Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus
Whole-genome sequencing (WGS) is essential for monitoring the genetic diversity of influenza A virus (IAV) across host species. We optimized a multisegment RT-PCR (mRT-PCR) protocol to enhance amplification of all eight IAV segments using modified RT and PCR conditions. Additionally, we introduced a dual-barcoding approach for the Oxford Nanopore platform, enabling high-throughput multiplexing without compromising sensitivity. The resulting workflow is robust, scalable, and effective for avian, swine, and human IAV samples, even at low viral loads. This approach strengthens genomic surveillance at the human-animal interface, supporting early detection, evolutionary monitoring, and rapid identification of IAV spillover events.
Authors
- Pascal Bittel (ORCID: https://orcid.org/0000-0002-0416-3996)
- Jenna N. Kelly (ORCID: https://orcid.org/0000-0001-7265-2233)
- Ronald Dijkman (ORCID: https://orcid.org/0000-0003-0320-2743)
- Manon Flore Licheri
- Matthias Licheri
- Annika Graaf (ORCID: https://orcid.org/0000-0002-9590-8550)
- Mike J. Mwanga (ORCID: https://orcid.org/0000-0003-1481-1405)
- Franziska Suter‐Riniker (ORCID: https://orcid.org/0000-0001-8568-578X)
- Timm Harder (ORCID: https://orcid.org/0000-0003-2387-378X)
- Cora Sägesser
Institutions
- University of Bern (CH)
- Bern University of Applied Sciences (CH)
- Friedrich-Loeffler-Institut (DE)
- Universidad Iberoamericana (DO)
- Jena Bioscience (Germany) (DE)
- Institute of Virology of the Slovak Academy of Sciences (SK)
Publication Details
- Journal
- Genome Medicine
- Published
- 2025-09-26
- DOI
- https://doi.org/10.1186/s13073-025-01512-x
- Primary Topic
- Influenza Virus Research Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Science Foundation
- University of Bern
- Ministerul Cercetării, Inovării şi Digitalizării
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung