NCM 2022: Exploration of Oxford Nanopore long-read sequencing to contribute to Influenza surveillance at the state level
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Influenza (flu) is a rapidly mutating virus which can cause severe respiratory disease and is responsible for tens of thousands of deaths and millions of illnesses annually in the United States. Influenza virus circulation and genetic diversity were severely reduced starting in fall and winter of 2020/2021, likely due to measures that were taken to mitigate the transmission of SARSCoV-2. This dramatic decline in genetic diversity has resulted in reduced detection across different influenza subtypes and no reported isolations of influenza B/Yamagata. As travel and other social behavioral changes trend towards a pre-pandemic state, we observed changes in Minnesota’s seasonal flu trends at Minnesota Department of Health Public Health Laboratory (MDH-PHL). Influenza detections were lower than years prior due to the COVID-19 pandemic. The public health response to the ongoing SARS-CoV-2 pandemic has included significant update of respiratory pathogen genomic surveillance utilizing next-generation sequencing including ONT. We piloted a method using Oxford Nanopore sequencing platform and existing CDC-developed wet laboratory methods to characterize influenza virus found in specimens collected for influenza surveillance. 46 specimens (26 flu A and 20 flu B) submitted to the MDH-PHL between 2014 and 2022 were included in this study. We analyzed the sequencing data using IRMA (iterative refinement metaassembler) pipeline, Nextclade (Nextstrain), and Geneious Prime 2019.2.1. In future studies we will continue to assess the public health merit of expanded state-level influenza genomic surveillance from the perspective of cost, turn-around-time, genomic resolution, and external stakeholder needs.
