ArticleNature communications2025
varVAMP: degenerate primer design for tiled full genome sequencing and qPCR.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- DivergentViruses · 2026Article
- Seqwin: ultrafast identification of signature sequences in microbial genomes.Bioinformatics (Oxford, England) · 2026Article
- Rocahepevirus ratti: molecular evolution, zoonotic potential and public health impact.Nature communications · 2026Review
- [Overview of PCR-based Diagnostic Assays for Emerging Infectious Disease Pathogens].Jugan geon-gang gwa jilbyeong · 2025Review
- Seqwin: Ultrafast identification of signature sequences in microbial genomes.bioRxiv : the preprint server for biology · 2025Article
- Sequence Variation and In Silico Protein Characterization ofInternational journal of molecular sciences · 2025Article
Corrections and comments
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Authors and funding
24 authors.
Funding
No grant is acknowledged in the PubMed record.
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 .
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Registered trials
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