Influenza Sequencing

Influenza (Flu) Sequencing

Monitoring the spread of Flu within a population can be accomplished with simple and affordable RT-PCR-based assays at relatively high throughputs, but those assays fail to collect information on the variants that may be introduced into the circulating strains of the virus. Full-length sequencing of the Flu virus is the best method for monitoring for and responding to mutations in the virus.

The NEBNext^® Flu A Integrated Indexing Primer Module (NEB #E3436S) includes a curated set of 48 RT-PCR primers with integrated indices, that allow for subsequent NGS library prep for sequencing on Oxford Nanopore Technologies^® platforms. The inclusion of indices during the RT-PCR step saves time and standardizes the library prep process. The integrated indices were intentionally positioned within the RT-PCR primers in highly stable regions, thereby minimizing the risk for variants to negatively impact amplification efficiency. For more information about the Primer Module, visit the E3436S product page.

The NEBNext Flu A Integrated Indexing Primer Module was developed in collaboration with scientists at the Johns Hopkins University Applied Physics Laboratory, and features a so-called “integrated indexing, multi-segment PCR” (iiMS-PCR) approach. By incorporating sequencing indices during RT-PCR, the sample is able to move straight into library prep, saving precious time. Compatibility with ONT^® platforms also enables the use of the NEBNext Flu A Integrated Indexing Primer Module in locations where speed and mobility are of paramount importance, such as field sites and regions where access to power and other utilities is unreliable.

Collaborators at Ceres Nanoscience worked with NEBNext Applications Scientists to demonstrate the use of the NEBNext Flu A Integrated Indexing Primer Module in a workflow for viral detection and sequencing from wastewater samples, using their Nanotrap^® Microbiome A particles along with Monarch^® Mag Viral DNA/RNA Extraction Kit. Download the application note to learn more about the convenient same-day workflow.

The RT-PCR primers found in the NEBNext Flu A Integrated Indexing Primer Module were used in concert with Monarch^® Mag Viral DNA/RNA Extraction Kit (NEB #T4010) to support the detection of Highly Pathogenic Avian Influenza from milk samples during an outbreak of avian flu that spread to dairy cows. Download the application note to learn more.