PRJNA528211
Influenza A virus Genome sequencing and assembly
Working overnight at a large swine exhibition, we identified an influenza A virus (IAV) outbreak, nanopore-sequenced 13 IAV genomes collected from swine, and in real-time determined that these viruses posed a novel risk to humans due to mismatches between the viruses and current candidate vaccine viruses (CVV). We developed and used a portable IAV sequencing and analysis platform called Mia (Mobile Influenza Analysis) to complete and characterize full-length consensus genomes roughly 18 hours after unpacking the mobile lab. Swine are important animal IAV reservoirs that have given rise to pandemic viruses via zoonotic transmission. Genomic analyses of IAV in swine are critical to understanding pandemic risk of viruses in this reservoir, and characterization of viruses circulating in exhibition swine enables analysis of protection offered by current human vaccine viruses. The Mia system rapidly identified three genetically and antigenically distinct swine IAV lineages from three subtypes: A(H1N1), A(H3N2) and A(H1N2). Additional analysis of the HA protein sequences of the A(H1N2) viruses identified >20 amino acid differences, likely to result in vaccine failure, between the hemagglutinin of these viruses and the most closely related pre-pandemic CVV. All virus sequences were emailed to colleagues at CDC who initiated development of a synthetically derived CVV designed to provide optimal protections against these new viruses emerging in the US swine population. Later, this virus began appearing in humans and would go on to be the dominant virus of the summer variant season. Had this virus caused a severe outbreak or pandemic, our proactive surveillance efforts would have given us an approximate 8 week time advantage. This is the first report of the use of field-derived nanopore sequencing data to effect a real-time, actionable public health response.