Mitigating Pandemic Risk with Influenza A Virus Field Surveillance at a Swine-Human Interface

Abstract

Working overnight at a large swine exhibition, we identified an influenza A virus (IAV) outbreak in swine, nanopore-sequenced 13 IAV genomes from samples collected, and in real-time, determined that these viruses posed a novel risk to humans due to genetic mismatches between the viruses and current pre-pandemic candidate vaccine viruses (CVV). We developed and used a portable IAV sequencing and analysis platform calledMia (Mobile Influenza Analysis)to complete and characterize full-length consensus genomes approximately 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 rapid comparison to current seasonal influenza vaccines and CVVs. TheMiasystem rapidly identified three genetically 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 >30 amino acid differences between the HA1 portion of the hemagglutinin of these viruses and the most closely related pre-2009 CVV. All virus sequences were emailed to colleagues at CDC who initiated development of a synthetically derived CVV designed to provide an optimal antigenic match with the viruses detected in the exhibition. In subsequent months, this virus caused 13 infections in humans, and was the dominant variant virus in the US detected in 2018. Had this virus caused a severe outbreak or pandemic, our proactive surveillance efforts and CVV derivation would have provided an approximate 8 week time advantage for vaccine manufacturing. This is the first report of the use of field-derived nanopore sequencing data to initiate a real-time, actionable public health countermeasure.

Field-Adapted Full Genome Sequencing of Peste-Des-Petits-Ruminants Virus Using Nanopore Sequencing

“…With the development of new and portable sequencing equipment, it is now possible to perform-in very basic laboratories-sequencing that was previously limited to well-equipped laboratories (1)(2)(3)(4). With a small thermocycler such as the miniPCR (Amplyus, Cambridge, United States), the hand-held MinION sequencer (Oxford Nanopore Technologies, Oxford, United Kingdom), and portable computational resources, full genome sequencing and advanced molecular epidemiology can be performed in almost any setting (1)(2)(3)(4). This is highly advantageous for the diagnosis and control of viral diseases.…”

Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples

“…ONT offers a "third-generation," portable, real-time approach to generating long-read single-molecule sequence data, with demonstrated success across a range of viruses (20,(22)(23)(24). To date, Nanopore sequencing of influenza virus has been reported using high-titer virus from an in vitro culture system, producing full-length genome sequences through direct RNA sequencing (25), or using targeted enrichment by either hybridization of cDNA (26) or influenza virus-specific PCR amplification (27).…”