NCM 2022: Exploration of Oxford Nanopore long-read sequencing to contribute to influenza surveillance at the state level

Influenza is a rapidly mutating virus that can cause severe respiratory disease and is responsible for excessive illness and death in the United States. Influenza virus circulation and genetic diversity were reduced in the fall and winter of 2020/2021, likely due to measures that were taken to mitigate the transmission of SARS-CoV-2. As social behavioral changes trended towards a pre-pandemic state, we observed changes in Minnesota’s seasonal flu trends at the Minnesota Department of Health Public Health Laboratory. Influenza detections were lower than years prior to the COVID-19 pandemic, resulting in a prolonged flu season. The public health response to the ongoing SARS-CoV-2 pandemic has shown the significance of respiratory pathogen genomic surveillance utilizing next-generation sequencing, including Oxford Nanopore sequencing. We piloted a method using the Oxford Nanopore sequencing platform and existing CDC-developed wet laboratory methods to characterize the influenza virus found in specimens collected for influenza surveillance.