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How does next-generation sequencing work and how long does it take?

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The next-generation sequencing and data analysis pipeline (© Illustration: Zsofia Keszei, Thomas Winkler-Penz, Andreas Bergthaler / CeMM).

An interdisciplinary team led by Andreas Bergthaler and Christoph Bock at CeMM is sequencing around 400 virus samples from Austria per week for the Austrian Agency for Health and Food Safety (AGES). The goal is to look for specific SARS-CoV-2 variants with multiple spike protein mutations, and to learn more about the molecular understanding of the COVID-19 pandemic and the causative pathogen.

The enclosed illustration demonstrates the standard next-generation sequencing and data analysis pipeline for SARS-CoV-2 viral genomes which takes approximately seven days. The aim is to obtain viral full-length genomes with low frequency variants at high quality. 

More information on the project can be found at sarscov2-austria.org and in the scientific publication Popa et al. Science Translational Medicine (December 2020).