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Khalil AM, Yoshida R, Masatani T, Takada A, Ozawa M. Variation in the HA antigenicity of A(H1N1)pdm09-related swine influenza viruses. J Gen Virol 2021; 102. [PMID: 33616517 DOI: 10.1099/jgv.0.001569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Since the influenza pandemic in 2009, the causative agent 'A(H1N1)pdm09 virus', has been circulating in both human and swine populations. Although phylogenetic analyses of the haemagglutinin (HA) gene segment have revealed broader genetic diversity of A(H1N1)pdm09-related swine influenza A viruses (swIAVs) compared with human A(H1N1)pdm09 viruses, it remains unclear whether the genetic diversity reflects the antigenic differences in HA. To assess the impact of the diversity of the HA gene of A(H1N1)pdm09-related swIAVs on HA antigenicity, we characterized 12 swIAVs isolated in Japan from 2013 to 2018. We used a ferret antiserum and a panel of anti-HA mouse monoclonal antibodies (mAbs) raised against an early A(H1N1)pdm09 isolate. The neutralization assay with the ferret antiserum revealed that five of the 12 swIAVs were significantly different in their HA antigenicity from the early A(H1N1)pdm09 isolate. The mAbs also showed differential neutralization patterns depending on the swIAV strains. In addition, the single amino acid substitution at position 190 of HA, which was found in one of the five antigenically different swIAVs but not in human isolates, was shown to be one of the critical determinants for the antigenic difference of swIAV HAs. Two potential N-glycosylation sites at amino acid positions 185 and 276 of the HA molecule were identified in two antigenically different swIAVs. These results indicated that the genetic diversity of HA in the A(H1N1)pdm09-related swIAVs is associated with their HA antigenic variation. Our findings highlighted the need for surveillance to monitor the emergence of swIAV antigenic variants with public health importance.
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Affiliation(s)
- Ahmed Magdy Khalil
- Joint Faculty of Veterinary Medicine, Kagoshima University, Japan.,United Graduate School of Veterinary Science, Yamaguchi University, Japan.,Faculty of Veterinary Medicine, Zagazig University, Egypt
| | - Reiko Yoshida
- Research Center for Zoonosis Control, Hokkaido University, Japan
| | - Tatsunori Masatani
- United Graduate School of Veterinary Science, Yamaguchi University, Japan.,Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
| | - Ayato Takada
- Research Center for Zoonosis Control, Hokkaido University, Japan
| | - Makoto Ozawa
- United Graduate School of Veterinary Science, Yamaguchi University, Japan.,Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
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Ayim-Akonor M, Mertens E, May J, Harder T. Exposure of domestic swine to influenza A viruses in Ghana suggests unidirectional, reverse zoonotic transmission at the human-animal interface. Zoonoses Public Health 2020; 67:697-707. [PMID: 32710707 DOI: 10.1111/zph.12751] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/14/2020] [Accepted: 06/08/2020] [Indexed: 01/02/2023]
Abstract
Influenza A viruses (IAVs) have both zoonotic and anthroponotic potential and are of public and veterinary importance. Swine are intermediate hosts and 'mixing vessels' for generating reassortants, progenies of which may harbour pandemic propensity. Swine handlers are at the highest risk of becoming infected with IAVs from swine but there is little information on the ecology of IAVs at the human-animal interface in Africa. We analysed and characterized nasal and throat swabs from swine and farmers respectively, for IAVs using RT-qPCR, from swine farms in the Ashanti region, Ghana. Sera were also analysed for IAVs antibodies and serotyped using ELISA and HI assays. IAV was detected in 1.4% (n = 17/1,200) and 2.0% (n = 2/99) of swine and farmers samples, respectively. Viral subtypes H3N2 and H1N1pdm09 were found in human samples. All virus-positive swine samples were subtyped as H1N1pdm09 phylogenetically clustering closely with H1N1pdm09 that circulated among humans during the study period. Phenotypic markers that confer sensitivity to Oseltamivir were found. Serological prevalence of IAVs in swine and farmers by ELISA was 3.2% (n = 38/1,200) and 18.2% (n = 18/99), respectively. Human H1N1pdm09 and H3N2 antibodies were found in both swine and farmers sera. Indigenous swine influenza A viruses and/or antibodies were not detected in swine or farmers samples. Majority (98%, n = 147/150) of farmers reported of not wearing surgical mask and few (4%, n = 6) reported to wear gloves when working. Most (n = 74, 87.7%) farmers reported of working on the farm when experiencing influenza-like illness. Poor husbandry and biosafety practices of farmers could facilitate virus transmission across the human-swine interface. Farmers should be educated on the importance of good farm practices to mitigate influenza transmission at the human-animal interface.
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Affiliation(s)
- Matilda Ayim-Akonor
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,Department of Animal Health and Food Safety, Council for Scientific and Industrial Research-Animal Research Institute, Accra, Ghana
| | - Eva Mertens
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Timm Harder
- Institute for Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
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3
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Keay S, Poljak Z, Klapwyk M, O’Connor A, Friendship RM, O’Sullivan TL, Sargeant JM. Influenza A virus vaccine research conducted in swine from 1990 to May 2018: A scoping review. PLoS One 2020; 15:e0236062. [PMID: 32673368 PMCID: PMC7365442 DOI: 10.1371/journal.pone.0236062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/27/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Influenza A viruses of swine (IAV-S) are a global zoonotic and economic concern. Primary control is through vaccination yet a formal evidence map summarizing vaccine research conducted in pigs is not available. OBJECTIVE Ten characteristics of English language primary IAV-S vaccine research, conducted at the level of the pig or higher, were charted to identify research gaps, topics for systematic review, and coverage across different publication types. DESIGN Six online databases and grey literature were searched, without geographic, population, or study type restrictions, and abstracts screened independently and in duplicate for relevant research published between 1990 and May 2018. Full text data was charted by a single reviewer. RESULTS Over 11,000 unique citations were screened, identifying 376 for charting, including 175 proceedings from 60 conferences, and 170 journal articles from 51 journals. Reported outcomes were heterogeneous with measures of immunity (86%, n = 323) and virus detection (65%, n = 246) reported far more than production metrics (9%, n = 32). Study of transmissibility under conditions of natural exposure (n = 7), use of mathematical modelling (n = 11), and autogenous vaccine research reported in journals (n = 7), was limited. CONCLUSIONS Most research used challenge trials (n = 219) and may have poor field relevance or suitability for systematic review if the purpose is to inform clinical decisions. Literature on vaccinated breeding herds (n = 89) and weaned pigs (n = 136) is potentially sufficient for systematic review. Research under field conditions is limited, disproportionately reported in conference proceedings versus journal articles, and may be insufficient to support systematic review.
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Affiliation(s)
- Sheila Keay
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Zvonimir Poljak
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Mackenzie Klapwyk
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Annette O’Connor
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Robert M. Friendship
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Terri L. O’Sullivan
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Jan M. Sargeant
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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4
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Mon PP, Thurain K, Janetanakit T, Nasamran C, Bunpapong N, Aye AM, San YY, Tun TN, Amonsin A. Swine influenza viruses and pandemic H1N1-2009 infection in pigs, Myanmar. Transbound Emerg Dis 2020; 67:2653-2666. [PMID: 32385913 DOI: 10.1111/tbed.13616] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 11/28/2022]
Abstract
Swine influenza virus (SIV) causes respiratory diseases in pigs and has impacts on both animal and human health. In this study, we conducted swine influenza surveillance in pig farms in the Yangon and Bago regions, Myanmar, during 2017-2019. Nasal swabs (n = 500) were collected from pigs in 10 swine farms. Our results showed that 11 out of 100 pooled samples (11%) were positive for influenza A virus (IAV) by real-time RT-PCR. Five SIVs could be isolated and could be subtyped as SIV-H1N1 (n = 4) or SIV-H3N2 (n = 1). The viruses were further characterized by whole-genome sequencing and classified as pdmH1N1-2009 (n = 3), reassortant H1N1 (n = 1) or reassortant H3N2 (n = 1). Phylogenetic analysis of Myanmar SIVs showed that all genes of the three SIV-H1N1 (pdmH1N1-2009) were clustered with viruses of the pdm/09 lineage. For one SIV-H1N1 (rH1N1), the HA1 gene was clustered with those of endemic SIVs of the classical swine lineage, and seven genes were clustered with those of viruses of the pdm/09 lineage. For SIV-H3N2 (rH3N2), the HA3 and NA2 genes were clustered with those of endemic SIVs of the human-like swine lineage, while six internal genes were clustered with those of viruses of the pdm/09 lineage. Genetic analysis indicated that all the Myanmar SIVs possessed amino acids that favour binding to the human receptor. All the Myanmar SIVs contained amino acids related to amantadine resistance but not oseltamivir resistance. Notably, the pdmH1N1-2009 virus might have been circulating in the Myanmar pig population for a period of time after pdmH1N1-2009 outbreaks in humans. Then, reassortment between endemic SIV-H1N1 or SIV-H3N2 and pdmH1N1-2009 in pig farms in Myanmar could have occurred. Our findings ascertained the genetic diversity of SIVs, especially pdmH1N1-2009, in the pig population in Myanmar, with zoonotic and reverse zoonotic potentials.
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Affiliation(s)
- Pont Pont Mon
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Khin Thurain
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Taveesak Janetanakit
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Chanakarn Nasamran
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Napawan Bunpapong
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Aung Myo Aye
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Yin Yin San
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Than Naing Tun
- Livestock Breeding and Veterinary Department, Ministry of Agriculture, Livestock and Irrigation, Nay Pyi Taw, Myanmar
| | - Alongkorn Amonsin
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals (CUEIDAs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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5
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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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6
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Deng YM, Wong FYK, Spirason N, Kaye M, Beazley R, Grau MLL, Shan S, Stevens V, Subbarao K, Sullivan S, Barr IG, Dhanasekaran V. Locally Acquired Human Infection with Swine-Origin Influenza A(H3N2) Variant Virus, Australia, 2018. Emerg Infect Dis 2020; 26:143-147. [PMID: 31661057 PMCID: PMC6924914 DOI: 10.3201/eid2601.191144] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In 2018, a 15-year-old female adolescent in Australia was infected with swine influenza A(H3N2) variant virus. The virus contained hemagglutinin and neuraminidase genes derived from 1990s-like human seasonal viruses and internal protein genes from influenza A(H1N1)pdm09 virus, highlighting the potential risk that swine influenza A virus poses to human health in Australia.
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7
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Deng YM, Wong FY, Spirason N, Kaye M, Beazley R, Grau M, Shan S, Stevens V, Subbarao K, Sullivan S, Barr IG, Dhanasekaran V. Locally Acquired Human Infection with Swine-Origin Influenza A(H3N2) Variant Virus, Australia, 2018. Emerg Infect Dis 2020. [DOI: 10.3201/2601.191144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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8
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Smith DW, Barr IG, Loh R, Levy A, Tempone S, O'Dea M, Watson J, Wong FYK, Effler PV. Respiratory Illness in a Piggery Associated with the First Identified Outbreak of Swine Influenza in Australia: Assessing the Risk to Human Health and Zoonotic Potential. Trop Med Infect Dis 2019; 4:tropicalmed4020096. [PMID: 31242646 PMCID: PMC6632059 DOI: 10.3390/tropicalmed4020096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 12/15/2022] Open
Abstract
Australia was previously believed to be free of enzootic swine influenza viruses due strict quarantine practices and use of biosecure breeding facilities. The first proven Australian outbreak of swine influenza occurred in Western Australian in 2012, revealing an unrecognized zoonotic risk, and a potential future pandemic threat. A public health investigation was undertaken to determine whether zoonotic infections had occurred and to reduce the risk of further transmission between humans and swine. A program of monitoring, testing, treatment, and vaccination was commenced, and a serosurvey of workers was also undertaken. No acute infections with the swine influenza viruses were detected. Serosurvey results were difficult to interpret due to previous influenza infections and past and current vaccinations. However, several workers had elevated haemagglutination inhibition (HI) antibody levels to the swine influenza viruses that could not be attributed to vaccination or infection with contemporaneous seasonal influenza A viruses. However, we lacked a suitable control population, so this was inconclusive. The experience was valuable in developing better protocols for managing outbreaks at the human–animal interface. Strict adherence to biosecurity practices, and ongoing monitoring of swine and their human contacts is important to mitigate pandemic risk. Strain specific serological assays would greatly assist in identifying zoonotic transmission.
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Affiliation(s)
- David W Smith
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, WA 6009, Australia.
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA 6009, Australia.
| | - Ian G Barr
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Richmond Loh
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, Perth, WA 6151, Australia.
| | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, WA 6009, Australia.
| | - Simone Tempone
- Communicable Disease Control Directorate, Department of Health Western Australia, Perth, WA 6004, Australia.
| | - Mark O'Dea
- School of Veterinary Medicine, Murdoch University, Perth, WA 6150, Australia.
| | - James Watson
- CSIRO Australian Animal Health Laboratory, Geelong, VIC 3219, Australia.
| | - Frank Y K Wong
- CSIRO Australian Animal Health Laboratory, Geelong, VIC 3219, Australia.
| | - Paul V Effler
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA 6009, Australia.
- Communicable Disease Control Directorate, Department of Health Western Australia, Perth, WA 6004, Australia.
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9
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Divergent Human-Origin Influenza Viruses Detected in Australian Swine Populations. J Virol 2018; 92:JVI.00316-18. [PMID: 29875251 DOI: 10.1128/jvi.00316-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 05/28/2018] [Indexed: 11/20/2022] Open
Abstract
Global swine populations infected with influenza A viruses pose a persistent pandemic risk. With the exception of a few countries, our understanding of the genetic diversity of swine influenza viruses is limited, hampering control measures and pandemic risk assessment. Here we report the genomic characteristics and evolutionary history of influenza A viruses isolated in Australia from 2012 to 2016 from two geographically isolated swine populations in the states of Queensland and Western Australia. Phylogenetic analysis with an expansive human and swine influenza virus data set comprising >40,000 sequences sampled globally revealed evidence of the pervasive introduction and long-term establishment of gene segments derived from several human influenza viruses of past seasons, including the H1N1/1977, H1N1/1995, H3N2/1968, and H3N2/2003, and the H1N1 2009 pandemic (H1N1pdm09) influenza A viruses, and a genotype that contained gene segments derived from the past three pandemics (1968, reemerged 1977, and 2009). Of the six human-derived gene lineages, only one, comprising two viruses isolated in Queensland during 2012, was closely related to swine viruses detected from other regions, indicating a previously undetected circulation of Australian swine lineages for approximately 3 to 44 years. Although the date of introduction of these lineages into Australian swine populations could not be accurately ascertained, we found evidence of sustained transmission of two lineages in swine from 2012 to 2016. The continued detection of human-origin influenza virus lineages in swine over several decades with little or unpredictable antigenic drift indicates that isolated swine populations can act as antigenic archives of human influenza viruses, raising the risk of reemergence in humans when sufficient susceptible populations arise.IMPORTANCE We describe the evolutionary origins and antigenic properties of influenza A viruses isolated from two separate Australian swine populations from 2012 to 2016, showing that these viruses are distinct from each other and from those isolated from swine globally. Whole-genome sequencing of virus isolates revealed a high genotypic diversity that had been generated exclusively through the introduction and establishment of human influenza viruses that circulated in past seasons. We detected six reassortants with gene segments derived from human H1N1/H1N1pdm09 and various human H3N2 viruses that circulated during various periods since 1968. We also found that these swine viruses were not related to swine viruses collected elsewhere, indicating independent circulation. The detection of unique lineages and genotypes in Australia suggests that isolated swine populations that are sufficiently large can sustain influenza virus for extensive periods; we show direct evidence of a sustained transmission for at least 4 years between 2012 and 2016.
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10
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Okuya K, Matsuu A, Kawabata T, Koike F, Ito M, Furuya T, Taneno A, Akimoto S, Deguchi E, Ozawa M. Distribution of gene segments of the pandemic A(H1N1) 2009 virus lineage in pig populations. Transbound Emerg Dis 2018; 65:1502-1513. [PMID: 29732720 DOI: 10.1111/tbed.12887] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 11/28/2022]
Abstract
Swine influenza viruses (SIVs) are important not only for pig farming, but also for public health. In fact, pandemic A(H1N1) 2009 viruses [A(H1N1)pdm09] were derived from SIVs. Therefore, timely characterization of locally circulating SIVs is necessary for understanding the global status of SIVs. To genetically characterize SIVs circulating in Japanese pig populations, we isolated 24 SIVs of three subtypes (17 H1N1, four H1N2 and three H3N2 strains) from 14 pig farms in Japan from 2013 to 2016. Genetic analyses revealed that the haemagglutinin (HA) and neuraminidase (NA) genes of the 17 H1N1 and the HA gene of one H1N2, A/swine/Aichi/02/2016 (H1N2), SIVs belonged to the A(H1N1)pdm09 lineage. More importantly, all of the remaining six gene segments (i.e., PB1, PB1, PA, NP, M and NS) of the 24 SIVs, regardless of the HA and NA subtype, were also classified as belonging to the A(H1N1)pdm09 lineage. These results indicate that gene segments of A(H1N1)pdm09 lineage are widely distributed in SIVs circulating in Japanese pig populations In addition, the NA gene of A/swine/Aichi/02/2016 (H1N2) shared less than 88.5% nucleotide identity with that of the closest relative A/swine/Miyagi/5/2003 (H1N2), which was isolated in Japan in 2003. These results indicate the sustained circulation of classical H1N2-derived SIVs with remarkable diversity in the NA genes in Japanese pig populations. These findings highlight the necessity of both intensive biosecurity systems and active SIV surveillance in pig populations worldwide for both animal and public health.
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Affiliation(s)
- K Okuya
- Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - A Matsuu
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.,United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - T Kawabata
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - F Koike
- Swine Management Consultation K.K., Atsugi, Japan
| | - M Ito
- Central Livestock Hygiene Service Center of Aichi Prefecture, Okazaki, Japan
| | - T Furuya
- Kyodoken Institute for Animal Science Research & Development, Kyoto, Japan
| | - A Taneno
- Vaxxinova Japan K.K., Minato-ku, Japan
| | - S Akimoto
- Matsuoka Research Institute for Science, Koganei, Japan
| | - E Deguchi
- Laboratory of Farm Animal Production Medicine, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - M Ozawa
- Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.,Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.,United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
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11
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Molecular detection of influenza A(H1N1)pdm09 viruses with M genes from human pandemic strains among Nigerian pigs, 2013-2015: implications and associated risk factors. Epidemiol Infect 2017; 145:3345-3360. [PMID: 29166978 DOI: 10.1017/s0950268817002503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
In the post-pandemic period, influenza A(H1N1)pdm09 virus has been detected in swine populations in different parts of the world. This study was conducted to determine the presence and spatial patterns of this human pandemic virus among Nigerian pigs and identify associated risk factors. Using a two-stage stratified random sampling method, nasal swab specimens were obtained from pigs in Ibadan, Nigeria during the 2013-2014 and 2014-2015 influenza seasons, and the virus was detected by reverse transcriptase-polymerase chain reaction (RT-PCR). Purified RT-PCR products were sequenced in both directions, and sequences were aligned using MUSCLE. Phylogenetic analysis was conducted in MEGA6. Purely spatial scan statistics and a spatial lag regression model were used to identify spatial clusters and associated risk factors. The virus was detected in both seasons, with an overall prevalence of 8·7%. Phylogenetic analyses revealed that the M genes were similar to those of pandemic strains which circulated in humans prior to and during the study. Cluster analysis revealed a significant primary spatial cluster (RR = 4·71, LLR = 5·66, P = 0·0046), while 'hours spent with pigs (R 2 = 0·90, P = 0·0018)' and 'hours spent with pigs from different farms (R 2 = 0·91, P = 0·0001)' were identified as significant risk factors (P < 0·05). These findings reveal that there is considerable risk of transmission of the pandemic virus, either directly from pig handlers or through fomites, to swine herds in Ibadan, Nigeria. Active circulation of the virus among Nigerian pigs could enhance its reassortment with endemic swine influenza viruses. Campaigns for adoption of biosecurity measures in West African piggeries and abattoirs should be introduced and sustained in order to prevent the emergence of a new influenza epicentre in the sub-region.
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12
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Nelson MI, Culhane MR, Trovão NS, Patnayak DP, Halpin RA, Lin X, Shilts MH, Das SR, Detmer SE. The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States. J Gen Virol 2017; 98:2663-2675. [PMID: 29058649 DOI: 10.1099/jgv.0.000924] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Swine are a key reservoir host for influenza A viruses (IAVs), with the potential to cause global pandemics in humans. Gaps in surveillance in many of the world's largest swine populations impede our understanding of how novel viruses emerge and expand their spatial range in pigs. Although US swine are intensively sampled, little is known about IAV diversity in Canada's population of ~12 million pigs. By sequencing 168 viruses from multiple regions of Canada, our study reveals that IAV diversity has been underestimated in Canadian pigs for many years. Critically, a new H1 clade has emerged in Canada (H1α-3), with a two-amino acid deletion at H1 positions 146-147, that experienced rapid growth in Manitoba's swine herds during 2014-2015. H1α-3 viruses also exhibit a higher capacity to invade US swine herds, resulting in multiple recent introductions of the virus into the US Heartland following large-scale movements of pigs in this direction. From the Heartland, H1α-3 viruses have disseminated onward to both the east and west coasts of the United States, and may become established in Appalachia. These findings demonstrate how long-distance trading of live pigs facilitates the spread of IAVs, increasing viral genetic diversity and complicating pathogen control. The proliferation of novel H1α-3 viruses also highlights the need for expanded surveillance in a Canadian swine population that has long been overlooked, and may have implications for vaccine design.
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Affiliation(s)
- Martha I Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Nídia S Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.,Icahn School of Medicine at Mount Sinai University, New York, USA
| | | | | | - Xudong Lin
- J. Craig Venter Institute, Rockville, MD, USA
| | - Meghan H Shilts
- J. Craig Venter Institute, Rockville, MD, USA.,Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Suman R Das
- J. Craig Venter Institute, Rockville, MD, USA.,Vanderbilt University School of Medicine, Nashville, TN, USA
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13
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McAuley J, Deng YM, Gilbertson B, Mackenzie-Kludas C, Barr I, Brown L. Rapid evolution of the PB1-F2 virulence protein expressed by human seasonal H3N2 influenza viruses reduces inflammatory responses to infection. Virol J 2017; 14:162. [PMID: 28830486 PMCID: PMC5568198 DOI: 10.1186/s12985-017-0827-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/14/2017] [Indexed: 11/10/2022] Open
Abstract
Influenza A virus (IAV) PB1-F2 protein has been linked to viral virulence. Strains of the H3N2 subtype historically express full-length PB1-F2 proteins but during the 2010-2011 influenza seasons, nearly half of the circulating H3N2 IAVs encoded truncated PB1-F2 protein. Using a panel of reverse engineered H3N2 IAVs differing only in the origin of the PB1 gene segment, we found that only the virus encoding the avian-derived 1968 PB1 gene matching the human pandemic strain enhanced cellular infiltrate into the alveolar spaces of infected mice. We linked this phenomenon to expression of full-length PB1-F2 protein encompassing critical "inflammatory" residues.
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Affiliation(s)
- Julie McAuley
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, VIC, 3000, Australia.
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza (WHO-CCRRI) at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Brad Gilbertson
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Charley Mackenzie-Kludas
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza (WHO-CCRRI) at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Lorena Brown
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth St, Melbourne, VIC, 3000, Australia
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14
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Baudon E, Peyre M, Peiris M, Cowling BJ. Epidemiological features of influenza circulation in swine populations: A systematic review and meta-analysis. PLoS One 2017; 12:e0179044. [PMID: 28591202 PMCID: PMC5462427 DOI: 10.1371/journal.pone.0179044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/23/2017] [Indexed: 11/25/2022] Open
Abstract
Background The emergence of the 2009 influenza pandemic virus with a swine origin stressed the importance of improving influenza surveillance in swine populations. The objectives of this systematic review and meta-analysis were to describe epidemiological features of swine influenza (SI) across the world and identify factors impacting swine influenza virus surveillance. Methods The systematic review followed the PRISMA guidelines. Articles published after 1990 containing data on SI on pig and herd-level seroprevalence, isolation and detection rates, and risk factors were included. Meta-regression analyses using seroprevalence and virological rates were performed. Results A total of 217 articles were included. Low avian influenza (AI) seroprevalence (means pig = 4.1%; herd = 15%) was found, showing that AIV do not readily establish themselves in swine while SIV seroprevalence was usually high across continents (influenza A means pig = 32.6–87.8%; herd = 29.3–100%). Higher pig density and number of pigs per farm were shown by the meta-regression analyses and/or the risk factor articles to be associated with higher SI seroprevalence. Lower seroprevalence levels were observed for countries with low-to-medium GDP. These results suggest that larger industrial farms could be more at risk of SIV circulation. Sampling swine with influenza-like illness (ILI) was positively associated with higher isolation rates; most studies in Europe, Latin and North America were targeting swine with ILI. Conclusions To improve understanding of SI epidemiology, standardization of the design and reporting of SI epidemiological studies is desirable. Performance of SI surveillance systems in low-to-medium GDP countries should be evaluated to rule out technical issues linked to lower observed SIV prevalence. Targeting certain swine age groups, farming systems and swine with ILI may improve the surveillance cost-effectiveness. However, focusing on pigs with ILI may bias virus detection against strains less virulent for swine but which may be important as pandemic threats.
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Affiliation(s)
- Eugénie Baudon
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Animal and Integrated Risk Management Research Unit (AGIRs), French Agricultural Research Center for International Development (CIRAD), Montpellier, France
| | - Marisa Peyre
- Animal and Integrated Risk Management Research Unit (AGIRs), French Agricultural Research Center for International Development (CIRAD), Montpellier, France
| | - Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin John Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
- * E-mail:
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15
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Growth and Pathogenic Potential of Naturally Selected Reassortants after Coinfection with Pandemic H1N1 and Highly Pathogenic Avian Influenza H5N1 Viruses. J Virol 2015; 90:616-23. [PMID: 26491154 DOI: 10.1128/jvi.01572-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/05/2015] [Indexed: 01/21/2023] Open
Abstract
Coinfection of ferrets with H5N1 and pH1N1 viruses resulted in two predominate genotypes in the lungs containing surface genes of highly pathogenic avian influenza H5N1 virus in the backbone of pandemic H1N1 2009 (pH1N1). Compared to parental strains, these reassortants exhibited increased growth and virulence in vitro and in mice but failed to be transmitted indirectly to naive contact ferrets. Thus, this demonstrates a possible natural reassortment following coinfection as well as the pathogenicity of the potential reassortants.
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16
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Watson SJ, Langat P, Reid SM, Lam TTY, Cotten M, Kelly M, Van Reeth K, Qiu Y, Simon G, Bonin E, Foni E, Chiapponi C, Larsen L, Hjulsager C, Markowska-Daniel I, Urbaniak K, Dürrwald R, Schlegel M, Huovilainen A, Davidson I, Dán Á, Loeffen W, Edwards S, Bublot M, Vila T, Maldonado J, Valls L, Brown IH, Pybus OG, Kellam P. Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013. J Virol 2015; 89:9920-31. [PMID: 26202246 PMCID: PMC4577897 DOI: 10.1128/jvi.00840-15] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/14/2015] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED The emergence in humans of the A(H1N1)pdm09 influenza virus, a complex reassortant virus of swine origin, highlighted the importance of worldwide influenza virus surveillance in swine. To date, large-scale surveillance studies have been reported for southern China and North America, but such data have not yet been described for Europe. We report the first large-scale genomic characterization of 290 swine influenza viruses collected from 14 European countries between 2009 and 2013. A total of 23 distinct genotypes were identified, with the 7 most common comprising 82% of the incidence. Contrasting epidemiological dynamics were observed for two of these genotypes, H1huN2 and H3N2, with the former showing multiple long-lived geographically isolated lineages, while the latter had short-lived geographically diffuse lineages. At least 32 human-swine transmission events have resulted in A(H1N1)pdm09 becoming established at a mean frequency of 8% across European countries. Notably, swine in the United Kingdom have largely had a replacement of the endemic Eurasian avian virus-like ("avian-like") genotypes with A(H1N1)pdm09-derived genotypes. The high number of reassortant genotypes observed in European swine, combined with the identification of a genotype similar to the A(H3N2)v genotype in North America, underlines the importance of continued swine surveillance in Europe for the purposes of maintaining public health. This report further reveals that the emergences and drivers of virus evolution in swine differ at the global level. IMPORTANCE The influenza A(H1N1)pdm09 virus contains a reassortant genome with segments derived from separate virus lineages that evolved in different regions of the world. In particular, its neuraminidase and matrix segments were derived from the Eurasian avian virus-like ("avian-like") lineage that emerged in European swine in the 1970s. However, while large-scale genomic characterization of swine has been reported for southern China and North America, no equivalent study has yet been reported for Europe. Surveillance of swine herds across Europe between 2009 and 2013 revealed that the A(H1N1)pdm09 virus is established in European swine, increasing the number of circulating lineages in the region and increasing the possibility of the emergence of a genotype with human pandemic potential. It also has implications for veterinary health, making prevention through vaccination more challenging. The identification of a genotype similar to the A(H3N2)v genotype, causing zoonoses at North American agricultural fairs, underlines the importance of continued genomic characterization in European swine.
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Affiliation(s)
- Simon J Watson
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Pinky Langat
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Scott M Reid
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | | | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Michael Kelly
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | | | - Yu Qiu
- Laboratory of Virology, Ghent University, Merelbeke, Belgium
| | - Gaëlle Simon
- Anses, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France
| | - Emilie Bonin
- Anses, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France
| | - Emanuela Foni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Chiara Chiapponi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Lars Larsen
- Department of Veterinary Diagnostics and Research, Technical University of Denmark, Copenhagen, Denmark
| | - Charlotte Hjulsager
- Department of Veterinary Diagnostics and Research, Technical University of Denmark, Copenhagen, Denmark
| | | | - Kinga Urbaniak
- Department of Swine Diseases, Panstwowy Instytut Weterynaryjny, Pulawy, Poland
| | | | | | | | - Irit Davidson
- Division of Avian Diseases, Kimron Veterinary Institute, Bet Dagan, Israel
| | - Ádám Dán
- National Food Chain Safety Office, Budapest, Hungary
| | - Willie Loeffen
- Central Veterinary Institute, Wageningen UR, Lelystad, The Netherlands
| | | | - Michel Bublot
- Virology Department, Discovery Research, Merial, Lyon, France
| | - Thais Vila
- Virology Department, Discovery Research, Merial, Lyon, France
| | - Jaime Maldonado
- Veterinary Diagnostic Services DIAGNOS, Laboratorios HIPRA SA, Gerona, Spain
| | - Laura Valls
- Veterinary Diagnostic Services DIAGNOS, Laboratorios HIPRA SA, Gerona, Spain
| | - Ian H Brown
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom Division of Infection & Immunity, University College London, London, United Kingdom
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17
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Deng YM, Spirason N, Iannello P, Jelley L, Lau H, Barr IG. A simplified Sanger sequencing method for full genome sequencing of multiple subtypes of human influenza A viruses. J Clin Virol 2015; 68:43-8. [PMID: 26071334 DOI: 10.1016/j.jcv.2015.04.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/20/2015] [Accepted: 04/25/2015] [Indexed: 01/31/2023]
Abstract
BACKGROUND Full genome sequencing of influenza A viruses (IAV), including those that arise from annual influenza epidemics, is undertaken to determine if reassorting has occurred or if other pathogenic traits are present. Traditionally IAV sequencing has been biased toward the major surface glycoproteins haemagglutinin and neuraminidase, while the internal genes are often ignored. Despite the development of next generation sequencing (NGS), many laboratories are still reliant on conventional Sanger sequencing to sequence IAV. OBJECTIVES To develop a minimal and robust set of primers for Sanger sequencing of the full genome of IAV currently circulating in humans. STUDY DESIGN A set of 13 primer pairs was designed that enabled amplification of the six internal genes of multiple human IAV subtypes including the recent avian influenza A(H7N9) virus from China. Specific primers were designed to amplify the HA and NA genes of each IAV subtype of interest. Each of the primers also incorporated a binding site at its 5'-end for either a forward or reverse M13 primer, such that only two M13 primers were required for all subsequent sequencing reactions. RESULTS This minimal set of primers was suitable for sequencing the six internal genes of all currently circulating human seasonal influenza A subtypes as well as the avian A(H7N9) viruses that have infected humans in China. CONCLUSIONS This streamlined Sanger sequencing protocol could be used to generate full genome sequence data more rapidly and easily than existing influenza genome sequencing protocols.
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Affiliation(s)
- Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.
| | - Natalie Spirason
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Pina Iannello
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Lauren Jelley
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Hilda Lau
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; School of Applied and Biomedical Sciences, Federation University, Churchill, Victoria 3842, Australia
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18
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Nelson MI, Viboud C, Vincent AL, Culhane MR, Detmer SE, Wentworth DE, Rambaut A, Suchard MA, Holmes EC, Lemey P. Global migration of influenza A viruses in swine. Nat Commun 2015; 6:6696. [PMID: 25813399 PMCID: PMC4380236 DOI: 10.1038/ncomms7696] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 02/19/2015] [Indexed: 11/13/2022] Open
Abstract
The complex and unresolved evolutionary origins of the 2009 H1N1 influenza pandemic exposed major gaps in our knowledge of the global spatial ecology and evolution of influenza A viruses in swine (swIAVs). Here we undertake an expansive phylogenetic analysis of swIAV sequence data and demonstrate that the global live swine trade strongly predicts the spatial dissemination of swIAVs, with Europe and North America acting as sources of viruses in Asian countries. In contrast, China has the world’s largest swine population but is not a major exporter of live swine, and is not an important source of swIAVs in neighboring Asian countries or globally. A meta-population simulation model incorporating trade data predicts that the global ecology of swIAVs is more complex than previously thought, and the US and China’s large swine populations are unlikely to be representative of swIAV diversity in their respective geographic regions, requiring independent surveillance efforts throughout Latin America and Asia.
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Affiliation(s)
- Martha I Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Amy L Vincent
- Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa 50010, USA
| | - Marie R Culhane
- University of Minnesota Veterinary Diagnostic Laboratory, St Paul, Minnesota 55108, USA
| | - Susan E Detmer
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | | | - Andrew Rambaut
- 1] Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA [2] Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 FLT, UK [3] Centre for Immunology, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 FLT, UK
| | - Marc A Suchard
- Departments of Biomathematics, Biostatistics, and Human Genetics, University of California, Los Angeles, California 90095, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, University of Sydney, Sydney New South Wales 2006, Australia
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
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19
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Nelson MI, Vincent AL. Reverse zoonosis of influenza to swine: new perspectives on the human-animal interface. Trends Microbiol 2015; 23:142-53. [PMID: 25564096 DOI: 10.1016/j.tim.2014.12.002] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 01/09/2023]
Abstract
The origins of the 2009 influenza A (H1N1) pandemic in swine are unknown, highlighting gaps in our understanding of influenza A virus (IAV) ecology and evolution. We review how recently strengthened influenza virus surveillance in pigs has revealed that influenza virus transmission from humans to swine is far more frequent than swine-to-human zoonosis, and is central in seeding swine globally with new viral diversity. The scale of global human-to-swine transmission represents the largest 'reverse zoonosis' of a pathogen documented to date. Overcoming the bias towards perceiving swine as sources of human viruses, rather than recipients, is key to understanding how the bidirectional nature of the human-animal interface produces influenza threats to both hosts.
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Affiliation(s)
- Martha I Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Amy L Vincent
- Virus and Prion Research Unit, National Animal Disease Center, US Department of Agriculture (USDA) Agricultural Research Service (ARS), Ames, IA 50010, USA
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20
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Qiao C, Liu L, Yang H, Chen Y, Xu H, Chen H. Novel triple reassortant H1N2 influenza viruses bearing six internal genes of the pandemic 2009/H1N1 influenza virus were detected in pigs in China. J Clin Virol 2014; 61:529-34. [PMID: 25467861 DOI: 10.1016/j.jcv.2014.10.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/30/2014] [Accepted: 10/20/2014] [Indexed: 01/10/2023]
Abstract
BACKGROUND The pandemic A/H1N1 influenza viruses emerged in both Mexico and the United States in March 2009, and were transmitted efficiently in the human population. Transmissions of the pandemic 2009/H1N1 virus from humans to poultry and other species of mammals were reported from several continents during the course of the 2009 H1N1 pandemic. Reassortant H1N1, H1N2, and H3N2 viruses containing genes of the pandemic 2009/H1N1 viruses appeared in pigs in some countries. STUDY DESIGN In winter of 2012, a total of 2600 nasal swabs were collected from healthy pigs in slaughterhouses located throughout 10 provinces in China. The isolated viruses were subjected to genetic and antigenic analysis. Two novel triple-reassortant H1N2 influenza viruses were isolated from swine in China in 2012, with the HA gene derived from Eurasian avian-like swine H1N1, the NA gene from North American swine H1N2, and the six internal genes from the pandemic 2009/H1N1 viruses. The two viruses had similar antigenic features and some significant changes in antigenic characteristics emerged when compared to the previously identified isolates. CONCLUSION We inferred that the novel reassortant viruses in China may have arisen from the accumulation of the three types of influenza viruses, which further indicates that swine herds serve as "mixing vessels" for influenza viruses. Influenza virus reassortment is an ongoing process, and our findings highlight the urgent need for continued influenza surveillance among swine herds.
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Affiliation(s)
- Chuanling Qiao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Liping Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Huanliang Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Yan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Huiyang Xu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China.
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21
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Abstract
Emergence and ongoing reassortment of these viruses among animals and humans suggest potential for pandemics. The emergence and transition to pandemic status of the influenza A(H1N1)A(H1N1)pdm09) virus in 2009 illustrated the potential for previously circulating human viruses to re-emerge in humans and cause a pandemic after decades of circulating among animals. Within a short time of the initial emergence of A(H1N1)pdm09 virus, novel reassortants were isolated from swine. In late 2011, a variant (v) H3N2 subtype was isolated from humans, and by 2012, the number of persons infected began to increase with limited person-to-person transmission. During 2012 in the United States, an A(H1N2)v virus was transmitted to humans from swine. During the same year, Australia recorded its first H1N2 subtype infection among swine. The A(H3N2)v and A(H1N2)v viruses contained the matrix protein from the A(H1N1)pdm09 virus, raising the possibility of increased transmissibility among humans and underscoring the potential for influenza pandemics of novel swine-origin viruses. We report on the differing histories of A(H1N2) viruses among humans and animals.
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MESH Headings
- Animals
- Evolution, Molecular
- History, 20th Century
- History, 21st Century
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H1N2 Subtype/classification
- Influenza A Virus, H1N2 Subtype/genetics
- Influenza A Virus, H1N2 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza A virus
- Influenza, Human/epidemiology
- Influenza, Human/history
- Influenza, Human/transmission
- Orthomyxoviridae Infections
- Reassortant Viruses/classification
- Reassortant Viruses/genetics
- Reassortant Viruses/isolation & purification
- Swine
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22
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Forberg H, Hauge AG, Gjerset B, Hungnes O, Kilander A. Swine influenza in Norway: a distinct lineage of influenza A(H1N1)pdm09 virus. Influenza Other Respir Viruses 2014; 7 Suppl 4:21-6. [PMID: 24224816 DOI: 10.1111/irv.12194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Since the influenza A(H1N1)pdm09 virus was first introduced to the Norwegian pig population in September 2009, it has repeatedly been detected in pigs in Norway. No other subtypes of influenza virus are circulating in Norwegian pigs. OBJECTIVE To follow the diversity of A(H1N1)pdm09 viruses circulating in pigs in Norway and to investigate the relationship between viruses circulating in Norwegian pigs and in humans. METHODS Between January 2011 and January 2013, nasal swabs from 507 pigs were tested for A(H1N1)pdm09 virus by real-time RT-PCR. The hemagglutinin (HA) gene of virus-positive samples was sequenced and compared with publically available sequences from viruses circulating in humans at the time. RESULTS Sequencing and phylogenetic analysis of the HA gene showed that the A(H1N1)pdm09 virus circulating in Norwegian pigs early in 2011 resembled the A(H1N1)pdm09 virus circulating in humans during this time. Viruses detected in pigs by the end of 2011 had acquired four characteristic amino acid substitutions (N31D, S84I S164F, and N473D) and formed a distinct phylogenetic group. CONCLUSIONS A(H1N1)pdm09 virus detected in Norwegian pigs by the end of 2011 formed a distinct genetic lineage. Also, our findings indicate that reverse-zoonotic transmission from humans to pigs of the A(H1N1)pdm09 virus is still important.
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Affiliation(s)
- Hilde Forberg
- Section of Virology, Norwegian Veterinary Institute, Oslo, Norway
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23
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The recent establishment of North American H10 lineage influenza viruses in Australian wild waterfowl and the evolution of Australian avian influenza viruses. J Virol 2013; 87:10182-9. [PMID: 23864623 DOI: 10.1128/jvi.03437-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influenza A H10N7 virus with a hemagglutinin gene of North American origin was detected in Australian chickens and poultry abattoir workers in New South Wales, Australia, in 2010 and in chickens in Queensland, Australia, on a mixed chicken and domestic duck farm in 2012. We investigated their genomic origins by sequencing full and partial genomes of H10 viruses isolated from wild aquatic birds and poultry in Australia and analyzed them with all available avian influenza virus sequences from Oceania and representative viruses from North America and Eurasia. Our analysis showed that the H10N7 viruses isolated from poultry were similar to those that have been circulating since 2009 in Australian aquatic birds and that their initial transmission into Australia occurred during 2007 and 2008. The H10 viruses that appear to have developed endemicity in Australian wild aquatic birds were derived from several viruses circulating in waterfowl along various flyways. Their hemagglutinin gene was derived from aquatic birds in the western states of the United States, whereas the neuraminidase was closely related to that from viruses previously detected in waterfowl in Japan. The remaining genes were derived from Eurasian avian influenza virus lineages. Our analysis of virological data spanning 40 years in Oceania indicates that the long-term evolutionary dynamics of avian influenza viruses in Australia may be determined by climatic changes. The introduction and long-term persistence of avian influenza virus lineages were observed during periods with increased rainfall, whereas bottlenecks and extinction were observed during phases of widespread decreases in rainfall. These results extend our understanding of factors affecting the dynamics of avian influenza and provide important considerations for surveillance and disease control strategies.
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Vincent A, Awada L, Brown I, Chen H, Claes F, Dauphin G, Donis R, Culhane M, Hamilton K, Lewis N, Mumford E, Nguyen T, Parchariyanon S, Pasick J, Pavade G, Pereda A, Peiris M, Saito T, Swenson S, Van Reeth K, Webby R, Wong F, Ciacci-Zanella J. Review of Influenza A Virus in Swine Worldwide: A Call for Increased Surveillance and Research. Zoonoses Public Health 2013; 61:4-17. [DOI: 10.1111/zph.12049] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Indexed: 11/30/2022]
Affiliation(s)
- A. Vincent
- Virus and Prion Research Unit; USDA-ARS NADC; Ames IA USA
| | - L. Awada
- World Organization for Animal Health (OIE); Paris France
| | - I. Brown
- Animal Health and Veterinary Laboratories Agency; Weybridge UK
| | - H. Chen
- Harbin Veterinary Research Institute; Harbin China
| | - F. Claes
- Food and Agriculture Organization of the United Nations (FAO); Rome Italy
| | - G. Dauphin
- Food and Agriculture Organization of the United Nations (FAO); Rome Italy
| | | | - M. Culhane
- University of Minnesota Veterinary Diagnostic Lab; St. Paul MN USA
| | - K. Hamilton
- World Organization for Animal Health (OIE); Paris France
| | - N. Lewis
- Department of Zoology; University of Cambridge; Cambridge UK
| | - E. Mumford
- World Health Organization (WHO); Geneva Switzerland
| | - T. Nguyen
- Department of Animal Health; National Centre for Veterinary Diagnostics; Hanoi Vietnam
| | | | - J. Pasick
- Canadian Food Inspection Agency; Winnepeg Canada
| | - G. Pavade
- World Organization for Animal Health (OIE); Paris France
| | - A. Pereda
- Instituto de Virología - INTA; Buenos Aires Argentina
| | - M. Peiris
- Hong Kong University; Hong Kong City Hong Kong
| | - T. Saito
- National Institute of Animal Health; Ibaraki Japan
| | | | | | - R. Webby
- St. Jude Children's Research Hospital; Memphis TN USA
| | - F. Wong
- Australian Animal Health Laboratory; CSIRO Livestock Industries; Geelong Vic. Australia
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Matsuu A, Uchida Y, Takemae N, Mawatari T, Kasai Yoneyama S, Kasai T, Nakamura R, Eto M, Saito T. Genetic characterization of swine influenza viruses isolated in Japan between 2009 and 2012. Microbiol Immunol 2012; 56:792-803. [DOI: 10.1111/j.1348-0421.2012.00501.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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McKimm-Breschkin JL, Rootes C, Mohr PG, Barrett S, Streltsov VA. In vitro passaging of a pandemic H1N1/09 virus selects for viruses with neuraminidase mutations conferring high-level resistance to oseltamivir and peramivir, but not to zanamivir. J Antimicrob Chemother 2012; 67:1874-83. [DOI: 10.1093/jac/dks150] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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