Influenza A Virus Field Surveillance at a Swine-Human Interface

Autor: Amy L. Vincent, C. Todd Davis, Tavis K. Anderson, Ujwal R. Bagal, Elizabeth B. Neuhaus, Matthew W. Keller, David E. Wentworth, Benjamin L. Rambo-Martin, Andrew S. Bowman, Jacqueline M. Nolting, Malania M. Wilson, Yunho Jang, John Barnes
Rok vydání: 2020
Předmět:
Genotype
Swine
viruses
lcsh:QR1-502
Hemagglutinin (influenza)
Genome
Viral
medicine.disease_cause
Microbiology
Genome
mobile sequencing
lcsh:Microbiology
Virus
Clinical Science and Epidemiology
03 medical and health sciences
Influenza A Virus
H1N1 Subtype
Orthomyxoviridae Infections
Influenza A Virus
H1N2 Subtype
Pandemic
Influenza A virus
medicine
Animals
Humans
Molecular Biology
Phylogeny
030304 developmental biology
Swine Diseases
0303 health sciences
swine influenza
biology
030306 microbiology
Transmission (medicine)
Influenza A Virus
H3N2 Subtype
Genetic Variation
Outbreak
Hemagglutination Inhibition Tests
Virology
QR1-502
United States
3. Good health
Epidemiological Monitoring
nanopore sequencing
biology.protein
RNA
Viral
pandemic preparedness
Nanopore sequencing
influenza
Research Article
Zdroj: mSphere, Vol 5, Iss 1, p e00822-19 (2020)
mSphere
mSphere, Vol 5, Iss 1 (2020)
ISSN: 2379-5042
DOI: 10.1128/msphere.00822-19
Popis: Swine are influenza virus reservoirs that have caused outbreaks and pandemics. Genomic characterization of these viruses enables pandemic risk assessment and vaccine comparisons, though this typically occurs after a novel swine virus jumps into humans. The greatest risk occurs where large groups of swine and humans comingle. At a large swine exhibition, we used Nanopore sequencing and on-site analytics to interpret 13 swine influenza virus genomes and identified an influenza virus cluster that was genetically highly varied to currently available vaccines. As part of the National Strategy for Pandemic Preparedness exercises, the sequences were emailed to colleagues at the CDC who initiated the development of a synthetically derived vaccine designed to match the viruses at the exhibition. Subsequently, this virus caused 14 infections in humans and was the dominant U.S. variant virus in 2018.
While working overnight at a swine exhibition, we identified an influenza A virus (IAV) outbreak in swine, Nanopore sequenced 13 IAV genomes from samples we collected, and predicted in real time that these viruses posed a novel risk to humans due to genetic mismatches between the viruses and current prepandemic candidate vaccine viruses (CVVs). We developed and used a portable IAV sequencing and analysis platform called Mia (Mobile Influenza Analysis) to complete and characterize full-length consensus genomes approximately 18 h after unpacking the mobile lab. Exhibition swine are a known source for zoonotic transmission of IAV to humans and pose a potential pandemic risk. Genomic analyses of IAV in swine are critical to understanding this risk, the types of viruses circulating in swine, and whether current vaccines developed for use in humans would be predicted to provide immune protection. Nanopore sequencing technology has enabled genome sequencing in the field at the source of viral outbreaks or at the bedside or pen-side of infected humans and animals. The acquired data, however, have not yet demonstrated real-time, actionable public health responses. The Mia system rapidly identified three genetically distinct swine IAV lineages from three subtypes, A(H1N1), A(H3N2), and A(H1N2). Analysis of the hemagglutinin (HA) sequences of the A(H1N2) viruses identified >30 amino acid differences between the HA1 of these viruses and the most closely related CVV. As an exercise in pandemic preparedness, all sequences were emailed to CDC collaborators who initiated the development of a synthetically derived CVV. IMPORTANCE Swine are influenza virus reservoirs that have caused outbreaks and pandemics. Genomic characterization of these viruses enables pandemic risk assessment and vaccine comparisons, though this typically occurs after a novel swine virus jumps into humans. The greatest risk occurs where large groups of swine and humans comingle. At a large swine exhibition, we used Nanopore sequencing and on-site analytics to interpret 13 swine influenza virus genomes and identified an influenza virus cluster that was genetically highly varied to currently available vaccines. As part of the National Strategy for Pandemic Preparedness exercises, the sequences were emailed to colleagues at the CDC who initiated the development of a synthetically derived vaccine designed to match the viruses at the exhibition. Subsequently, this virus caused 14 infections in humans and was the dominant U.S. variant virus in 2018.
Databáze: OpenAIRE
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