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Lagan P, Hamil M, Cull S, Hanrahan A, Wregor RM, Lemon K. Swine influenza A virus infection dynamics and evolution in intensive pig production systems. Virus Evol 2024; 10:veae017. [PMID: 38476866 PMCID: PMC10930190 DOI: 10.1093/ve/veae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Swine influenza A virus (swIAV) is one of the main viral pathogens responsible for respiratory disease in farmed pigs. While outbreaks are often epidemic in nature, increasing reports suggest that continuous, endemic infection of herds is now common. The move towards larger herd sizes and increased intensification in the commercial pig industry may promote endemic infection; however, the impact that intensification has on swIAV infection dynamics and evolution is unclear. We carried out a longitudinal surveillance study for over 18 months on two enzootically infected, intensive, indoor, and multi-site pig production flows. Frequent sampling of all production stages using individual and group sampling methods was performed, followed by virological and immunological testing and whole-genome sequencing. We identified weaned pigs between 4 and 12-weeks old as the main reservoir of swIAV in the production flows, with continuous, year-round infection. Despite the continuous nature of viral circulation, infection levels were not uniform, with increasing exposure at the herd level associated with reduced viral prevalence followed by subsequent rebound infection. A single virus subtype was maintained on each farm for the entire duration of the study. Viral evolution was characterised by long periods of stasis punctuated by periods of rapid change coinciding with increasing exposure within the herd. An accumulation of mutations in the surface glycoproteins consistent with antigenic drift was observed, in addition to amino acid substitutions in the internal gene products as well as reassortment exchange of internal gene segments from newly introduced strains. These data demonstrate that long-term, continuous infection of herds with a single subtype is possible and document the evolutionary mechanisms utilised to achieve this.
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Affiliation(s)
- Paula Lagan
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, 12 Stoney Road, Belfast BT4 3SD, Northern Ireland
| | - Michael Hamil
- JMW Farms Ltd., 50 Hamiltonsbawn Road, Armagh BT60 1HW, Northern Ireland
| | - Susan Cull
- Craigavon Area Hospital, 68 Lurgan Road, Craigavon BT63 5QQ, Northern Ireland
| | - Anthony Hanrahan
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland
| | - Rosanna M Wregor
- JMW Farms Ltd., 50 Hamiltonsbawn Road, Armagh BT60 1HW, Northern Ireland
| | - Ken Lemon
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, 12 Stoney Road, Belfast BT4 3SD, Northern Ireland
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Opriessnig T, Gauger PC, Filippsen Favaro P, Rawal G, Magstadt DR, Digard P, Lee HM, Halbur PG. An experimental universal swine influenza a virus (IAV) vaccine candidate based on the M2 ectodomain (M2e) peptide does not provide protection against H1N1 IAV challenge in pigs. Vaccine 2024; 42:220-228. [PMID: 38087714 DOI: 10.1016/j.vaccine.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/13/2023] [Accepted: 12/02/2023] [Indexed: 01/01/2024]
Abstract
Swine flu is a common disease problem in North American pig populations and swine influenza A viruses (IAV) are extremely diverse and the lack of cross protection between heterologous strains is impacting vaccine efficacy in the field. The objective of this study was to design and test a novel swine flu vaccine targeting the M2 ectodomain (M2e) of IAV, a highly conserved region within the IAV proteome. In brief, an M2e peptide was designed to match the predominant swine IAV M2 sequence based on global analysis of sequences from pigs and humans. The resulting sequence was used to synthesize the M2e peptide coupled to a carrier protein. The final vaccine concentration was 200 µg per dose, and a commercial, microemulsion-based aqueous adjuvant was added. Nine 3-week-old IAV negative piglets were randomly assigned to three groups and rooms including non-vaccinated pigs (NEG-CONTROLs) and vaccinated pigs using the intramuscular (M2e-IM) or the intranasal route (M2e-IN). Vaccinations were done at weaning and again at 2 weeks later. An in-house enzyme-linked immunosorbent assay (ELISA) was developed and validated to study the M2e IgG antibody response and demonstrated M2e-IM pigs had a higher systemic antibody response compared to M2e-IN pigs. Subsequently, an IAV challenge study was conducted. The results indicated that M2e-IM vaccinated pigs were not protected from H1N1 (US pandemic clade, global clade 1A.3.3.2) challenge despite having a strong humoral anti-M2e immune response. In conclusion, while the experimental IAV vaccine was able to induce anti-M2e antibodies, when challenged with H1N1, the vaccinated pigs were not protected, perhaps indicating that reactivity to the M2e antigen alone is not sufficient to reduce clinical signs, lesions or shedding associated with experimental IAV challenge.
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Affiliation(s)
- Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA; Vaccines and Diagnostics Department, Moredun Research Institute, Penicuik, Edinburgh, UK.
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
| | | | - Gaurav Rawal
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
| | - Drew R Magstadt
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
| | - Paul Digard
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
| | - Hui-Min Lee
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK.
| | - Patrick G Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
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Kristensen C, Laybourn HA, Crumpton JC, Martiny K, Webb A, Ryt-Hansen P, Trebbien R, Jensen HE, Nissen JN, Skovgaard K, Webby RJ, Larsen LE. Experimental infection of pigs and ferrets with "pre-pandemic," human-adapted, and swine-adapted variants of the H1N1pdm09 influenza A virus reveals significant differences in viral dynamics and pathological manifestations. PLoS Pathog 2023; 19:e1011838. [PMID: 38048355 PMCID: PMC10721187 DOI: 10.1371/journal.ppat.1011838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 12/14/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
Influenza A viruses are RNA viruses that cause epidemics in humans and are enzootic in the pig population globally. In 2009, pig-to-human transmission of a reassortant H1N1 virus (H1N1pdm09) caused the first influenza pandemic of the 21st century. This study investigated the infection dynamics, pathogenesis, and lesions in pigs and ferrets inoculated with natural isolates of swine-adapted, human-adapted, and "pre-pandemic" H1N1pdm09 viruses. Additionally, the direct-contact and aerosol transmission properties of the three H1N1pdm09 isolates were assessed in ferrets. In pigs, inoculated ferrets, and ferrets infected by direct contact with inoculated ferrets, the pre-pandemic H1N1pdm09 virus induced an intermediary viral load, caused the most severe lesions, and had the highest clinical impact. The swine-adapted H1N1pdm09 virus induced the highest viral load, caused intermediary lesions, and had the least clinical impact in pigs. The human-adapted H1N1pdm09 virus induced the highest viral load, caused the mildest lesions, and had the least clinical impact in ferrets infected by direct contact. The discrepancy between viral load and clinical impact presumably reflects the importance of viral host adaptation. Interestingly, the swine-adapted H1N1pdm09 virus was transmitted by aerosols to two-thirds of the ferrets. Further work is needed to assess the risk of human-to-human aerosol transmission of swine-adapted H1N1pdm09 viruses.
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Affiliation(s)
- Charlotte Kristensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Helena A. Laybourn
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jeri-Carol Crumpton
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Karen Martiny
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Ashley Webb
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Pia Ryt-Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Ramona Trebbien
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Henrik E. Jensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Jakob N. Nissen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Lars E. Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Keay S, Poljak Z, Alberts F, O’Connor A, Friendship R, O’Sullivan TL, Sargeant JM. Does Vaccine-Induced Maternally-Derived Immunity Protect Swine Offspring against Influenza a Viruses? A Systematic Review and Meta-Analysis of Challenge Trials from 1990 to May 2021. Animals (Basel) 2023; 13:3085. [PMID: 37835692 PMCID: PMC10571953 DOI: 10.3390/ani13193085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
It is unclear if piglets benefit from vaccination of sows against influenza. For the first time, methods of evidence-based medicine were applied to answer the question: "Does vaccine-induced maternally-derived immunity (MDI) protect swine offspring against influenza A viruses?". Challenge trials were reviewed that were published from 1990 to April 2021 and measured at least one of six outcomes in MDI-positive versus MDI-negative offspring (hemagglutination inhibition (HI) titers, virus titers, time to begin and time to stop shedding, risk of infection, average daily gain (ADG), and coughing) (n = 15). Screening and extraction of study characteristics was conducted in duplicate by two reviewers, with data extraction and assessment for risk of bias performed by one. Homology was defined by the antigenic match of vaccine and challenge virus hemagglutinin epitopes. Results: Homologous, but not heterologous MDI, reduced virus titers in piglets. There was no difference, calculated as relative risks (RR), in infection incidence risk over the entire study period; however, infection hazard (instantaneous risk) was decreased in pigs with MDI (log HR = -0.64, 95% CI: -1.13, -0.15). Overall, pigs with MDI took about a ½ day longer to begin shedding virus post-challenge (MD = 0.51, 95% CI: 0.03, 0.99) but the hazard of infected pigs ceasing to shed was not different (log HR = 0.32, 95% CI: -0.29, 0.93). HI titers were synthesized qualitatively and although data on ADG and coughing was extracted, details were insufficient for conducting meta-analyses. Conclusion: Homology of vaccine strains with challenge viruses is an important consideration when assessing vaccine effectiveness. Herd viral dynamics are complex and may include concurrent or sequential exposures in the field. The practical significance of reduced weaned pig virus titers is, therefore, not known and evidence from challenge trials is insufficient to make inferences on the effects of MDI on incidence risk, time to begin or to cease shedding virus, coughing, and ADG. The applicability of evidence from single-strain challenge trials to field practices is limited. Despite the synthesis of six outcomes, challenge trial evidence does not support or refute vaccination of sows against influenza to protect piglets. Additional research is needed; controlled trials with multi-strain concurrent or sequential heterologous challenges have not been conducted, and sequential homologous exposure trials were rare. Consensus is also warranted on (1) the selection of core outcomes, (2) the sizing of trial populations to be reflective of field populations, (3) the reporting of antigenic characterization of vaccines, challenge viruses, and sow exposure history, and (4) on the collection of non-aggregated individual pig data.
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Affiliation(s)
- Sheila Keay
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (Z.P.); (F.A.); (R.F.); (T.L.O.); (J.M.S.)
| | - Zvonimir Poljak
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (Z.P.); (F.A.); (R.F.); (T.L.O.); (J.M.S.)
| | - Famke Alberts
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (Z.P.); (F.A.); (R.F.); (T.L.O.); (J.M.S.)
| | - Annette O’Connor
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA;
| | - Robert Friendship
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (Z.P.); (F.A.); (R.F.); (T.L.O.); (J.M.S.)
| | - Terri L. O’Sullivan
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (Z.P.); (F.A.); (R.F.); (T.L.O.); (J.M.S.)
| | - Jan M. Sargeant
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada; (Z.P.); (F.A.); (R.F.); (T.L.O.); (J.M.S.)
- Centre for Public Health and Zoonoses, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
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Yang Y, Huang Y, Huang K, Zhang Y, Hu X, Zou W, Wu C, Hui X, Li C, Zhao Y, Sun X, Zou Z, Jin M. Isolation and identification of Eurasian avian-like H1N1 swine influenza virus and evaluation of their pathogenicity and immune protective effects in pigs. Vet Microbiol 2023; 284:109827. [PMID: 37542928 DOI: 10.1016/j.vetmic.2023.109827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 08/07/2023]
Abstract
Swine influenza (SI) is a severe disease affecting pigs, with a huge economic impact on pig farmers. Currently, available SIV vaccines do not meet the requirements for Swine influenza prevention and control, indicating the need for vaccine development using predominant strains. Here, we isolated and identified the swine influenza virus in farms and slaughterhouses in nine provinces in China to determine the most prevalent strain. A total of 8383 samples were collected between 2013 and 2022, from which 87 swine influenza virus strains were isolated. Genome sequencing identified 62 strains of the H1N1 subtype, three strains of the H1N2 subtype, and 22 strains of the H3N2 subtype. The 521# strain virus possesses the viral ribonucleoprotein (vRNP) and matrix (M) genes from the pdm/09 lineage, the HA, NA from the original Eurasian avian-like (EA) H1N1 lineage, and the nonstructural (NS) gene from the triple-reassortant (TR) lineage. The 431# strain was also a TR, except its M-gene was derived from the original EA H1N1 lineage. The pathogenicity of two 431# strains and one typical 521# strain was evaluated in mice, and the 431# strain exhibited higher pathogenicity. Therefore, a new 521# strain was selected for vaccine production because it is the current circulating strain. The vaccine produced using the 521# strain and pre-evaluated adjuvants was effective against the homologous H05 strain, as evidenced by the normal body temperature of vaccinated pigs and low virus titer of nasal swabs. In contrast, infection with the H05 strain significantly increased the body temperature of unvaccinated pigs and increased the virus titer of nasal swabs. Notably, vaccination with the 521#-based vaccine conferred some level of protection against the heterologous B15 strain (H3N2 subtype), thus reducing the viral load in pigs.
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Affiliation(s)
- Ying Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China; Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Yunfu Huang
- Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China
| | - Kun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yufei Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaotong Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weihua Zou
- Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China
| | - Chao Wu
- Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China
| | - Xianfeng Hui
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengfei Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ya Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaomei Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhong Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China; Hubei Jiangxia Laboratory, Wuhan 430200, China.
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Wuhan Keqian Biological Co. Ltd., Wuhan 430200, China; Hubei Jiangxia Laboratory, Wuhan 430200, China.
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Andraud M, Hervé S, Gorin S, Barbier N, Quéguiner S, Paboeuf F, Simon G, Rose N. Evaluation of early single dose vaccination on swine influenza A virus transmission in piglets: From experimental data to mechanistic modelling. Vaccine 2023; 41:3119-3127. [PMID: 37061373 DOI: 10.1016/j.vaccine.2023.04.018] [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: 09/30/2022] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/17/2023]
Abstract
Swine influenza A virus (swIAV) is a major pathogen affecting pigs with a huge economic impact and potentially zoonotic. Epidemiological studies in endemically infected farms permitted to identify critical factors favoring on-farm persistence, among which maternally-derived antibodies (MDAs). Vaccination is commonly practiced in breeding herds and might be used for immunization of growing pigs at weaning. Althoughinterference between MDAs and vaccination was reported in young piglets, its impact on swIAV transmission was not yet quantified. To this aim, this study reports on a transmission experiment in piglets with or without MDAs, vaccinated with a single dose injection at four weeks of age, and challenged 17 days post-vaccination. To transpose small-scale experiments to real-life situation, estimated parameters were used in a simulation tool to assess their influence at the herd level. Based on a thorough follow-up of the infection chain during the experiment, the transmission of the swIAV challenge strain was highly dependent on the MDA status of the pigs when vaccinated. MDA-positive vaccinated animals showed a direct transmission rate 3.6-fold higher than the one obtained in vaccinated animals without MDAs, estimated to 1.2. Vaccination nevertheless reduced significantly the contribution of airborne transmission when compared with previous estimates obtained in unvaccinated animals. The integration of parameter estimates in a large-scale simulation model, representing a typical farrow-to-finish pig herd, evidenced an extended persistence of viral spread when vaccination of sows and single dose vaccination of piglets was hypothesized. When extinction was quasi-systematic at year 5 post-introduction in the absence of sow vaccination but with single dose early vaccination of piglets, the extinction probability fell down to 33% when batch-to-batch vaccination was implemented both in breeding herd and weaned piglets. These results shed light on a potential adverse effect of single dose vaccination in MDA-positive piglets, which might lead to longer persistence of the SwIAV at the herd level.
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Affiliation(s)
- M Andraud
- Anses, Ploufragan-Plouzané-Niort Laboratory, Epidemiology, Health and Welfare Unit, France.
| | - S Hervé
- Anses, Ploufragan-Plouzané-Niort Laboratory, Swine Virology Immunology Unit, France
| | - S Gorin
- Anses, Ploufragan-Plouzané-Niort Laboratory, Swine Virology Immunology Unit, France
| | - N Barbier
- Anses, Ploufragan-Plouzané-Niort Laboratory, Swine Virology Immunology Unit, France
| | - S Quéguiner
- Anses, Ploufragan-Plouzané-Niort Laboratory, Swine Virology Immunology Unit, France
| | - F Paboeuf
- Anses, Ploufragan-Plouzané-Niort Laboratory, SPF Pig Production and Experimentation, France
| | - G Simon
- Anses, Ploufragan-Plouzané-Niort Laboratory, Swine Virology Immunology Unit, France
| | - N Rose
- Anses, Ploufragan-Plouzané-Niort Laboratory, Epidemiology, Health and Welfare Unit, France
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Karl CA, Andres D, Carlos M, Peña M, Juan HO, Jorge O. Farm management practices, biosecurity and influenza a virus detection in swine farms: a comprehensive study in colombia. Porcine Health Manag 2022; 8:42. [PMID: 36199147 PMCID: PMC9532805 DOI: 10.1186/s40813-022-00287-6] [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] [Received: 04/27/2022] [Revised: 07/22/2022] [Accepted: 09/22/2022] [Indexed: 12/01/2022] Open
Abstract
Biosecurity protocols (BP) and good management practices are key to reduce the risk of introduction and transmission of infectious diseases into the pig farms. In this observational cross-sectional study, survey data were collected from 176 pig farms with inventories over 100 sows in Colombia. We analyzed a complex survey dataset to explore the structure and identify clustering patterns using Multiple Correspondence Analysis (MCA) of swine farms in Colombia, and estimated its association with Influenza A virus detection. Two principal dimensions contributed to 27.6% of the dataset variation. Farms with highest contribution to dimension 1 were larger farrow-to-finish farms, using self-replacement of gilts and implementing most of the measures evaluated. In contrast, farms with highest contribution to dimension 2 were medium to large farrow-to-finish farms, but implemented biosecurity in a lower degree. Additionally, two farm clusters were identified by Hierarchical Cluster Analysis (HCA), and the odds of influenza A virus detection was statistically different between clusters (OR 7.29, CI: 1.7,66, p = < 0.01). Moreover, after logistic regression analysis, three important variables were associated with higher odds of influenza detection: (1) “location in an area with a high density of pigs”, (2) “farm size”, and (3) “after cleaning and disinfecting, the facilities are allowed to dry before use”. Our results revealed two clustering patterns of swine farms. This systematic analysis of complex survey data identified relationships between biosecurity, husbandry practices and influenza status. This approach helped to identify gaps on biosecurity and key elements for designing successful strategies to prevent and control swine respiratory diseases in the swine industry.
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Affiliation(s)
- Ciuoderis-Aponte Karl
- Universidad Nacional de Colombia sede Medellín. Consortium Colombia Wisconsin One Health, Cra 75#61-85, 050034, Medellín, Colombia.
| | - Diaz Andres
- Pig Improvement Company, Hendersonville, North Carolina , USA
| | - Muskus Carlos
- Programa de Estudio y Control de Enfermedades Tropicales- PECET, Universidad de Antioquia, Medellín, Colombia
| | - Mario Peña
- Asociación Porkcolombia - Fondo nacional de la porcicultura, Bogotá, Colombia
| | - Hernández-Ortiz Juan
- Universidad Nacional de Colombia sede Medellín. Consortium Colombia Wisconsin One Health, Cra 75#61-85, 050034, Medellín, Colombia
| | - Osorio Jorge
- Department of Pathobiological sciences, University of Wisconsin-Madison. Consortium Colombia Wisconsin One Health, 53706, Madison, USA
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Ryt-Hansen P, Nielsen HG, Sørensen SS, Larsen I, Kristensen CS, Larsen LE. The role of gilts in transmission dynamics of swine influenza virus and impacts of vaccination strategies and quarantine management. Porcine Health Manag 2022; 8:19. [PMID: 35513878 PMCID: PMC9069814 DOI: 10.1186/s40813-022-00261-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Along with an expanding global swine production, the commercial housing and management of swine herds, provide an optimal environment for constant circulation of swine influenza virus (swIAV), thereby challenging farmers and veterinarian in determining optimal control measures. The aim of this study was to investigate the role of gilts in the swIAV transmission dynamics, and to evaluate the impact of different control measures such as quarantine and gilt vaccination. METHODS The study was conducted as a cross-sectional study in ten Danish sow herds, including five swIAV vaccinated and five unvaccinated herds. Blood- and nasal swab samples of gilts, first parity sows and their piglets were collected at different stages in the production system (quarantine in/out, mating, gestation and farrowing) and analyzed for the presence of swIAV and swIAV antibodies. Associations between the detection of swIAV, seroprevalence, antibody levels, sow and gilt vaccination strategy and quarantine biosecurity were thereafter investigated to identify possible risk factors for swIAV introductions and persistence within the herds. RESULTS Nine of the ten herds of the study had swIAV circulation and swIAV was detected in the quarantine, mating- and farrowing unit. The prevalence of seropositive gilts and first parity sows was significantly higher in the vaccinated herds, but swIAV was still present in nasal swabs from both gilts, first parity sows and piglets in these herds. Quarantine gilt vaccination and all-in/all-out management resulted in a significant reduction of swIAV positive gilts at the end of the quarantine period. CONCLUSION The results underline that herd vaccination and/or quarantine facilities are crucial to avoid swIAV introductions into sow herds.
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Affiliation(s)
- Pia Ryt-Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, 1870, Frederiksberg C, Denmark.
| | - Henriette Guldberg Nielsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, 1870, Frederiksberg C, Denmark
| | - Simon Smed Sørensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, 1870, Frederiksberg C, Denmark
| | - Inge Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, 1870, Frederiksberg C, Denmark
| | | | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, 1870, Frederiksberg C, Denmark
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Chrun T, Maze EA, Vatzia E, Martini V, Paudyal B, Edmans MD, McNee A, Manjegowda T, Salguero FJ, Wanasen N, Koonpaew S, Graham SP, Tchilian E. Simultaneous Infection With Porcine Reproductive and Respiratory Syndrome and Influenza Viruses Abrogates Clinical Protection Induced by Live Attenuated Porcine Reproductive and Respiratory Syndrome Vaccination. Front Immunol 2021; 12:758368. [PMID: 34858411 PMCID: PMC8632230 DOI: 10.3389/fimmu.2021.758368] [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: 08/13/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022] Open
Abstract
The porcine respiratory disease complex (PRDC) is responsible for significant economic losses in the pig industry worldwide. Porcine reproductive and respiratory syndrome virus (PRRSV) and swine influenza virus are major viral contributors to PRDC. Vaccines are cost-effective measures for controlling PRRS, however, their efficacy in the context of co-infections has been poorly investigated. In this study, we aimed to determine the effect of PRRSV-2 and swine influenza H3N2 virus co-infection on the efficacy of PRRSV modified live virus (MLV) vaccination, which is widely used in the field. Following simultaneous challenge with contemporary PRRSV-2 and H3N2 field isolates, we found that the protective effect of PRRS MLV vaccination on clinical disease and pathology was abrogated, although viral load was unaffected and antibody responses were enhanced. In contrast, co-infection in non-immunized animals reduced PRRSV-2 viremia and H3N2 virus load in the upper respiratory tract and potentiated T cell responses against both PRRSV-2 and H3N2 in the lung. Further analysis suggested that an upregulation of inhibitory cytokines gene expression in the lungs of vaccinated pigs may have influenced responses to H3N2 and PRRSV-2. These findings provide important insights into the effect of viral co-infections on PRRS vaccine efficacy that may help identify more effective vaccination strategies against PRDC in the field.
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Affiliation(s)
| | | | | | | | | | | | - Adam McNee
- The Pirbright Institute, Woking, United Kingdom
| | | | | | - Nanchaya Wanasen
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Surapong Koonpaew
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
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10
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Unterweger C, Debeerst S, Klingler E, Auer A, Redlberger-Fritz M, Stadler J, Pesch S, Lillie-Jaschniski K, Ladinig A. [Challenges in Influenza diagnostics in a swine herd - a case report]. Tierarztl Prax Ausg G Grosstiere Nutztiere 2021; 49:425-431. [PMID: 34861735 DOI: 10.1055/a-1580-6938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In a gilt producing farm in Lower Austria, respiratory diseases occurred over the previous years in self-reared gilts after being introduced into the sow herd. In addition, fertility disorders in terms of late abortions and re-breeders were observed in the fall of 2019. Nasal swabs of 3 gilts with respiratory signs and fever were tested positive for influenza A virus (IAV) subtype H1avN1 by PCR. However, examination of serum samples from these animals at 2 different time points did not detect antibodies using the standard hemagglutination inhibition (HI) test of the laboratory. Examination of additional age groups likewise failed to detect H1avN1 antibody titers. In consequence to the extension of the diagnostic panel of the HI test by 7 additional H1avN1 test antigens, a clear seroconversion of the PCR positive sows against 2 different H1avN1 isolates could be measured. In addition, high antibody titers against these 2 H1avN1 strains were also detectable in the majority of the remaining age groups tested. Following the administration of the trivalent influenza vaccine, which has been approved throughout Europe, a significant improvement of the clinical presentation in the herd was achieved. The present case report illustrates that direct and indirect pathogen detection should be used in combination for targeted influenza diagnostics. In addition, it was shown that the continuous adaptation of test antigens to the isolates circulating in the field would be extremely crucial for the significance of the HI test.
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Affiliation(s)
- Christine Unterweger
- Universitätsklinik für Schweine, Department für Nutztiere und öffentliches Gesundheitswesen in der Veterinärmedizin, Veterinärmedizinische Universität Wien
| | | | | | - Angelika Auer
- Institut für Virologie, Department für Pathobiologie, Veterinärmedizinische Universität Wien
| | | | - Julia Stadler
- Klinik für Schweine, Ludwig-Maximilians-Universität München
| | | | | | - Andrea Ladinig
- Universitätsklinik für Schweine, Department für Nutztiere und öffentliches Gesundheitswesen in der Veterinärmedizin, Veterinärmedizinische Universität Wien
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11
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Aira C, Klett-Mingo JI, Ruiz T, Garcia-Sacristán A, Martín-Valls GE, Mateu E, Gómez-Laguna J, Rueda P, González VM, Rodríguez MJ, López L. Development of an antigen Enzyme-Linked AptaSorbent Assay (ELASA) for the detection of swine influenza virus in field samples. Anal Chim Acta 2021; 1181:338933. [PMID: 34556218 DOI: 10.1016/j.aca.2021.338933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 08/04/2021] [Accepted: 08/08/2021] [Indexed: 02/08/2023]
Abstract
Influenza viruses are highly variable pathogens that infect a wide range of mammalian and avian species. According to the internal conserved proteins (nucleoprotein: NP, and matrix proteins: M), these viruses are classified into type A, B, C, and D. Influenza A virus in swine is of significant importance to the industry since it is responsible for endemic infections that lead to high economic loses derived from poor weight gain, reproductive disorders, and the role it plays in Porcine Respiratory Disease Complex (PRDC). To date, swine influenza virus (SIV) diagnosis continues to be based in complex and expensive technologies such as RT-qPCR. In this study, we aimed to improve actual tools by the implementation of aptamers as capture molecules. First, three different aptamers have been selected using as target the recombinant NP of Influenza A virus expressed in insect cells. Then, these molecules have been used for the development of an Enzyme-Linked AptaSorbent Assay (ELASA) in combination with specific monoclonal antibodies for Influenza A detection. A total of 171 field samples (nasal swabs) have been evaluated with the newly developed assay obtaining a 79.7% and 98.1% sensitivity and specificity respectively, using real time RT-PCR as standard assay. These results suggest that the assay is a promising method that could be used for Influenza A detection in analysis laboratories facilitating surveillance labours.
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Affiliation(s)
- Cristina Aira
- Eurofins-Inmunología y Genética Aplicada S.A. (Eurofins-INGENASA), Madrid, Spain.
| | | | - Tamara Ruiz
- Eurofins-Inmunología y Genética Aplicada S.A. (Eurofins-INGENASA), Madrid, Spain
| | | | | | - Enric Mateu
- Institut de Recerca I Tecnologia Alimentaria, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Jaime Gómez-Laguna
- Department of Anatomy, Comparative Pathology, and Toxicology, University of Córdoba, Córdoba, Spain
| | - Paloma Rueda
- Eurofins-Inmunología y Genética Aplicada S.A. (Eurofins-INGENASA), Madrid, Spain
| | - Víctor Manuel González
- Aptamer Group. IRYCIS-Hospital Ramón y Cajal, Madrid, Spain; Aptus Biotech SL, Madrid, Spain
| | - María José Rodríguez
- Eurofins-Inmunología y Genética Aplicada S.A. (Eurofins-INGENASA), Madrid, Spain
| | - Lissette López
- Eurofins-Inmunología y Genética Aplicada S.A. (Eurofins-INGENASA), Madrid, Spain
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12
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Ryt-Hansen P, Krog JS, Breum SØ, Hjulsager CK, Pedersen AG, Trebbien R, Larsen LE. Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses. eLife 2021; 10:60940. [PMID: 34313225 PMCID: PMC8397370 DOI: 10.7554/elife.60940] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 07/21/2021] [Indexed: 12/11/2022] Open
Abstract
Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018. In total, 3800 submissions were received with a steady increase in swIAV-positive submissions, reaching 56% in 2018. Full-genome sequences were obtained from 129 swIAV-positive samples. Altogether, 17 different circulating genotypes were identified including six novel reassortants harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx (clade 1A.3.3.2) viruses. The results provide essential data for the control of swIAV in pigs and emphasize the importance of contemporary surveillance for discovering novel swIAV strains posing a potential threat to the human population.
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Affiliation(s)
- Pia Ryt-Hansen
- Technical University of Denmark, National Veterinary Institute, Lyngby, Denmark.,University of Copenhagen, Department of Health Sciences, Institute for Animal and Veterinary Sciences, Frederiksberg, Denmark
| | | | | | | | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Lars Erik Larsen
- Technical University of Denmark, National Veterinary Institute, Lyngby, Denmark.,University of Copenhagen, Department of Health Sciences, Institute for Animal and Veterinary Sciences, Frederiksberg, Denmark
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13
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Vaccines That Reduce Viral Shedding Do Not Prevent Transmission of H1N1 Pandemic 2009 Swine Influenza A Virus Infection to Unvaccinated Pigs. J Virol 2021; 95:JVI.01787-20. [PMID: 33268518 PMCID: PMC7851569 DOI: 10.1128/jvi.01787-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/15/2020] [Indexed: 01/19/2023] Open
Abstract
Swine influenza A virus (swIAV) infection causes substantial economic loss and disease burden in humans and animals. The 2009 pandemic H1N1 (pH1N1) influenza A virus is now endemic in both populations. In this study, we evaluated the efficacy of different vaccines in reducing nasal shedding in pigs following pH1N1 virus challenge. We also assessed transmission from immunized and challenged pigs to naive, directly in-contact pigs. Pigs were immunized with either adjuvanted, whole inactivated virus (WIV) vaccines or virus-vectored (ChAdOx1 and MVA) vaccines expressing either the homologous or heterologous influenza A virus hemagglutinin (HA) glycoprotein, as well as an influenza virus pseudotype (S-FLU) vaccine expressing heterologous HA. Only two vaccines containing homologous HA, which also induced high hemagglutination inhibitory antibody titers, significantly reduced virus shedding in challenged animals. Nevertheless, virus transmission from challenged to naive, in-contact animals occurred in all groups, although it was delayed in groups of vaccinated animals with reduced virus shedding.IMPORTANCE This study was designed to determine whether vaccination of pigs with conventional WIV or virus-vectored vaccines reduces pH1N1 swine influenza A virus shedding following challenge and can prevent transmission to naive in-contact animals. Even when viral shedding was significantly reduced following challenge, infection was transmissible to susceptible cohoused recipients. This knowledge is important to inform disease surveillance and control strategies and to determine the vaccine coverage required in a population, thereby defining disease moderation or herd protection. WIV or virus-vectored vaccines homologous to the challenge strain significantly reduced virus shedding from directly infected pigs, but vaccination did not completely prevent transmission to cohoused naive pigs.
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14
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A universal RT-qPCR assay for "One Health" detection of influenza A viruses. PLoS One 2021; 16:e0244669. [PMID: 33471840 PMCID: PMC7817021 DOI: 10.1371/journal.pone.0244669] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/15/2020] [Indexed: 12/27/2022] Open
Abstract
The mutual dependence of human and animal health is central to the One Health initiative as an integrated strategy for infectious disease control and management. A crucial element of the One Health includes preparation and response to influenza A virus (IAV) threats at the human-animal interface. The IAVs are characterized by extensive genetic variability, they circulate among different hosts and can establish host-specific lineages. The four main hosts are: avian, swine, human and equine, with occasional transmission to other mammalian species. The host diversity is mirrored in the range of the RT-qPCR assays for IAV detection. Different assays are recommended by the responsible health authorities for generic IAV detection in birds, swine or humans. In order to unify IAV monitoring in different hosts and apply the One Health approach, we developed a single RT-qPCR assay for universal detection of all IAVs of all subtypes, species origin and global distribution. The assay design was centred on a highly conserved region of the IAV matrix protein (MP)-segment identified by a comprehensive analysis of 99,353 sequences. The reaction parameters were effectively optimised with efficiency of 93–97% and LOD95% of approximately ten IAV templates per reaction. The assay showed high repeatability, reproducibility and robustness. The extensive in silico evaluation demonstrated high inclusivity, i.e. perfect sequence match in the primers and probe binding regions, established as 94.6% for swine, 98.2% for avian and 100% for human H3N2, pandemic H1N1, as well as other IAV strains, resulting in an overall predicted detection rate of 99% on the analysed dataset. The theoretical predictions were confirmed and extensively validated by collaboration between six veterinary or human diagnostic laboratories on a total of 1970 specimens, of which 1455 were clinical and included a diverse panel of IAV strains.
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15
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Bhatta TR, Ryt-Hansen P, Nielsen JP, Larsen LE, Larsen I, Chamings A, Goecke NB, Alexandersen S. Infection Dynamics of Swine Influenza Virus in a Danish Pig Herd Reveals Recurrent Infections with Different Variants of the H1N2 Swine Influenza A Virus Subtype. Viruses 2020; 12:v12091013. [PMID: 32927910 PMCID: PMC7551734 DOI: 10.3390/v12091013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 12/15/2022] Open
Abstract
Influenza A virus (IAV) in swine, so-called swine influenza A virus (swIAV), causes respiratory illness in pigs around the globe. In Danish pig herds, a H1N2 subtype named H1N2dk is one of the main circulating swIAV. In this cohort study, the infection dynamic of swIAV was evaluated in a Danish pig herd by sampling and PCR testing of pigs from two weeks of age until slaughter at 22 weeks of age. In addition, next generation sequencing (NGS) was used to identify and characterize the complete genome of swIAV circulating in the herd, and to examine the antigenic variability in the antigenic sites of the virus hemagglutinin (HA) and neuraminidase (NA) proteins. Overall, 76.6% of the pigs became PCR positive for swIAV during the study, with the highest prevalence at four weeks of age. Detailed analysis of the virus sequences obtained showed that the majority of mutations occurred at antigenic sites in the HA and NA proteins of the virus. At least two different H1N2 variants were found to be circulating in the herd; one H1N2 variant was circulating at the sow and nursery sites, while another H1N2 variant was circulating at the finisher site. Furthermore, it was demonstrated that individual pigs had recurrent swIAV infections with the two different H1N2 variants, but re-infection with the same H1N2 variant was also observed. Better understandings of the epidemiology, genetic and antigenic diversity of swIAV may help to design better health interventions for the prevention and control of swIAV infections in the herds.
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Affiliation(s)
- Tarka Raj Bhatta
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC 3220, Australia;
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (P.R.-H.); (J.P.N.); (L.E.L.); (I.L.); (N.B.G.)
- Correspondence: (T.R.B.); (S.A.); Tel.: +61-0-452199095 (T.R.B.); +61-0-342159635 (S.A.)
| | - Pia Ryt-Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (P.R.-H.); (J.P.N.); (L.E.L.); (I.L.); (N.B.G.)
| | - Jens Peter Nielsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (P.R.-H.); (J.P.N.); (L.E.L.); (I.L.); (N.B.G.)
| | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (P.R.-H.); (J.P.N.); (L.E.L.); (I.L.); (N.B.G.)
| | - Inge Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (P.R.-H.); (J.P.N.); (L.E.L.); (I.L.); (N.B.G.)
| | - Anthony Chamings
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC 3220, Australia;
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
| | - Nicole B. Goecke
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; (P.R.-H.); (J.P.N.); (L.E.L.); (I.L.); (N.B.G.)
- Division for Diagnostics & Scientific Advice, National Veterinary Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Soren Alexandersen
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC 3220, Australia;
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Barwon Health, University Hospital Geelong, Geelong, VIC 3220, Australia
- Correspondence: (T.R.B.); (S.A.); Tel.: +61-0-452199095 (T.R.B.); +61-0-342159635 (S.A.)
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16
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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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17
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Chamba Pardo FO, W Allerson M, R Culhane M, B Morrison R, R Davies P, Perez A, Torremorell M. Effect of influenza A virus sow vaccination on infection in pigs at weaning: A prospective longitudinal study. Transbound Emerg Dis 2020; 68:183-193. [PMID: 32652870 DOI: 10.1111/tbed.13688] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 05/12/2020] [Accepted: 06/10/2020] [Indexed: 12/28/2022]
Abstract
Although vaccination is the main measure to control influenza A virus (IAV) in swine, there is limited information on the efficacy of sow vaccination on reducing IAV infections in pigs at weaning. We assessed the effect of sow vaccination on IAV infection in pigs at weaning in a cohort of 52 breeding herds studied prospectively. Herds were voluntarily enrolled according to their IAV history, sow vaccination protocol and monitored during six months (prospective longitudinal study). On each herd, nasal swabs were collected monthly from 30 pigs at weaning and tested for IAV by RT-PCR. IAV was detected in 25% (75/305) of sampling events. Of 9,150 nasal swab pools (3 individual nasal swabs/pool), 15% (458/3050) of pools tested IAV positive. IAV infections in pigs at weaning were lower in vaccinated herds compared to non-vaccinated ones. Moreover, no significant differences were seen between prefarrow and whole herd protocols, or the use of commercial versus autogenous IAV vaccines. Prefarrow and whole herd vaccination protocols reduced the odds of groups testing IAV positive at weaning in comparison with no vaccination. Our results are relevant when considering implementation of sow vaccination to control influenza infections in pigs at weaning and, hence, minimize transmission to growing pigs and other farms.
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Affiliation(s)
- Fabian O Chamba Pardo
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, USA
| | | | - Marie R Culhane
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, USA
| | - Robert B Morrison
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, USA
| | - Peter R Davies
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, USA
| | - Andres Perez
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, USA
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18
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Genetic Characterization of Influenza A Viruses in Japanese Swine in 2015 to 2019. J Virol 2020; 94:JVI.02169-19. [PMID: 32350072 PMCID: PMC7343197 DOI: 10.1128/jvi.02169-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 04/10/2020] [Indexed: 11/20/2022] Open
Abstract
Understanding the current status of influenza A viruses of swine (IAVs-S) and their evolution at the farm level is important for controlling these pathogens. Efforts to monitor IAVs-S during 2015 to 2019 yielded H1N1, H1N2, and H3N2 viruses. H1 genes in Japanese swine formed a unique clade in the classical swine H1 lineage of 1A.1, and H3 genes originating from 1999–2000 human seasonal influenza viruses appear to have become established among Japanese swine. A(H1N1)pdm09-derived H1 genes became introduced repeatedly and reassorted with endemic IAVs-S, resulting in various combinations of surface and internal genes among pig populations in Japan. At the farm level, multiple introductions of IAVs-S with phylogenetically distinct HA sequences occurred, or IAVs-S derived from a single introduction have persisted for at least 3 years with only a single mutation at the antigenic site of the HA protein. Continued monitoring of IAVs-S is necessary to update and maximize control strategies. To assess the current status of influenza A viruses of swine (IAVs-S) throughout Japan and to investigate how these viruses persisted and evolve on pig farms, we genetically characterized IAVs-S isolated during 2015 to 2019. Nasal swab samples collected through active surveillance and lung tissue samples collected for diagnosis yielded 424 IAVs-S, comprising 78 H1N1, 331 H1N2, and 15 H3N2 viruses, from farms in 21 sampled prefectures in Japan. Phylogenetic analyses of surface genes revealed that the 1A.1 classical swine H1 lineage has evolved uniquely since the late 1970s among pig populations in Japan. During 2015 to 2019, A(H1N1)pdm09 viruses repeatedly became introduced into farms and reassorted with endemic H1N2 and H3N2 IAVs-S. H3N2 IAVs-S isolated during 2015 to 2019 formed a clade that originated from 1999–2000 human seasonal influenza viruses; this situation differs from previous reports, in which H3N2 IAVs-S derived from human seasonal influenza viruses were transmitted sporadically from humans to swine but then disappeared without becoming established within the pig population. At farms where IAVs-S were frequently isolated for at least 3 years, multiple introductions of IAVs-S with phylogenetically distinct hemagglutinin (HA) genes occurred. In addition, at one farm, IAVs-S derived from a single introduction persisted for at least 3 years and carried no mutations at the deduced antigenic sites of the hemagglutinin protein, except for one at the antigenic site (Sa). Our results extend our understanding regarding the status of IAVs-S currently circulating in Japan and how they genetically evolve at the farm level. IMPORTANCE Understanding the current status of influenza A viruses of swine (IAVs-S) and their evolution at the farm level is important for controlling these pathogens. Efforts to monitor IAVs-S during 2015 to 2019 yielded H1N1, H1N2, and H3N2 viruses. H1 genes in Japanese swine formed a unique clade in the classical swine H1 lineage of 1A.1, and H3 genes originating from 1999–2000 human seasonal influenza viruses appear to have become established among Japanese swine. A(H1N1)pdm09-derived H1 genes became introduced repeatedly and reassorted with endemic IAVs-S, resulting in various combinations of surface and internal genes among pig populations in Japan. At the farm level, multiple introductions of IAVs-S with phylogenetically distinct HA sequences occurred, or IAVs-S derived from a single introduction have persisted for at least 3 years with only a single mutation at the antigenic site of the HA protein. Continued monitoring of IAVs-S is necessary to update and maximize control strategies.
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Ryt-Hansen P, Pedersen AG, Larsen I, Kristensen CS, Krog JS, Wacheck S, Larsen LE. Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses. Viruses 2020; 12:v12020248. [PMID: 32102230 PMCID: PMC7077184 DOI: 10.3390/v12020248] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022] Open
Abstract
The degree of antigenic drift in swine influenza A viruses (swIAV) has historically been regarded as minimal compared to that of human influenza A virus strains. However, as surveillance activities on swIAV have increased, more isolates have been characterized, revealing a high level of genetic and antigenic differences even within the same swIAV lineage. The objective of this study was to investigate the level of genetic drift in one enzootically infected swine herd over one year. Nasal swabs were collected monthly from sows (n = 4) and piglets (n = 40) in the farrowing unit, and from weaners (n = 20) in the nursery. Virus from 1-4 animals were sequenced per month. Analyses of the sequences revealed that the hemagglutinin (HA) gene was the main target for genetic drift with a substitution rate of 7.6 × 10-3 substitutions/site/year and evidence of positive selection. The majority of the mutations occurred in the globular head of the HA protein and in antigenic sites. The phylogenetic tree of the HA sequences displayed a pectinate typology, where only a single lineage persists and forms the ancestor for subsequent lineages. This was most likely caused by repeated selection of a single immune-escape variant, which subsequently became the founder of the next wave of infections.
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Affiliation(s)
- Pia Ryt-Hansen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet Building 204, DK-2800 Kongens Lyngby, Denmark
- Dpt. of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, DK-1870 Frederiksberg C, Denmark; (I.L.); (L.E.L.)
- Correspondence:
| | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kemitorvet Building 208, DK-2800 Kongens Lyngby, Denmark;
| | - Inge Larsen
- Dpt. of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, DK-1870 Frederiksberg C, Denmark; (I.L.); (L.E.L.)
| | | | - Jesper Schak Krog
- Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark;
| | - Silke Wacheck
- Ceva Santé Animale 10 Avenue de la Ballastière, 33500 Libourne, France;
| | - Lars Erik Larsen
- Dpt. of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, DK-1870 Frederiksberg C, Denmark; (I.L.); (L.E.L.)
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