New England Biolabs (NEB) has unveiled a new tool designed to accelerate the world’s response to seasonal and emerging influenza threats.

The NEBNext Flu A Integrated Indexing Primer Module, released recently, promises to streamline whole-genome sequencing of Influenza A virus across species and sample types using Oxford Nanopore Technologies (ONT) platforms. By enabling rapid, high-throughput processing of subtypes like H3N2, H1N1, and the increasingly scrutinized H5N1, the launch marks a significant advance for global flu surveillance efforts.

Developed in partnership with the Johns Hopkins Applied Physics Laboratory (APL), the module is built around a multi-segment RT-PCR method with integrated indexing, known as iiMS-PCR. The approach allows labs to multiplex up to 48 samples in a single sequencing run—an efficiency boost with major implications for outbreak monitoring, zoonotic pathogen tracking, and wastewater-based epidemiology.

For APL molecular biologist Peter Thielen, the stakes couldn’t be clearer. “To effectively limit the spread of emerging biological threats—such as highly pathogenic avian influenza—genetic characterization methods must become as fast and simple to perform as diagnostic assays,” he said.

Streamlined, low-cost whole-genome sequencing, he added, is essential for rapid local response and for feeding high-resolution data into global monitoring networks that strengthen predictive modelling.

Real-world applications are already proving the impact. At Institut Pasteur du Cambodge, virologist Erik Karlsson credits the iiMS workflow with transforming responses to H5 outbreaks. “It enables us to confirm poultry-to-human transmission within 24 hours, which is essential for timely public-health action,” Karlsson said.

The system now supports weekly assessments of circulating influenza strains across Cambodia and, he noted, is adaptable enough to be deployed quickly in low-resource settings—precisely where frontline surveillance is most urgently needed.

The new primer module includes reagents for indexed cDNA synthesis, amplification, and library prep, and is fully compatible with NEB’s Monarch Mag Viral DNA/RNA Extraction Kit, LunaScript Multiplex One-Step RT-PCR Kit, and ONT’s Native Barcoding Workflow. The protocol has already been validated across a wide array of sample types, from clinical specimens to agricultural products and wastewater.

Influenza A remains a persistent global health challenge due to its rapid evolution and seasonal variability,” said Betsy Young, Senior Product Marketing Manager for Next Generation Sequencing at NEB. “With this primer module, we’re equipping researchers and surveillance teams with a robust, scalable workflow to track genetic changes and inform deployment of public health resources.”