varVAMP: automated pan-specific primer design for tiled full genome sequencing and qPCR of highly diverse viral pathogens. DOI Creative Commons
Jonas Fuchs,

Johanna Kleine,

Mathias Schemmerer

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 9, 2024

ABSTRACT Time- and cost-saving surveillance of viral pathogens is achieved by tiled sequencing in which a genome amplified overlapping PCR amplicons qPCR. However, designing pan-specific primers for that have high genomic variability represents major challenge. Here, we present bioinformatics command-line tool, called varVAMP ( var iable v irus amp licons). It relies on multiple sequence alignments highly variable virus sequences enables automatic primer design qPCR or amplicon whole sequencing. The software guarantees pan-specificity two means: it designs regions with minimal introduces degenerate nucleotides into to compensate common variations. We demonstrate varVAMP’s utility evaluating novel schemes suitable the genomes SARS-CoV-2, Hepatitis E virus, rat A Borna-disease-virus-1, Poliovirus. Moreover, established sensitive specific Poliovirus assays could potentially simplify current surveillance. Importantly, wet-lab bioinformatic techniques SARS-CoV-2 were readily transferable these new will allow laboratories extend their methodology other human pathogens.

Language: Английский

The zoonotic LCK-3110 strain of Rocahepevirus ratti leads to mild infection in chickens after experimental inoculation DOI Creative Commons
Kush Kumar Yadav, Patricia A. Boley, Saroj Khatiwada

et al.

Virus Research, Journal Year: 2024, Volume and Issue: 350, P. 199477 - 199477

Published: Oct. 13, 2024

Language: Английский

Citations

1
varVAMP: automated pan-specific primer design for tiled full genome sequencing and qPCR of highly diverse viral pathogens. DOI Creative Commons
Jonas Fuchs,

Johanna Kleine,

Mathias Schemmerer

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 9, 2024

ABSTRACT Time- and cost-saving surveillance of viral pathogens is achieved by tiled sequencing in which a genome amplified overlapping PCR amplicons qPCR. However, designing pan-specific primers for that have high genomic variability represents major challenge. Here, we present bioinformatics command-line tool, called varVAMP ( var iable v irus amp licons). It relies on multiple sequence alignments highly variable virus sequences enables automatic primer design qPCR or amplicon whole sequencing. The software guarantees pan-specificity two means: it designs regions with minimal introduces degenerate nucleotides into to compensate common variations. We demonstrate varVAMP’s utility evaluating novel schemes suitable the genomes SARS-CoV-2, Hepatitis E virus, rat A Borna-disease-virus-1, Poliovirus. Moreover, established sensitive specific Poliovirus assays could potentially simplify current surveillance. Importantly, wet-lab bioinformatic techniques SARS-CoV-2 were readily transferable these new will allow laboratories extend their methodology other human pathogens.

Language: Английский

Citations

0