Influenza A Virus Field Surveillance at a Swine-Human Interface

ABSTRACT 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 an...

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Autores principales:	Benjamin L. Rambo-Martin, Matthew W. Keller, Malania M. Wilson, Jacqueline M. Nolting, Tavis K. Anderson, Amy L. Vincent, Ujwal R. Bagal, Yunho Jang, Elizabeth B. Neuhaus, C. Todd Davis, Andrew S. Bowman, David E. Wentworth, John R. Barnes
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	influenza mobile sequencing Nanopore sequencing pandemic preparedness swine influenza Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/69b4fadc25ee4696a45a24d4fb896cfd
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spelling	oai:doaj.org-article:69b4fadc25ee4696a45a24d4fb896cfd2021-11-15T15:27:52ZInfluenza A Virus Field Surveillance at a Swine-Human Interface10.1128/mSphere.00822-192379-5042https://doaj.org/article/69b4fadc25ee4696a45a24d4fb896cfd2020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00822-19https://doaj.org/toc/2379-5042ABSTRACT 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.Benjamin L. Rambo-MartinMatthew W. KellerMalania M. WilsonJacqueline M. NoltingTavis K. AndersonAmy L. VincentUjwal R. BagalYunho JangElizabeth B. NeuhausC. Todd DavisAndrew S. BowmanDavid E. WentworthJohn R. BarnesAmerican Society for Microbiologyarticleinfluenzamobile sequencingNanopore sequencingpandemic preparednessswine influenzaMicrobiologyQR1-502ENmSphere, Vol 5, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	influenza mobile sequencing Nanopore sequencing pandemic preparedness swine influenza Microbiology QR1-502
spellingShingle	influenza mobile sequencing Nanopore sequencing pandemic preparedness swine influenza Microbiology QR1-502 Benjamin L. Rambo-Martin Matthew W. Keller Malania M. Wilson Jacqueline M. Nolting Tavis K. Anderson Amy L. Vincent Ujwal R. Bagal Yunho Jang Elizabeth B. Neuhaus C. Todd Davis Andrew S. Bowman David E. Wentworth John R. Barnes Influenza A Virus Field Surveillance at a Swine-Human Interface
description	ABSTRACT 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.
format	article
author	Benjamin L. Rambo-Martin Matthew W. Keller Malania M. Wilson Jacqueline M. Nolting Tavis K. Anderson Amy L. Vincent Ujwal R. Bagal Yunho Jang Elizabeth B. Neuhaus C. Todd Davis Andrew S. Bowman David E. Wentworth John R. Barnes
author_facet	Benjamin L. Rambo-Martin Matthew W. Keller Malania M. Wilson Jacqueline M. Nolting Tavis K. Anderson Amy L. Vincent Ujwal R. Bagal Yunho Jang Elizabeth B. Neuhaus C. Todd Davis Andrew S. Bowman David E. Wentworth John R. Barnes
author_sort	Benjamin L. Rambo-Martin
title	Influenza A Virus Field Surveillance at a Swine-Human Interface
title_short	Influenza A Virus Field Surveillance at a Swine-Human Interface
title_full	Influenza A Virus Field Surveillance at a Swine-Human Interface
title_fullStr	Influenza A Virus Field Surveillance at a Swine-Human Interface
title_full_unstemmed	Influenza A Virus Field Surveillance at a Swine-Human Interface
title_sort	influenza a virus field surveillance at a swine-human interface
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/69b4fadc25ee4696a45a24d4fb896cfd
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Influenza A Virus Field Surveillance at a Swine-Human Interface

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