Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater.

ABSTRACT: Influenza A viruses (IAV) remain a persistent One Health threat, and whole-genome sequencing from wastewater offers a promising surveillance tool. However, IAV is at low abundance in wastewater, making it difficult to sequence. We benchmarked four targeted enrichment methods suited for whole-genome sequencing including custom and off-the-shelf amplicon and probe-based methods. Our custom HA tiled-amplicon panel was sensitive, fast, and cost-effective, making it suitable for monitoring low-abundance seasonal variants of known subtypes. However, its reliance on conserved and intact primer-binding sites limited primer design to fewer subtypes. A previously published universal amplicon method targeted all IAV subtypes, but it performed poorly in wastewater due to its reliance on intact genome

SUBMITTER: Jiang M 

PROVIDER: S-EPMC12458313 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature