVID spike classification software
• Web App: SSI BioLib COVID Spike Classification App

Note: The method discussed is specific to the spike protein of SARS-CoV-2, and emphasizes the use of Sanger sequencing for variant identification.

Key Points

1. Rapid Variant Detection Method

• Developed a simplified Sanger sequencing approach for COVID-19 variant screening
• Uses existing RT-PCR infrastructure and ARTIC protocol primers
• Can process up to 200 samples per day with minimal additional resources

2. Detection and Reporting Process

• Targets a 1,001-base region in the spike protein
• Results available within 50-60 hours from sample collection
• Immediate reporting to hospitals and contact tracing authorities

3. Practical Implementation

• Initially focused on detecting B.1.1.7 variant
• Successfully identified first P1 variant in Denmark
• Serves as a preliminary screening before whole genome sequencing

Take-Home Messages

• Rapid, accessible method for COVID-19 variant tracking
• Simplifies variant detection using existing laboratory infrastructure
• Enables quick public health response to emerging variants