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Holgado-Martín R, Arnal JL, Sibila M, Franzo G, Martín-Jurado D, Risco D, Segalés J, Gómez L. First detection of porcine circovirus 4 (PCV-4) in Europe. Virol J 2023; 20:230. [PMID: 37817216 PMCID: PMC10566016 DOI: 10.1186/s12985-023-02181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/08/2023] [Indexed: 10/12/2023] Open
Abstract
Porcine circovirus 4 (PCV-4) is a novel virus recently discovered (2019) in domestic pigs from China, although several studies have proven its circulation since 2008. Later, PCV-4 was also detected in wild boar populations from China and domestic pigs from South Korea and Thailand. Currently, Asia is so far the only continent where this novel virus has been reported; few studies carried out in South America and Europe failed in the attempt to detect it. The objective of this Comment is to communicate the first detection of PCV-4 in Europe, specifically in wild boar and domestic pigs from Mid-South-Western Spain. A retrospective study was carried out on wild boar and domestic pigs, both extensively (Iberian breed) and intensively raised, from Spain and Italy, sampled between 1998 and 2022. PCV-4 genome detection was attempted using different conventional or quantitative real time PCR (qPCR) protocols and some positive results were confirmed through Sanger sequencing. A total of 57 out of 166 (34.3%) Spanish wild boar and 9 out of 223 (4%) Iberian pigs (both geographically located in the Mid-South-Western Spain) were qPCR positive, while the rest of tested animals from North-Eastern Spain and Italy were negative. Partial sequences of Rep or Cap genes of selected samples confirmed the presence of PCV-4. The relatively high prevalence in wild boar and the low one in Iberian pigs from the same areas suggests intra- and interspecific transmission, being the wild boar a potential viral reservoir. The epidemiological and clinical importance of these findings are currently unknown, but guarantees further research on this novel virus.
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Affiliation(s)
- Rocío Holgado-Martín
- Departamento de Medicina Animal, Unidad de Anatomía Patológica y Anatomía Comparada, Facultad de Veterinaria de Cáceres, Universidad de Extremadura, Cáceres, 10003, Spain
| | - José Luís Arnal
- Exopol, Autovaccines and Veterinary Diagnostics, Polígono Río Gállego D/14, San Mateo de Gállego, Zaragoza, 50840, Spain
| | - Marina Sibila
- Programa de Sanitat Animal, IRTA, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Campus, Bellaterra, 08193, Spain
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autónoma de Barcelona (UAB), Bellaterra, 08193, Spain
- WOAH collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Spain
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), Padua University, Legnaro, 35020, Italy
| | - Desireé Martín-Jurado
- Exopol, Autovaccines and Veterinary Diagnostics, Polígono Río Gállego D/14, San Mateo de Gállego, Zaragoza, 50840, Spain
| | - David Risco
- Departamento de Medicina Animal, Unidad de Anatomía Patológica y Anatomía Comparada, Facultad de Veterinaria de Cáceres, Universidad de Extremadura, Cáceres, 10003, Spain
| | - Joaquim Segalés
- Programa de Sanitat Animal, IRTA, Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona (UAB), Campus, Bellaterra, 08193, Spain.
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autónoma de Barcelona (UAB), Bellaterra, 08193, Spain.
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
| | - Luís Gómez
- Departamento de Medicina Animal, Unidad de Anatomía Patológica y Anatomía Comparada, Facultad de Veterinaria de Cáceres, Universidad de Extremadura, Cáceres, 10003, Spain.
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2
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Cui Y, Li J, Guo J, Pan Y, Tong X, Liu C, Wang D, Xu W, Shi Y, Ji Y, Qiu Y, Yang X, Hou L, Zhou J, Feng X, Wang Y, Liu J. Evolutionary Origin, Genetic Recombination, and Phylogeography of Porcine Kobuvirus. Viruses 2023; 15:240. [PMID: 36680281 PMCID: PMC9867129 DOI: 10.3390/v15010240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The newly identified porcine Kobuvirus (PKV) has raised concerns owing to its association with diarrheal symptom in pigs worldwide. The process involving the emergence and global spread of PKV remains largely unknown. Here, the origin, genetic diversity, and geographic distribution of PKV were determined based on the available PKV sequence information. PKV might be derived from the rabbit Kobuvirus and sheep were an important intermediate host. The most recent ancestor of PKV could be traced back to 1975. Two major clades are identified, PKVa and PKVb, and recombination events increase PKV genetic diversity. Cross-species transmission of PKV might be linked to interspecies conserved amino acids at 13-17 and 25-40 residue motifs of Kobuvirus VP1 proteins. Phylogeographic analysis showed that Spain was the most likely location of PKV origin, which then spread to pig-rearing countries in Asia, Africa, and Europe. Within China, the Hubei province was identified as a primary hub of PKV, transmitting to the east, southwest, and northeast regions of the country. Taken together, our findings have important implications for understanding the evolutionary origin, genetic recombination, and geographic distribution of PKV thereby facilitating the design of preventive and containment measures to combat PKV infection.
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Affiliation(s)
- Yongqiu Cui
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jingyi Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jinshuo Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yang Pan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xinxin Tong
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Changzhe Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Dedong Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Weiyin Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yongyan Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Ying Ji
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yonghui Qiu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyu Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Lei Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jianwei Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xufei Feng
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yong Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Jue Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
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3
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Development of CRISPR-Mediated Nucleic Acid Detection Technologies and Their Applications in the Livestock Industry. Genes (Basel) 2022; 13:genes13112007. [PMID: 36360244 PMCID: PMC9690124 DOI: 10.3390/genes13112007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
The rapid rate of virus transmission and pathogen mutation and evolution highlight the necessity for innovative approaches to the diagnosis and prevention of infectious diseases. Traditional technologies for pathogen detection, mostly PCR-based, involve costly/advanced equipment and skilled personnel and are therefore not feasible in resource-limited areas. Over the years, many promising methods based on clustered regularly interspaced short palindromic repeats and the associated protein systems (CRISPR/Cas), i.e., orthologues of Cas9, Cas12, Cas13 and Cas14, have been reported for nucleic acid detection. CRISPR/Cas effectors can provide one-tube reaction systems, amplification-free strategies, simultaneous multiplex pathogen detection, visual colorimetric detection, and quantitative identification as alternatives to quantitative PCR (qPCR). This review summarizes the current development of CRISPR/Cas-mediated molecular diagnostics, as well as their design software and readout methods, highlighting technical improvements for integrating CRISPR/Cas technologies into on-site applications. It further highlights recent applications of CRISPR/Cas-based nucleic acid detection in livestock industry, including emerging infectious diseases, authenticity and composition of meat/milk products, as well as sex determination of early embryos.
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Petukhova T, Pearl DL, Spinato M, Fairles J, Hazlett M, Poljak Z. The impact of the initial public health response to COVID-19 on swine health surveillance in Ontario. One Health 2021; 13:100338. [PMID: 34692972 PMCID: PMC8523356 DOI: 10.1016/j.onehlt.2021.100338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/21/2022] Open
Abstract
COVID-19 restrictions and the pandemic have affected animal health and food production through the disease's effects on human activities. COVID-19 impact on swine health surveillance can be assessed by investigating submissions and test positivity for pathogens before and after COVID-19 restrictions. PRRSV, Influenza A virus, Mycoplasma hyopneumoniae and PCV-2 are considered important and economically challenging respiratory diseases for the swine populations. By reviewing test results from swine samples submitted for diagnostic testing to a regional diagnostic laboratory, and by assessing total submissions, total positive tests, and the proportion of positive tests at weekly intervals with time series techniques and generalized linear regression models, we evaluated COVID-19's impact on the monitoring of these respiratory pathogens in Ontario, Canada. We classified weeks that fell from week 12 through week 24 in each year as pandemic equivalent weeks and the non-pandemic weeks included all other weeks. The pandemic period in 2020 resulted in a significantly higher number of submissions (p < 0.05) and PRRSV positive submission counts (p < 0.05) when compared to equivalent time periods in previous years; however, no changes could be detected in the odds of weekly PRRSV submission positivity. Weekly positive proportions of PCV-2 tests were higher during the pandemic period in 2020 compared with the pandemic equivalent period in 2018 and 2017. The counts of submissions that requested tests for PRRSV, Influenza A virus and M. hyopneumonia combined, as well as the number of submissions and the proportions of submissions that tested negative for these multiple respiratory pathogens were not significantly different between the pandemic period in 2020 and other periods examined. Our findings indicate that swine producers, in conjunction with various private and public veterinary support services, continued monitoring and performing diagnostic screening on farms for economically important animal diseases despite complications resulting from COVID-19 public health restrictions. PRRSV continues to have a serious impact on swine health. The absence of an increased proportion of negative tests for individual or groups of pathogens, or an accompanying increase in submissions during the 2020 pandemic period suggests that no new undetected pathogens with an impact on respiratory signs in swine were introduced during this time.
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Affiliation(s)
- Tatiana Petukhova
- Department of Population Medicine, University of Guelph, ON N1G 2W1, Canada
| | - David L. Pearl
- Department of Population Medicine, University of Guelph, ON N1G 2W1, Canada
| | - Maria Spinato
- Animal Health Laboratory, University of Guelph, ON N1G 2W1, Canada
| | - Jim Fairles
- Animal Health Laboratory, University of Guelph, ON N1G 2W1, Canada
| | - Murray Hazlett
- Animal Health Laboratory, University of Guelph, ON N1G 2W1, Canada
| | - Zvonimir Poljak
- Department of Population Medicine, University of Guelph, ON N1G 2W1, Canada
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5
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Otte J, Pica-Ciamarra U. Emerging infectious zoonotic diseases: The neglected role of food animals. One Health 2021; 13:100323. [PMID: 34522761 PMCID: PMC8426280 DOI: 10.1016/j.onehlt.2021.100323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 01/13/2023] Open
Abstract
This paper compares the relative frequency of zoonotic disease emergence associated with food animals versus emergence from other animal sources and explores differences in disease characteristics and drivers of emergence between the two sources. It draws on a published compilation of 202 Emerging Infectious Zoonotic Disease (EIZD) events for the period 1940–2004. Of the 202 zoonotic EID events in the dataset, 74 (36.6%) were associated with animals kept for food production, which acted as reservoir for the zoonotic pathogen in 64 events and as intermediate / amplifying host in 8 events. Significant differences exist both in the characteristics of the causal agents and the drivers of emergence of zoonotic diseases from food animals and non-food animals. However, the prevailing policy debate on prevention, detection and control of EIZDs largely focuses on diseases of non-food animal origin (wildlife), neglecting the role of food animals. Policies and investments that ensure appropriate veterinary public health measures along and within food animal value chains are essential to mitigate the global risk of EIZDs, particularly in developing regions where the livestock sector is experiencing rapid growth and structural transformation. Over 36% of emerging infectious zoonotic diseases (EIZDs) are associated with animals kept for food production. The prevailing policy debate on managing EIZDs largely focuses on diseases of non-food animal origin (wildlife) The causal agents and drivers of emergence of zoonotic diseases from food animals and non-food animals are significantly different. Policies that ensure appropriate veterinary public health measures are essential to mitigate the global risk of EIZDs.
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Affiliation(s)
- Joachim Otte
- Food and Agriculture Organization of the United Nations, Italy
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6
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Saporiti V, Franzo G, Sibila M, Segalés J. Porcine circovirus 3 (PCV-3) as a causal agent of disease in swine and a proposal of PCV-3 associated disease case definition. Transbound Emerg Dis 2021; 68:2936-2948. [PMID: 34184834 PMCID: PMC9291921 DOI: 10.1111/tbed.14204] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/09/2021] [Accepted: 06/23/2021] [Indexed: 01/14/2023]
Abstract
Porcine circovirus 3 (PCV‐3) was discovered in 2015 using next‐generation sequencing (NGS) methods. Since then, the virus has been detected worldwide in pigs displaying several clinical–pathological outcomes as well as in healthy animals. The objective of this review is to critically discuss the evidence existing so far regarding PCV‐3 as a swine pathogen. In fact, a significant number of publications claim PCV‐3 as a disease causal infectious agent, but very few of them have shown strong evidence of such potential causality. The most convincing proofs of disease association are those that demonstrate a clinical picture linked to multisystemic lymphoplasmacytic to lymphohistiocytic perivascular inflammation and presence of viral nucleic acid within these lesions. Based on these evidence, individual case definitions for PCV‐3‐reproductive disease and PCV‐3‐systemic disease are proposed to standardize diagnostic criteria for PCV‐3‐associated diseases. However, the real frequency of these clinical–pathological conditions linked to the novel virus is unknown, and the most frequent outcome of PCV‐3 infection is likely subclinical based on its worlwide distribution.
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Affiliation(s)
- Viviane Saporiti
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Padua, Italy
| | - Marina Sibila
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain.,OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain
| | - Joaquim Segalés
- OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain.,UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
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Franzo G, He W, Correa‐Fiz F, Li G, Legnardi M, Su S, Segalés J. A Shift in Porcine Circovirus 3 (PCV-3) History Paradigm: Phylodynamic Analyses Reveal an Ancient Origin and Prolonged Undetected Circulation in the Worldwide Swine Population. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1901004. [PMID: 31763138 PMCID: PMC6865002 DOI: 10.1002/advs.201901004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/12/2019] [Indexed: 06/10/2023]
Abstract
The identification of a new circovirus (Porcine circovirus 3, PCV-3) has raised a remarkable concern because of some analogies with Porcine circovirus 2 (PCV-2). Preliminary results suggest an extremely recent PCV-3 emergence and high mutation rate. Retrospective studies prove its circulation at least since the early 1990s, revealing that PCV-3 could have been infecting pigs for an even longer period. Therefore, a new evaluation, based on an updated collection of PCV-3 sequences spanning more than 20 years, is performed using a phylodynamic approach. The obtained results overrule the previous PCV-3 history concept, indicating an ancient origin. These evidences are associated with an evolutionary rate far lower (10-5-10-6 substitution/site/year) than the PCV-2 one. Accordingly, the action of selective pressures on PCV-3 open reading frames (ORFs) seems to be remarkably lower compared to those acting on PCV-2, suggesting either a reduced PCV-3 plasticity or a less efficient host-induced natural selection. A complex and not-directional viral flow network is evidenced through phylogeographic analysis, indicating a long lasting circulation rather than a recent emergence followed by spreading. Being recent emergence has been ruled out, efforts should be devoted to understand whether its recent discovery is simply due to improved detection capabilities or to the breaking of a previous equilibrium.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal MedicineProduction and Health (MAPS)University of PaduaViale, dell'Università 1635020Legnaro (PD)Italy
| | - Wanting He
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food SafetyJiangsu Engineering Laboratory of Animal ImmunologyInstitute of ImmunologyCollege of Veterinary MedicineNanjing Agricultural UniversityNanjing210000China
| | - Florencia Correa‐Fiz
- IRTACentre de Recerca en Sanitat Animal (CReSA, IRTA‐UAB)Campus de la Universitat Autònoma de BarcelonaBellaterra08913Spain
| | - Gairu Li
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food SafetyJiangsu Engineering Laboratory of Animal ImmunologyInstitute of ImmunologyCollege of Veterinary MedicineNanjing Agricultural UniversityNanjing210000China
| | - Matteo Legnardi
- Department of Animal MedicineProduction and Health (MAPS)University of PaduaViale, dell'Università 1635020Legnaro (PD)Italy
| | - Shuo Su
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food SafetyJiangsu Engineering Laboratory of Animal ImmunologyInstitute of ImmunologyCollege of Veterinary MedicineNanjing Agricultural UniversityNanjing210000China
| | - Joaquim Segalés
- UABCentre de Recerca en Sanitat Animal (CReSA, IRTA‐UAB)Campus de la Universitat Autònoma de BarcelonaBellaterra08913Spain
- Departament de Sanitat i Anatomia AnimalsFacultat de VeterinàriaUniversitat Autònoma de BarcelonaBellaterra08913Spain
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Klaumann F, Correa-Fiz F, Franzo G, Sibila M, Núñez JI, Segalés J. Current Knowledge on Porcine circovirus 3 (PCV-3): A Novel Virus With a Yet Unknown Impact on the Swine Industry. Front Vet Sci 2018; 5:315. [PMID: 30631769 PMCID: PMC6315159 DOI: 10.3389/fvets.2018.00315] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/28/2018] [Indexed: 12/21/2022] Open
Abstract
Porcine circovirus 3 (PCV-3) is a recently described virus belonging to the family Circoviridae. It represents the third member of genus Circovirus able to infect swine, together with PCV-1, considered non-pathogenic, and PCV-2, one of the most economically relevant viruses for the swine worldwide industry. PCV-3 was originally found by metagenomics analyses in 2015 in tissues of pigs suffering from porcine dermatitis and nephropathy syndrome, reproductive failure, myocarditis and multisystemic inflammation. The lack of other common pathogens as potential infectious agents of these conditions prompted the suspicion that PCV-3 might etiologically be involved in disease occurrence. Subsequently, viral genome was detected in apparently healthy pigs, and retrospective studies indicated that PCV-3 was already present in pigs by early 1990s. In fact, current evidence suggests that PCV-3 is a rather widespread virus worldwide. Recently, the virus DNA has also been found in wild boar, expanding the scope of infection susceptibility among the Suidae family; also, the potential reservoir role of this species for the domestic pig has been proposed. Phylogenetic studies with available PCV-3 partial and complete sequences from around the world have revealed high nucleotide identity (>96%), although two main groups and several subclusters have been described as well. Moreover, it has been proposed the existence of a most common ancestor dated around 50 years ago. Taking into account the economic importance and the well-known effects of PCV-2 on the swine industry, a new member of the same family like PCV-3 should not be neglected. Studies on epidemiology, pathogenesis, immunity and diagnosis are guaranteed in the next few years. Therefore, the present review will update the current knowledge and future trends of research on PCV-3.
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Affiliation(s)
- Francini Klaumann
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil.,IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Florencia Correa-Fiz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Padua, Italy
| | - Marina Sibila
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José I Núñez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joaquim Segalés
- UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
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9
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Melmer DJ, O'Sullivan TL, Poljak Z. A descriptive analysis of swine movements in Ontario (Canada) as a contributor to disease spread. Prev Vet Med 2018; 159:211-219. [PMID: 30314784 DOI: 10.1016/j.prevetmed.2018.09.021] [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: 03/12/2018] [Revised: 08/18/2018] [Accepted: 09/19/2018] [Indexed: 01/30/2023]
Abstract
In recent times, considerable efforts have been made to develop infrastructure and processes of tracing livestock movements. One of common use of this type of data is to assess the potential for spread of infections in source populations. The objectives of this research were to describe Ontario pig movements in 2015, and to understand the potential for disease transmission through animal movement on a weekly and yearly basis. Swine shipments from January to December 2015 represented 224 production facilities and a total of 5398 unique animal movements. This one-mode directed network of animal movements was then analyzed using common descriptive network measures. The maximum yearly (y) weak component (WCy) size and maximum weekly (w) weak component size (WCw) was 224 facilities, and 83 facilities, respectively. The maximum WCw did not change significantly (p > 0.05) over time. The maximum strong component (SC) consisted of two facilities both on a weekly, and on a yearly basis. The size of the maximum ingoing contact chain on a yearly basis (ICCy) was 173 nodes with one abattoir as the end point, and the maximum ICCw consisted of 53 nodes. The size of the maximum outgoing contact chain (OCCy) contained 79 nodes, with one sow herd as a starting point. The maximum OCCw was 6 nodes. Regression models resulted in significant quadratic associations between weekly count of finisher facilities with betweenness >0 (p = 0.02) and weekly count of finisher facilities with in-degree and out-degree >0 (p = 0.01) and week number. Higher weekly counts of nursery and finisher facilities with betweenness >0 and in-degree and out-degree both >0 values occurred during summer months. All study facilities were connected when direction of animal movement was not taken into consideration in the yearly network. As such, yearly networks are potentially representative of infections with long incubation periods, subclinical infections, or endemic infections for which active control measures have not being taken. When the direction of animal movement was considered, such infection could still spread substantially and affect 35% of the study population (79/224). In the study population, finisher sites were proportionally and consistently most represented in WCw (min = 51%, max = 78%), which reflects current Ontario herd demographics. However, abattoirs were over-represented when the number of facilities in the study population was taken into consideration. This, and the size of the maximum ICCw both suggest that abattoirs could be, at least for some infectious diseases, suitable establishments for targeted sampling.
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Affiliation(s)
- Dylan John Melmer
- Department of Population Medicine, University of Guelph, ON, N1G 2W1, Canada.
| | - Terri L O'Sullivan
- Department of Population Medicine, University of Guelph, ON, N1G 2W1, Canada
| | - Zvonimir Poljak
- Department of Population Medicine, University of Guelph, ON, N1G 2W1, Canada
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10
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Segalés J. Diagnosis by ruling out other diseases or conditions. Vet Rec 2018; 183:93-94. [DOI: 10.1136/vr.k3132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Joaquim Segalés
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària; Universitat Autònoma de Barcelona, and Centre de Recerca en Sanitat Animal (CReSA) - Institut de Recerca i Tecnologia Agroalimentàries (IRTA); Campus UAB Barcelona Spain
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11
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Assessment of autoregressive integrated moving average (ARIMA), generalized linear autoregressive moving average (GLARMA), and random forest (RF) time series regression models for predicting influenza A virus frequency in swine in Ontario, Canada. PLoS One 2018; 13:e0198313. [PMID: 29856881 PMCID: PMC5983852 DOI: 10.1371/journal.pone.0198313] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 05/17/2018] [Indexed: 12/18/2022] Open
Abstract
Influenza A virus commonly circulating in swine (IAV-S) is characterized by large genetic and antigenic diversity and, thus, improvements in different aspects of IAV-S surveillance are needed to achieve desirable goals of surveillance such as to establish the capacity to forecast with the greatest accuracy the number of influenza cases likely to arise. Advancements in modeling approaches provide the opportunity to use different models for surveillance. However, in order to make improvements in surveillance, it is necessary to assess the predictive ability of such models. This study compares the sensitivity and predictive accuracy of the autoregressive integrated moving average (ARIMA) model, the generalized linear autoregressive moving average (GLARMA) model, and the random forest (RF) model with respect to the frequency of influenza A virus (IAV) in Ontario swine. Diagnostic data on IAV submissions in Ontario swine between 2007 and 2015 were obtained from the Animal Health Laboratory (University of Guelph, Guelph, ON, Canada). Each modeling approach was examined for predictive accuracy, evaluated by the root mean square error, the normalized root mean square error, and the model’s ability to anticipate increases and decreases in disease frequency. Likewise, we verified the magnitude of improvement offered by the ARIMA, GLARMA and RF models over a seasonal-naïve method. Using the diagnostic submissions, the occurrence of seasonality and the long-term trend in IAV infections were also investigated. The RF model had the smallest root mean square error in the prospective analysis and tended to predict increases in the number of diagnostic submissions and positive virological submissions at weekly and monthly intervals with a higher degree of sensitivity than the ARIMA and GLARMA models. The number of weekly positive virological submissions is significantly higher in the fall calendar season compared to the summer calendar season. Positive counts at weekly and monthly intervals demonstrated a significant increasing trend. Overall, this study shows that the RF model offers enhanced prediction ability over the ARIMA and GLARMA time series models for predicting the frequency of IAV infections in diagnostic submissions.
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Phylogenetic analysis of Hepatitis E virus strains isolated from slaughter-age pigs in Colombia. INFECTION GENETICS AND EVOLUTION 2017; 49:138-145. [DOI: 10.1016/j.meegid.2017.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 12/06/2016] [Accepted: 01/03/2017] [Indexed: 12/11/2022]
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13
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Thibault PA, Watkinson RE, Moreira-Soto A, Drexler JF, Lee B. Zoonotic Potential of Emerging Paramyxoviruses: Knowns and Unknowns. Adv Virus Res 2017; 98:1-55. [PMID: 28433050 PMCID: PMC5894875 DOI: 10.1016/bs.aivir.2016.12.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The risk of spillover of enzootic paramyxoviruses and the susceptibility of recipient human and domestic animal populations are defined by a broad collection of ecological and molecular factors that interact in ways that are not yet fully understood. Nipah and Hendra viruses were the first highly lethal zoonotic paramyxoviruses discovered in modern times, but other paramyxoviruses from multiple genera are present in bats and other reservoirs that have unknown potential to spillover into humans. We outline our current understanding of paramyxovirus reservoir hosts and the ecological factors that may drive spillover, and we explore the molecular barriers to spillover that emergent paramyxoviruses may encounter. By outlining what is known about enzootic paramyxovirus receptor usage, mechanisms of innate immune evasion, and other host-specific interactions, we highlight the breadth of unexplored avenues that may be important in understanding paramyxovirus emergence.
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Affiliation(s)
| | - Ruth E Watkinson
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Jan F Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany; German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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14
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Abstract
Senecavirus A (SVA) is the only member of the genus Senecavirus within the family Picornaviridae. This virus was discovered as a serendipitous finding in 2002 (and named Seneca Valley virus 001 [SVV-001]) while cultivating viral vectors in cell culture and has been proposed for use as an oncolytic virus to treat different types of human neoplasia. SVA was found in lesions in pigs affected by porcine idiopathic vesicular disease in Canada and the USA in 2008 and 2012, respectively. In 2014 and 2015, SVA infection was associated with outbreaks of vesicular disease in sows as well as neonatal pig mortality in Brazil and the USA. Phylogenetic analysis of the SVA VP1 indicates the existence of 3 clades of the virus. Clade I contains the historical strain SVV-001, clade II contains USA SVA strains identified between 1988 and 1997, and clade III contains global SVA strains from Brazil, Canada, China, and the USA identified between 2001 and 2015. The aim of this review is to draw the attention of veterinarians and researchers to a recently described infectious clinical-pathologic condition caused by a previously known agent (SVA). Apart from the intrinsic interest in a novel virus infecting pigs and causing economic losses, the major current concern is the similarity of the clinical picture to that of other swine diseases, because one of them-foot and mouth disease-is a World Organization for Animal Health-listed disease. Because the potential association of SVA with disease is rather new, there are still many questions to be resolved.
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Affiliation(s)
- J Segalés
- 1 UAB, Centre de Recerca en Sanitat Animal (CReSA), IRTA-UAB, Campus de la Universitat Autònoma de Barcelona, Spain.,2 Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Spain
| | - D Barcellos
- 3 Departamento de Medicina Animal, Federal University of Rio Grande do Sul/UFRGS, Porto Alegre, RS, Brazil
| | - A Alfieri
- 4 Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - E Burrough
- 5 Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - D Marthaler
- 6 Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
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