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<p>Genomic surveillance of Usutu virus (USUV) in blood donors is hampered by extremely low viral loads, which usually prevent reliable genome sequencing. We developed and validated a tiled amplicon-based sequencing protocol optimized for low-titer samples. Serial dilutions of four phylogenetically distinct USUV lineages showed ≥ 95% genome recovery above 100 RNA copies/µL and 65–98% recovery between 3 and 100 copies/µL. We applied the method to 27 USUV-positive blood donors from Germany (median 1.70 copies/µL), achieving lineage assignment in 74% and ≥ 70% genome coverage in 63% of samples. This approach enables routine genomic surveillance of USUV in blood donors.</p>

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A highly sensitive amplicon sequencing workflow for genomic surveillance of Usutu virus

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月10日

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  • Gábor Endre Tóth,
  • Anna Nagy,
  • Jaime A. Costales,
  • M. Alejandra Camacho,
  • Santiago F. Burneo,
  • Marike Petersen,
  • Alexandra Bialonski,
  • Heike Baum,
  • Balázs Horváth,
  • Anna Heitmann,
  • Renke Lühken,
  • Michael Schmidt,
  • Jonas Schmidt-Chanasit,
  • Zsófia Tauber,
  • Dániel Cadar

摘要

Genomic surveillance of Usutu virus (USUV) in blood donors is hampered by extremely low viral loads, which usually prevent reliable genome sequencing. We developed and validated a tiled amplicon-based sequencing protocol optimized for low-titer samples. Serial dilutions of four phylogenetically distinct USUV lineages showed ≥ 95% genome recovery above 100 RNA copies/µL and 65–98% recovery between 3 and 100 copies/µL. We applied the method to 27 USUV-positive blood donors from Germany (median 1.70 copies/µL), achieving lineage assignment in 74% and ≥ 70% genome coverage in 63% of samples. This approach enables routine genomic surveillance of USUV in blood donors.