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<p>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.</p>

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Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年9月26日

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  • Matthias Licheri,
  • Mike Mwanga,
  • Manon F. Licheri,
  • Annika Graaf-Rau,
  • Cora Sägesser,
  • Pascal Bittel,
  • Timm Harder,
  • Franziska Suter-Riniker,
  • Jenna N. Kelly,
  • Ronald Dijkman

摘要

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.