Medizinische Universität Graz Austria/Österreich - Forschungsportal - Medical University of Graz
Gewählte Publikation:
SHR Neuro Krebs Kardio Lipid Stoffw Microb
Wagner, GE; Totaro, MG; Volland, A; Lipp, M; Saiger, S; Lichtenegger, S; Forstner, P; von, Laer, D; Oberdorfer, G; Steinmetz, I.
A Novel High-Throughput Nanopore-Sequencing-Based Strategy for Rapid and Automated S-Protein Typing of SARS-CoV-2 Variants.
Viruses. 2021; 13(12):
Doi: 10.3390/v13122548
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- Führende Autor*innen der Med Uni Graz
- Wagner-Lichtenegger Gabriel
- Co-Autor*innen der Med Uni Graz
- Forstner Patrick
- Lipp Michaela
- Saiger Sabine
- Steinmetz Ivo
- Wagner-Lichtenegger Sabine
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- Abstract:
- Rapid molecular surveillance of SARS-CoV-2 S-protein variants leading to immune escape and/or increased infectivity is of utmost importance. Among global bottlenecks for variant monitoring in diagnostic settings are sequencing and bioinformatics capacities. In this study, we aimed to establish a rapid and user-friendly protocol for high-throughput S-gene sequencing and subsequent automated identification of variants. We designed two new primer pairs to amplify only the immunodominant part of the S-gene for nanopore sequencing. Furthermore, we developed an automated "S-Protein-Typer" tool that analyzes and reports S-protein mutations on the amino acid level including a variant of concern indicator. Validation of our primer panel using SARS-CoV-2-positive respiratory specimens covering a broad Ct range showed successful amplification for 29/30 samples. Restriction to the region of interest freed sequencing capacity by a factor of 12-13, compared with whole-genome sequencing. Using either the MinION or Flongle flow cell, our sequencing strategy reduced the time required to identify SARS-CoV-2 variants accordingly. The S-Protein-Typer tool identified all mutations correctly when challenged with our sequenced samples and 50 deposited sequences covering all VOCs (December 2021). Our proposed S-protein variant screening offers a simple, more rapid, and low-cost entry into NGS-based SARS-CoV-2 analysis, compared with current whole-genome approaches.
- Find related publications in this database (Keywords)
- SARS-CoV-2
- next-generation sequencing
- vaccine escape
- S-protein
- nanopore
- surveillance
- typing