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Szablewski CM, McBride DS, Trock SC, Habing GG, Hoet AE, Nelson SW, Nolting JM, Bowman AS. Evolution of influenza A viruses in exhibition swine and transmission to humans, 2013-2015. Zoonoses Public Health 2024; 71:281-293. [PMID: 38110691 PMCID: PMC10994755 DOI: 10.1111/zph.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/14/2023] [Accepted: 12/09/2023] [Indexed: 12/20/2023]
Abstract
AIMS Swine are a mixing vessel for the emergence of novel reassortant influenza A viruses (IAV). Interspecies transmission of swine-origin IAV poses a public health and pandemic risk. In the United States, the majority of zoonotic IAV transmission events have occurred in association with swine exposure at agricultural fairs. Accordingly, this human-animal interface necessitates mitigation strategies informed by understanding of interspecies transmission mechanisms in exhibition swine. Likewise, the diversity of IAV in swine can be a source for novel reassortant or mutated viruses that pose a risk to both swine and human health. METHODS AND RESULTS In an effort to better understand those risks, here we investigated the epidemiology of IAV in exhibition swine and subsequent transmission to humans by performing phylogenetic analyses using full genome sequences from 272 IAV isolates collected from exhibition swine and 23 A(H3N2)v viruses from human hosts during 2013-2015. Sixty-seven fairs (24.2%) had at least one pig test positive for IAV with an overall estimated prevalence of 8.9% (95% CI: 8.3-9.6, Clopper-Pearson). Of the 19 genotypes found in swine, 5 were also identified in humans. There was a positive correlation between the number of human cases of a genotype and its prevalence in exhibition swine. Additionally, we demonstrated that A(H3N2)v viruses clustered tightly with exhibition swine viruses that were prevalent in the same year. CONCLUSIONS These data indicate that multiple genotypes of swine-lineage IAV have infected humans, and highly prevalent IAV genotypes in exhibition swine during a given year are also the strains detected most frequently in human cases of variant IAV. Continued surveillance and rapid characterization of IAVs in exhibition swine can facilitate timely phenotypic evaluation and matching of candidate vaccine strains to those viruses present at the human-animal interface which are most likely to spillover into humans.
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Affiliation(s)
| | - Dillon S. McBride
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, OH, USA
| | - Susan C. Trock
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gregory G. Habing
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, OH, USA
| | - Armando E. Hoet
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, OH, USA
| | - Sarah W. Nelson
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, OH, USA
| | - Jacqueline M. Nolting
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, OH, USA
| | - Andrew S. Bowman
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, OH, USA
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2
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Padykula I, Damodaran L, Young KT, Krunkosky M, Griffin EF, North JF, Neasham PJ, Pliasas VC, Siepker CL, Stanton JB, Howerth EW, Bahl J, Kyriakis CS, Tompkins SM. Pandemic Risk Assessment for Swine Influenza A Virus in Comparative In Vitro and In Vivo Models. Viruses 2024; 16:548. [PMID: 38675891 PMCID: PMC11053818 DOI: 10.3390/v16040548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Swine influenza A viruses pose a public health concern as novel and circulating strains occasionally spill over into human hosts, with the potential to cause disease. Crucial to preempting these events is the use of a threat assessment framework for human populations. However, established guidelines do not specify which animal models or in vitro substrates should be used. We completed an assessment of a contemporary swine influenza isolate, A/swine/GA/A27480/2019 (H1N2), using animal models and human cell substrates. Infection studies in vivo revealed high replicative ability and a pathogenic phenotype in the swine host, with replication corresponding to a complementary study performed in swine primary respiratory epithelial cells. However, replication was limited in human primary cell substrates. This contrasted with our findings in the Calu-3 cell line, which demonstrated a replication profile on par with the 2009 pandemic H1N1 virus. These data suggest that the selection of models is important for meaningful risk assessment.
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Affiliation(s)
- Ian Padykula
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - Lambodhar Damodaran
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - Kelsey T. Young
- Department of Pathology, University of Georgia, Athens, GA 30602, USA
| | - Madelyn Krunkosky
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - Emily F. Griffin
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - James F. North
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Department of Pathobiology, Auburn University, Auburn, AL 36849, USA
| | - Peter J. Neasham
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Department of Pathobiology, Auburn University, Auburn, AL 36849, USA
| | - Vasilis C. Pliasas
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Department of Pathobiology, Auburn University, Auburn, AL 36849, USA
| | - Chris L. Siepker
- Department of Pathology, University of Georgia, Athens, GA 30602, USA
| | - James B. Stanton
- Department of Pathology, University of Georgia, Athens, GA 30602, USA
| | | | - Justin Bahl
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
| | - Constantinos S. Kyriakis
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Department of Pathobiology, Auburn University, Auburn, AL 36849, USA
| | - Stephen Mark Tompkins
- Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
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3
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Griffin EF, Tompkins SM. Fitness Determinants of Influenza A Viruses. Viruses 2023; 15:1959. [PMID: 37766365 PMCID: PMC10535923 DOI: 10.3390/v15091959] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A (IAV) is a major human respiratory pathogen that causes illness, hospitalizations, and mortality annually worldwide. IAV is also a zoonotic pathogen with a multitude of hosts, allowing for interspecies transmission, reassortment events, and the emergence of novel pandemics, as was seen in 2009 with the emergence of a swine-origin H1N1 (pdmH1N1) virus into humans, causing the first influenza pandemic of the 21st century. While the 2009 pandemic was considered to have high morbidity and low mortality, studies have linked the pdmH1N1 virus and its gene segments to increased disease in humans and animal models. Genetic components of the pdmH1N1 virus currently circulate in the swine population, reassorting with endemic swine viruses that co-circulate and occasionally spillover into humans. This is evidenced by the regular detection of variant swine IAVs in humans associated with state fairs and other intersections of humans and swine. Defining genetic changes that support species adaptation, virulence, and cross-species transmission, as well as mutations that enhance or attenuate these features, will improve our understanding of influenza biology. It aids in surveillance and virus risk assessment and guides the establishment of counter measures for emerging viruses. Here, we review the current understanding of the determinants of specific IAV phenotypes, focusing on the fitness, transmission, and virulence determinants that have been identified in swine IAVs and/or in relation to the 2009 pdmH1N1 virus.
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Affiliation(s)
- Emily Fate Griffin
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
| | - Stephen Mark Tompkins
- Center for Vaccines and Immunology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
- Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA 30602, USA
- Center for Influenza Disease and Emergence Response (CIDER), Athens, GA 30602, USA
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4
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Graaf A, Hennig C, Jaschniski KL, Koechling M, Stadler J, Boehmer J, Ripp U, Pohlmann A, Schwarz BA, Beer M, Harder T. Emergenceof swine influenza A virus, porcine respirovirus 1 and swine orthopneumovirus in porcine respiratory disease in Germany. Emerg Microbes Infect 2023:2239938. [PMID: 37470510 PMCID: PMC10402848 DOI: 10.1080/22221751.2023.2239938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Respiratory disease is a significant economic issue in pig farming, with a complex aetiology that includes swine influenza A viruses (swIAV), which are common in European domestic pig populations. The most recent human influenza pandemic in 2009 showed swIAV's zoonotic potential. Monitoring pathogens and disease control are critical from a preventive standpoint, and are based on quick, sensitive, and specific diagnostic assays capable of detecting and distinguishing currently circulating swIAV in clinical samples. For passive surveillance, a set of multiplex quantitative reverse transcription real-time PCRs (mRT-qPCR) and MinION-directed sequencing was updated and deployed. Several lineages and genotypes of swIAV were shown to be dynamically developing, including novel reassortants between human pandemic H1N1 and the avian-derived H1 lineage of swIAV. Despite this, nearly 70% (842/1216) of individual samples from pigs with respiratory symptoms were swIAV-negative, hinting to different aetiologies. The complex and synergistic interactions of swIAV infections with other viral and bacterial infectious agents contribute to the aggravation of pig respiratory diseases. Using a newly developed mRT-qPCR for the combined detection of swIAV and the recently described porcine respirovirus 1 (PRV1) and swine orthopneumovirus (SOV) widespread co-circulation of PRV1 (19.6%, 238/1216 samples) and SOV (14.2%, 173/1216 samples) was evident. Because of the high incidence of PRV1 and SOV infections in pigs with respiratory disease, these viruses may emerge as new allies in the porcine respiratory disease syndrome.
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Affiliation(s)
- Annika Graaf
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Christin Hennig
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | | | - Julia Stadler
- Clinic for Swine at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleissheim, Germany
| | - Jan Boehmer
- IVD Society for Innovative Veterinary Diagnostics mbH, Seelze-Letter, Germany
| | - Ulrike Ripp
- Vaxxinova diagnostics GmbH, Leipzig, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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5
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Cheung J, Bui AN, Younas S, Edwards KM, Nguyen HQ, Pham NT, Bui VN, Peiris M, Dhanasekaran V. Long-Term Epidemiology and Evolution of Swine Influenza Viruses, Vietnam. Emerg Infect Dis 2023; 29:1397-1406. [PMID: 37347532 PMCID: PMC10310380 DOI: 10.3201/eid2907.230165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023] Open
Abstract
Influenza A viruses are a One Health threat because they can spill over between host populations, including among humans, swine, and birds. Surveillance of swine influenza virus in Hanoi, Vietnam, during 2013-2019 revealed gene pool enrichment from imported swine from Asia and North America and showed long-term maintenance, persistence, and reassortment of virus lineages. Genome sequencing showed continuous enrichment of H1 and H3 diversity through repeat introduction of human virus variants and swine influenza viruses endemic in other countries. In particular, the North American H1-δ1a strain, which has a triple-reassortant backbone that potentially results in increased human adaptation, emerged as a virus that could pose a zoonotic threat. Co-circulation of H1-δ1a viruses with other swine influenza virus genotypes raises concerns for both human and animal health.
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Affiliation(s)
- Jonathan Cheung
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Anh Ngoc Bui
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Sonia Younas
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Kimberly M. Edwards
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Huy Quang Nguyen
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Ngoc Thi Pham
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
| | - Vuong Nghia Bui
- The University of Hong Kong, Hong Kong, China (J. Cheung, S. Younas, K.M. Edwards, M. Peiris, V. Dhanasekaran)
- National Institute of Veterinary Research, Hanoi, Vietnam (A.N. Bui, H.Q. Nguyen, N.T. Pham, V.N. Bui)
- Centre for Immunology & Infection, Hong Kong (M. Peiris)
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6
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Markin A, Ciacci Zanella G, Arendsee ZW, Zhang J, Krueger KM, Gauger PC, Vincent Baker AL, Anderson TK. Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential. PLoS Pathog 2023; 19:e1011476. [PMID: 37498825 PMCID: PMC10374098 DOI: 10.1371/journal.ppat.1011476] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/12/2023] [Indexed: 07/29/2023] Open
Abstract
The 2009 H1N1 pandemic (pdm09) lineage of influenza A virus (IAV) crosses interspecies barriers with frequent human-to-swine spillovers each year. These spillovers reassort and drift within swine populations, leading to genetically and antigenically novel IAV that represent a zoonotic threat. We quantified interspecies transmission of the pdm09 lineage, persistence in swine, and identified how evolution in swine impacted zoonotic risk. Human and swine pdm09 case counts between 2010 and 2020 were correlated and human pdm09 burden and circulation directly impacted the detection of pdm09 in pigs. However, there was a relative absence of pdm09 circulation in humans during the 2020-21 season that was not reflected in swine. During the 2020-21 season, most swine pdm09 detections originated from human-to-swine spillovers from the 2018-19 and 2019-20 seasons that persisted in swine. We identified contemporary swine pdm09 representatives of each persistent spillover and quantified cross-reactivity between human seasonal H1 vaccine strains and the swine strains using a panel of monovalent ferret antisera in hemagglutination inhibition (HI) assays. The swine pdm09s had variable antigenic reactivity to vaccine antisera, but each swine pdm09 clade exhibited significant reduction in cross-reactivity to one or more of the human seasonal vaccine strains. Further supporting zoonotic risk, we showed phylogenetic evidence for 17 swine-to-human transmission events of pdm09 from 2010 to 2021, 11 of which were not previously classified as variants, with each of the zoonotic cases associated with persistent circulation of pdm09 in pigs. These data demonstrate that reverse-zoonoses and evolution of pdm09 in swine results in viruses that are capable of zoonotic transmission and represent a potential pandemic threat.
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Affiliation(s)
- Alexey Markin
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Giovana Ciacci Zanella
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Zebulun W Arendsee
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Karen M Krueger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Amy L Vincent Baker
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
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7
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Petro-Turnquist E, Pekarek M, Jeanjaquet N, Wooledge C, Steffen D, Vu H, Weaver EA. Adenoviral-vectored epigraph vaccine elicits robust, durable, and protective immunity against H3 influenza A virus in swine. Front Immunol 2023; 14:1143451. [PMID: 37256131 PMCID: PMC10225514 DOI: 10.3389/fimmu.2023.1143451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
Current methods of vaccination against swine Influenza A Virus (IAV-S) in pigs are infrequently updated, induce strain-specific responses, and have a limited duration of protection. Here, we characterize the onset and duration of adaptive immune responses after vaccination with an adenoviral-vectored Epigraph vaccine. In this longitudinal study we observed robust and durable antibody responses that remained above protective titers six months after vaccination. We further identified stable levels of antigen-specific T cell responses that remained detectable in the absence of antigen stimulation. Antibody isotyping revealed robust class switching from IgM to IgG induced by Epigraph vaccination, while the commercial comparator vaccine failed to induce strong antibody class switching. Swine were challenged six months after initial vaccination, and Epigraph-vaccinated animals demonstrated significant protection from microscopic lesion development in the trachea and lungs, reduced duration of viral shedding, lower presence of infectious virus and viral antigens in the lungs, and significant recall of antigen-specific T cell responses following challenge. The results obtained from this study are useful in determining the kinetics of adaptive immune responses after vaccination with adjuvanted whole inactivated virus vaccines compared to adenoviral vectored vaccines and contribute to the continued efforts of creating a universal IAV-S vaccine.
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Affiliation(s)
- Erika Petro-Turnquist
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Matthew Pekarek
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Nicholas Jeanjaquet
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Cedric Wooledge
- Office of Research and Development, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - David Steffen
- Nebraska Veterinary Diagnostic Center, Lincoln, NE, United States
| | - Hiep Vu
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Eric A. Weaver
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
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8
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Hu M, Kackos C, Banoth B, Ojha CR, Jones JC, Lei S, Li L, Kercher L, Webby RJ, Russell CJ. Hemagglutinin destabilization in H3N2 vaccine reference viruses skews antigenicity and prevents airborne transmission in ferrets. SCIENCE ADVANCES 2023; 9:eadf5182. [PMID: 36989367 PMCID: PMC10058244 DOI: 10.1126/sciadv.adf5182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/28/2023] [Indexed: 06/14/2023]
Abstract
During influenza virus entry, the hemagglutinin (HA) protein binds receptors and causes membrane fusion after endosomal acid activation. To improve vaccine efficiency and pandemic risk assessment for currently-dominant H3N2 influenza viruses, we investigated HA stability of 6 vaccine reference viruses and 42 circulating viruses. Recent vaccine reference viruses had destabilized HA proteins due to egg-adaptive mutation HA1-L194P. Virus growth in cell culture was independent of HA stability. In ferrets, the vaccine reference viruses and circulating viruses required a relatively stable HA (activation and inactivation pH < 5.5) for airborne transmissibility. The recent vaccine reference viruses with destabilized HA proteins had reduced infectivity, had no airborne transmissibility unless reversion to HA1-P194L occurred, and had skewed antigenicity away from the studied viruses and circulating H3N2 viruses. Other vaccine reference viruses with stabilized HAs retained infectivity, transmissibility, and antigenicity. Therefore, HA stabilization should be prioritized over destabilization in vaccine reference virus selection to reduce mismatches between vaccine and circulating viruses.
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Affiliation(s)
- Meng Hu
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Christina Kackos
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
- St. Jude Children’s Research Hospital Graduate School of Biomedical Sciences, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Balaji Banoth
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Chet Raj Ojha
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Jeremy C. Jones
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Shaohua Lei
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
- Center of Excellence for Leukemia Studies, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Lei Li
- Drukier Institute for Children’s Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lisa Kercher
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Charles J. Russell
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
- Department of Microbiology, Immunology and Biochemistry, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
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9
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Wang M, Li H, Liu S, Ge L, Muhmood A, Liu D, Gan F, Liu Y, Chen X, Huang K. Lipopolysaccharide aggravates canine influenza a (H3N2) virus infection and lung damage via mTOR/autophagy in vivo and in vitro. Food Chem Toxicol 2023; 172:113597. [PMID: 36596444 DOI: 10.1016/j.fct.2022.113597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Influenza A (H3N2) accounts for the majority of influenza worldwide and continues to challenge human health. Disturbance in the gut microbiota caused by many diseases leads to increased production of lipopolysaccharide (LPS), and LPS induces sepsis and conditions associated with local or systemic inflammation. However, to date, little attention has been paid to the potential impact of LPS on influenza A (H3N2) infection and the potential mechanism. Hence, in this study we used canine influenza A (H3N2) virus (CIV) as a model of influenza A virus to investigate the effect of low-dose of LPS on CIV replication and lung damage and explore the underlying mechanism in mice and A549 and HPAEpiC cells. The results showed that LPS (25 μg/kg) increased CIV infection and lung damage in mice, as indicated by pulmonary virus titer, viral NP levels, lung index, and pulmonary histopathology. LPS (1 μg/ml) also increased CIV replication in A549 cells as indicated by the above same parameters. Furthermore, low doses of LPS reduced CIV-induced p-mTOR protein expression and enhanced CIV-induced autophagy-related mRNA/protein expressions in vivo and in vitro. In addition, the use of the mTOR activator, MHY1485, reversed CIV-induced autophagy and CIV replication in A549 and HPAEpiC cells, respectively. siATG5 alleviated CIV replication exacerbated by LPS in the two lines. In conclusion, LPS aggravates CIV infection and lung damage via mTOR/autophagy.
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Affiliation(s)
- Mengmeng Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; Institute of Nutritional and Metabolic Disorders in Domestic Animals and Fowls, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Haolei Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; Institute of Nutritional and Metabolic Disorders in Domestic Animals and Fowls, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Shuiping Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; Institute of Nutritional and Metabolic Disorders in Domestic Animals and Fowls, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Lei Ge
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; Institute of Nutritional and Metabolic Disorders in Domestic Animals and Fowls, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Azhar Muhmood
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; Institute of Nutritional and Metabolic Disorders in Domestic Animals and Fowls, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Dandan Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; Institute of Nutritional and Metabolic Disorders in Domestic Animals and Fowls, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Fang Gan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; Institute of Nutritional and Metabolic Disorders in Domestic Animals and Fowls, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Yunhuan Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; Institute of Nutritional and Metabolic Disorders in Domestic Animals and Fowls, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Xingxiang Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; Institute of Nutritional and Metabolic Disorders in Domestic Animals and Fowls, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Kehe Huang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; Institute of Nutritional and Metabolic Disorders in Domestic Animals and Fowls, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China.
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10
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McBride DS, Nolting JM, Nelson SW, Spurck MM, Bliss NT, Kenah E, Trock SC, Bowman AS. Shortening Duration of Swine Exhibitions to Reduce Risk for Zoonotic Transmission of Influenza A Virus. Emerg Infect Dis 2022; 28:2035-2042. [PMID: 36084650 PMCID: PMC9514346 DOI: 10.3201/eid2810.220649] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Reducing zoonotic influenza A virus (IAV) risk in the United States necessitates mitigation of IAV in exhibition swine. We evaluated the effectiveness of shortening swine exhibitions to <72 hours to reduce IAV risk. We longitudinally sampled every pig daily for the full duration of 16 county fairs during 2014-2015 (39,768 nasal wipes from 6,768 pigs). In addition, we estimated IAV prevalence at 195 fairs during 2018-2019 to test the hypothesis that <72-hour swine exhibitions would have lower IAV prevalence. In both studies, we found that shortening duration drastically reduces IAV prevalence in exhibition swine at county fairs. Reduction of viral load in the barn within a county fair is critical to reduce the risk for interspecies IAV transmission and pandemic potential. Therefore, we encourage fair organizers to shorten swine shows to protect the health of both animals and humans.
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11
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Merced-Morales A, Daly P, Abd Elal AI, Ajayi N, Annan E, Budd A, Barnes J, Colon A, Cummings CN, Iuliano AD, DaSilva J, Dempster N, Garg S, Gubareva L, Hawkins D, Howa A, Huang S, Kirby M, Kniss K, Kondor R, Liddell J, Moon S, Nguyen HT, O'Halloran A, Smith C, Stark T, Tastad K, Ujamaa D, Wentworth DE, Fry AM, Dugan VG, Brammer L. Influenza Activity and Composition of the 2022-23 Influenza Vaccine - United States, 2021-22 Season. MMWR. MORBIDITY AND MORTALITY WEEKLY REPORT 2022; 71:913-919. [PMID: 35862284 PMCID: PMC9310632 DOI: 10.15585/mmwr.mm7129a1] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Peter Daly
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Anwar Isa Abd Elal
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Noreen Ajayi
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Ekow Annan
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Alicia Budd
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - John Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Arielle Colon
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Charisse N Cummings
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - A Danielle Iuliano
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Juliana DaSilva
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Nick Dempster
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Shikha Garg
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Larisa Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Daneisha Hawkins
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Amanda Howa
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Stacy Huang
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Marie Kirby
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Krista Kniss
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Rebecca Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Jimma Liddell
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Shunte Moon
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Ha T Nguyen
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Alissa O'Halloran
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Catherine Smith
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Thomas Stark
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Katie Tastad
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Dawud Ujamaa
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Dave E Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Alicia M Fry
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Vivien G Dugan
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Lynnette Brammer
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
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12
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Hennig C, Graaf A, Petric PP, Graf L, Schwemmle M, Beer M, Harder T. Are pigs overestimated as a source of zoonotic influenza viruses? Porcine Health Manag 2022; 8:30. [PMID: 35773676 PMCID: PMC9244577 DOI: 10.1186/s40813-022-00274-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/20/2022] [Indexed: 11/23/2022] Open
Abstract
Background Swine influenza caused by influenza A viruses (IAV) directly affects respiratory health and indirectly impairs reproduction rates in pigs causing production losses. In Europe, and elsewhere, production systems have intensified featuring fewer holdings but, in turn, increased breeding herd and litter sizes. This seems to foster swine IAV (swIAV) infections with respect to the entrenchment within and spread between holdings. Disease management of swine influenza is difficult and relies on biosecurity and vaccination measures. Recently discovered and widely proliferating forms of self-sustaining modes of swIAV infections in large swine holdings challenge these preventive concepts by generating vaccine-escape mutants in rolling circles of infection. Main body The most recent human IAV pandemic of 2009 rooted at least partly in IAV of porcine origin highlighting the zoonotic potential of swIAV. Pigs constitute a mixing vessel of IAV from different species including avian and human hosts. However, other host species such as turkey and quail but also humans themselves may also act in this way; thus, pigs are not essentially required for the generation of IAV reassortants with a multispecies origin. Since 1918, all human pandemic influenza viruses except the H2N2 virus of 1958 have been transmitted in a reverse zoonotic mode from human into swine populations. Swine populations act as long-term reservoirs of these viruses. Human-derived IAV constitute a major driver of swIAV epidemiology in pigs. Swine-to-human IAV transmissions occurred rarely and mainly sporadically as compared to avian-to-human spill-over events of avian IAV. Yet, new swIAV variants that harbor zoonotic components continue to be detected. This increases the risk that such components might eventually reassort into viruses with pandemic potential. Conclusions Domestic pig populations should not be globally stigmatized as the only or most important reservoir of potentially zoonotic IAV. The likely emergence from swine of the most recent human IAV pandemic in 2009, however, emphasized the principal risks of swine populations in which IAV circulate unimpededly. Implementation of regular and close-meshed IAV surveillance of domestic swine populations to follow the dynamics of swIAV evolution is clearly demanded. Improved algorithms for directly inferring zoonotic potential from whole IAV genome sequences as well as improved vaccines are still being sought.
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Affiliation(s)
- Christin Hennig
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Annika Graaf
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Philipp P Petric
- Institute of Virology, Medical Center, University of Freiburg, 79104, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Laura Graf
- Institute of Virology, Medical Center, University of Freiburg, 79104, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center, University of Freiburg, 79104, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493, Greifswald-Insel Riems, Germany.
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13
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Vandoorn E, Parys A, Chepkwony S, Chiers K, Van Reeth K. Efficacy of the NS1-truncated live attenuated influenza virus vaccine for swine against infection with viruses of major North American and European H3N2 lineages. Vaccine 2022; 40:2723-2732. [PMID: 35367071 DOI: 10.1016/j.vaccine.2022.03.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022]
Abstract
Control of swine influenza A virus (swIAV) in North America and Europe is complicated because multiple antigenically distinct swIAV strains co-circulate in the field, and no vaccine is available that can provide broad cross-protection against all these swIAVs. In 2017, the first live attenuated influenza vaccine (LAIV) for swine was licensed in the US. The non-structural protein 1 (NS1)-truncated cluster I H3N2 strain A/swine/Texas/4199-2/98 NS1del126 (TX98 LAIV) in this vaccine provides partial cross-protection against heterologous North American cluster II and IV H3N2 swIAV strains. Its efficacy against European or more recent North American H3N2 lineages remains to be investigated. In this study, we evaluated the level of cross-protection against heterologous IAVs representative of the major H3N2 swIAV lineages in Europe and North America. TX98 LAIV prevented both nasal shedding and replication in the lungs of a North American cluster IV H3N2 swIAV for 2/4 pigs, prevented considerable nasal shedding of a North American novel human-like H3N2 swIAV for 2/4 pigs, and reduced replication of a European H3N2 swIAV in the lower respiratory tract to minimal titers for 1/3 pigs. Although TX98 LAIV elicited neutralizing antibodies against the homologous virus in serum and to a lesser extent in nose and lungs, no significant cross-reactive antibody titers against the heterologous swIAVs were detected. Partial cross-protection therefore likely relies on cellular and mucosal immune responses against conserved parts of the swIAV proteins. Since TX98 LAIV can offer partial protection against a broad range of H3N2 swIAVs, it might be a suitable priming vaccine for use in a heterologous prime-boost vaccination strategy.
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Affiliation(s)
- Elien Vandoorn
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Anna Parys
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Sharon Chepkwony
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Koen Chiers
- Laboratory of Veterinary Pathology, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Kristien Van Reeth
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
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14
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Markin A, Wagle S, Anderson TK, Eulenstein O. RF-Net 2: fast inference of virus reassortment and hybridization networks. Bioinformatics 2022; 38:2144-2152. [PMID: 35150239 PMCID: PMC9004648 DOI: 10.1093/bioinformatics/btac075] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method called RF-Net for accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens. RESULTS Here, we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, called Fast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. In addition, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical IAV evolutionary analyses. AVAILABILITY AND IMPLEMENTATION RF-Net 2 is available at https://github.com/flu-crew/rf-net-2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alexey Markin
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| | - Sanket Wagle
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| | - Oliver Eulenstein
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
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15
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Characterization of a 2016-2017 Human Seasonal H3 Influenza A Virus Spillover Now Endemic to U.S. Swine. mSphere 2022; 7:e0080921. [PMID: 35019669 PMCID: PMC8754165 DOI: 10.1128/msphere.00809-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In 2017, the Iowa State University Veterinary Diagnostic Laboratory detected a reverse-zoonotic transmission of a human seasonal H3 influenza A virus into swine (IAV-S) in Oklahoma. Pairwise comparison between the recently characterized human seasonal H3 IAV-S (H3.2010.2) hemagglutinin (HA) sequences detected in swine and the most similar 2016-2017 human seasonal H3 revealed 99.9% nucleotide identity. To elucidate the origin of H3.2010.2 IAV-S, 45 HA and 27 neuraminidase (NA) sequences from 2017 to 2020 as well as 11 whole-genome sequences (WGS) were genetically characterized. Time to most recent common human ancestor was estimated between August and September 2016. The N2 NA was of human origin in all but one strain from diagnostic submissions with NA sequences, and the internal gene segments from WGS consisted of matrix genes originating from the 2009 pandemic H1N1 and another 5 internal genes of triple reassortant swine origin (TTTTPT). Pigs experimentally infected with H3.2010.2 demonstrated efficient nasal shedding and replication in the lungs, mild pneumonia, and minimal microscopic lung lesions and transmitted the virus to indirect contact swine. Antigenically, H3.2010.2 viruses were closer to a human seasonal vaccine strain, A/Hong Kong/4801/2014, than to the H3.2010.1 human seasonal H3 viruses detected in swine in 2012. This was the second sustained transmission of a human seasonal IAV into swine from the 2010 decade after H3.2010.1. Monitoring the spillover and detection of novel IAV from humans to swine may help vaccine antigen selection and could impact pandemic preparedness. IMPORTANCE H3.2010.2 is a new phylogenetic clade of H3N2 circulating in swine that became established after the spillover of a human seasonal H3N2 from the 2016-2017 influenza season. The novel H3.2010.2 transmitted and adapted to the swine host and demonstrated reassortment with internal genes from strains endemic to pigs, but it maintained human-like HA and NA. It is genetically and antigenically distinct from the H3.2010.1 H3N2 introduced earlier in the 2010 decade. Human seasonal IAV spillovers into swine become established in the population through adaptation and sustained transmission and contribute to the genetic and antigenic diversity of IAV circulating in swine. Continued IAV surveillance is necessary to detect emergence of novel strains in swine and assist with vaccine antigen selection to improve the ability to prevent respiratory disease in swine as well as the risk of zoonotic transmission.
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16
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Antigenic distance between North American swine and human seasonal H3N2 influenza A viruses as an indication of zoonotic risk to humans. J Virol 2021; 96:e0137421. [PMID: 34757846 DOI: 10.1128/jvi.01374-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human-to-swine transmission of influenza A virus (IAV) repeatedly occurs, leading to sustained transmission and increased diversity in swine; human seasonal H3N2 introductions occurred in the 1990s and 2010s and were maintained in North American swine. Swine H3N2 were subsequently associated with zoonotic infections, highlighting the need to understand the risk of endemic swine IAV to humans. We quantified antigenic distances between swine H3N2 and human seasonal vaccine strains from 1973 to 2014 using a panel of monovalent antisera raised in pigs in hemagglutination inhibition (HI) assays. Swine H3N2 lineages retained closest antigenic similarity to human vaccine strains from the decade of incursion. Swine lineages from the 1990s were antigenically more similar to human vaccine strains of the mid-1990s but had substantial distance from recent human vaccine strains. In contrast, lineages from the 2010s were closer to human vaccine strains from 2011 and 2014 and most antigenically distant from human vaccine strains prior to 2007. HI assays using ferret antisera demonstrated that swine lineages from the 1990s and 2010s had significant fold-reduction compared with the homologous HI titer of the nearest pandemic preparedness candidate vaccine virus (CVV) or seasonal vaccine strain. The assessment of post-infection and post-vaccination human sera cohorts demonstrated limited cross-reactivity to swine H3N2 from the 1990s, especially in older adults born before 1970s. We identified swine strains to which humans are likely to lack population immunity or are not protected against by a current human seasonal vaccine or CVV to use in prioritizing future human CVV strain selection. IMPORTANCE Human H3N2 influenza A viruses spread to pigs in North America in the 1990s and more recently in the 2010s. These cross-species events led to sustained circulation and increased H3N2 diversity in pig populations. Evolution of H3N2 in swine led to a reduced similarity with human seasonal H3N2 and the vaccine strains used to protect human populations. We quantified the antigenic phenotypes and found that North American swine H3N2 lineages retained more antigenic similarity to historical human vaccine strains from the decade of incursion but had substantial difference compared with recent human vaccine strains. Additionally, pandemic preparedness vaccine strains demonstrated a loss in similarity with contemporary swine strains. Lastly, human sera revealed that although these adults had antibodies against human H3N2 strains, many had limited immunity to swine H3N2, especially older adults born before 1970. Antigenic assessment of swine H3N2 provides critical information for pandemic preparedness and candidate vaccine development.
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17
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Zeller MA, Chang J, Vincent AL, Gauger PC, Anderson TK. Spatial and Temporal Coevolution of N2 Neuraminidase and H1 and H3 Hemagglutinin Genes of Influenza A Virus in United States Swine. Virus Evol 2021; 7:veab090. [PMID: 35223081 PMCID: PMC8864744 DOI: 10.1093/ve/veab090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 09/14/2021] [Accepted: 10/07/2021] [Indexed: 11/12/2022] Open
Abstract
Abstract
The neuraminidase (NA) and hemagglutinin (HA) are essential surface glycoproteins of influenza A virus (IAV). In this study, the evolution of subtype N2 NA paired with H1 and H3 subtype HA in swine was evaluated to understand if genetic diversity of HA and NA were linked. Using time-scaled Bayesian phylodynamic analyses, the relationships of paired swine N2 with H1 or H3 from 2009 to 2018 were evaluated. These data demonstrated increased relative genetic diversity within the major N2 clades circulating in swine in the United States (N2.1998 between 2014-2017 and N2.2002 between 2010-2016). Preferential pairing was observed among specific NA and HA genetic clades. Gene reassortment between cocirculating influenza A strains resulted in novel pairings that persisted. The changes of genetic diversity in the NA gene were quantified using Bayesian phylodynamic analyses and increases in diversity were observed subsequent to novel NA-HA reassortment events. The rate of evolution among NA-N2 clades and HA-H1 and HA-H3 clades were similar. Bayesian phylodynamic analyses demonstrated strong spatial patterns in N2 genetic diversity, but frequent interstate movement of rare N2 clades provided opportunity for reassortment and emergence of new N2-HA pairings. The frequent regional movement of pigs and their influenza viruses is an explanation for the documented patterns of reassortment and subsequent changes in gene diversity. The reassortment and evolution of NA and linked HA evolution may result in antigenic drift of both major surface glycoproteins, reducing vaccine efficacy, with subsequent impact on animal health.
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Affiliation(s)
- Michael A Zeller
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
| | - Jennifer Chang
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA
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Glud HA, George S, Skovgaard K, Larsen LE. Zoonotic and reverse zoonotic transmission of viruses between humans and pigs. APMIS 2021; 129:675-693. [PMID: 34586648 PMCID: PMC9297979 DOI: 10.1111/apm.13178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/28/2021] [Indexed: 12/30/2022]
Abstract
Humans and pigs share a close contact relationship, similar biological traits, and one of the highest estimated number of viruses compared to other mammalian species. The contribution and directionality of viral exchange between humans and pigs remain unclear for some of these viruses, but their transmission routes are important to characterize in order to prevent outbreaks of disease in both host species. This review collects and assesses the evidence to determine the likely transmission route of 27 viruses between humans and pigs.
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Affiliation(s)
- Helena Aagaard Glud
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sophie George
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
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19
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McBride DS, Perofsky AC, Nolting JM, Nelson MI, Bowman AS. Tracing the Source of Influenza A Virus Zoonoses in Interconnected Circuits of Swine Exhibitions. J Infect Dis 2021; 224:458-468. [PMID: 33686399 PMCID: PMC7989509 DOI: 10.1093/infdis/jiab122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Since 2011, influenza A viruses circulating in US swine exhibited at county fairs are associated with >460 zoonotic infections, presenting an ongoing pandemic risk. Swine "jackpot shows" that occur before county fairs each summer intermix large numbers of exhibition swine from diverse geographic locations. We investigated the role of jackpot shows in influenza zoonoses. METHODS We collected snout wipe or nasal swab samples from 17 009 pigs attending 350 national, state, and local swine exhibitions across 8 states during 2016-2018. RESULTS Influenza was detected in 13.9% of swine sampled at jackpot shows, and 76.3% of jackpot shows had at least 1 pig test positive. Jackpot shows had 4.3-fold higher odds of detecting at least 1 influenza-positive pig compared to county fairs. When influenza was detected at a county fair, almost half of pigs tested positive, clarifying why zoonotic infections occur primarily at county fairs. CONCLUSIONS The earlier timing of jackpot shows and long-distance travel for repeated showing of individual pigs provide a pathway for the introduction of influenza into county fairs. Mitigation strategies aimed at curtailing influenza at jackpot shows are likely to have downstream effects on disease transmission at county fairs and zoonoses.
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Affiliation(s)
- Dillon S McBride
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Amanda C Perofsky
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jacqueline M Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Martha I Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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20
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Lorbach JN, Nelson SW, Lauterbach SE, Nolting JM, Kenah E, McBride DS, Culhane MR, Goodell C, Bowman AS. Influenza Vaccination of Swine Reduces Public Health Risk at the Swine-Human Interface. mSphere 2021; 6:e0117020. [PMID: 34190586 PMCID: PMC8265676 DOI: 10.1128/msphere.01170-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/08/2021] [Indexed: 11/20/2022] Open
Abstract
Influenza A viruses (IAV) in swine (IAV-S) pose serious risk to public health through spillover at the human-animal interface. Continued zoonotic transmission increases the likelihood novel IAV-S capable of causing the next influenza pandemic will emerge from this animal reservoir. Because current mitigation strategies are insufficient to prevent IAV zoonosis, we investigated the ability of swine vaccination to decrease IAV-S zoonotic transmission risk. We assessed postchallenge viral shedding in market-age swine vaccinated with either live-attenuated influenza virus (LAIV), killed influenza virus (KV), or sham vaccine (NV). We also assessed postchallenge transmission by exposing naive ferrets to pigs with contact types reflective of those experienced by humans in a field setting. LAIV and KV swine groups exhibited a nearly 100-fold reduction in peak nasal titer (LAIV mean, 4.55 log 50% tissue culture infectious dose [TCID50]/ml; KV mean, 4.53 log TCID50/ml) compared to NV swine (mean, 6.40 log TCID50/ml). Air sampling during the postchallenge period revealed decreased cumulative IAV in LAIV and KV study room air (LAIV, area under the concentration-time curve [AUC] of 57.55; KV, AUC = 24.29) compared to the NV study room (AUC = 86.92). Pairwise survival analysis revealed a significant delay in onset of infection among ferrets exposed to LAIV pigs versus NV pigs (rate ratio, 0.66; P = 0.028). Ferrets exposed to vaccinated pigs had lower cumulative virus titers in nasal wash samples (LAIV versus NV, P < 0.0001; KV versus NV, P= 0.3490) and experienced reduced clinical signs during infection. Our findings support the implementation of preexhibition influenza vaccination of swine to reduce the public health risk posed by IAV-S at agricultural exhibitions. IMPORTANCE Swine exhibited at agricultural fairs in North America have been the source of repeated zoonotic influenza A virus transmission, which creates a pathway for influenza pandemic emergence. We investigated the effect of using either live-attenuated influenza virus or killed influenza virus vaccines as prefair influenza vaccination of swine on zoonotic influenza transmission risk. Ferrets were exposed to the pigs in order to simulate human exposure in a field setting. We observed reductions in influenza A virus shedding in both groups of vaccinated pigs as well as the corresponding ferret exposure groups, indicating vaccination improved outcomes on both sides of the interface. There was also significant delay in onset of infection among ferrets that were exposed to live-attenuated virus-vaccinated pigs, which might be beneficial during longer fairs. Our findings indicate that policies mandating influenza vaccination of swine before fairs, while not currently common, would reduce the public health risk posed by influenza zoonosis.
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Affiliation(s)
| | | | | | | | - Eben Kenah
- The Ohio State University, Columbus, Ohio, USA
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21
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Genetic and antigenic evolution of H1 swine influenza A viruses isolated in Belgium and the Netherlands from 2014 through 2019. Sci Rep 2021; 11:11276. [PMID: 34050216 PMCID: PMC8163766 DOI: 10.1038/s41598-021-90512-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/06/2021] [Indexed: 12/17/2022] Open
Abstract
Surveillance of swine influenza A viruses (swIAV) allows timely detection and identification of new variants with potential zoonotic risks. In this study, we aimed to identify swIAV subtypes that circulated in pigs in Belgium and the Netherlands between 2014 and 2019, and characterize their genetic and antigenic evolution. We subtyped all isolates and analyzed hemagglutinin sequences and hemagglutination inhibition assay data for H1 swIAV, which were the dominant HA subtype. We also analyzed whole genome sequences (WGS) of selected isolates. Out of 200 samples, 89 tested positive for swIAV. swIAV of H1N1, H1N2 and H3N2 subtypes were detected. Analysis of WGS of 18 H1 swIAV isolates revealed three newly emerged genotypes. The European avian-like H1 swIAV (lineage 1C) were predominant and accounted for 47.2% of the total isolates. They were shown to evolve faster than the European human-like H1 (1B lineage) swIAV, which represented 27% of the isolates. The 2009 pandemic H1 swIAV (lineage 1A) accounted for only 5.6% of the isolates and showed divergence from their precursor virus. These results point to the increasing divergence of swIAV and stress the need for continuous surveillance of swIAV.
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22
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Danilenko DM, Komissarov AB, Fadeev AV, Bakaev MI, Ivanova AA, Petrova PA, Vassilieva AD, Komissarova KS, Zheltukhina AI, Konovalova NI, Vasin AV. Antigenic and Genetic Characterization of Swine Influenza Viruses Identified in the European Region of Russia, 2014-2020. Front Microbiol 2021; 12:662028. [PMID: 33936018 PMCID: PMC8081852 DOI: 10.3389/fmicb.2021.662028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/25/2021] [Indexed: 12/05/2022] Open
Abstract
Pigs have long been recognized as “mixing vessels” in which new viruses are formed by reassortment involving various influenza virus lineages (avian, animal, human). However, surveillance of swine influenza viruses only gained real significance after the 2009 pandemic. A fundamentally important point is the fact that there is still no regular surveillance of swine flu in Russia, and the role of swine viruses is underestimated since, as a rule, they do not cause serious disease in animals. Since the pig population in Russia is large, it is obvious that the lack of monitoring and insufficient study of swine influenza evolution constitutes a gap in animal influenza surveillance, not only for Russia, but globally. A 6 year joint effort enabled identification of SIV subtypes that circulate in the pig population of Russia’s European geographic region. The swine influenza viruses isolated were antigenically and genetically diverse. Some were similar to human influenza viruses of A(H1N1)pdm09 and A(H3N2) subtype, while others were reassortant A(H1pdm09N2) and A(H1avN2) and were antigenically distinct from human H1N1 and H1N1pdm09 strains. Analysis of swine serum samples collected throughout the seasons showed that the number of sera positive for influenza viruses has increased in recent years. This indicates that swine populations are highly susceptible to infection with human influenza viruses. It also stresses the need for regular SIV surveillance, monitoring of viral evolution, and strengthening of pandemic preparedness.
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Affiliation(s)
- Daria M Danilenko
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia
| | - Andrey B Komissarov
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia
| | - Artem V Fadeev
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia
| | - Mikhail I Bakaev
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia
| | - Anna A Ivanova
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia
| | - Polina A Petrova
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia
| | - Anastasia D Vassilieva
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia
| | - Kseniya S Komissarova
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia
| | - Alyona I Zheltukhina
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia
| | - Nadezhda I Konovalova
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia
| | - Andrey V Vasin
- WHO-Recognized National Influenza Centre (NIC), Smorodintsev Research Institute of Influenza, Ministry of Health, Saint Petersburg, Russia.,Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
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23
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Anderson TK, Chang J, Arendsee ZW, Venkatesh D, Souza CK, Kimble JB, Lewis NS, Davis CT, Vincent AL. Swine Influenza A Viruses and the Tangled Relationship with Humans. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038737. [PMID: 31988203 PMCID: PMC7919397 DOI: 10.1101/cshperspect.a038737] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Influenza A viruses (IAVs) are the causative agents of one of the most important viral respiratory diseases in pigs and humans. Human and swine IAV are prone to interspecies transmission, leading to regular incursions from human to pig and vice versa. This bidirectional transmission of IAV has heavily influenced the evolutionary history of IAV in both species. Transmission of distinct human seasonal lineages to pigs, followed by sustained within-host transmission and rapid adaptation and evolution, represent a considerable challenge for pig health and production. Consequently, although only subtypes of H1N1, H1N2, and H3N2 are endemic in swine around the world, extensive diversity can be found in the hemagglutinin (HA) and neuraminidase (NA) genes, as well as the remaining six genes. We review the complicated global epidemiology of IAV in swine and the inextricably entangled implications for public health and influenza pandemic planning.
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Affiliation(s)
- Tavis K. Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - Jennifer Chang
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - Zebulun W. Arendsee
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - Divya Venkatesh
- Department of Pathology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire AL9 7TA, United Kingdom
| | - Carine K. Souza
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - J. Brian Kimble
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - Nicola S. Lewis
- Department of Pathology and Population Sciences, Royal Veterinary College, University of London, Hertfordshire AL9 7TA, United Kingdom
| | - C. Todd Davis
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Amy L. Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
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24
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Lorbach JN, Fitzgerald T, Nolan C, Nolting JM, Treanor JJ, Topham DJ, Bowman AS. Gaps in Serologic Immunity against Contemporary Swine-Origin Influenza A Viruses among Healthy Individuals in the United States. Viruses 2021; 13:v13010127. [PMID: 33477472 PMCID: PMC7830885 DOI: 10.3390/v13010127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
Influenza A Viruses (IAV) in domestic swine (IAV-S) are associated with sporadic zoonotic transmission at the human–animal interface. Previous pandemic IAVs originated from animals, which emphasizes the importance of characterizing human immunity against the increasingly diverse IAV-S. We analyzed serum samples from healthy human donors (n = 153) using hemagglutination-inhibition (HAI) assay to assess existing serologic protection against a panel of contemporary IAV-S isolated from swine in the United States (n = 11). Age-specific seroprotection rates (SPR), which are the proportion of individuals with HAI ≥ 1:40, corresponded with lower or moderate pandemic risk classifications for the multiple IAV-S examined (one H1-δ1, one H1-δ2, three H3-IVA, one H3-IVB, one H3-IVF). Individuals born between 2004 and 2013 had SPRs of 0% for the five classified H3 subtype IAV-S, indicating youth may be particularly predisposed to infection with these viruses. Expansion of existing immunologic gaps over time could increase likelihood of future IAV-S spillover to humans and facilitate subsequent sustained human-to-human transmission resulting in disease outbreaks with pandemic potential.
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Affiliation(s)
- Joshua N. Lorbach
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (J.N.L.); (J.M.N.)
| | - Theresa Fitzgerald
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14627, USA; (T.F.); (C.N.); (D.J.T.)
| | - Carolyn Nolan
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14627, USA; (T.F.); (C.N.); (D.J.T.)
| | - Jacqueline M. Nolting
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (J.N.L.); (J.M.N.)
| | - John J. Treanor
- Department of Medicine, University of Rochester Medical Center, Rochester, NY 14627, USA;
| | - David J. Topham
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14627, USA; (T.F.); (C.N.); (D.J.T.)
| | - Andrew S. Bowman
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; (J.N.L.); (J.M.N.)
- Correspondence:
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25
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Dürrwald R, Wedde M, Biere B, Oh DY, Heßler-Klee M, Geidel C, Volmer R, Hauri AM, Gerst K, Thürmer A, Appelt S, Reiche J, Duwe S, Buda S, Wolff T, Haas W. Zoonotic infection with swine A/H1 avN1 influenza virus in a child, Germany, June 2020. ACTA ACUST UNITED AC 2021; 25. [PMID: 33094718 PMCID: PMC7651875 DOI: 10.2807/1560-7917.es.2020.25.42.2001638] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A zoonotic A/sw/H1avN1 1C.2.2 influenza virus infection was detected in a German child that presented with influenza-like illness, including high fever. There was a history of close contact with pigs 3 days before symptom onset. The child recovered within 3 days. No other transmissions were observed. Serological investigations of the virus isolate revealed cross-reactions with ferret antisera against influenza A(H1N1)pdm09 virus, indicating a closer antigenic relationship with A(H1N1)pdm09 than with the former seasonal H1N1 viruses.
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Affiliation(s)
| | | | | | | | | | | | - Renate Volmer
- Landesbetrieb Hessisches Landeslabor (LHL), Fachgebiet II.4 Tiergesundheitsdienste, Gießen, Germany
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26
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Tabaszewski P, Gorecki P, Markin A, Anderson T, Eulenstein O. Consensus of All Solutions for Intractable Phylogenetic Tree Inference. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:149-161. [PMID: 31613775 DOI: 10.1109/tcbb.2019.2947051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Solving median tree problems is a classic approach for inferring species trees from a collection of discordant gene trees. Median tree problems are typically NP-hard and dealt with by local search heuristics. Unfortunately, such heuristics generally lack provable correctness and precision. Algorithmic advances addressing this uncertainty have led to exact dynamic programming formulations suitable to solve a well-studied group of median tree problems for smaller phylogenetic analyses. However, these formulations allow computing only very few optimal species trees out of possibly many such trees, and phylogenetic studies often require the analysis of all optimal solutions through their consensus tree. Here, we describe a significant algorithmic modification of the dynamic programming formulations that compute the cluster counts of all optimal species trees from which various types of consensus trees can be efficiently computed. Through experimental studies, we demonstrate that our parallel implementation of the modified dynamic programming formulation is more efficient than a previous implementation of the original formulation. Finally, we show that the parallel implementation can rapidly identify novel reassorted influenza A viruses potentially facilitating pandemic preparedness efforts.
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27
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Powell JD, Abente EJ, Chang J, Souza CK, Rajao DS, Anderson TK, Zeller MA, Gauger PC, Lewis NS, Vincent AL. Characterization of contemporary 2010.1 H3N2 swine influenza A viruses circulating in United States pigs. Virology 2020; 553:94-101. [PMID: 33253936 DOI: 10.1016/j.virol.2020.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 01/17/2023]
Abstract
In 2012, swine influenza surveillance detected a novel reassorted influenza A virus (IAV) strain containing human-seasonal hemagglutinin (HA) and neuraminidase (NA). Subsequently, these viruses reassorted, maintaining only the human-origin H3, which resulted in a new lineage of viruses that became the most frequently detected H3 clade in US swine (2010.1 HA clade). Here, we assessed the antigenic phenotype, virulence, and transmission characteristics of this virus lineage following its introduction to swine. Relative to 2010.1 viruses from 2012 and 2014, recent 2010.1 contemporary strains from 2015 to 2017 resulted in equivalent macroscopic lung lesions and transmission in pigs. A single mutation at amino acid residue 145 within the previously defined HA antigenic motif was associated with a change of antigenic phenotype, potentially impairing vaccine efficacy. Contemporary 2010.1 viruses circulating in swine since 2012 were significantly different from both pre-2012H3N2 in swine and human-seasonal H3N2 viruses and demonstrated continued evolution within the lineage.
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Affiliation(s)
- Joshua D Powell
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Eugenio J Abente
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Jennifer Chang
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Carine K Souza
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Daniela S Rajao
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Michael A Zeller
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Nicola S Lewis
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA.
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28
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Chepkwony S, Parys A, Vandoorn E, Chiers K, Van Reeth K. Efficacy of Heterologous Prime-Boost Vaccination with H3N2 Influenza Viruses in Pre-Immune Individuals: Studies in the Pig Model. Viruses 2020; 12:v12090968. [PMID: 32882956 PMCID: PMC7552030 DOI: 10.3390/v12090968] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/26/2020] [Accepted: 08/30/2020] [Indexed: 12/25/2022] Open
Abstract
In a previous study in influenza-naïve pigs, heterologous prime-boost vaccination with monovalent, adjuvanted whole inactivated vaccines (WIV) based on the European swine influenza A virus (SwIAV) strain, A/swine/Gent/172/2008 (G08), followed by the US SwIAV strain, A/swine/Pennsylvania/A01076777/2010 (PA10), was shown to induce broadly cross-reactive hemagglutination inhibition (HI) antibodies against 12 out of 15 antigenically distinct H3N2 influenza strains. Here, we used the pig model to examine the efficacy of that particular heterologous prime-boost vaccination regimen, in individuals with pre-existing infection-immunity. Pigs were first inoculated intranasally with the human H3N2 strain, A/Nanchang/933/1995. Seven weeks later, they were vaccinated intramuscularly with G08 followed by PA10 or vice versa. We examined serum antibody responses against the hemagglutinin and neuraminidase, and antibody-secreting cell (ASC) responses in peripheral blood, draining lymph nodes, and nasal mucosa (NMC), in ELISPOT assays. Vaccination induced up to 10-fold higher HI antibody titers than in naïve pigs, with broader cross-reactivity, and protection against challenge with an antigenically distant H3N2 strain. It also boosted ASC responses in lymph nodes and NMC. Our results show that intramuscular administration of WIV can lead to enhanced antibody responses and cross-reactivity in pre-immune subjects, and recall of ASC responses in lymph nodes and NMC.
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Affiliation(s)
- Sharon Chepkwony
- Laboratory of Virology, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Ghent University, 9820 Merelbeke, Belgium; (S.C.); (A.P.); (E.V.)
| | - Anna Parys
- Laboratory of Virology, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Ghent University, 9820 Merelbeke, Belgium; (S.C.); (A.P.); (E.V.)
| | - Elien Vandoorn
- Laboratory of Virology, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Ghent University, 9820 Merelbeke, Belgium; (S.C.); (A.P.); (E.V.)
| | - Koen Chiers
- Laboratory of Veterinary Pathology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium;
| | - Kristien Van Reeth
- Laboratory of Virology, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Ghent University, 9820 Merelbeke, Belgium; (S.C.); (A.P.); (E.V.)
- Correspondence: ; Tel.: +32-92647369
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29
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Lauterbach SE, Nelson SW, Martin AM, Spurck MM, Mathys DA, Mollenkopf DF, Nolting JM, Wittum TE, Bowman AS. Adoption of recommended hand hygiene practices to limit zoonotic disease transmission at agricultural fairs. Prev Vet Med 2020; 182:105116. [PMID: 32768662 PMCID: PMC7494593 DOI: 10.1016/j.prevetmed.2020.105116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 11/23/2022]
Abstract
Rapid transmission and spread of infectious pathogens are enhanced by the agricultural fair environment, where large numbers of livestock and people from numerous backgrounds congregate for several days. The transmission of influenza A virus and zoonotic enteric pathogens to fairgoers is a considerable risk and has occurred several times over the past decade. In an effort to mitigate zoonotic disease transmission in these settings, public health guidelines and recommendations including hand sanitation stations have been implemented. While hand hygiene recommendations to prevent the spread of zoonotic disease are well communicated, it is hypothesized that the adoption of these recommendations by agricultural fairs and fairgoers is low. To test this hypothesis, hand hygiene data collected from 658 agricultural fairs between 2012 and 2019 was analyzed to determine frequency and function of hand sanitation stations at the fairs, as well as utilization of educational signage. In addition, an observational study was performed to calculate the proportion of fairgoers who use hand sanitation stations at the fair. Lastly, samples were taken from working hand sanitation stations present at the exits of livestock barns and tested for the presence of influenza A virus and antimicrobial resistant coliform bacteria. Hand sanitation stations were present at most fairs (77.4 %) as recommended, but only 142 out of 2021 (7.0 %) visitors were observed using the stations. Health risk signage was displayed at more than half of fairs while the proper wash procedure was displayed at less than half. No influenza A virus was detected on any of the hand sanitation stations, however antimicrobial resistant coliform bacteria were recovered from 75.5 % of the sampled hand sanitation stations. Fairs should employ educational material along with functional hand sanitation stations in order to promote hand hygiene at fairs. Stations should be maintained and cleaned often to ensure effectiveness, as hand hygiene continues to be recommended to fairgoers when exiting animal barns to reduce zoonotic disease transmission.
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Affiliation(s)
- Sarah E Lauterbach
- The Ohio State University, Department of Veterinary Preventive Medicine, 1920 Coffey Road, Columbus, OH, 43210, USA.
| | - Sarah W Nelson
- The Ohio State University, Department of Veterinary Preventive Medicine, 1920 Coffey Road, Columbus, OH, 43210, USA.
| | - Alison M Martin
- The Ohio State University, Department of Veterinary Preventive Medicine, 1920 Coffey Road, Columbus, OH, 43210, USA.
| | - Michele M Spurck
- The Ohio State University, Department of Veterinary Preventive Medicine, 1920 Coffey Road, Columbus, OH, 43210, USA.
| | - Dimitria A Mathys
- The Ohio State University, Department of Veterinary Preventive Medicine, 1920 Coffey Road, Columbus, OH, 43210, USA.
| | - Dixie F Mollenkopf
- The Ohio State University, Department of Veterinary Preventive Medicine, 1920 Coffey Road, Columbus, OH, 43210, USA.
| | - Jacqueline M Nolting
- The Ohio State University, Department of Veterinary Preventive Medicine, 1920 Coffey Road, Columbus, OH, 43210, USA.
| | - Thomas E Wittum
- The Ohio State University, Department of Veterinary Preventive Medicine, 1920 Coffey Road, Columbus, OH, 43210, USA.
| | - Andrew S Bowman
- The Ohio State University, Department of Veterinary Preventive Medicine, 1920 Coffey Road, Columbus, OH, 43210, USA.
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Mahoney JA, Widmar NJO, Bir CL. #GoingtotheFair: a social media listening analysis of agricultural fairs. Transl Anim Sci 2020; 4:txaa139. [PMID: 32832858 PMCID: PMC7433905 DOI: 10.1093/tas/txaa139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 11/26/2022] Open
Abstract
Agricultural fairs provide one of the last frontiers, and largest stages, for showcasing livestock agriculture to the public. However, public funding, attendance revenue, animal biosecurity, and public health concerns are all aspects worthy of conversation and increased research attention given the interaction between livestock animals and the general public in fair and festival settings. A prominent social media listening and data analytics platform was used to quantify online and social media chatter concerning agricultural fairs during a 27-mo period. A general search for online media referencing agricultural fair keywords was designed; social and online media mentions of agricultural fairs (n = 2,091,350 mentions) were further queried according to their reference to livestock, fair food, or the major agricultural product producing species of dairy and beef cattle (n = 68,900), poultry (n = 39,600), and swine (n = 31,250). Numbers of search results were found to be seasonal and Twitter was the single largest domain for all fair-related results; in contrast, the majority of livestock-related media was generated by news sources rather than from Twitter. On a weekly basis, the percentage of fair livestock mentions with species-specific reference was highly variable ranging from 0% to 86.8% for cattle, 0% to 85.7% for poultry, and 0% to 76.9% for swine. In addition to quantifying total search hits or mentions, the positivity/negativity of the search results was analyzed using natural language processing capabilities. The net sentiment quantified is the total percentage of positive posts minus the percentage of negative posts, which results in a necessarily bounded net sentiment between −100% and +100%. Overall net sentiment associated with mentions of agricultural fairs was positive; the topics garnering the highest positive sentiments were fair food and cattle (both 98% positive). Online discussion pertaining to agricultural fairs and swine was overall positive despite references to swine flu outbreaks. In conclusion, livestock and animal products had positive net sentiment over the time period studied, but there are multiple aspects of agricultural fairs worthy of further investigation and continued vigilance, including zoonotic disease risk and public perceptions of livestock industries.
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Affiliation(s)
| | - Nicole J O Widmar
- Department of Agricultural Economics, Purdue University, West Lafayette, IN
| | - Courtney L Bir
- Department of Agricultural Economics, Oklahoma State University, Stillwater, OK
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Aerosol Transmission from Infected Swine to Ferrets of an H3N2 Virus Collected from an Agricultural Fair and Associated with Human Variant Infections. J Virol 2020; 94:JVI.01009-20. [PMID: 32522849 DOI: 10.1128/jvi.01009-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
Influenza A viruses (IAV) sporadically transmit from swine to humans, typically associated with agricultural fairs in the United States. A human seasonal H3 virus from the 2010-2011 IAV season was introduced into the U.S. swine population and termed H3.2010.1 to differentiate it from the previous swine H3 virus. This H3N2 lineage became widespread in the U.S. commercial swine population, subsequently spilling over into exhibition swine, and caused a majority of H3N2 variant (H3N2v) cases in humans in 2016 and 2017. A cluster of human H3N2v cases were reported at an agricultural fair in 2017 in Ohio, where 2010.1 H3N2 IAV was concurrently detected in exhibition swine. Genomic analysis showed that the swine and human isolates were nearly identical. In this study, we evaluated the propensity of a 2010.1 H3N2 IAV (A/swine/Ohio/A01354299/2017 [sw/OH/2017]) isolated from a pig in the agricultural fair outbreak to replicate in ferrets and transmit from swine to ferret. sw/OH/2017 displayed robust replication in the ferret respiratory tract, causing slight fever and moderate weight loss. Further, sw/OH/2017 was capable of efficient respiratory droplet transmission from infected pigs to contact ferrets. These findings establish a model for evaluating the propensity of swine IAV to transmit from pig to ferret as a measure of risk to the human population. The identification of higher-risk swine strains can then be targeted for control measures to limit the dissemination at human-swine interfaces to reduce the risk of zoonotic infections and to inform pandemic planning.IMPORTANCE A recently emerged lineage of human-like H3N2 (H3.2010.1) influenza A virus (IAV) from swine has been frequently detected in commercial and exhibition swine in recent years and has been associated with H3N2 variant cases in humans from 2016 and 2017. To demonstrate a model for characterizing the potential for zoonotic transmission associated with swine IAV, we performed an in vivo study of transmission between pigs infected with an H3.2010.1 H3N2 IAV and aerosol contact ferrets. The efficient interspecies transmission demonstrated for the H3.2010.1 IAV in swine emphasizes the need for further characterization of viruses circulating at the swine-human interface for transmission potential prior to human spillover and the development and implementation of more robust vaccines and control strategies to mitigate human exposure to higher-risk swine strains.
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32
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Henritzi D, Petric PP, Lewis NS, Graaf A, Pessia A, Starick E, Breithaupt A, Strebelow G, Luttermann C, Parker LMK, Schröder C, Hammerschmidt B, Herrler G, Beilage EG, Stadlbauer D, Simon V, Krammer F, Wacheck S, Pesch S, Schwemmle M, Beer M, Harder TC. Surveillance of European Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza A Viruses. Cell Host Microbe 2020; 28:614-627.e6. [PMID: 32721380 DOI: 10.1016/j.chom.2020.07.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/22/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Swine influenza A viruses (swIAVs) can play a crucial role in the generation of new human pandemic viruses. In this study, in-depth passive surveillance comprising nearly 2,500 European swine holdings and more than 18,000 individual samples identified a year-round presence of up to four major swIAV lineages on more than 50% of farms surveilled. Phylogenetic analyses show that intensive reassortment with human pandemic A(H1N1)/2009 (H1pdm) virus produced an expanding and novel repertoire of at least 31 distinct swIAV genotypes and 12 distinct hemagglutinin/neuraminidase combinations with largely unknown consequences for virulence and host tropism. Several viral isolates were resistant to the human antiviral MxA protein, a prerequisite for zoonotic transmission and stable introduction into human populations. A pronounced antigenic variation was noted in swIAV, and several H1pdm lineages antigenically distinct from current seasonal human H1pdm co-circulate in swine. Thus, European swine populations represent reservoirs for emerging IAV strains with zoonotic and, possibly, pre-pandemic potential.
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Affiliation(s)
- Dinah Henritzi
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Philipp Peter Petric
- Institute of Virology, Medical Center, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine, University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nicola Sarah Lewis
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, Hertfordshire AL9 7TA, UK; OIE/FAO International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease, Animal and Plant Health Agency (APHA) - Weybridge, Addlestone, Surrey KT15 3NB, UK
| | - Annika Graaf
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Alberto Pessia
- Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
| | - Elke Starick
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Günter Strebelow
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Christine Luttermann
- Institute of Immunology, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Larissa Mareike Kristin Parker
- Institute of Virology, Medical Center, University of Freiburg, 79104 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Charlotte Schröder
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Bärbel Hammerschmidt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Georg Herrler
- Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Bünteweg 2, 30559 Hannover, Germany
| | - Elisabeth Große Beilage
- Field Station for Epidemiology, University of Veterinary Medicine Hannover, Büscheler Str. 9, 49456 Bakum, Germany
| | - Daniel Stadlbauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Silke Wacheck
- Ceva Santé Animale (former IDT Biologika GmbH), 06861 Dessau-Rosslau, Germany
| | - Stefan Pesch
- Ceva Santé Animale (former IDT Biologika GmbH), 06861 Dessau-Rosslau, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center, University of Freiburg, 79104 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald-Insel Riems, Germany.
| | - Timm Clemens Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Suedufer 10, 17493 Greifswald-Insel Riems, Germany.
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A feasibility study of conducting surveillance for swine pathogens in slurry from North Carolina swine farms. Sci Rep 2020; 10:10059. [PMID: 32572119 PMCID: PMC7308328 DOI: 10.1038/s41598-020-67313-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/21/2020] [Indexed: 12/02/2022] Open
Abstract
Despite close contact between humans and animals on large scale farms, little to no infectious disease research is conducted at this interface. Our goal in this preliminary study was to explore if we could detect swine pathogens using a non-invasive, indirect approach through the study of swine slurry. From April to November 2018, 105 swine slurry samples were collected by farm personnel from waste pits at two sites on a swine farm in North Carolina. These samples were tested for DNA and RNA viruses using a real-time PCR and RT-PCR. Statistical analyses were performed to measure association between virus positive outcomes and potential predictors such as date of sample collection, weight of pigs, number of pigs in barn, temperature, and weather conditions. Overall, 86% of the samples had evidence of at least one of the targeted viruses. Ultimately, this study demonstrated the utility of conducting noninvasive surveillance for swine pathogens through the study of swine slurry. Such swine slurry surveillance may supplant the need to handle, restrain, and collect specimens directly from pigs thus providing an approach to emerging pathogen detection that appeals to the swine industry.
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34
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Chauhan RP, Gordon ML. A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide. Pathogens 2020; 9:pathogens9050355. [PMID: 32397138 PMCID: PMC7281378 DOI: 10.3390/pathogens9050355] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/02/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023] Open
Abstract
The global anxiety and a significant threat to public health due to the current COVID-19 pandemic reiterate the need for active surveillance for the zoonotic virus diseases of pandemic potential. Influenza virus due to its wide host range and zoonotic potential poses such a significant threat to public health. Swine serve as a “mixing vessel” for influenza virus reassortment and evolution which as a result may facilitate the emergence of new strains or subtypes of zoonotic potential. In this context, the currently available scientific data hold a high significance to unravel influenza virus epidemiology and evolution. With this objective, the current systematic review summarizes the original research articles and case reports of all the four types of influenza viruses reported in swine populations worldwide. A total of 281 articles were found eligible through screening of PubMed and Google Scholar databases and hence were included in this systematic review. The highest number of research articles (n = 107) were reported from Asia, followed by Americas (n = 97), Europe (n = 55), Africa (n = 18), and Australia (n = 4). The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were the most common influenza A virus subtypes reported in swine in most countries across the globe, however, few strains of influenza B, C, and D viruses were also reported in certain countries. Multiple reports of the avian influenza virus strains documented in the last two decades in swine in China, the United States, Canada, South Korea, Nigeria, and Egypt provided the evidence of interspecies transmission of influenza viruses from birds to swine. Inter-species transmission of equine influenza virus H3N8 from horse to swine in China expanded the genetic diversity of swine influenza viruses. Additionally, numerous reports of the double and triple-reassortant strains which emerged due to reassortments among avian, human, and swine strains within swine further increased the genetic diversity of swine influenza viruses. These findings are alarming hence active surveillance should be in place to prevent future influenza pandemics.
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Park MS, Kim JI, Bae JY, Park MS. Animal models for the risk assessment of viral pandemic potential. Lab Anim Res 2020; 36:11. [PMID: 32337177 PMCID: PMC7175453 DOI: 10.1186/s42826-020-00040-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Pandemics affect human lives severely and globally. Experience predicts that there will be a pandemic for sure although the time is unknown. When a viral epidemic breaks out, assessing its pandemic risk is an important part of the process that characterizes genomic property, viral pathogenicity, transmission in animal model, and so forth. In this review, we intend to figure out how a pandemic may occur by looking into the past influenza pandemic events. We discuss interpretations of the experimental evidences resulted from animal model studies and extend implications of viral pandemic potentials and ingredients to emerging viral epidemics. Focusing on the pandemic potential of viral infectious diseases, we suggest what should be assessed to prevent global catastrophes from influenza virus, Middle East respiratory syndrome coronavirus, dengue and Zika viruses.
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Affiliation(s)
- Mee Sook Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Jin Il Kim
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
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36
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Rambo-Martin BL, Keller MW, Wilson MM, Nolting JM, Anderson TK, Vincent AL, Bagal UR, Jang Y, Neuhaus EB, Davis CT, Bowman AS, Wentworth DE, Barnes JR. Influenza A Virus Field Surveillance at a Swine-Human Interface. mSphere 2020; 5:e00822-19. [PMID: 32024713 PMCID: PMC7002310 DOI: 10.1128/msphere.00822-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/07/2020] [Indexed: 12/20/2022] Open
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.
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Affiliation(s)
| | - Matthew W Keller
- Oak Ridge Institute of Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | - Malania M Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Jacqueline M Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Tavis K Anderson
- National Animal Disease Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Ames, Iowa, USA
| | - Amy L Vincent
- National Animal Disease Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Ames, Iowa, USA
| | | | - Yunho Jang
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Elizabeth B Neuhaus
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - C Todd Davis
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - David E Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
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37
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Abstract
Influenza A viruses (IAVs) of the Orthomyxoviridae virus family cause one of the most important respiratory diseases in pigs and humans. Repeated outbreaks and rapid spread of genetically and antigenically distinct IAVs represent a considerable challenge for animal production and public health. Bidirection transmission of IAV between pigs and people has altered the evolutionary dynamics of IAV, and a "One Health" approach is required to ameliorate morbidity and mortality in both hosts and improve control strategies. Although only subtypes of H1N1, H1N2, and H3N2 are endemic in swine around the world, considerable diversity can be found not only in the hemagglutinin (HA) and neuraminidase (NA) genes but in the remaining six genes as well. Human and swine IAVs have demonstrated a particular propensity for interspecies transmission, leading to regular and sometimes sustained incursions from man to pig and vice versa. The diversity of IAVs in swine remains a critical challenge in the diagnosis and control of this important pathogen for swine health and in turn contributes to a significant public health risk.
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Affiliation(s)
- Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, USA.
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, USA
| | - Kelly M Lager
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, USA
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38
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Nirmala J, Bender JB, Lynfield R, Yang M, Rene Culhane M, Nelson MI, Sreevatsan S, Torremorell M. Genetic diversity of influenza A viruses circulating in pigs between winter and summer in a Minnesota live animal market. Zoonoses Public Health 2019; 67:243-250. [PMID: 31868300 DOI: 10.1111/zph.12679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 10/07/2019] [Accepted: 11/19/2019] [Indexed: 11/26/2022]
Abstract
There has been little surveillance of influenza A viruses (IAVs) circulating in swine at live animal markets, particularly in the United States. To address this gap, we conducted active surveillance of IAVs in pigs, the air, and the environment during a summer and winter season in a live animal market in St. Paul, Minnesota, that had been epidemiologically associated with swine-origin influenza cases in humans previously. High rates of IAV were detected by PCR in swine lungs and oral fluids during both summer and winter seasons. Rates of IAV detection by PCR in the air were similar during summer and winter, although rates of successful virus isolation in the air were lower during summer than in winter (26% and 67%, respectively). H3N2 was the most prevalent subtype in both seasons, followed by H1N2. Genetically diverse viruses with multiple gene constellations were isolated from both winter and summer, with a total of 19 distinct genotypes identified. Comparative phylogenetic analysis of all eight segments of 40 virus isolates from summer and 122 isolates from winter revealed that the summer and winter isolates were genetically distinct, indicating IAVs are not maintained in the market, but rather are re-introduced, likely from commercial swine. These findings highlight the extent of IAV genetic diversity circulating in swine in live animal markets, even during summer months, and the ongoing risk to humans.
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Affiliation(s)
- Jayaveeramuthu Nirmala
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Jeff B Bender
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.,School of Public Health, Environmental Health Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Ruth Lynfield
- Minnesota State Health Department, St. Paul, MN, USA
| | - My Yang
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Marie Rene Culhane
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Martha Irene Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI, USA
| | - Montserrat Torremorell
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
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39
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Lauterbach SE, Nelson SW, Robinson ME, Lorbach JN, Nolting JM, Bowman AS. Assessing exhibition swine as potential disseminators of infectious disease through the detection of five respiratory pathogens at agricultural exhibitions. Vet Res 2019; 50:63. [PMID: 31533860 PMCID: PMC6749708 DOI: 10.1186/s13567-019-0684-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/27/2019] [Indexed: 11/17/2022] Open
Abstract
Widespread geographic movement and extensive comingling of exhibition swine facilitates the spread and transmission of infectious pathogens. Nasal samples were collected from 2862 pigs at 102 exhibitions and tested for five pathogens. At least one pathogen was molecularly detected in pigs at 63 (61.8%) exhibitions. Influenza A virus was most prevalent and was detected in 498 (17.4%) samples. Influenza D virus was detected in two (0.07%) samples. More than one pathogen was detected in 165 (5.8%) samples. Influenza A virus remains a top threat to animal and human health, but other pathogens may be disseminated through the exhibition swine population.
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Affiliation(s)
- Sarah E Lauterbach
- Department of Veterinary Preventive Medicine, The Ohio State University, 1920 Coffey Road, Columbus, OH, 43210, USA
| | - Sarah W Nelson
- Department of Veterinary Preventive Medicine, The Ohio State University, 1920 Coffey Road, Columbus, OH, 43210, USA
| | - Meghann E Robinson
- Health Science District, University of California Davis, 1 Garrod Drive, Davis, CA, 95616, USA
| | - Josh N Lorbach
- Department of Veterinary Preventive Medicine, The Ohio State University, 1920 Coffey Road, Columbus, OH, 43210, USA
| | - Jacqueline M Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, 1920 Coffey Road, Columbus, OH, 43210, USA
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, 1920 Coffey Road, Columbus, OH, 43210, USA.
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40
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Borkenhagen LK, Salman MD, Ma MJ, Gray GC. Animal influenza virus infections in humans: A commentary. Int J Infect Dis 2019; 88:113-119. [PMID: 31401200 DOI: 10.1016/j.ijid.2019.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/29/2019] [Accepted: 08/04/2019] [Indexed: 12/19/2022] Open
Abstract
Here we review evidence for influenza A viruses (IAVs) moving from swine, avian, feline, equine, and canine species to infect humans. We review case reports, sero-epidemiological, archeo-epidemiological, environmental, and historical studies and consider trends in livestock farming. Although this focused review is not systematic, the aggregated data point to industrialized swine farming as the most likely source of future pandemic viruses, yet IAV surveillance on such farms is remarkably sparse. We recommend increased biosafety and biosecurity training for farm administrators and swine workers with One Health-oriented virus surveillance throughout industrialized farming and meat production lines. Collaborative partnerships with human medical researchers could aid in efforts to mitigate emerging virus threats by offering new surveillance and diagnostic technologies to livestock farming industries.
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Affiliation(s)
- Laura K Borkenhagen
- Division of Infectious Diseases, School of Medicine, & Global Health Institute, Duke University, Durham, NC, USA
| | - Mo D Salman
- Animal Population Health Institute, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Mai-Juan Ma
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Gregory C Gray
- Division of Infectious Diseases, School of Medicine, & Global Health Institute, Duke University, Durham, NC, USA; Global Health Research Center, Duke Kunshan University, Kunshan, China; Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore.
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41
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Xu X, Blanton L, Elal AIA, Alabi N, Barnes J, Biggerstaff M, Brammer L, Budd AP, Burns E, Cummings CN, Garg S, Kondor R, Gubareva L, Kniss K, Nyanseor S, O'Halloran A, Rolfes M, Sessions W, Dugan VG, Fry AM, Wentworth DE, Stevens J, Jernigan D. Update: Influenza Activity in the United States During the 2018-19 Season and Composition of the 2019-20 Influenza Vaccine. MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT 2019; 68:544-551. [PMID: 31220057 PMCID: PMC6586370 DOI: 10.15585/mmwr.mm6824a3] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Influenza activity* in the United States during the 2018-19 season (September 30, 2018-May 18, 2019) was of moderate severity (1). Nationally, influenza-like illness (ILI)† activity began increasing in November, peaked during mid-February, and returned to below baseline in mid-April; the season lasted 21 weeks,§ making it the longest season in 10 years. Illness attributed to influenza A viruses predominated, with very little influenza B activity. Two waves of influenza A were notable during this extended season: influenza A(H1N1)pdm09 viruses from October 2018 to mid-February 2019 and influenza A(H3N2) viruses from February through May 2019. Compared with the 2017-18 influenza season, rates of hospitalization this season were lower for adults, but were similar for children. Although influenza activity is currently below surveillance baselines, testing for seasonal influenza viruses and monitoring for novel influenza A virus infections should continue year-round. Receiving a seasonal influenza vaccine each year remains the best way to protect against seasonal influenza and its potentially severe consequences.
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Affiliation(s)
- Xiyan Xu
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Lenee Blanton
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Anwar Isa Abd Elal
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Noreen Alabi
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - John Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Matthew Biggerstaff
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Lynnette Brammer
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Alicia P Budd
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Erin Burns
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Charisse N Cummings
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Shikha Garg
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Rebecca Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Larisa Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Krista Kniss
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Sankan Nyanseor
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Alissa O'Halloran
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Melissa Rolfes
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Wendy Sessions
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Vivien G Dugan
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Alicia M Fry
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - David E Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - James Stevens
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
| | - Daniel Jernigan
- Influenza Division, National Center for Immunization and Respiratory Diseases, CDC
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42
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Stewart RJ, Rossow J, Eckel S, Bidol S, Ballew G, Signs K, Conover JT, Burns E, Bresee JS, Fry AM, Olsen SJ, Biggerstaff M. Text-Based Illness Monitoring for Detection of Novel Influenza A Virus Infections During an Influenza A (H3N2)v Virus Outbreak in Michigan, 2016: Surveillance and Survey. JMIR Public Health Surveill 2019; 5:e10842. [PMID: 31025948 PMCID: PMC6658270 DOI: 10.2196/10842] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/13/2018] [Accepted: 12/20/2018] [Indexed: 01/23/2023] Open
Abstract
Background Rapid reporting of human infections with novel influenza A viruses accelerates detection of viruses with pandemic potential and implementation of an effective public health response. After detection of human infections with influenza A (H3N2) variant (H3N2v) viruses associated with agricultural fairs during August 2016, the Michigan Department of Health and Human Services worked with the US Centers for Disease Control and Prevention (CDC) to identify infections with variant influenza viruses using a text-based illness monitoring system. Objective To enhance detection of influenza infections using text-based monitoring and evaluate the feasibility and acceptability of the system for use in future outbreaks of novel influenza viruses. Methods During an outbreak of H3N2v virus infections among agricultural fair attendees, we deployed a text-illness monitoring (TIM) system to conduct active illness surveillance among households of youth who exhibited swine at fairs. We selected all fairs with suspected H3N2v virus infections. For fairs without suspected infections, we selected only those fairs that met predefined criteria. Eligible respondents were identified and recruited through email outreach and/or on-site meetings at fairs. During the fairs and for 10 days after selected fairs, enrolled households received daily, automated text-messages inquiring about illness; reports of illness were investigated by local health departments. To understand the feasibility and acceptability of the system, we monitored enrollment and trends in participation and distributed a Web-based survey to households of exhibitors from five fairs. Results Among an estimated 500 households with a member who exhibited swine at one of nine selected fairs, representatives of 87 (17.4%) households were enrolled, representing 392 household members. Among fairs that were ongoing when the TIM system was deployed, the number of respondents peaked at 54 on the third day of the fair and then steadily declined throughout the rest of the monitoring period; 19 out of 87 household representatives (22%) responded through the end of the 10-day monitoring period. We detected 2 H3N2v virus infections using the TIM system, which represents 17% (2/12) of all H3N2v virus infections detected during this outbreak in Michigan. Of the 70 survey respondents, 16 (23%) had participated in the TIM system. A total of 73% (11/15) participated because it was recommended by fair coordinators and 80% (12/15) said they would participate again. Conclusions Using a text-message system, we monitored for illness among a large number of individuals and households and detected H3N2v virus infections through active surveillance. Text-based illness monitoring systems are useful for detecting novel influenza virus infections when active monitoring is necessary. Participant retention and testing of persons reporting illness are critical elements for system improvement.
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Affiliation(s)
- Rebekah J Stewart
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - John Rossow
- Epidemiology Elective Program, Division of Scientific Education and Professional Development, Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA, United States.,College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Seth Eckel
- Michigan Department of Health and Human Services, Lansing, MI, United States
| | - Sally Bidol
- Michigan Department of Health and Human Services, Lansing, MI, United States
| | - Grant Ballew
- Compliant Campaign, Scottsdale, AZ, United States
| | - Kimberly Signs
- Michigan Department of Health and Human Services, Lansing, MI, United States
| | | | - Erin Burns
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joseph S Bresee
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Alicia M Fry
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sonja J Olsen
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Matthew Biggerstaff
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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43
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Prost K, Kloeze H, Mukhi S, Bozek K, Poljak Z, Mubareka S. Bioaerosol and surface sampling for the surveillance of influenza A virus in swine. Transbound Emerg Dis 2019; 66:1210-1217. [PMID: 30715792 DOI: 10.1111/tbed.13139] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/19/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022]
Abstract
Influenza A virus in swine is of significant importance to human and veterinary public health. Environmental sampling techniques that prove practical would enhance surveillance for influenza viruses in swine. The primary objective of this study was to demonstrate the feasibility of bioaerosol and surface sampling for the detection of influenza virus in swine barns with a secondary objective of piloting a mobile application for data collection. Sampling was conducted at a large swine operation between July 2016 and August 2017. Swine oral fluids and surface swabs were collected from multiple rooms. Room-level air samples were collected using four bioaerosol samplers: a low volume polytetrafluoroethylene (PTFE) filter sampler, the National Institute for Occupational Safety and Health's low volume cyclone sampler, a 2-stage Andersen impactor and/or one high volume cyclonic sampler. Samples were analysed using quantitative RT-PCR. Data and results were reported using a mobile data application. Eighty-nine composite oral fluid samples, 70 surface swabs and 122 bioaerosol samples were analysed. Detection rates for influenza virus RNA in swine barn samples were 71.1% for oral fluids, 70.8% for surface swabs and 71.1% for the PTFE sampler. Analysis revealed a statistically significant relationship between the results of the PTFE sampler and the surface swabs with oral fluid results (p < 0.001 and p < 0.01 respectively). In addition, both the PTFE sampler (p < 0.01) and surface swabs (p = 0.03) significantly correlated with, and predicted oral fluid results. Bioaerosol sampling using PTFE samplers is an effective hands-off approach for detecting influenza virus activity among swine. Further study is required for the implementation of this approach for surveillance and risk assessment of circulating influenza viruses of swine origin. In addition, mobile data collection stands to be an invaluable tool in the field by allowing secure, real-time reporting of sample collection and results.
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Affiliation(s)
- Karren Prost
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - Harold Kloeze
- Canadian Network for Public Health Intelligence, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Shamir Mukhi
- Canadian Network for Public Health Intelligence, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Katie Bozek
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - Zvonimir Poljak
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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44
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Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clin Microbiol Rev 2018; 32:32/1/e00042-18. [PMID: 30541871 DOI: 10.1128/cmr.00042-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.
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45
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Souza CK, Oldiges DP, Poeta APS, Vaz IDS, Schaefer R, Gava D, Ciacci-Zanella JR, Canal CW, Corbellini LG. Serological surveillance and factors associated with influenza A virus in backyard pigs in Southern Brazil. Zoonoses Public Health 2018; 66:125-132. [PMID: 30485723 DOI: 10.1111/zph.12542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 10/26/2018] [Accepted: 11/03/2018] [Indexed: 11/27/2022]
Abstract
Backyard pig populations are not monitored for influenza A virus (IAV) in Brazil and there are limited data about seroprevalence and risk factors in these populations. Our goal was to assess possible factors associated with IAV seroprevalence in backyard pig populations using an indirect ELISA protocol based on a recombinant nucleoprotein. Following the IAV screening using NP-ELISA, subtype-specific serology based on hemagglutination inhibition (HI) assay of the ELISA-positive pigs was conducted. The survey comprised a total of 1,667 sera samples collected in 2012 and 2014 in 479 holdings and the estimated seroprevalence was 5.3% (3.84%-7.33%) and 2.3% (1.34%-3.71%) in the respective years. In both years, H1N1pdm09 was the most prevalent subtype. The multivariable analysis showed main factors such as "age," "sex," "number of suckling pigs" and "neighbours raising pigs" that presented the greatest effect on IAV seroprevalence in these pig populations. These factors may be associated with the low biosecurity measures and management of backyard holdings. In addition, the low IAV seroprevalences found in these backyard pig populations could be related to a low number of animals in each pig holding and low animal movement/replacement that do not favour IAV transmission dynamics. This low frequency of H1N1pdm09 seropositive pigs could also be due to sporadic human-to-pig transmission of what is now a human seasonal influenza A virus; however, these factors should be explored in future studies. Herein, these results highlight the importance of IAV continued surveillance in backyard pig holdings, since it is poorly known which IAVs are circulating in these populations and the risk they could pose to public health and virus transmission to commercial farms.
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Affiliation(s)
- Carine K Souza
- Laboratório de Virologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Daiane P Oldiges
- Laboratório de Imunologia Aplicada à Sanidade Animal, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil
| | - Ana Paula S Poeta
- Laboratório de Medicina Veterinária Preventiva, Faculdade de Veterinária, UFRGS, Porto Alegre, Brazil
| | - Itabajara da S Vaz
- Laboratório de Imunologia Aplicada à Sanidade Animal, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil
| | | | | | | | - Cláudio W Canal
- Laboratório de Virologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luís G Corbellini
- Laboratório de Medicina Veterinária Preventiva, Faculdade de Veterinária, UFRGS, Porto Alegre, Brazil
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46
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Berger KA, Pigott DM, Tomlinson F, Godding D, Maurer-Stroh S, Taye B, Sirota FL, Han A, Lee RTC, Gunalan V, Eisenhaber F, Hay SI, Russell CA. The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine. Open Forum Infect Dis 2018; 5:ofy318. [PMID: 30619908 PMCID: PMC6309522 DOI: 10.1093/ofid/ofy318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/23/2018] [Indexed: 12/14/2022] Open
Abstract
Background Avian and swine influenza viruses circulate worldwide and pose threats to both animal and human health. The design of global surveillance strategies is hindered by information gaps on the geospatial variation in virus emergence potential and existing surveillance efforts. Methods We developed a spatial framework to quantify the geographic variation in outbreak emergence potential based on indices of potential for animal-to-human and secondary human-to-human transmission. We then compared our resultant raster model of variation in emergence potential with the global distribution of recent surveillance efforts from 359105 reports of surveillance activities. Results Our framework identified regions of Southeast Asia, Eastern Europe, Central America, and sub-Saharan Africa with high potential for influenza virus spillover. In the last 15 years, however, we found that 78.43% and 49.01% of high-risk areas lacked evidence of influenza virus surveillance in swine and domestic poultry, respectively. Conclusions Our work highlights priority areas where improved surveillance and outbreak mitigation could enhance pandemic preparedness strategies.
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Affiliation(s)
- Kathryn A Berger
- Department of Veterinary Medicine, University of Cambridge, United Kingdom.,Agrimetrics Ltd., Harpenden, United Kingdom
| | - David M Pigott
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | | | - David Godding
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | | | - Biruhalem Taye
- Bioinformatics Institute, ASTAR, Singapore.,European Molecular Biology Laboratory, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | | | - Alvin Han
- Bioinformatics Institute, ASTAR, Singapore.,National University of Singapore
| | | | | | - Frank Eisenhaber
- Bioinformatics Institute, ASTAR, Singapore.,National University of Singapore
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Colin A Russell
- Academic Medical Center, University of Amsterdam, The Netherlands
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47
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Saito S, Nakauchi M, Takayama I, Nagata S, Odagiri T, Kageyama T. Development and Evaluation of New Real-Time RT-PCR Assays for Identifying the Influenza A Virus Cluster IV H3N2 Variant. Jpn J Infect Dis 2018; 72:127-129. [PMID: 30381693 DOI: 10.7883/yoken.jjid.2018.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
From 2005 to July 6, 2018, a total of 435 swine-origin influenza A H3N2 variant virus (H3N2v) infections in humans were reported in the USA. The largest H3N2v outbreak in the USA occurred in 2011-2012. This virus obtained the HA gene from the human seasonal H3N2 influenza A viruses (seasonal H3N2) via human-to-swine transmission in the mid-1990s and was classified as Cluster IV H3N2v. For early detection of public health threats associated with Cluster IV H3N2v distinct from seasonal H3N2, we developed highly specific and sensitive one-step real-time RT-PCR assays directly targeting the HA genes of Cluster IV H3N2v and seasonal H3N2. These assays are useful for the systematic surveillance and identification of Cluster IV H3N2v.
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Affiliation(s)
- Shinji Saito
- Influenza Virus Research Center, National Institute of Infectious Diseases
| | - Mina Nakauchi
- Influenza Virus Research Center, National Institute of Infectious Diseases
| | - Ikuyo Takayama
- Influenza Virus Research Center, National Institute of Infectious Diseases
| | - Shiho Nagata
- Influenza Virus Research Center, National Institute of Infectious Diseases
| | - Takato Odagiri
- Influenza Virus Research Center, National Institute of Infectious Diseases
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48
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Bolton MJ, Abente EJ, Venkatesh D, Stratton JA, Zeller M, Anderson TK, Lewis NS, Vincent AL. Antigenic evolution of H3N2 influenza A viruses in swine in the United States from 2012 to 2016. Influenza Other Respir Viruses 2018; 13:83-90. [PMID: 30216671 PMCID: PMC6304321 DOI: 10.1111/irv.12610] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 12/27/2022] Open
Abstract
Background Six amino acid positions (145, 155, 156, 158, 159, and 189, referred to as the antigenic motif; H3 numbering) in the globular head region of hemagglutinin (HA1 domain) play an important role in defining the antigenic phenotype of swine Clade IV (C‐IV) H3N2 IAV, containing an H3 from a late 1990s human‐to‐swine introduction. We hypothesized that antigenicity of a swine C‐IV H3 virus could be inferred based upon the antigenic motif if it matched a previously characterized antigen with the same motif. An increasing number of C‐IV H3 genes encoding antigenic motifs that had not been previously characterized were observed in the U.S. pig population between 2012 and 2016. Objectives A broad panel of contemporary H3 viruses with uncharacterized antigenic motifs was selected across multiple clades within C‐IV to assess the impact of HA1 genetic diversity on the antigenic phenotype. Methods Hemagglutination inhibition (HI) assays were performed with isolates selected based on antigenic motif, tested against a panel of swine antisera, and visualized by antigenic cartography. Results A previously uncharacterized motif with low but sustained circulation in the swine population demonstrated a distinct phenotype from those previously characterized. Antigenic variation increased for viruses with similar antigenic motifs, likely due to amino acid substitutions outside the motif. Conclusions Although antigenic motifs were largely associated with antigenic distances, substantial diversity among co‐circulating viruses poses a significant challenge for effective vaccine development. Continued surveillance and antigenic characterization of circulating strains is critical for improving vaccine efforts to control C‐IV H3 IAV in U.S. swine.
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Affiliation(s)
- Marcus J Bolton
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa
| | - Eugenio J Abente
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa
| | - Divya Venkatesh
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jered A Stratton
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa
| | - Michael Zeller
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa.,Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Tavis K Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa
| | - Nicola S Lewis
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa
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49
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Nelson SW, Hammons CT, Bliss NT, Lauterbach SE, Zentkovich MM, Lorbach JN, Nolting JM, Bowman AS. Evaluation of nonwoven fabrics for nasal wipe sampling for influenza A virus in swine. J Vet Diagn Invest 2018; 30:920-923. [PMID: 30264670 DOI: 10.1177/1040638718803999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Influenza A virus (IAV) is a zoonotic pathogen threatening animal and public health; therefore, detection and monitoring of IAV in animal populations are critical components of a surveillance program. Swine are important hosts of IAV, wherein the virus can undergo rapid evolution. Several methods (i.e., nasal swabs, nasal wipes, and oral fluids) have been used to collect samples from swine for IAV surveillance. We utilized nasal wipes made from cotton gauze and multiple, polyester or mixed polyester fabrics to compare performance in the molecular detection and isolation of IAV. In vitro experiments revealed that no polyester or mixed polyester fabric was superior to cotton gauze for molecular IAV detection; however, 3 polyester or mixed polyester fabrics yielded significantly more viable IAV than cotton. In a field trial, both cotton gauze and the polyester or mixed polyester fabric yielded similar proportions of IAV isolates from swine. The results indicate that cotton gauze remains a practical and useful material for swine nasal wipes.
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Affiliation(s)
- Sarah W Nelson
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Christie T Hammons
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Nola T Bliss
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Sarah E Lauterbach
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Michele M Zentkovich
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Joshua N Lorbach
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Jacqueline M Nolting
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH
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50
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Lauterbach SE, Nelson SN, Nolting JM, Trujillo JD, Richt JA, Bowman AS. Evaluation of a Field-Deployable Insulated Isothermal Polymerase Chain Reaction Nucleic Acid Analyzer for Influenza A Virus Detection at Swine Exhibitions. Vector Borne Zoonotic Dis 2018; 19:212-216. [PMID: 30183529 DOI: 10.1089/vbz.2018.2345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Rapid detection of influenza A virus (IAV) at swine exhibitions, where zoonotic transmission has occurred, can allow exhibition officials to quickly implement mitigation strategies and reduce public health risk. While laboratory diagnostic methods using PCR exist, pen-side detection of IAV can reduce lag time between sample collection and results. Portable insulated isothermal PCR (RT-iiPCR) has been used for point-of-care pathogen detection in veterinary medicine. This study compared laboratory methods of real-time reverse transcription PCR (rRT-PCR) to RT-iiPCR to determine the potential effectiveness of RT-iiPCR for detection of IAV in swine in the field. Two methods of extraction (magnetic bead and spin-column) and the two PCR platforms were used in a crossover study design to detect IAV in nasal wipes of 150 individual swine from one exhibition. Magnetic bead extraction is considered the laboratory gold standard while spin-column purification is considered the field-deployable method. IAV RNA was detected in 17 samples using Mag/rRT-PCR (reference assay) and 16 samples using Mag/RT-iiPCR (Sensitivity-S 76.5%), whereas only 14 samples using Spin/rRT-PCR (S 88.2%) and 12 samples using Spin/RT-iiPCR (field method) (S 58.8%) were positive, demonstrating a reduction in detection of viral RNA using column purification. There is moderate agreement (Cohen's kappa = 0.6575) between Mag/rRT-PCR and Spin/RT-iiPCR. There is good agreement between both PCR assays when using the same method of extraction (Mag: Cohen's kappa = 0.8203, Spin: Cohen's kappa = 0.7642). RT-iiPCR requires testing of 10 more samples than the rRT-PCR to detect disease at the 95% confidence level in a population of 300 animals with a disease prevalence of 20%. In conclusion, although there is some reduction in sensitivity, RT-iiPCR used in conjunction with spin-column purification is an acceptable method of IAV in swine detection at exhibitions where it may help reduce lag time and allow for rapid control of an IAV outbreak.
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Affiliation(s)
- Sarah E Lauterbach
- 1 Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio
| | - Sarah N Nelson
- 1 Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio
| | - Jacqueline M Nolting
- 1 Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio
| | - Jessie D Trujillo
- 2 Diagnostic Medicine Pathobiology, Kansas State University, College of Veterinary Medicine, Manhattan, Kansas
| | - Jürgen A Richt
- 2 Diagnostic Medicine Pathobiology, Kansas State University, College of Veterinary Medicine, Manhattan, Kansas
| | - Andrew S Bowman
- 1 Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio
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