Fuchs, Jonas and Kleine, Johanna and Schemmerer, Mathias and Kreibich, Julian and Maier, Wolfgang and Battur, Namuun and Krannich, Thomas and Sedaghatjoo, Somayyeh and Jaki, Lena and Maks, Anastasija and Boehm, Christina and Wilhelm, Carina and Schulze, Jessica and Mache, Christin and Berger, Elischa and Panajotov, Jessica and Arnold, Lisa and Gruening, Bjoern and Bauswein, Markus and Boettcher, Sindy and Johne, Reimar and Wenzel, Juergen and Hoelzer, Martin and Panning, Marcus (2025) varVAMP: degenerate primer design for tiled full genome sequencing and qPCR. NATURE COMMUNICATIONS, 16 (1): 5067. ISSN 2041-1723
Full text not available from this repository. (Request a copy)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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | VIRUS; PCR; ALIGNMENT; ZIKA |
| Subjects: | 600 Technology > 610 Medical sciences Medicine |
| Divisions: | Medicine > Lehrstuhl für Medizinische Mikrobiologie und Hygiene |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 28 Jul 2026 06:45 |
| Last Modified: | 28 Jul 2026 06:45 |
| URI: | https://pred.uni-regensburg.de/id/eprint/66960 |
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