Efficient primer design for broad-range virus detection: A semi-automated workflow using sequence clustering and varVAMP
- 1Statens Serum Institut
Abstract
Broad-range RT-qPCR assays are essential for detecting highly diverse viruses within virus families, but designing suitable primers remains challenging because of extensive sequence diversity and biases in public sequence databases. Here, we present a semi-automated workflow that combines sequence clustering and varVAMP to streamline pan-RT-qPCR primer design. The workflow reduces sequence redundancy, improves the representation of viral diversity, and facilitates the identification of broadly reactive primer candidates. We demonstrate the workflow using the arboviral genera Orthoflavivirus and Alphavirus as proof-of-concept datasets, showing its applicability to large and genetically diverse viral sequence collections. The workflow provides a practical, scalable, and reproducible framework for developing broad-range primer candidates and may support surveillance, diagnostics, and preparedness for emerging or divergent viruses.
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BibTeX
@misc{johnston2026efficient,
title = {{Efficient primer design for broad-range virus detection: A semi-automated workflow using sequence clustering and varVAMP}},
author = {C. M. Johnston and A. Mingoli and A. M. Hoegh and L. Lohse and T. B. Rasmussen},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.21.753121},
url = {https://www.biorxiv.org/content/10.64898/2026.09.21.753121v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Efficient primer design for broad-range virus detection: A semi-automated workflow using sequence clustering and varVAMP
AU - C. M. Johnston
AU - A. Mingoli
AU - A. M. Hoegh
AU - L. Lohse
AU - T. B. Rasmussen
PY - 2026
DA - 2026/09/21
PB - bioRxiv
DO - 10.64898/2026.09.21.753121
UR - https://www.biorxiv.org/content/10.64898/2026.09.21.753121v1
AB - Broad-range RT-qPCR assays are essential for detecting highly diverse viruses within virus families, but designing suitable primers remains challenging because of extensive sequence diversity and biases in public sequence databases. Here, we present a semi-automated workflow that combines sequence clustering and varVAMP to streamline pan-RT-qPCR primer design. The workflow reduces sequence redundancy, improves the representation of viral diversity, and facilitates the identification of broadly reactive primer candidates. We demonstrate the workflow using the arboviral genera Orthoflavivirus and Alphavirus as proof-of-concept datasets, showing its applicability to large and genetically diverse viral sequence collections. The workflow provides a practical, scalable, and reproducible framework for developing broad-range primer candidates and may support surveillance, diagnostics, and preparedness for emerging or divergent viruses.
ER -