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De Marco MA, Cotti C, Raffini E, Frasnelli M, Prosperi A, Zanni I, Romanini C, Castrucci MR, Chiapponi C, Delogu M. Long-Term Serological Investigations of Influenza A Virus in Free-Living Wild Boars (Sus scrofa) from Northern Italy (2007–2014). Microorganisms 2022; 10:microorganisms10091768. [PMID: 36144370 PMCID: PMC9506564 DOI: 10.3390/microorganisms10091768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Influenza A viruses (IAV) have been repeatedly demonstrated to circulate in wild suid populations. In this study, serum samples were collected from 2618 free-ranging wild boars in a protected area of Northern Italy between 2007 and 2014, and firstly screened by enzyme-linked immunosorbent assay (ELISA) for the presence of antibodies against IAV. The ELISA-positive samples were further tested by hemagglutination inhibition (HI) assays performed using antigen strains representative of the four major swine IAV (sIAV) lineages circulating in Italy: avian-like swine H1N1, pandemic-like swine H1N1, human-like swine H1N2 and human-like swine H3N2. An overall seroprevalence of 5.5% (145/2618) was detected by ELISA, with 56.7% (80/141) of screened sera tests positive by HI assay. Antibodies against H1N1 subtypes were the most prevalent beginning in 2009—with the highest detection in the first quarter of the year—until 2013, although at a low level. In addition, antibodies to H3N2 subtype were found during six years (2007, 2009, 2010, 2011, 2012 and 2014) whereas H1N2 antibodies were detected in 2012 only. Of the HI-positive samples, 30% showed reactivity to both H1N1 and H3N2 subtypes. These results provide additional insight into the circulation dynamics of IAV in wild suid populations, suggesting the occurrence of sIAV spillover events from pigs to wild boars.
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Affiliation(s)
- Maria Alessandra De Marco
- Institute for Environmental Protection and Research (ISPRA), 40064 Ozzano dell’Emilia, Italy
- Correspondence: (M.A.D.M.); (M.D.); Tel.: +39-051-6512205 (M.A.D.M.); +39-051-2097078 (M.D.)
| | - Claudia Cotti
- Wildlife and Exotic Animal Service, Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, Italy
| | - Elisabetta Raffini
- WOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
| | - Matteo Frasnelli
- WOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
| | - Alice Prosperi
- WOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
| | - Irene Zanni
- WOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
| | - Chiara Romanini
- WOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
| | - Maria Rita Castrucci
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Chiara Chiapponi
- WOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy
- Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Mauro Delogu
- Wildlife and Exotic Animal Service, Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell’Emilia, Italy
- Correspondence: (M.A.D.M.); (M.D.); Tel.: +39-051-6512205 (M.A.D.M.); +39-051-2097078 (M.D.)
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2
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Chauhan RP, Gordon ML. Review of genome sequencing technologies in molecular characterization of influenza A viruses in swine. J Vet Diagn Invest 2022; 34:177-189. [PMID: 35037523 PMCID: PMC8921814 DOI: 10.1177/10406387211068023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The rapidly evolving antigenic diversity of influenza A virus (IAV) genomes in swine makes it imperative to detect emerging novel strains and track their circulation. We analyzed in our review the sequencing technologies used for subtyping and characterizing swine IAV genomes. Google Scholar, PubMed, and International Nucleotide Sequence Database Collaboration (INSDC) database searches identified 216 studies that have utilized Sanger, second-, and third-generation sequencing techniques to subtype and characterize swine IAV genomes up to 31 March 2021. Sanger dideoxy sequencing was by far the most widely used sequencing technique for generating either full-length (43.0%) or partial (31.0%) IAV genomes in swine globally; however, in the last decade, other sequencing platforms such as Illumina have emerged as serious competitors for the generation of whole-genome sequences of swine IAVs. Although partial HA and NA gene sequences were sufficient to determine swine IAV subtypes, whole-genome sequences were critical for determining reassortments and identifying unusual or less frequently occurring IAV subtypes. The combination of Sanger and second-generation sequencing technologies also greatly improved swine IAV characterization. In addition, the rapidly evolving third-generation sequencing platform, MinION, appears promising for on-site, real-time sequencing of complete swine IAV genomes. With a higher raw read accuracy, the use of the MinION could enhance the scalability of swine IAV testing in the field and strengthen the swine IAV disease outbreak response.
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Affiliation(s)
| | - Michelle L. Gordon
- Michelle L. Gordon, School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Rd, Durban 4001, South Africa.
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3
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Chauhan RP, Gordon ML. A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide. Pathogens 2020; 9:pathogens9050355. [PMID: 32397138 PMCID: PMC7281378 DOI: 10.3390/pathogens9050355] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/02/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023] Open
Abstract
The global anxiety and a significant threat to public health due to the current COVID-19 pandemic reiterate the need for active surveillance for the zoonotic virus diseases of pandemic potential. Influenza virus due to its wide host range and zoonotic potential poses such a significant threat to public health. Swine serve as a “mixing vessel” for influenza virus reassortment and evolution which as a result may facilitate the emergence of new strains or subtypes of zoonotic potential. In this context, the currently available scientific data hold a high significance to unravel influenza virus epidemiology and evolution. With this objective, the current systematic review summarizes the original research articles and case reports of all the four types of influenza viruses reported in swine populations worldwide. A total of 281 articles were found eligible through screening of PubMed and Google Scholar databases and hence were included in this systematic review. The highest number of research articles (n = 107) were reported from Asia, followed by Americas (n = 97), Europe (n = 55), Africa (n = 18), and Australia (n = 4). The H1N1, H1N2, H3N2, and A(H1N1)pdm09 viruses were the most common influenza A virus subtypes reported in swine in most countries across the globe, however, few strains of influenza B, C, and D viruses were also reported in certain countries. Multiple reports of the avian influenza virus strains documented in the last two decades in swine in China, the United States, Canada, South Korea, Nigeria, and Egypt provided the evidence of interspecies transmission of influenza viruses from birds to swine. Inter-species transmission of equine influenza virus H3N8 from horse to swine in China expanded the genetic diversity of swine influenza viruses. Additionally, numerous reports of the double and triple-reassortant strains which emerged due to reassortments among avian, human, and swine strains within swine further increased the genetic diversity of swine influenza viruses. These findings are alarming hence active surveillance should be in place to prevent future influenza pandemics.
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4
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Pepin KM, Pedersen K, Wan XF, Cunningham FL, Webb CT, Wilber MQ. Individual-Level Antibody Dynamics Reveal Potential Drivers of Influenza A Seasonality in Wild Pig Populations. Integr Comp Biol 2020; 59:1231-1242. [PMID: 31251341 DOI: 10.1093/icb/icz118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Swine are important in the ecology of influenza A virus (IAV) globally. Understanding the ecological role of wild pigs in IAV ecology has been limited because surveillance in wild pigs is often for antibodies (serosurveillance) rather than IAVs, as in humans and domestic swine. As IAV antibodies can persist long after an infection, serosurveillance data are not necessarily indicative of current infection risk. However, antibody responses to IAV infections cause a predictable antibody response, thus time of infection can be inferred from antibody levels in serological samples, enabling identification of risk factors of infection at estimated times of infection. Recent work demonstrates that these quantitative antibody methods (QAMs) can accurately recover infection dates, even when individual-level variation in antibody curves is moderately high. Also, the methodology can be implemented in a survival analysis (SA) framework to reduce bias from opportunistic sampling. Here we integrated QAMs and SA and applied this novel QAM-SA framework to understand the dynamics of IAV infection risk in wild pigs seasonally and spatially, and identify risk factors. We used national-scale IAV serosurveillance data from 15 US states. We found that infection risk was highest during January-March (54% of 61 estimated peaks), with 24% of estimated peaks occurring from May to July, and some low-level of infection risk occurring year-round. Time-varying IAV infection risk in wild pigs was positively correlated with humidity and IAV infection trends in domestic swine and humans, and did not show wave-like spatial spread of infection among states, nor more similar levels of infection risk among states with more similar meteorological conditions. Effects of host sex on IAV infection risk in wild pigs were generally not significant. Because most of the variation in infection risk was explained by state-level factors or infection risk at long-distances, our results suggested that predicting IAV infection risk in wild pigs is complicated by local ecological factors and potentially long-distance translocation of infection. In addition to revealing factors of IAV infection risk in wild pigs, our framework is broadly applicable for quantifying risk factors of disease transmission using opportunistic serosurveillance sampling, a common methodology in wildlife disease surveillance. Future research on the factors that determine individual-level antibody kinetics will facilitate the design of serosurveillance systems that can extract more accurate estimates of time-varying disease risk from quantitative antibody data.
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Affiliation(s)
- Kim M Pepin
- National Wildlife Research Center, USDA-APHIS, Wildlife Services, Fort Collins, CO 80521-2154, USA
| | - Kerri Pedersen
- USDA-APHIS, Wildlife Services, 920 Main Campus Drive, Suite 200, Raleigh, NC 27606, USA
| | - Xiu-Feng Wan
- Missouri University Center for Research on Influenza Systems Biology (CRISB), University of Missouri, Columbia, MO 65211, USA.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.,Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,MU Informatics Institute, University of Missouri, Columbia, MO, USA.,Department of Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Fred L Cunningham
- National Wildlife Research Center, USDA-APHIS, Wildlife Services, Mississippi Field Station, MS 39762, USA
| | - Colleen T Webb
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Mark Q Wilber
- National Wildlife Research Center, USDA-APHIS, Wildlife Services, Fort Collins, CO 80521-2154, USA.,Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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5
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Ferguson L, Luo K, Olivier AK, Cunningham FL, Blackmon S, Hanson-Dorr K, Sun H, Baroch J, Lutman MW, Quade B, Epperson W, Webby R, DeLiberto TJ, Wan XF. Influenza D Virus Infection in Feral Swine Populations, United States. Emerg Infect Dis 2019; 24:1020-1028. [PMID: 29774857 PMCID: PMC6004836 DOI: 10.3201/eid2406.172102] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Influenza D virus (IDV) has been identified in domestic cattle, swine, camelid, and small ruminant populations across North America, Europe, Asia, South America, and Africa. Our study investigated seroprevalence and transmissibility of IDV in feral swine. During 2012-2013, we evaluated feral swine populations in 4 US states; of 256 swine tested, 57 (19.1%) were IDV seropositive. Among 96 archived influenza A virus-seropositive feral swine samples collected from 16 US states during 2010-2013, 41 (42.7%) were IDV seropositive. Infection studies demonstrated that IDV-inoculated feral swine shed virus 3-5 days postinoculation and seroconverted at 21 days postinoculation; 50% of in-contact naive feral swine shed virus, seroconverted, or both. Immunohistochemical staining showed viral antigen within epithelial cells of the respiratory tract, including trachea, soft palate, and lungs. Our findings suggest that feral swine might serve an important role in the ecology of IDV.
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6
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Tissue tropisms opt for transmissible reassortants during avian and swine influenza A virus co-infection in swine. PLoS Pathog 2018; 14:e1007417. [PMID: 30507946 PMCID: PMC6292640 DOI: 10.1371/journal.ppat.1007417] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/13/2018] [Accepted: 10/18/2018] [Indexed: 01/28/2023] Open
Abstract
Genetic reassortment between influenza A viruses (IAVs) facilitate emergence of pandemic strains, and swine are proposed as a "mixing vessel" for generating reassortants of avian and mammalian IAVs that could be of risk to mammals, including humans. However, how a transmissible reassortant emerges in swine are not well understood. Genomic analyses of 571 isolates recovered from nasal wash samples and respiratory tract tissues of a group of co-housed pigs (influenza-seronegative, avian H1N1 IAV-infected, and swine H3N2 IAV-infected pigs) identified 30 distinct genotypes of reassortants. Viruses recovered from lower respiratory tract tissues had the largest genomic diversity, and those recovered from turbinates and nasal wash fluids had the least. Reassortants from lower respiratory tracts had the largest variations in growth kinetics in respiratory tract epithelial cells, and the cold temperature in swine nasal cells seemed to select the type of reassortant viruses shed by the pigs. One reassortant in nasal wash samples was consistently identified in upper, middle, and lower respiratory tract tissues, and it was confirmed to be transmitted efficiently between pigs. Study findings suggest that, during mixed infections of avian and swine IAVs, genetic reassortments are likely to occur in the lower respiratory track, and tissue tropism is an important factor selecting for a transmissible reassortant.
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7
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Feral Swine in the United States Have Been Exposed to both Avian and Swine Influenza A Viruses. Appl Environ Microbiol 2017; 83:AEM.01346-17. [PMID: 28733290 DOI: 10.1128/aem.01346-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 07/18/2017] [Indexed: 01/23/2023] Open
Abstract
Influenza A viruses (IAVs) in swine can cause sporadic infections and pandemic outbreaks among humans, but how avian IAV emerges in swine is still unclear. Unlike domestic swine, feral swine are free ranging and have many opportunities for IAV exposure through contacts with various habitats and animals, including migratory waterfowl, a natural reservoir for IAVs. During the period from 2010 to 2013, 8,239 serum samples were collected from feral swine across 35 U.S. states and tested against 45 contemporary antigenic variants of avian, swine, and human IAVs; of these, 406 (4.9%) samples were IAV antibody positive. Among 294 serum samples selected for antigenic characterization, 271 cross-reacted with ≥1 tested virus, whereas the other 23 did not cross-react with any tested virus. Of the 271 IAV-positive samples, 236 cross-reacted with swine IAVs, 1 with avian IAVs, and 16 with avian and swine IAVs, indicating that feral swine had been exposed to both swine and avian IAVs but predominantly to swine IAVs. Our findings suggest that feral swine could potentially be infected with both avian and swine IAVs, generating novel IAVs by hosting and reassorting IAVs from wild birds and domestic swine and facilitating adaptation of avian IAVs to other hosts, including humans, before their spillover. Continued surveillance to monitor the distribution and antigenic diversities of IAVs in feral swine is necessary to increase our understanding of the natural history of IAVs.IMPORTANCE There are more than 5 million feral swine distributed across at least 35 states in the United States. In contrast to domestic swine, feral swine are free ranging and have unique opportunities for contact with wildlife, livestock, and their habitats. Our serological results indicate that feral swine in the United States have been exposed to influenza A viruses (IAVs) consistent with those found in both domestic swine and wild birds, with the predominant infections consisting of swine-adapted IAVs. Our findings suggest that feral swine have been infected with IAVs at low levels and could serve as hosts for the generation of novel IAVs at the interface of feral swine, wild birds, domestic swine, and humans.
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8
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Denner J. The porcine virome and xenotransplantation. Virol J 2017; 14:171. [PMID: 28874166 PMCID: PMC5585927 DOI: 10.1186/s12985-017-0836-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/27/2017] [Indexed: 12/29/2022] Open
Abstract
The composition of the porcine virome includes viruses that infect pig cells, ancient virus-derived elements including endogenous retroviruses inserted in the pig chromosomes, and bacteriophages that infect a broad array of bacteria that inhabit pigs. Viruses infecting pigs, among them viruses also infecting human cells, as well as porcine endogenous retroviruses (PERVs) are of importance when evaluating the virus safety of xenotransplantation. Bacteriophages associated with bacteria mainly in the gut are not relevant in this context. Xenotransplantation using pig cells, tissues or organs is under development in order to alleviate the shortage of human transplants. Here for the first time published data describing the viromes in different pigs and their relevance for the virus safety of xenotransplantation is analysed. In conclusion, the analysis of the porcine virome has resulted in numerous new viruses being described, although their impact on xenotransplantation is unclear. Most importantly, viruses with known or suspected zoonotic potential were often not detected by next generation sequencing, but were revealed by more sensitive methods.
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Affiliation(s)
- Joachim Denner
- Robert Koch Fellow, Robert Koch Institute, Nordufer, 20, Berlin, Germany.
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9
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Pedersen K, Bauer NE, Rodgers S, Bazan LR, Mesenbrink BT, Gidlewski T. Antibodies to Various Zoonotic Pathogens Detected in Feral Swine (Sus scrofa) at Abattoirs in Texas, USA. J Food Prot 2017; 80:1239-1242. [PMID: 28686494 DOI: 10.4315/0362-028x.jfp-17-016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The zoonotic risk posed to employees by slaughtering feral swine (Sus scrofa) at two abattoirs in Texas was assessed by testing feral swine serum samples for exposure to influenza A virus, Leptospira, Trichinella spiralis, and Toxoplasma gondii. Blood was collected from a total of 376 feral swine between the two facilities during six separate collection periods in 2015. Antibodies to one or more serovars of Leptospira were identified in 48.9% of feral swine tested, with Bratislava and Pomona as the most commonly detected serovars, and antibodies to influenza A virus were detected in 14.1% of feral swine. Antibodies to T. gondii and T. spiralis were identified in 9.0 and 3.5%, respectively, of feral swine tested. Our results suggest that abattoir employees should be aware of the potential for exposure to various zoonotic pathogens when slaughtering feral swine, wear appropriate personal protective equipment, and participate in medical monitoring programs to ensure detection and prompt treatment. In addition, consumers of feral swine should cook the meat to the appropriate temperature and wash hands and kitchen surfaces thoroughly after preparing meat.
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Affiliation(s)
- Kerri Pedersen
- 1 U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, 4101 LaPorte Avenue, Fort Collins, Colorado 80521 (ORCID: http://orcid.org/000-0002-2980-9618 )
| | - Nathan E Bauer
- 2 U.S. Department of Agriculture, Food Safety Inspection Service, 2881 F&B Road, College Station, Texas 77845
| | - Sandra Rodgers
- 3 Texas A&M University Veterinary Medical Diagnostic Laboratory, 483 Agronomy Road, College Station, Texas 77840
| | - Luis R Bazan
- 4 U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, 5730 Northwest Parkway, Suite 700, San Antonio, Texas 78249
| | - Brian T Mesenbrink
- 4 U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, 5730 Northwest Parkway, Suite 700, San Antonio, Texas 78249
| | - Thomas Gidlewski
- 5 U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 LaPorte Avenue, Fort Collins, Colorado 80521, USA
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10
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Ali R, Blackburn RM, Kozlakidis Z. Next-Generation Sequencing and Influenza Virus: A Short Review of the Published Implementation Attempts. HAYATI JOURNAL OF BIOSCIENCES 2016. [DOI: 10.1016/j.hjb.2016.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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11
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Hause BM, Padmanabhan A, Pedersen K, Gidlewski T. Feral swine virome is dominated by single-stranded DNA viruses and contains a novel Orthopneumovirus which circulates both in feral and domestic swine. J Gen Virol 2016; 97:2090-2095. [PMID: 27417702 DOI: 10.1099/jgv.0.000554] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Feral swine are known reservoirs for various pathogens that can adversely affect domestic animals. To assess the viral ecology of feral swine in the USA, metagenomic sequencing was performed on 100 pooled nasal swabs. The virome was dominated by small, ssDNA viruses belonging to the families Circoviridae, Anelloviridae and Parvovirinae. Only four RNA viruses were identified: porcine kobuvirus, porcine sapelovirus, atypical porcine pestivirus and a novel Orthopneumovirus, provisionally named swine orthopneumovirus (SOV). SOV shared ~90 % nucleotide identity to murine pneumonia virus (MPV) and canine pneumovirus. A modified, commercially available ELISA for MPV found that approximately 30 % of both feral and domestic swine sera were positive for antibodies cross-reactive with MPV. Quantitative reverse transcription-PCR identified two (2 %) and four (5.0 %) positive nasal swab pools from feral and domestic swine, respectively, confirming that SOV circulates in both herds.
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Affiliation(s)
- Ben M Hause
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas 66549, USA.,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, Kansas 66549, USA
| | - Aiswaria Padmanabhan
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, Kansas 66549, USA
| | - Kerri Pedersen
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, Colorado 80521, USA
| | - Thomas Gidlewski
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, Colorado 80521, USA
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12
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Molecular Diagnostic Assays for the Detection and Control of Zoonotic Diseases. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Sun H, Cunningham FL, Harris J, Xu Y, Long LP, Hanson-Dorr K, Baroch JA, Fioranelli P, Lutman MW, Li T, Pedersen K, Schmit BS, Cooley J, Lin X, Jarman RG, DeLiberto TJ, Wan XF. Dynamics of virus shedding and antibody responses in influenza A virus-infected feral swine. J Gen Virol 2015; 96:2569-2578. [PMID: 26297148 DOI: 10.1099/jgv.0.000225] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Given their free-ranging habits, feral swine could serve as reservoirs or spatially dynamic 'mixing vessels' for influenza A virus (IAV). To better understand virus shedding patterns and antibody response dynamics in the context of IAV surveillance amongst feral swine, we used IAV of feral swine origin to perform infection experiments. The virus was highly infectious and transmissible in feral swine, and virus shedding patterns and antibody response dynamics were similar to those in domestic swine. In the virus-inoculated and sentinel groups, virus shedding lasted ≤ 6 and ≤ 9 days, respectively. Antibody titres in inoculated swine peaked at 1 : 840 on day 11 post-inoculation (p.i.), remained there until 21 days p.i. and dropped to < 1 : 220 at 42 days p.i. Genomic sequencing identified changes in wildtype (WT) viruses and isolates from sentinel swine, most notably an amino acid divergence in nucleoprotein position 473. Using data from cell culture as a benchmark, sensitivity and specificity of a matrix gene-based quantitative reverse transcription-PCR method using nasal swab samples for detection of IAV in feral swine were 78.9 and 78.1 %, respectively. Using data from haemagglutination inhibition assays as a benchmark, sensitivity and specificity of an ELISA for detection of IAV-specific antibody were 95.4 and 95.0 %, respectively. Serological surveillance from 2009 to 2014 showed that ∼7.58 % of feral swine in the USA were positive for IAV. Our findings confirm the susceptibility of IAV infection and the high transmission ability of IAV amongst feral swine, and also suggest the need for continued surveillance of IAVs in feral swine populations.
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Affiliation(s)
- Hailiang Sun
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MI, USA
| | - Fred L Cunningham
- Mississippi Field Station, National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Mississippi State, MI, USA
| | - Jillian Harris
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MI, USA
| | - Yifei Xu
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MI, USA
| | - Li-Ping Long
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MI, USA
| | - Katie Hanson-Dorr
- Mississippi Field Station, National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Mississippi State, MI, USA
| | - John A Baroch
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA
| | - Paul Fioranelli
- Mississippi Field Station, National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Mississippi State, MI, USA
| | - Mark W Lutman
- US Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Kerri Pedersen
- US Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO, USA
| | - Brandon S Schmit
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA
| | - Jim Cooley
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MI, USA
| | - Xiaoxu Lin
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Thomas J DeLiberto
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO, USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MI, USA
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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Bevins SN, Pedersen K, Lutman MW, Gidlewski T, Deliberto TJ. Consequences Associated with the Recent Range Expansion of Nonnative Feral Swine. Bioscience 2014. [DOI: 10.1093/biosci/biu015] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Foni E, Garbarino C, Chiapponi C, Baioni L, Zanni I, Cordioli P. Epidemiological survey of swine influenza A virus in the wild boar population of two Italian provinces. Influenza Other Respir Viruses 2013; 7 Suppl 4:16-20. [PMID: 24224815 PMCID: PMC5655886 DOI: 10.1111/irv.12198] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES An epidemiological survey was carried out in order to obtain a better understanding of the role of wild boars in the epidemiology of the influenza virus. DESIGN The samples were submitted to Real-Time PCR testing for gene M of the swine influenza virus (SIV), and virus isolation was performed from the positive PCR samples. Genome sequence analysis was performed on the isolates. Additionally, 1,977 boar sera samples were analyzed using ELISA and hemoagglutination inhibition. SETTING Over recent years, the wild boar population has greatly increased in Italy, including in areas of high-density industrial pig farming, where the influenza virus is widespread. From July to December 2012, wild boar lung samples were collected in the Parma and Piacenza area, in the Emilia Romagna region. SAMPLE 354 wild boar lung samples were collected. MAIN OUTCOME MEASURES Wild-boar influenza A virus infection should be studied more broadly in order to obtain a better understanding of the epidemiological role played by this species. RESULTS Three SIV strains were isolated out of 12 samples that resulted positive using PCR analysis and they were identified as avian-like SIV subtype H1N1. Phylogenetic analysis of the sequences obtained from isolate A/wild boar/291320/2012 showed that it clustered with recent Italian avian-like H1N1 SIVs isolated from domestic pigs. Sixty-eight sera samples showed a positive titer to the isolate A/wild boar/291320/2012. CONCLUSIONS This study suggests that SIV actively circulates in the wild boar population in the investigated. area.
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Affiliation(s)
- Emanuela Foni
- OIE Reference Laboratory for Swine InfluenzaIstituto Zooprofilattico Sperimentale della Lombardia ed Emilia RomagnaParmaItaly
| | - Chiara Garbarino
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia RomagnaPiacenzaItaly
| | - Chiara Chiapponi
- OIE Reference Laboratory for Swine InfluenzaIstituto Zooprofilattico Sperimentale della Lombardia ed Emilia RomagnaParmaItaly
| | - Laura Baioni
- OIE Reference Laboratory for Swine InfluenzaIstituto Zooprofilattico Sperimentale della Lombardia ed Emilia RomagnaParmaItaly
| | - Irene Zanni
- OIE Reference Laboratory for Swine InfluenzaIstituto Zooprofilattico Sperimentale della Lombardia ed Emilia RomagnaParmaItaly
| | - Paolo Cordioli
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia RomagnaBresciaItaly
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