1
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Vendruscolo FE, Pissetti C, de Freitas Costa E, Zanella JRC. Evaluation of nasal swab and nasal wipe for detection of Influenza A in swine using Bayesian latent class analysis. Prev Vet Med 2024; 230:106292. [PMID: 39068789 DOI: 10.1016/j.prevetmed.2024.106292] [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: 11/20/2023] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024]
Abstract
Influenza A virus (IAV) is an important pathogen in Brazilian swine herds, and monitoring the viral circulation is essential to control and reduce the transmission. Surveillance programs for IAV are often based on individual piglets level sampling, making the evaluation of the available diagnostic tools crucial to assessing IAV circulation in herds. Thus, two sample collection methodologies were compared in pig herds in southern Brazil to detect IAV by RT-qPCR: nasal swab (NS) and nasal wipe (NW). A Bayesian latent class model (BLCM) was set for two tests and two populations. The NW and NS used are more specific (higher than 95 % for both) than sensitive. The sensitivity for NW was lower than the NS, 84.14 % (70 % - 95 %; posterior probability interval (PPI): 95 %) and 87.15 % (73 % - 97 %; PPI: 95 %), respectively, and the specificity was 95 % (90 % - 99 %; PPI: 95 %) and 99 % (96 % - 100 %; PPI: 95 %), respectively. Although the wipe sample collection loses both sensitivity and specificity compared with nasal swab, differences in test performance were very limited and PPIs largely overlapped. Therefore NW can also be considered a valuable tool. The decision about the use of both techniques should be based on the trade-off between their performance limitations and feasibility in routine monitoring.
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Affiliation(s)
- Francisco Elias Vendruscolo
- Programa de Pós-Graduação em Produção e Sanidade Animal (PPGPSA), Instituto Federal Catarinense, IFC, Campus Concórdia, Concórdia, SC, Brazil.
| | - Caroline Pissetti
- Centro de Diagnóstico de Sanidade Animal, CEDISA, Concórdia, SC, Brazil.
| | - Eduardo de Freitas Costa
- Department of Epidemiology, Bioinformatics and Animal Models, Wageningen Bioveterinary Research, Lelystad, the Netherlands.
| | - Janice Reis Ciacci Zanella
- Brazilian Agricultural Research Corporation (EMBRAPA), Embrapa Swine and Poultry, Concórdia, SC, Brazil.
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2
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Encinas P, del Real G, Dutta J, Khan Z, van Bakel H, del Burgo MÁM, García-Sastre A, Nelson MI. Evolution of influenza A virus in intensive and free-range swine farms in Spain. Virus Evol 2022; 7:veab099. [PMID: 35039784 PMCID: PMC8754697 DOI: 10.1093/ve/veab099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/21/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Swine harbor genetically diverse influenza A viruses (IAVs) with the capacity to host-switch to humans, causing global pandemics. Spain is the largest swine producer in Europe and has a mixed production system that includes 'white coat' pigs raised intensively in modern buildings and free-range Iberian pigs that interface differently with humans, wildlife, and other swine. Through active longitudinal IAV surveillance in nine Spanish provinces during 2015-9, we generated forty-seven complete or near-complete genome sequences from IAVs collected from swine in both systems. Genetically diverse IAVs were identified in intensively raised white pigs and free-range Iberian pigs, including new H3N1 reassortants. Both systems are dynamic environments for IAV evolution, but driven by different processes. IAVs in white pigs were genetically related to viruses found in swine raised intensively in other European countries, reflecting high rates of viral introduction following European trade routes. In contrast, IAVs in Iberian pigs have a genetic makeup shaped by frequent introductions of human IAVs, reflecting rearing practices with high rates of human contact. Transmission between white and Iberian pigs also occurred. In conclusion, Iberian swine with high rates of human contact harbor genetically diverse IAVs and potentially serve as intermediary hosts between white pigs and humans, presenting an understudied zoonotic risk that requires further investigation.
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Affiliation(s)
- Paloma Encinas
- Department of Biotechnology, National Institute of Agricultural and Food Research and Technology (INIA, CSIC), Ctra. de La Coruña Km 7.5, Madrid 28040, Spain
| | - Gustavo del Real
- Department of Biotechnology, National Institute of Agricultural and Food Research and Technology (INIA, CSIC), Ctra. de La Coruña Km 7.5, Madrid 28040, Spain
| | - Jayeeta Dutta
- Genetics and Genomic Sciences, Hess Center for Science and Medicine, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Zenab Khan
- Genetics and Genomic Sciences, Hess Center for Science and Medicine, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Harm van Bakel
- Genetics and Genomic Sciences, Hess Center for Science and Medicine, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - M Ángeles Martín del Burgo
- Department of Biotechnology, National Institute of Agricultural and Food Research and Technology (INIA, CSIC), Ctra. de La Coruña Km 7.5, Madrid 28040, Spain
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Martha I Nelson
- Laboratory of Parasitic Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
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3
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de Lara AC, Garrido-Mantilla J, Lopez-Moreno G, Yang M, Barcellos DESN, Torremorell M. Effect of pooling udder skin wipes on the detection of influenza A virus in preweaning pigs. J Vet Diagn Invest 2021; 34:133-135. [PMID: 34404296 DOI: 10.1177/10406387211039462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Influenza A virus (IAV) active surveillance in pigs prior to weaning is commonly conducted by collecting individual samples, mostly nasal swabs. Recently, the use of udder skin wipes collected from lactating sows was identified as an effective sampling method to indicate IAV status of suckling piglets prior to weaning. However, there is limited information on the effect of pooling multiple udder wipes on the ability to detect IAV. We evaluated the effect of pooling 3, 5, or 10 udder wipes on the sensitivity of detecting IAV and compared the results with testing the wipes individually. The likelihood of detecting positive udder wipes decreased with pooling when the initial positive cycle threshold value was ≥31.5; pooling of up to 3 samples could be performed without affecting sensitivity significantly. Our results support pooling of udder skin wipes to conduct surveillance of IAV in pigs prior to weaning.
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Affiliation(s)
- Anne C de Lara
- Universidade Federal do Rio Grande do Sul, Faculdade de Veterinária, Porto Alegre, RS, Brazil
| | | | - Gustavo Lopez-Moreno
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
| | - My Yang
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
| | - David E S N Barcellos
- Universidade Federal do Rio Grande do Sul, Faculdade de Veterinária, Porto Alegre, RS, Brazil
| | - Montserrat Torremorell
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
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4
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Bakre AA, Jones LP, Bennett HK, Bobbitt DE, Tripp RA. Detection of swine influenza virus in nasal specimens by reverse transcription-loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 2021; 288:114015. [PMID: 33271254 PMCID: PMC7799534 DOI: 10.1016/j.jviromet.2020.114015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/31/2022]
Abstract
Detection of swine influenza virus (SIV) in commercial swine herds is important for understanding the infection status of the herd and for controlling disease. Current molecular diagnostics require that specimens be submitted to a laboratory which provides results to the growers after some time which is generally too late to intercede in disease control. Moreover, current diagnostic assays are time-consuming, typically costly, and require skilled technical expertise. We have instituted a reverse transcription loop-mediated isothermal amplification (RT-LAMP) diagnostic assay based on conserved regions of the SIV matrix (M) gene and H1N1 hemagglutinin (HA) sequences. The RT-LAMP assay was optimized to use both colorimetric and fluorescent endpoints and was validated. The M and HA RT-LAMP assays have a limit-of-detection (LOD) sensitive to 11 and 8-log-fold dilutions of viral RNA, respectively, and are capable of discriminating between H1 and H3 strains of SIV. Additionally, the RT-LAMP assay was optimized for direct amplification of SIV from field samples without the need for viral RNA isolation. The direct RT-LAMP detected >86 % of qRT-PCR validated SIV samples, and >66 % of negative samples when spiked with viral RNA or SIV. The diagnostic RT-LAMP assay is a rapid, sensitive, specific, and cost-effective method for the detection of SIV in herds substantially aiding diagnosis and surveillance.
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Affiliation(s)
- Abhijeet A Bakre
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Les P Jones
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Hailey K Bennett
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Davis E Bobbitt
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Ralph A Tripp
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.
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5
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Bakre AA, Jones LP, Kyriakis CS, Hanson JM, Bobbitt DE, Bennett HK, Todd KV, Orr-Burks N, Murray J, Zhang M, Steinhauer DA, Byrd-Leotis L, Cummings RD, Fent J, Coffey T, Tripp RA. Molecular epidemiology and glycomics of swine influenza viruses circulating in commercial swine farms in the southeastern and midwest United States. Vet Microbiol 2020; 251:108914. [PMID: 33181438 DOI: 10.1016/j.vetmic.2020.108914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022]
Abstract
Tracking the genetic diversity and spread of swine influenza viruses (SIVs) in commercial swine farms is central for control and to reduce the potential emergence of SIV reassortants. We analyzed the diversity of SIVs in nasal washes or oral fluids from commercial swine farms in North Carolina using influenza M qRT-PCR and hemagglutinin (HA) and neuraminidase (NA) subtyping. We found a predominance of H1 HAs and N2 NAs in the samples examined. The majority of the H1 HAs could be further classified into gamma and delta subclusters. We also identified HAs of the H1 alpha cluster, and those of human novel pandemic origin. Glycan binding profiles from a representative subset of these viruses revealed broad α2,6 sialylated glycan recognition, though some strains exhibited the ability to bind to α2,3 sialic acid. These data show that SIV surveillance can aid our understanding of viral transmission dynamics and help uncover the diversity at the human-swine interface.
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Affiliation(s)
| | - Les P Jones
- Department of Infectious Diseases, Athens, GA, United States
| | | | - Jarod M Hanson
- Department of Infectious Diseases, Athens, GA, United States
| | - Davis E Bobbitt
- Department of Infectious Diseases, Athens, GA, United States
| | | | - Kyle V Todd
- Department of Infectious Diseases, Athens, GA, United States
| | | | - Jackelyn Murray
- Department of Infectious Diseases, Athens, GA, United States
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, United States
| | | | | | - Richard D Cummings
- Beth Israel Deaconess Medical Center, Department of Surgery and Harvard Medical School Center for Glycoscience, Harvard Medical School, Boston, MA, United States
| | - Joseph Fent
- Smithfield Foods, Rose Hill, NC, United States
| | | | - Ralph A Tripp
- Department of Infectious Diseases, Athens, GA, United States.
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6
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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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7
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Li C, Culhane MR, Cheeran M, Galina Pantoja L, Jansen ML, Amodie D, Mellencamp MA, Torremorell M. Exploring heterologous prime-boost vaccination approaches to enhance influenza control in pigs. Vet Res 2020; 51:89. [PMID: 32646490 PMCID: PMC7344353 DOI: 10.1186/s13567-020-00810-z] [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: 02/14/2020] [Accepted: 06/11/2020] [Indexed: 12/23/2022] Open
Abstract
Influenza A viruses evolve rapidly to escape host immunity. In swine, this viral evolution has resulted in the emergence of multiple H1 and H3 influenza A virus (IAV) lineages in the United States (US) pig populations. The heterologous prime-boost vaccination strategy is a promising way to deal with diverse IAV infection in multiple animal models. However, whether or not this vaccination strategy is applicable to US swine to impart immunity against infection from North American strains of IAV is still unknown. We performed a vaccination-challenge study to evaluate the protective efficacy of using multivalent inactivated vaccine and/or a live attenuated IAV vaccine (LAIV) in pigs following multiple prime-boost vaccination protocols against a simultaneous H1N1 and H3N2 IAV infection. Our data show that pigs in the heterologous prime-boost vaccination group had more favorable outcomes consistent with a better response against virus challenge than non-vaccinated pigs. Additionally, delivering a multivalent heterologous inactivated vaccine boost to pigs following a single LAIV administration was also beneficial. We concluded the heterologous prime boost vaccination strategy may potentiate responses to suboptimal immunogens and holds the potential applicability to control IAV in the North American swine industry. However, more studies are needed to validate the application of this vaccination approach under field conditions.
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Affiliation(s)
- Chong Li
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Marie R Culhane
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Maxim Cheeran
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
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8
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Haach V, Gava D, Cantão ME, Schaefer R. Evaluation of two multiplex RT-PCR assays for detection and subtype differentiation of Brazilian swine influenza viruses. Braz J Microbiol 2020; 51:1447-1451. [PMID: 32125678 DOI: 10.1007/s42770-020-00250-z] [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: 09/19/2019] [Accepted: 02/20/2020] [Indexed: 11/27/2022] Open
Abstract
Influenza A virus (IAV) subtypes H1N1, H1N2, and H3N2 are endemic in swine herds in most pork producing countries; however, the viruses circulating in different geographic regions are antigenically and genetically distinct. In this sense, the availability of a rapid diagnostic assay to detect locally adapted IAVs and discriminate the virus subtype in clinical samples from swine is extremely important for monitoring and control of the disease. This study describes the development and validation of a multiplex RT-PCR assay for detection and subtyping of IAV from pigs. The analytical and diagnostic specificity of the assays was 100% (94.3-100.0, CI 95%), and the limit of detection was 10-3 TCID50/mL. A total of 100 samples (IAV isolates and clinical specimens) were tested, and the virus subtype was determined for 80 samples (80%; 71.1-86.7, CI 95%). From these, 50% were H1N1, 22.5% were H1N2, and 7.5% were H3N2. Partial subtyping was determined for 8.75% samples (H1pdmNx and HxN2). Additionally, mixed infections with two virus subtypes (H1N2 + H3N2 and H1N1pdm + H1pdmN2; 2.5%) and reassortant viruses (H1pdmN2, 6.25%; and H1N1hu, 2.5%) were detected by the assay. A rapid detection of the most prevalent IAV subtypes and lineages in swine is provided by the assays developed here, improving the IAV diagnosis in Brazilian laboratories, and contributing to the IAV monitoring.
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Affiliation(s)
- Vanessa Haach
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, 500, Porto Alegre, Rio Grande do Sul, CEP 90050-170, Brazil
| | - Danielle Gava
- Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, Santa Catarina, CEP 89715-899, Brazil
| | - Maurício Egídio Cantão
- Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, Santa Catarina, CEP 89715-899, Brazil
| | - Rejane Schaefer
- Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, Santa Catarina, CEP 89715-899, Brazil.
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9
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Zhang H, Wang Y, Porter E, Lu N, Li Y, Yuan F, Lohman M, Noll L, Zheng W, Stoy C, Lang Y, Huber VC, Ma W, Peddireddi L, Fang Y, Shi J, Anderson G, Liu X, Bai J. Development of a multiplex real-time RT-PCR assay for simultaneous detection and differentiation of influenza A, B, C, and D viruses. Diagn Microbiol Infect Dis 2019; 95:59-66. [PMID: 31130238 PMCID: PMC6697560 DOI: 10.1016/j.diagmicrobio.2019.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 01/18/2023]
Abstract
Influenza is a common and contagious respiratory disease caused by influenza A, B, C, and D viruses (IAV, IBV, ICV, and IDV). A multiplex real-time RT-PCR assay was developed for simultaneous detection of IAV, IBV, ICV, and IDV. The assay was designed to target unique sequences in the matrix gene of IBV and ICV, the RNA polymerase subunit PB1 of IDV, and combined with USDA and CDC IAV assays, both target the matrix gene. The host 18S rRNA gene was included as an internal control. In silico analyses indicated high strain coverages: 97.9% for IBV, 99.5% for ICV, and 100% for IDV. Transcribed RNA, viral isolates and clinical samples were used for validation. The assay specifically detected target viruses without cross-reactivity, nor detection of other common pathogens. The limit of detection was approximately 30 copies for each viral RNA template, which was equivalent to a threshold cycle value of ~37.
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Affiliation(s)
- Hewei Zhang
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; College of Food and Drugs, Luoyang Polytechnic, Luo Yang, Henan, China
| | - Yin Wang
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Elizabeth Porter
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Nanyan Lu
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yanhua Li
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Fangfeng Yuan
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Molly Lohman
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Wanglong Zheng
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Colin Stoy
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yuekun Lang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Victor C Huber
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD, USA
| | - Wenjun Ma
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Lalitha Peddireddi
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Ying Fang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jishu Shi
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Gary Anderson
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Xuming Liu
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
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10
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Nelson MI, Souza CK, Trovão NS, Diaz A, Mena I, Rovira A, Vincent AL, Torremorell M, Marthaler D, Culhane MR. Human-Origin Influenza A(H3N2) Reassortant Viruses in Swine, Southeast Mexico. Emerg Infect Dis 2019; 25:691-700. [PMID: 30730827 PMCID: PMC6433011 DOI: 10.3201/eid2504.180779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The genetic diversity of influenza A viruses circulating in swine in Mexico complicates control efforts in animals and presents a threat to humans, as shown by influenza A(H1N1)pdm09 virus. To describe evolution of swine influenza A viruses in Mexico and evaluate strains for vaccine development, we sequenced the genomes of 59 viruses and performed antigenic cartography on strains from 5 regions. We found that genetic and antigenic diversity were particularly high in southeast Mexico because of repeated introductions of viruses from humans and swine in other regions in Mexico. We identified novel reassortant H3N2 viruses with genome segments derived from 2 different viruses that were independently introduced from humans into swine: pandemic H1N1 viruses and seasonal H3N2 viruses. The Mexico swine viruses are antigenically distinct from US swine lineages. Protection against these viruses is unlikely to be afforded by US virus vaccines and would require development of new vaccines specifically targeting these diverse strains.
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11
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Haach V, Gava D, Mauricio EC, Franco AC, Schaefer R. One-step multiplex RT-qPCR for the detection and subtyping of influenza A virus in swine in Brazil. J Virol Methods 2019; 269:43-48. [PMID: 30959063 DOI: 10.1016/j.jviromet.2019.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 11/19/2022]
Abstract
Pandemic H1N1, human-like H1N2 and H3N2 influenza A (IAV) viruses are co-circulating in swine herds in Brazil. The genetic analysis of the Brazilian IAVs has shown that they are genetically distinct from viruses found in swine in other countries; therefore, an update of the diagnostic assays for IAV detection and subtyping is needed. This study describes the development and validation of a TaqMan based - one-step multiplex RT-qPCR to discriminate the hemagglutinin and neuraminidase genes of the three major IAV subtypes circulating in pigs in Brazil. The RT-qPCR assays presented 100% (95.7-100, CI 95%) of diagnostic sensitivity in the analysis of 85 IAVs, previously characterized by sequencing. The limits of detection ranged from 5.09 × 101 to 5.09 × 103 viral RNA copies/μL. For the analytical specificity, 73 pig samples collected during 2017 and 2018 were analyzed, resulting in the identification of the subtype in 74.0% (62.9-82.7, CI 95%) of samples. From these, 46.3% were H3N2, 33.3% were H1N1, 11.1% were H1N2 and 3.7% were HxN1. Mixed viral infections (3.7%) and reassortant viruses (1.9%) were also detected by the test. This multiplex RT-qPCR assay provides a fast and specific diagnostic tool for identification of different subtypes and lineages of IAV in pigs, contributing to the monitoring of influenza in swine.
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Affiliation(s)
- Vanessa Haach
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, 500, Porto Alegre, CEP 90050-170, Rio Grande do Sul, Brazil
| | - Danielle Gava
- Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, CEP 89715-899, Santa Catarina, Brazil
| | - Egídio Cantão Mauricio
- Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, CEP 89715-899, Santa Catarina, Brazil
| | - Ana Cláudia Franco
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, 500, Porto Alegre, CEP 90050-170, Rio Grande do Sul, Brazil
| | - Rejane Schaefer
- Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, CEP 89715-899, Santa Catarina, Brazil.
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Nelson MI, Souza C, Trovão NS, Diaz A, Mena I, Rovira A, Vincent AL, Torremorell M, Marthaler D, Culhane MR. Human-Origin Influenza A(H3N2) Reassortant Viruses in Swine, Southeast Mexico. Emerg Infect Dis 2019. [DOI: 10.3201/eid2503.180779] [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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13
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Chamba Pardo FO, Wayne S, Culhane MR, Perez A, Allerson M, Torremorell M. Effect of strain-specific maternally-derived antibodies on influenza A virus infection dynamics in nursery pigs. PLoS One 2019; 14:e0210700. [PMID: 30640929 PMCID: PMC6331129 DOI: 10.1371/journal.pone.0210700] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 12/31/2018] [Indexed: 12/25/2022] Open
Abstract
Reducing the number of influenza A virus (IAV) infected pigs at weaning is critical to minimize IAV spread to other farms. Sow vaccination is a common measure to reduce influenza levels at weaning. However, the impact of maternally-derived antibodies on IAV infection dynamics in growing pigs is poorly understood. We evaluated the effect of maternally-derived antibodies at weaning on IAV prevalence at weaning, time of influenza infection, number of weeks that pigs tested IAV positive, and estimated quantity of IAV in nursery pigs. We evaluated 301 pigs within 10 cohorts for their influenza serological (seroprevalence estimated by hemagglutination inhibition (HI) test) and virological (prevalence) status. Nasal swabs were collected weekly and pigs were bled 3 times throughout the nursery period. There was significant variability in influenza seroprevalence, HI titers and influenza prevalence after weaning. Increase in influenza seroprevalence at weaning was associated with low influenza prevalence at weaning and delayed time to IAV infection throughout the nursery. Piglets with IAV HI titers of 40 or higher at weaning were also less likely to test IAV positive at weaning, took longer to become infected, tested IAV RT-PCR positive for fewer weeks, and had higher IAV RT-PCR cycle threshold values compared to piglets with HI titers less than 40. Our findings suggest that sow vaccination or infection status that results in high levels of IAV strain-specific maternally-derived antibodies may help to reduce IAV circulation in both suckling and nursery pigs.
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Affiliation(s)
| | - Spencer Wayne
- Health Services, Pipestone Veterinary Services, Pipestone, MN, United States of America
| | - Marie Rene Culhane
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, United States of America
| | - Andres Perez
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, United States of America
| | - Matthew Allerson
- Health and Research Division, Holden Farms Inc., Northfield, MN, United States of America
| | - Montserrat Torremorell
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, United States of America
- * E-mail:
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Almeida MN, Zimmerman JJ, Wang C, Linhares DCL. Assessment of abattoir based monitoring of PRRSV using oral fluids. Prev Vet Med 2018; 158:137-145. [PMID: 30220387 DOI: 10.1016/j.prevetmed.2018.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 07/12/2018] [Accepted: 08/07/2018] [Indexed: 02/06/2023]
Abstract
Various porcine reproductive and respiratory syndrome virus (PRRSV) regional elimination projects have been implemented in the U.S., but none have yet succeeded. In part, this reflects the need for efficient methods to monitor over time the progress of PRRSV status of participating herds. This study assessed the feasibility of monitoring PRRSV using oral fluids collected at the abattoir. A total of 36 pig lots were included in the study. On-farm oral fluid (n = 10) and serum (n = 10) collected within two days of shipment to the abattoir were used to establish the reference PRRSV status of the population. Oral fluids (n = 3 per lot) were successfully collected from 32 lots (89%) at the lairage. Three veterinary diagnostic laboratories (VDLs) tested the sera (VDL1 and VDL3: n = 316, VDL2: n = 315) and oral fluids (VDL1 and VDL3: n = 319, VDL2: n = 320) for PRRSV antibodies (ELISA) and RNA (rRT-PCR). Environmental samples (n = 64, 32 before and 32 after pigs were placed in lairage) were tested for PRRSV RNA at one VDL. All oral fluids (farm and abattoir) tested positive for PRRSV antibody at all VDLs. PRRSV positivity frequency on serum ranged from 92.4% to 94.6% among VDLs, with an overall agreement of 97.6%. RNA was detected on 1.3% to 1.9%, 8.1% to 17.7%, and 8.3% to 17.7% of sera, on-farm and abattoir oral fluids, respectively. Between-VDLs rRT-PCR agreement on sera and oral fluids (farm and abattoir) ranged from 97.8% to 99.0%, and 79.0% to 81.2%, respectively. Between-locations agreement of oral fluids varied from 31.3% to 50% depending on the VDL. This study reported the application of swine oral fluids collected at the abattoir for monitoring PRRSV, and describes the between-VDL agreement for PRRS testing of serum and oral fluid field samples.
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Affiliation(s)
- M N Almeida
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States
| | - J J Zimmerman
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States
| | - C Wang
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States
| | - D C L Linhares
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States.
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Haach V, Gava D, Coldebella A, Schaefer R. INFLUÊNCIA DAS CONDIÇÕES DE ARMAZENAMENTO DO VÍRUS INFLUENZA NA DETECÇÃO POR RT-qPCR E ISOLAMENTO VIRAL. CIÊNCIA ANIMAL BRASILEIRA 2018. [DOI: 10.1590/1809-6891v19e-46789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Resumo A infecção de suínos pelo vírus influenza causa perdas significativas na suinocultura e a doença tem implicações consideráveis para a saúde pública. Dessa forma, a rápida detecção viral em amostras biológicas de suínos é importante para a vigilância da influenza. Para o diagnóstico, as condições de manutenção das amostras biológicas (modo de acondicionamento, temperatura e período de acondicionamento), desde a colheita das amostras de suínos até o envio ao laboratório, podem interferir negativamente na detecção viral. Neste estudo foi analisada a viabilidade de uma amostra do vírus influenza A H1N1/2009 isolada de suínos, mantida em diferentes modos de acondicionamento (meio comercial UTM, meio in house VTM e sem meio de manutenção) e diferentes temperaturas (4, 23 e 37 °C) por um período de até 120 horas. As amostras foram avaliadas por RT-qPCR e isolamento em ovos embrionados. Foram observados efeitos significativos (p<0,05) para o modo e período de acondicionamento e da interação entre esses dois fatores com a carga viral. Dessa forma, as amostras biológicas enviadas para diagnóstico de influenza devem ser armazenadas, preferencialmente, em meio de manutenção viral a 4 °C e o tempo decorrido entre a colheita da amostra e a chegada ao laboratório deve ser de, no máximo, três dias.
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Houston DD, Azeem S, Lundy CW, Sato Y, Guo B, Blanchong JA, Gauger PC, Marks DR, Yoon KJ, Adelman JS. Evaluating the role of wild songbirds or rodents in spreading avian influenza virus across an agricultural landscape. PeerJ 2017; 5:e4060. [PMID: 29255648 PMCID: PMC5732541 DOI: 10.7717/peerj.4060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/28/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Avian influenza virus (AIV) infections occur naturally in wild bird populations and can cross the wildlife-domestic animal interface, often with devastating impacts on commercial poultry. Migratory waterfowl and shorebirds are natural AIV reservoirs and can carry the virus along migratory pathways, often without exhibiting clinical signs. However, these species rarely inhabit poultry farms, so transmission into domestic birds likely occurs through other means. In many cases, human activities are thought to spread the virus into domestic populations. Consequently, biosecurity measures have been implemented to limit human-facilitated outbreaks. The 2015 avian influenza outbreak in the United States, which occurred among poultry operations with strict biosecurity controls, suggests that alternative routes of virus infiltration may exist, including bridge hosts: wild animals that transfer virus from areas of high waterfowl and shorebird densities. METHODS Here, we examined small, wild birds (songbirds, woodpeckers, etc.) and mammals in Iowa, one of the regions hit hardest by the 2015 avian influenza epizootic, to determine whether these animals carry AIV. To assess whether influenza A virus was present in other species in Iowa during our sampling period, we also present results from surveillance of waterfowl by the Iowa Department of Natural Resources and Unites Stated Department of Agriculture. RESULTS Capturing animals at wetlands and near poultry facilities, we swabbed 449 individuals, internally and externally, for the presence of influenza A virus and no samples tested positive by qPCR. Similarly, serology from 402 animals showed no antibodies against influenza A. Although several species were captured at both wetland and poultry sites, the overall community structure of wild species differed significantly between these types of sites. In contrast, 83 out of 527 sampled waterfowl tested positive for influenza A via qPCR. DISCUSSION These results suggest that even though influenza A viruses were present on the Iowa landscape at the time of our sampling, small, wild birds and rodents were unlikely to be frequent bridge hosts.
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Affiliation(s)
- Derek D. Houston
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, United States of America
- Department of Natural and Environmental Sciences, Western State Colorado University, Gunnison, CO, United States of America
| | - Shahan Azeem
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States of America
| | - Coady W. Lundy
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, United States of America
- Animal and Plant Health Inspection Service, Wildlife Services, United States Department of Agriculture, Urbandale, IA, United States of America
| | - Yuko Sato
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States of America
| | - Baoqing Guo
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States of America
| | - Julie A. Blanchong
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, United States of America
| | - Phillip C. Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States of America
| | - David R. Marks
- Animal and Plant Health Inspection Service, Wildlife Services, United States Department of Agriculture, Urbandale, IA, United States of America
| | - Kyoung-Jin Yoon
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States of America
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States of America
| | - James S. Adelman
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, United States of America
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Tian D, Sooryanarain H, Matzinger SR, Gauger PC, Karuppannan AK, Elankumaran S, Opriessnig T, Meng XJ. Protective efficacy of a virus-vectored multi-component vaccine against porcine reproductive and respiratory syndrome virus, porcine circovirus type 2 and swine influenza virus. J Gen Virol 2017; 98:3026-3036. [DOI: 10.1099/jgv.0.000964] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Debin Tian
- Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Harini Sooryanarain
- Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Shannon R. Matzinger
- Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Phil C. Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Anbu K. Karuppannan
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Subbiah Elankumaran
- Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Tanja Opriessnig
- The Roslin Institute, University of Edinburgh, Midlothian, Scotland, UK
| | - Xiang-Jin Meng
- Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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Rech RR, Gava D, Silva MC, Fernandes LT, Haach V, Ciacci-Zanella JR, Schaefer R. Porcine respiratory disease complex after the introduction of H1N1/2009 influenza virus in Brazil. Zoonoses Public Health 2017; 65:e155-e161. [DOI: 10.1111/zph.12424] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Indexed: 02/03/2023]
Affiliation(s)
- R. R. Rech
- Department of Veterinary Pathobiology; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; College Station TX USA
| | - D. Gava
- Embrapa Suínos e Aves; Concórdia SC Brazil
| | - M. C. Silva
- Qualem Laboratorio Veterinário; Santa Maria RS Brazil
| | | | - V. Haach
- Departamento de Microbiologia, Imunologia e Parasitologia; Instituto de Ciências Básicas da Saúde; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
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Molecular epidemiology of swine influenza A viruses in the Southeastern United States, highlights regional differences in circulating strains. Vet Microbiol 2017; 211:174-179. [PMID: 29102115 DOI: 10.1016/j.vetmic.2017.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 01/13/2023]
Abstract
Swine influenza A virus (IAV) can cause widespread respiratory disease with high morbidity, low mortality, and have a substantial economic impact to the swine industry. Swine infection may contribute to pandemic IAV given their susceptibility to both avian and human IAVs. Currently, three IAV subtypes (H1N1, H3N2 and H1N2) circulate in swine in North America frequently combining gene segments from avian or human viruses. This study investigated the prevalence of IAV in commercial swine herds. A total of 1878 oral fluid samples were collected from pigs of all ages from 201 commercial farms located in North Carolina and South Carolina. Sixty-eight oral fluid samples from 35 farms were positive by MP gene PCR with an overall IAV-positivity of 3.6%. On the herd level, the percentage of IAV positivity was 17.4%. Fifty-six viruses were subtyped, while 12 were partly subtyped or not subtyped at all. Using de novo assembly, complete sequences were obtained for 59 HA genes. The majority of IAVs subtyped had an H1 HA demonstrating a considerable prevalence over H3 viruses. Furthermore, only six out of eleven HA types were detected which has implications for the selection of vaccines used by swine producers in the region.
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20
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Chamba Pardo FO, Alba-Casals A, Nerem J, Morrison RB, Puig P, Torremorell M. Influenza Herd-Level Prevalence and Seasonality in Breed-to-Wean Pig Farms in the Midwestern United States. Front Vet Sci 2017; 4:167. [PMID: 29075636 PMCID: PMC5641542 DOI: 10.3389/fvets.2017.00167] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/25/2017] [Indexed: 01/30/2023] Open
Abstract
Influenza is a costly disease for pig producers and understanding its epidemiology is critical to control it. In this study, we aimed to estimate the herd-level prevalence and seasonality of influenza in breed-to-wean pig farms, evaluate the correlation between influenza herd-level prevalence and meteorological conditions, and characterize influenza genetic diversity over time. A cohort of 34 breed-to-wean farms with monthly influenza status obtained over a 5-year period in piglets prior to wean was selected. A farm was considered positive in a given month if at least one oral fluid tested influenza positive by reverse transcriptase polymerase chain reaction. Influenza seasonality was assessed combining autoregressive integrated moving average (ARIMA) models with trigonometric functions as covariates. Meteorological conditions were gathered from local land-based weather stations, monthly aggregated and correlated with influenza herd-level prevalence. Influenza herd-level prevalence had a median of 28% with a range from 7 to 57% and followed a cyclical pattern with levels increasing during fall, peaking in both early winter (December) and late spring (May), and decreasing in summer. Influenza herd-level prevalence was correlated with mean outdoor air absolute humidity (AH) and temperature. Influenza genetic diversity was substantial over time with influenza isolates belonging to 10 distinct clades from which H1 delta 1 and H1 gamma 1 were the most common. Twenty-one percent of farms had three different clades co-circulating over time, 18% of farms had two clades, and 41% of farms had one clade. In summary, our study showed that influenza had a cyclical pattern explained in part by air AH and temperature changes over time, and highlighted the importance of active surveillance to identify high-risk periods when strategic control measures for influenza could be implemented.
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Affiliation(s)
| | - Ana Alba-Casals
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, United States
| | - Joel Nerem
- Pipestone Veterinary Services, Pipestone, MN, United States
| | - Robert B Morrison
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, United States
| | - Pedro Puig
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Montserrat Torremorell
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN, United States
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21
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Henritzi D, Zhao N, Starick E, Simon G, Krog JS, Larsen LE, Reid SM, Brown IH, Chiapponi C, Foni E, Wacheck S, Schmid P, Beer M, Hoffmann B, Harder TC. Rapid detection and subtyping of European swine influenza viruses in porcine clinical samples by haemagglutinin- and neuraminidase-specific tetra- and triplex real-time RT-PCRs. Influenza Other Respir Viruses 2016; 10:504-517. [PMID: 27397600 PMCID: PMC5059951 DOI: 10.1111/irv.12407] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2016] [Indexed: 12/26/2022] Open
Abstract
Background A diversifying pool of mammalian‐adapted influenza A viruses (IAV) with largely unknown zoonotic potential is maintained in domestic swine populations worldwide. The most recent human influenza pandemic in 2009 was caused by a virus with genes originating from IAV isolated from swine. Swine influenza viruses (SIV) are widespread in European domestic pig populations and evolve dynamically. Knowledge regarding occurrence, spread and evolution of potentially zoonotic SIV in Europe is poorly understood. Objectives Efficient SIV surveillance programmes depend on sensitive and specific diagnostic methods which allow for cost‐effective large‐scale analysis. Methods New SIV haemagglutinin (HA) and neuraminidase (NA) subtype‐ and lineage‐specific multiplex real‐time RT‐PCRs (RT‐qPCR) have been developed and validated with reference virus isolates and clinical samples. Results A diagnostic algorithm is proposed for the combined detection in clinical samples and subtyping of SIV strains currently circulating in Europe that is based on a generic, M‐gene‐specific influenza A virus RT‐qPCR. In a second step, positive samples are examined by tetraplex HA‐ and triplex NA‐specific RT‐qPCRs to differentiate the porcine subtypes H1, H3, N1 and N2. Within the HA subtype H1, lineages “av” (European avian‐derived), “hu” (European human‐derived) and “pdm” (human pandemic A/H1N1, 2009) are distinguished by RT‐qPCRs, and within the NA subtype N1, lineage “pdm” is differentiated. An RT‐PCR amplicon Sanger sequencing method of small fragments of the HA and NA genes is also proposed to safeguard against failure of multiplex RT‐qPCR subtyping. Conclusions These new multiplex RT‐qPCR assays provide adequate tools for sustained SIV monitoring programmes in Europe.
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Affiliation(s)
- Dinah Henritzi
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute (FLI), Greifswald-Insel Riems, Germany
| | - Na Zhao
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute (FLI), Greifswald-Insel Riems, Germany
| | - Elke Starick
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute (FLI), Greifswald-Insel Riems, Germany
| | - Gaelle Simon
- Anses, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France
| | - Jesper S Krog
- National Veterinary Institute; Technical University of Denmark (DTU), Frederiksberg C, Denmark
| | - Lars Erik Larsen
- National Veterinary Institute; Technical University of Denmark (DTU), Frederiksberg C, Denmark
| | - Scott M Reid
- Department of Virology, Animal and Plant Health Agency-Weybridge, New Haw, Addlestone, Surrey, UK
| | - Ian H Brown
- Department of Virology, Animal and Plant Health Agency-Weybridge, New Haw, Addlestone, Surrey, UK
| | - Chiara Chiapponi
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Parma, Italy
| | - Emanuela Foni
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Parma, Italy
| | | | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute (FLI), Greifswald-Insel Riems, Germany
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute (FLI), Greifswald-Insel Riems, Germany
| | - Timm C Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute (FLI), Greifswald-Insel Riems, Germany.
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22
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Abstract
Multiple divergent lineages challenge the design of cross-protective vaccines and highlight the need for additional surveillance. The evolutionary origins of the influenza A(H1N1)pdm09 virus that caused the first outbreak of the 2009 pandemic in Mexico remain unclear, highlighting the lack of swine surveillance in Latin American countries. Although Brazil has one of the largest swine populations in the world, influenza was not thought to be endemic in Brazil’s swine until the major outbreaks of influenza A(H1N1)pdm09 in 2009. Through phylogenetic analysis of whole-genome sequences of influenza viruses of the H1N1, H1N2, and H3N2 subtypes collected in swine in Brazil during 2009–2012, we identified multiple previously uncharacterized influenza viruses of human seasonal H1N2 and H3N2 virus origin that have circulated undetected in swine for more than a decade. Viral diversity has further increased in Brazil through reassortment between co-circulating viruses, including A(H1N1)pdm09. The circulation of multiple divergent hemagglutinin lineages challenges the design of effective cross-protective vaccines and highlights the need for additional surveillance.
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23
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Characterization of Viral Load, Viability and Persistence of Influenza A Virus in Air and on Surfaces of Swine Production Facilities. PLoS One 2016; 11:e0146616. [PMID: 26757362 PMCID: PMC4710569 DOI: 10.1371/journal.pone.0146616] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/18/2015] [Indexed: 01/26/2023] Open
Abstract
Indirect transmission of influenza A virus (IAV) in swine is poorly understood and information is lacking on levels of environmental exposure encountered by swine and people during outbreaks of IAV in swine barns. We characterized viral load, viability and persistence of IAV in air and on surfaces during outbreaks in swine barns. IAV was detected in pigs, air and surfaces from five confirmed outbreaks with 48% (47/98) of oral fluid, 38% (32/84) of pen railing and 43% (35/82) of indoor air samples testing positive by IAV RT-PCR. IAV was isolated from air and oral fluids yielding a mixture of subtypes (H1N1, H1N2 and H3N2). Detection of IAV RNA from air was sustained during the outbreaks with maximum levels estimated between 7 and 11 days from reported onset. Our results indicate that during outbreaks of IAV in swine, aerosols and surfaces in barns contain significant levels of IAV potentially representing an exposure hazard to both swine and people.
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Nolting JM, Szablewski CM, Edwards JL, Nelson SW, Bowman AS. Nasal Wipes for Influenza A Virus Detection and Isolation from Swine. J Vis Exp 2015:e53313. [PMID: 26709840 DOI: 10.3791/53313] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Surveillance for influenza A viruses in swine is critical to human and animal health because influenza A virus rapidly evolves in swine populations and new strains are continually emerging. Swine are able to be infected by diverse lineages of influenza A virus making them important hosts for the emergence and maintenance of novel influenza A virus strains. Sampling pigs in diverse settings such as commercial swine farms, agricultural fairs, and live animal markets is important to provide a comprehensive view of currently circulating IAV strains. The current gold-standard ante-mortem sampling technique (i.e. collection of nasal swabs) is labor intensive because it requires physical restraint of the pigs. Nasal wipes involve rubbing a piece of fabric across the snout of the pig with minimal to no restraint of the animal. The nasal wipe procedure is simple to perform and does not require personnel with professional veterinary or animal handling training. While slightly less sensitive than nasal swabs, virus detection and isolation rates are adequate to make nasal wipes a viable alternative for sampling individual pigs when low stress sampling methods are required. The proceeding protocol outlines the steps needed to collect a viable nasal wipe from an individual pig.
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Affiliation(s)
| | | | - Jody L Edwards
- Department of Veterinary Preventive Medicine, The Ohio State University
| | - Sarah W Nelson
- Department of Veterinary Preventive Medicine, The Ohio State University
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University;
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25
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Influenza A virus infection in Brazilian swine herds following the introduction of pandemic 2009 H1N1. Vet Microbiol 2015; 180:118-22. [DOI: 10.1016/j.vetmic.2015.08.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 08/17/2015] [Accepted: 08/27/2015] [Indexed: 11/23/2022]
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Nelson M, Culhane MR, Rovira A, Torremorell M, Guerrero P, Norambuena J. Novel Human-like Influenza A Viruses Circulate in Swine in Mexico and Chile. PLOS CURRENTS 2015; 7. [PMID: 26345598 PMCID: PMC4551470 DOI: 10.1371/currents.outbreaks.c8b3207c9bad98474eca3013fa933ca6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Further understanding of the genetic diversity and evolution of influenza A viruses circulating in swine (IAV-S) is important for the development of effective vaccines and our knowledge of pandemic threats. Until recently, very little was known of IAV-S diversity in Latin America, owing to a lack of surveillance. METHODS To address this gap, we sequenced and conducted a phylogenetic analysis of 69 hemagglutinin (HA) sequences from IAV-S isolates collected in swine in Mexico and Chile during 2010-2014, including the H1N1, H1N2, and H3N2 subtypes. RESULTS Our analysis identified multiple IAV-S lineages that appear to have been circulating undetected in swine for decades, including four novel IAV-S lineages of human seasonal virus origin that have not been previously identified in any swine populations globally. We also found evidence of repeated introductions of pandemic H1N1 viruses from humans into swine in Mexico and Chile since 2009, and incursions of H1 and H3 viruses from North American swine into Mexico. DISCUSSION Overall, our findings indicate that at least 12 genetically distinct HA lineages circulate in Latin American swine herds, only two of which have been found in North American swine herds. Human-to-swine transmission, spatial migration via swine movements, and genomic reassortment are the key evolutionary mechanisms that generate this viral diversity. Additional antigenic characterization and whole-genome sequencing is greatly needed to understand the diversity and independent evolution of IAV-S in Latin America.
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Affiliation(s)
- Martha Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Marie R Culhane
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Albert Rovira
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
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