varVAMP: degenerate primer design for tiled full genome sequencing and qPCR

Jonas Fuchs (), Johanna Kleine, Mathias Schemmerer, Julian Kreibich, Wolfgang Maier, Namuun Battur, Thomas Krannich, Somayyeh Sedaghatjoo, Lena Jaki, Anastasija Maks, Christina Boehm, Carina Wilhelm, Jessica Schulze, Christin Mache, Elischa Berger, Jessica Panajotov, Lisa Arnold, Björn Grüning, Markus Bauswein, Sindy Böttcher, Reimar Johne, Jürgen Wenzel, Martin Hölzer and Marcus Panning ()
Additional contact information
Jonas Fuchs: University of Freiburg
Johanna Kleine: University of Freiburg
Mathias Schemmerer: University Medical Center Regensburg
Julian Kreibich: Robert Koch Institute
Wolfgang Maier: Albert-Ludwigs-University Freiburg
Namuun Battur: Robert Koch Institute
Thomas Krannich: Robert Koch Institute
Somayyeh Sedaghatjoo: Robert Koch Institute
Lena Jaki: University of Freiburg
Anastasija Maks: University of Freiburg
Christina Boehm: University Medical Center Regensburg
Carina Wilhelm: University Medical Center Regensburg
Jessica Schulze: Robert Koch-Institute
Christin Mache: Robert Koch-Institute
Elischa Berger: Albert-Ludwigs-University Freiburg
Jessica Panajotov: German Federal Institute for Risk Assessment (BfR)
Lisa Arnold: University Hospital Regensburg
Björn Grüning: Albert-Ludwigs-University Freiburg
Markus Bauswein: University Hospital Regensburg
Sindy Böttcher: Robert Koch Institute
Reimar Johne: German Federal Institute for Risk Assessment (BfR)
Jürgen Wenzel: University Medical Center Regensburg
Martin Hölzer: Robert Koch Institute
Marcus Panning: University of Freiburg

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract Time- and cost-saving surveillance of viral pathogens is achieved by tiled sequencing in which a viral genome is amplified in overlapping PCR amplicons and qPCR. However, designing pan-specific primers for viral pathogens with high genomic variability represents a significant challenge. Here, we present a bioinformatics command-line tool, called varVAMP (variable virus amplicons), which addresses this issue. It relies on multiple sequence alignments of highly variable virus sequences and enables degenerate primer design for qPCR or tiled amplicon whole genome sequencing. We demonstrate the utility of varVAMP by designing and evaluating novel pan-specific primer schemes suitable for sequencing the genomes of SARS-CoV-2, Hepatitis E virus, rat Hepatitis E virus, Hepatitis A virus, Borna-disease-virus-1, and Poliovirus using clinical samples. Importantly, we also designed primers on the same input data using the software packages PrimalScheme and Olivar and showed that varVAMP minimizes primer mismatches most efficiently. Finally, we established highly sensitive and specific Poliovirus qPCR assays that could potentially simplify current Poliovirus surveillance. varVAMP is open-source and available through PyPI, UseGalaxy, Bioconda, and https://github.com/jonas-fuchs/varVAMP .

Date: 2025
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DOI: 10.1038/s41467-025-60175-9

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