Whole-Genome Sequencing of Influenza A from Wastewater Using Nanotrap Microbiome A Particles and NEBNext iiMS Influenza A DNA Library Preparation

Wastewater-based epidemiology (WBE) has emerged as a crucial tool for monitoring infectious diseases at the population level, providing early indicators of viral transmission and evolution. Influenza A viruses, known for their seasonal epidemics and pandemic potential, pose unique challenges for wastewater surveillance due to their low abundance and susceptibility to environmental degradation (1, 2). Traditional sequencing approaches for influenza A in wastewater often yield incomplete genomes due to low viral titers and matrix inhibitors, limiting their utility for public health surveillance(3).

This study presents an enhanced workflow combining Nanotrap® Microbiome A Particles for viral enrichment with the NEBNext iiMS Influenza A DNA Library Prep protocol, leveraging Oxford Nanopore sequencing for rapid whole-genome characterization. By integrating targeted cDNA synthesis and native barcoding, this approach enables same-day sequencing with improved genome coverage, offering a scalable and high-throughput solution for monitoring influenza A in wastewater.