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He W, Liao K, Li R, Peng W, Qian B, Zeng D, Tang F, Xue F, Jung YS, Dai J. Development of a CRISPR/Cas12a-based fluorescent detection method of Senecavirus A. BMC Vet Res 2024; 20:258. [PMID: 38877537 PMCID: PMC11179212 DOI: 10.1186/s12917-024-04116-6] [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: 10/12/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Senecavirus A (SVA), identified in 2002, is known to cause porcine idiopathic vesicular disease (PIVD), which presents with symptoms resembling other vesicular diseases. This similarity complicates field diagnosis. Conventional molecular diagnostic techniques are limited by their cost, sensitivity, and requirement for complicated instrumentation. Therefore, developing an effective and accurate diagnostic method is crucial for timely identification and isolation of affected pigs, thereby preventing further disease spread. METHODS In this study, we developed a highly-specific and ultra-sensitive SVA detection method powered by CRISPR/Cas12a. To enhance the availability in laboratories with varied equipment conditions, microplate reader and ultraviolet light transilluminator were introduced. Moreover, PCR amplification has also been incorporated into this method to improve sensitivity. The specificity and sensitivity of this method were determined following the preparation of the recombinant Cas12a protein and optimization of the CRISPR/Cas12a-based trans-cleavage system. RESULTS The method demonstrated no cross-reactivity with ten kinds of viruses of swine. The minimum template concentration required to activate substantial trans-cleavage activity was determined to be 106 copies/µL of SVA templates. However, when PCR amplification was incorporated, the method achieved a detection limit of one copy of SVA templates per reaction. It also exhibited 100% accuracy in simulated sample testing. The complete testing process does not exceed three hours. CONCLUSIONS Importantly, this method utilizes standard laboratory equipment, making it accessible for use in resource-limited settings and facilitating widespread and ultra-sensitive screening during epidemics. Overall, the development of this method not only broadens the array of tools available for detecting SVA but also holds significant promise for controlling the spread of PIVD.
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Affiliation(s)
- Wei He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
- Ningxia Hui Autonomous Region Food Testing and Research Institute, Yinchuan, 750002, China
| | - Kai Liao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruixue Li
- Ningxia Hui Autonomous Region Food Testing and Research Institute, Yinchuan, 750002, China
| | - Wanqing Peng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingxu Qian
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dexin Zeng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China.
- Sanya Institute of Nanjing Agricultural University, Sanya, 572024, China.
| | - Yong Sam Jung
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianjun Dai
- China Pharmaceutical University, Nanjing, 211198, China
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Ma L, Zhu M, Meng Q, Wang Y, Wang X. Real-time detection of Seneca Valley virus by one-tube RPA-CRISPR/Cas12a assay. Front Cell Infect Microbiol 2024; 13:1305222. [PMID: 38259970 PMCID: PMC10800940 DOI: 10.3389/fcimb.2023.1305222] [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: 10/10/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Senecavirus A (SVA) is a highly contagious virus that causes vesicular disease in pigs. At present, laboratory detection methods, such as virus isolation and polymerase chain reaction (PCR), required precision instruments and qualified personnel, making them unsuitable for point-of-care tests (POCT). Fortunately, the emergence of CRISPR/Cas system has provided new opportunities for fast and efficient pathogen detection. Methods This study successfully developed a precise and sensitive detection platform for diagnosing SVA by combining the CRISPR system with recombinase polymerase amplification (RPA). Results The minimum detection limit of the assay was 10 copies of the SVA genome. Meanwhile, the assay demonstrated high specificity. To validate the effectiveness of this system, we tested 85 swine clinical samples and found that the fluorescence method had a 100% coincidence rate compared to RT-qPCR. Discussion Overall, the RPA-CRISPR/Cas12a assay established in our study is a highly effective method for detecting SVA and holds great potential for practical applications in the resource-limited settings.
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Affiliation(s)
- Lei Ma
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
- College of Life Science, Henan University, Kaifeng, China
| | - Mengjie Zhu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Qingfeng Meng
- Testing Technology R&D Department, Shanghai Kaiwosha Biotechnology Co., Ltd, Shanghai, China
| | - Yao Wang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Xueping Wang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
- College of Life Science, Henan University, Kaifeng, China
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Ran X, Hu Z, Wang J, Yang Z, Li Z, Wen X. Prevalence of Senecavirus A in pigs from 2014 to 2020: a global systematic review and meta-analysis. J Vet Sci 2023; 24:e48. [PMID: 37271515 DOI: 10.4142/jvs.22307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/23/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND Senecavirus A (SVA), a member of the family Picornaviridae, is newly discovered, which causes vesicular lesions, lameness in swine, and even death in neonatal piglets. SVA has rapidly spread worldwide in recent years, especially in Asia. OBJECTIVES We conducted a global meta-analysis and systematic review to determine the status of SVA infection in pigs. METHODS Through PubMed, VIP Chinese Journals Database, China National Knowledge Infrastructure, and Wanfang Data search data from 2014 to July 26, 2020, a total of 34 articles were included in this analysis based on our inclusion criteria. We estimated the pooled prevalence of SVA in pigs by the random effects model. A risk of bias assessment of the studies and subgroup analysis to explain heterogeneity was undertaken. RESULTS We estimated the SVA prevalence to be 15.90% (1,564/9,839; 95% confidence interval [CI], 44.75-65.89) globally. The prevalence decreased to 11.06% (945/8,542; 95% CI, 28.25-50.64) after 2016. The highest SVA prevalence with the VP1-based RT-PCR and immunohistochemistry assay was 58.52% (594/1,015; 95% CI, 59.90-83.96) and 85.54% (71/83; 95% CI, 76.68-100.00), respectively. Besides, the SVA prevalence in piglet herds was the highest at 71.69% (119/166; 95% CI, 68.61-98.43) (p < 0.05). Moreover, our analysis confirmed that the subgroups, including country, sampling year, sampling position, detected gene, detection method, season, age, and climate, could be the heterogeneous factors associated with SVA prevalence. CONCLUSIONS The results indicated that SVA widely exists in various countries currently. Therefore, more prevention and control policies should be proposed to enhance the management of pig farms and improve breeding conditions and the environment to reduce the spread of SVA.
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Affiliation(s)
- Xuhua Ran
- School of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Zhenru Hu
- School of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Jun Wang
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Zhiyuan Yang
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Zhongle Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130018, China.
| | - Xiaobo Wen
- School of Animal Science and Technology, Hainan University, Haikou 570228, China.
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Chen W, Wang W, Wang X, Li Z, Wu K, Li X, Li Y, Yi L, Zhao M, Ding H, Fan S, Chen J. Advances in the differential molecular diagnosis of vesicular disease pathogens in swine. Front Microbiol 2022; 13:1019876. [PMID: 36386633 PMCID: PMC9641196 DOI: 10.3389/fmicb.2022.1019876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV), Senecavirus A (SVA) and swine vesicular disease virus (SVDV) are members of the family Picornaviridae, which can cause similar symptoms - vesicular lesions in the tissues of the mouth, nose, feet, skin and mucous membrane of animals. Rapid and accurate diagnosis of these viruses allows for control measures to prevent the spread of these diseases. Reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR are traditional and reliable methods for pathogen detection, while their amplification reaction requires a thermocycler. Isothermal amplification methods including loop-mediated isothermal amplification and recombinase polymerase amplification developed in recent years are simple, rapid and do not require specialized equipment, allowing for point of care diagnostics. Luminex technology allows for simultaneous detection of multiple pathogens. CRISPR-Cas diagnostic systems also emerging nucleic acid detection technologies which are very sensitivity and specificity. In this paper, various nucleic acid detection methods aimed at vesicular disease pathogens in swine (including FMDV, SVA and SVDV) are summarized.
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Affiliation(s)
- Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Weijun Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xinyan Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhaoyao Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yuwan Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Shuangqi Fan, ; Jinding Chen,
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Shuangqi Fan, ; Jinding Chen,
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Hawko S, Burrai GP, Polinas M, Angioi PP, Dei Giudici S, Oggiano A, Alberti A, Hosri C, Antuofermo E. A Review on Pathological and Diagnostic Aspects of Emerging Viruses—Senecavirus A, Torque teno sus virus and Linda Virus—In Swine. Vet Sci 2022; 9:vetsci9090495. [PMID: 36136710 PMCID: PMC9502770 DOI: 10.3390/vetsci9090495] [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: 07/29/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Worldwide demand for food is expected to increase due to population growth and swine accounts for more than one-third of meat produced worldwide. Several factors affect the success of livestock production systems, including animal disease control. Despite the importance of infectious diseases to animal health and the productivity of the global swine industry, pathogens of swine, in particular emerging viruses, such as Senecavirus A, Torque teno sus virus, and Linda virus, have gained limited interest. We performed a systematic analysis of the literature, with a focus on the main macroscopical and histological findings related to those viruses to fill the gap and highpoint these potentially hazardous pathogens. Abstract Swine production represents a significant component in agricultural economies as it occupies over 30% of global meat demand. Infectious diseases could constrain the swine health and productivity of the global swine industry. In particular, emerging swine viral diseases are omnipresent in swine populations, but the limited knowledge of the pathogenesis and the scarce information related to associated lesions restrict the development of data-based control strategies aimed to reduce the potentially great impact on the swine industry. In this paper, we reviewed and summarized the main pathological findings related to emerging viruses, such as Senecavirus A, Torque teno sus virus, and Linda virus, suggesting a call for further multidisciplinary studies aimed to fill this lack of knowledge and better clarify the potential role of those viral diseases in swine pathology.
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Affiliation(s)
- Salwa Hawko
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Giovanni P. Burrai
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Correspondence: ; Tel.: +39-079-229440
| | - Marta Polinas
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Paolo Angioi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy
| | - Silvia Dei Giudici
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy
| | - Annalisa Oggiano
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy
| | - Alberto Alberti
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Chadi Hosri
- Department of Veterinary Medicine, Faculty of Agronomy and Veterinary Sciences, Lebanese University, Beirut 14/6573, Lebanon
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Wang H, Dong J, Zhang T, Wang F, Yang R, Zhang Y, Zhao X. A novel rapid detection of Senecavirus A using recombinase polymerase amplification (RPA) coupled with lateral flow (LF) dipstrip. Anal Biochem 2022; 646:114627. [PMID: 35245488 DOI: 10.1016/j.ab.2022.114627] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/06/2022] [Accepted: 02/22/2022] [Indexed: 11/24/2022]
Abstract
SENECAVIRUS A: (SVA), an emerging picornavirus, has been associated with vesicular disease and neonatal mortality in swine, posing a great threat to the global swine industry. Accurate diagnosis of SVA is crucial for the effective prevention and control disease. In the present study, a simple, rapid and accurate diagnostic assay was developed combining recombinase polymerase amplification and a lateral flow dipstrip (RPA-LF) to detect SVA infection. Using recombinant plasmid pMD19-T-VP1 DNA as a template, the RPA-LF optimal reaction conditions were incubated at 35 °C for 25 min, and the result was visualized directly on the dipstrip. The specificity assay showed no cross-reactivity with other tested viruses, and the sensitivity assay revealed the minimum detection limit was 15 copies/μl. Moreover, the RPA-LF method was successfully applied with viral cDNA as template to test clinical samples, with no significant difference being observed between RPA-LF and qRT-PCR. Hence, the established RPA-LF assay could be used as a potential optional rapid, reliable, sensitive and low-cost method for field diagnosis of SVA, especially in resource-limited regions.
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Affiliation(s)
- Huibao Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, PR China; China Agricultural Veterinary Biological Science and Technology Co. Ltd., Lanzhou, PR China
| | - Jinjie Dong
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, PR China; China Agricultural Veterinary Biological Science and Technology Co. Ltd., Lanzhou, PR China; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, PR China
| | - Tao Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, PR China; China Agricultural Veterinary Biological Science and Technology Co. Ltd., Lanzhou, PR China
| | - Fan Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, PR China; China Agricultural Veterinary Biological Science and Technology Co. Ltd., Lanzhou, PR China
| | - Rui Yang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, PR China; China Agricultural Veterinary Biological Science and Technology Co. Ltd., Lanzhou, PR China
| | - Yong Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, PR China.
| | - Xingxu Zhao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, PR China.
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Ravn Warncke S, Rohde Knudsen C. Detection methods targeting the positive- and negative-sense RNA transcripts from plus-stranded RNA viruses. APMIS 2021; 130:284-292. [PMID: 34939239 PMCID: PMC9306919 DOI: 10.1111/apm.13202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/16/2021] [Indexed: 11/27/2022]
Abstract
The largest group of viruses in the Baltimore classification system comprises viruses with a positive-sense, single-stranded RNA genome. Once the viral genome is released into the cytoplasm of a specific host cell following virus entry, it functions directly as a mRNA and the virus-encoded proteins that are essential for genome replication, are produced by the translation apparatus of the host cell. The positive-sense genome is replicated in two stages, initially the positive strand is copied to make a negative-sense RNA, which then functions as the template for transcription of many new positive-sense genomes. Virus infections can be detected at different stages throughout the infection cycle for diagnostic and scientific purposes. Here, the advantages and disadvantages of some of the relevant methods for genome detection will be briefly reviewed with special emphasis on techniques allowing strand-specific RNA detection. Furthermore, tools of the future are considered.
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Affiliation(s)
- Signe Ravn Warncke
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000, Aarhus C, Denmark
| | - Charlotte Rohde Knudsen
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000, Aarhus C, Denmark
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Miyabe FM, Dall Agnol AM, Leme RA, Oliveira TES, Headley SA, Fernandes T, de Oliveira AG, Alfieri AF, Alfieri AA. Porcine rotavirus B as primary causative agent of diarrhea outbreaks in newborn piglets. Sci Rep 2020; 10:22002. [PMID: 33319798 PMCID: PMC7738533 DOI: 10.1038/s41598-020-78797-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/19/2020] [Indexed: 12/19/2022] Open
Abstract
Rotavirus (RV) is considered a major cause of acute viral gastroenteritis in young animals. RV is classified into nine species, five of which have been identified in pigs. Most studies worldwide have highlighted diarrhoea outbreaks caused by RVA, which is considered the most important RV species. In the present study, we described the detection and characterization of porcine RVB as a primary causative agent of diarrhoea outbreaks in pig herds in Brazil. The study showed a high frequency (64/90; 71.1%) of RVB diagnosis in newborn piglets associated with marked histopathological lesions in the small intestines. Phylogenetic analysis of the VP7 gene of wild-type RVB strains revealed a high diversity of G genotypes circulating in one geographic region of Brazil. Our findings suggest that RVB may be considered an important primary enteric pathogen in piglets and should be included in the routine differential diagnosis of enteric diseases in piglets.
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Affiliation(s)
- Flavia Megumi Miyabe
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, PO Box 10011, Londrina, Paraná, 86057-970, Brazil.,Multi-User Animal Health Laboratory-Molecular Biology Unit, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Alais Maria Dall Agnol
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, PO Box 10011, Londrina, Paraná, 86057-970, Brazil.,Multi-User Animal Health Laboratory-Molecular Biology Unit, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Raquel Arruda Leme
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, PO Box 10011, Londrina, Paraná, 86057-970, Brazil.,Multi-User Animal Health Laboratory-Molecular Biology Unit, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Thalita Evani Silva Oliveira
- Laboratory of Animal Pathology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Selwyn Arlington Headley
- Laboratory of Animal Pathology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Thiago Fernandes
- Laboratory of Electron Microscopy, Department of Microbiology, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Admilton Gonçalves de Oliveira
- Laboratory of Electron Microscopy, Department of Microbiology, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Alice Fernandes Alfieri
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, PO Box 10011, Londrina, Paraná, 86057-970, Brazil.,Multi-User Animal Health Laboratory-Molecular Biology Unit, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Amauri Alcindo Alfieri
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, PO Box 10011, Londrina, Paraná, 86057-970, Brazil. .,Multi-User Animal Health Laboratory-Molecular Biology Unit, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
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Tan S, Dvorak CMT, Murtaugh MP. Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model. Viruses 2020; 12:v12101136. [PMID: 33036361 PMCID: PMC7600144 DOI: 10.3390/v12101136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
Emerging viral infectious diseases present a major threat to the global swine industry. Since 2015, Senecavirus A (SVA) has been identified as a cause of vesicular disease in different countries and is considered an emerging disease. Despite the growing concern about SVA, there is a lack of preventive and diagnostic strategies, which is also a problem for all emerging infectious diseases. Using SVA as a model, we demonstrated that Oxford Nanopore MinION sequencing could be used as a robust tool for the investigation and surveillance of emerging viral diseases. Our results identified that MinION sequencing allowed for rapid, unbiased pathogen detection at the species and strain level for clinical cases. SVA whole genome sequences were generated using both direct RNA sequencing and PCR-cDNA sequencing methods, with an optimized consensus accuracy of 94% and 99%, respectively. The advantages of direct RNA sequencing lie in its shorter turnaround time, higher analytical sensitivity and its quantitative relationship between input RNA and output sequencing reads, while PCR-cDNA sequencing excelled at creating highly accurate sequences. This study developed whole genome sequencing methods to facilitate the control of SVA and provide a reference for the timely detection and prevention of other emerging infectious diseases.
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Liu F, Wang Q, Huang Y, Wang N, Shan H. A 5-Year Review of Senecavirus A in China since Its Emergence in 2015. Front Vet Sci 2020; 7:567792. [PMID: 33134352 PMCID: PMC7561413 DOI: 10.3389/fvets.2020.567792] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/21/2020] [Indexed: 12/15/2022] Open
Abstract
Senecavirus A (SVA), previously known as Seneca Valley virus, is classified into the genus Senecavirus in the family Picornaviridae. This virus can cause vesicular disease and epidemic transient neonatal losses in swine. Typical clinical signs include vesicular and/or ulcerative lesions on the snout, oral mucosa, coronary bands and hooves. SVA emerged in Guangdong Province of China in 2015, and thereafter gradually spread into other provinces, autonomous regions and municipalities (P.A.M.s). Nowadays more than half of the P.A.M.s have been affected by SVA, and asymptomatic infection has occurred in some areas. The phylogenetic analysis shows that China isolates are clustered into five genetic branches, implying a fast evolutionary speed since SVA emergence in 2015. This review presented current knowledge concerning SVA infection in China, including its history, epidemiology, evolutionary characteristics, diagnostics and vaccines.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yilan Huang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ning Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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11
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Mu S, Abdullah SW, Zhang Y, Han S, Guo H, Li M, Dong H, Xu J, Teng Z, Wen X, Sun S. Development of a novel SYBR green I-based quantitative RT-PCR assay for Senecavirus A detection in clinical samples of pigs. Mol Cell Probes 2020; 53:101643. [PMID: 32768439 DOI: 10.1016/j.mcp.2020.101643] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 11/26/2022]
Abstract
Porcine vesicular disease caused by Senecavirus A (SVA) is a newly emerging disease in many countries. Based on clinical signs only, it is very challenging to distinguish SVA infection from other similar diseases, such as foot and mouth disease, swine vesicular disease, and vesicular stomatitis. Therefore, it is crucial to establish a detection assay for the clinical diagnosis of SVA infection. In this study, a pair of specific primers were designed based on the highly conserved L/VP4 gene sequence of SVA. The established SYBR green I-based quantitative reverse transcription polymerase chain reaction (qRT-PCR) method was used to detect SVA nucleic acids in clinical samples. The limit of detection SVA nucleic acids by qRT-PCR was 6.4 × 101 copies/μL, which was significantly more sensitive than that by gel electrophoresis of 6.4 × 103 copes/μL. This assay was specific and had no cross-reaction with other seven swine viruses. Using SYBR green I-based qRT-PCR, the SVA positive rates in experimental animal samples and field samples were 67.60% (96/142) and 80% (24/30) respectively. The results demonstrate that SYBR green I-based qRT-PCR is a rapid and specific method for the clinical diagnosis and epidemiological investigation of related vesicular diseases caused by SVA.
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Affiliation(s)
- Suyu Mu
- State Key Laboratory of Veterinary Etiological Biology and National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Sahibzada Waheed Abdullah
- State Key Laboratory of Veterinary Etiological Biology and National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Yun Zhang
- State Key Laboratory of Veterinary Etiological Biology and National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Shichong Han
- State Key Laboratory of Veterinary Etiological Biology and National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Huichen Guo
- State Key Laboratory of Veterinary Etiological Biology and National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China; College of Animal Science, Yangtze University, Jingmi Street, Jingzhou District, Jingzhou, 434025, PR China
| | - Mei Li
- State Key Laboratory of Veterinary Etiological Biology and National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Hu Dong
- State Key Laboratory of Veterinary Etiological Biology and National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Jin Xu
- Bazhong Academy of Agriculture and Forestry, Jiangbei Avenue 1, Bazhong, Sichuan, PR China
| | - Zhidong Teng
- State Key Laboratory of Veterinary Etiological Biology and National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Xiaobo Wen
- College of Animal Science and Technology, Hainan University, Hainan Key Lab of Tropical Animal Reproduction and Breeding and Epidemic Disease Research, Haidian Island, Haikou, 570228, PR China
| | - Shiqi Sun
- State Key Laboratory of Veterinary Etiological Biology and National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China.
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12
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Houston E, Temeeyasen G, Piñeyro PE. Comprehensive review on immunopathogenesis, diagnostic and epidemiology of Senecavirus A. Virus Res 2020; 286:198038. [PMID: 32479975 DOI: 10.1016/j.virusres.2020.198038] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 01/19/2023]
Abstract
Senecavirus A (SVA), formerly known as Seneca Valley virus, is a single-strand, positive-sense RNA virus in the family Picornaviridae. This virus has been associated with recent outbreaks of vesicular disease (SVA-VD) and epidemic transient neonatal losses (ETNL) in several swine-producing countries. The clinical manifestation of and lesion caused by SVA are indistinguishable from other vesicular diseases. Pathogenicity studies indicate that SVA could regulate the host innate immune response to facilitate virus replication and the spread of the virus to bystander cells. SVA infection can induce specific humoral and cellular responses that can be detected within the first week of infection. However, SVA seems to produce persistent infection, and the virus can be shed in oral fluids for a month and detected in tissues for approximately two months after experimental infection. SVA transmission could be horizontal or vertical in infected herds of swine, while positive animals can also remain subclinical. In addition, mice seem to act as reservoirs, and the virus can persist in feed and feed ingredients, increasing the risk of introduction into naïve farms. Besides the pathological effects in swine, SVA possesses cytolytic activity, especially in neoplastic cells. Thus, SVA has been evaluated in phase II clinical trials as a virotherapy for neuroendocrine tumors. The goal of this review is summarize the current SVA-related research in pathogenesis, immunity, epidemiology and advances in diagnosis as well as discuses current challenges with subclinical/persistent presentation.
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Affiliation(s)
- Elizabeth Houston
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA; Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Gun Temeeyasen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Pablo Enrique Piñeyro
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
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13
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Wang Y, Das A, Zheng W, Porter E, Xu L, Noll L, Liu X, Dodd K, Jia W, Bai J. Development and evaluation of multiplex real-time RT-PCR assays for the detection and differentiation of foot-and-mouth disease virus and Seneca Valley virus 1. Transbound Emerg Dis 2019; 67:604-616. [PMID: 31550077 DOI: 10.1111/tbed.13373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 09/06/2019] [Accepted: 09/13/2019] [Indexed: 01/14/2023]
Abstract
Foot-and-mouth disease virus (FMDV) causes a highly contagious and economically important vesicular disease in cloven-hoofed animals that is clinically indistinguishable from symptoms caused by Seneca Valley virus 1 (SVV-1). To differentiate SVV-1 from FMDV infections, we developed a SVV-1 real-time RT-PCR (RT-qPCR) assay and multiplexed with published FMDV assays. Two published FMDV assays (Journal of the American Veterinary Medical Association, 220, 2002, 1636; Journal of Virological Methods, 236, 2016, 258) targeting the 3D polymerase (3D) region were selected and multiplexed with the SVV-1 assay that has two targets, one in the 5' untranslated region (5' UTR, this study) and the other in the 3D region (Journal of Virological Methods, 239, 2017, 34). In silico analysis showed that the primers and probes of SVV-1 assay matched 98.3% of the strain sequences (113/115). The primer and probe sequences of the Shi FMDV assay matched 85.4% (806/944), and that of the Callahan FMDV assay matched 62.7% (592/944) of the sequences. The limit of detection (LOD) for the two multiplex RT-qPCR assays for SVV-1 was both 9 copies per reaction by cloned positive plasmids and 0.16 TCID50 per reaction by cell culture. The LOD for FMDV by both multiplex assays was 11 copies per reaction using cloned positive plasmids. With cell cultures of the seven serotypes of FMDV, the Shi assay (Journal of Virological Methods, 236, 2016, 258) had LODs between 0.04 and 0.18 TCID50 per reaction that were either the same or lower than the Callahan assay. Interestingly, multiplexing with SVV-1 increased the amplification efficiencies of the Callahan assay (Journal of the American Veterinary Medical Association, 220, 2002, 1636) from 51.5%-66.7% to 89.5%-96.6%. Both assays specifically detected the target viruses without cross-reacting to SVV-1 or to other common porcine viruses. An 18S rRNA housekeeping gene that was amplified from multiple cloven-hoofed animal species was used as an internal control. The prevalence study did not detect any FMDV, but SVV-1 was detected from multiple types of swine samples with an overall positive rate of 10.5% for non-serum samples.
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Affiliation(s)
- Yin Wang
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Amaresh Das
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, Plum Island Animal Disease Center, NY, USA
| | - Wanglong Zheng
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Elizabeth Porter
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Lizhe Xu
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, Plum Island Animal Disease Center, NY, USA
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Xuming Liu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Kimberly Dodd
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, Plum Island Animal Disease Center, NY, USA
| | - Wei Jia
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, Plum Island Animal Disease Center, NY, USA
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
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Zhang J, Nfon C, Tsai CF, Lee CH, Fredericks L, Chen Q, Sinha A, Bade S, Harmon K, Piñeyro P, Gauger P, Tsai YL, Wang HTT, Lee PYA. Development and evaluation of a real-time RT-PCR and a field-deployable RT-insulated isothermal PCR for the detection of Seneca Valley virus. BMC Vet Res 2019; 15:168. [PMID: 31126297 PMCID: PMC6534938 DOI: 10.1186/s12917-019-1927-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
Background Seneca Valley virus (SVV) has emerged in multiple countries in recent years. SVV infection can cause vesicular lesions clinically indistinguishable from those caused by other vesicular disease viruses, such as foot-and-mouth disease virus (FMDV), swine vesicular disease virus (SVDV), vesicular stomatitis virus (VSV), and vesicular exanthema of swine virus (VESV). Sensitive and specific RT-PCR assays for the SVV detection is necessary for differential diagnosis. Real-time RT-PCR (rRT-PCR) has been used for the detection of many RNA viruses. The insulated isothermal PCR (iiPCR) on a portable POCKIT™ device is user friendly for on-site pathogen detection. In the present study, SVV rRT-PCR and RT-iiPCR were developed and validated. Results Neither the SVV rRT-PCR nor the RT-iiPCR cross-reacted with any of the vesicular disease viruses (20 FMDV, two SVDV, six VSV, and two VESV strains), classical swine fever virus (four strains), and 15 other common swine viruses. Analytical sensitivities of the SVV rRT-PCR and RT-iiPCR were determined using serial dilutions of in vitro transcribed RNA as well as viral RNA extracted from a historical SVV isolate and a contemporary SVV isolate. Diagnostic performances were further evaluated using 125 swine samples by two approaches. First, nucleic acids were extracted from the 125 samples using the MagMAX™ kit and then tested by both RT-PCR methods. One sample was negative by the rRT-PCR but positive by the RT-iiPCR, resulting in a 99.20% agreement (124/125; 95% CI: 96.59–100%, κ = 0.98). Second, the 125 samples were tested by the taco™ mini extraction/RT-iiPCR and by the MagMAX™ extraction/rRT-PCR system in parallel. Two samples were positive by the MagMAX™/rRT-PCR system but negative by the taco™ mini/RT-iiPCR system, resulting in a 98.40% agreement (123/125; 95% CI: 95.39–100%, κ = 0.97). The two samples with discrepant results had relatively high CT values. Conclusions The SVV rRT-PCR and RT-iiPCR developed in this study are very sensitive and specific and have comparable diagnostic performances for SVV RNA detection. The SVV rRT-PCR can be adopted for SVV detection in laboratories. The SVV RT-iiPCR in a simple field-deployable system could serve as a tool to help diagnose vesicular diseases in swine at points of need.
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Affiliation(s)
- Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA.
| | - Charles Nfon
- National Center for Foreign Animal Diseases, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | | | | | - Lindsay Fredericks
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Qi Chen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Avanti Sinha
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Sarah Bade
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Karen Harmon
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Pablo Piñeyro
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Phillip Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
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15
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Leme RA, Miyabe FM, Dall Agnol AM, Alfieri AF, Alfieri AA. Seneca Valley virus RNA detection in pig feed and feed ingredients in Brazil. Transbound Emerg Dis 2019; 66:1449-1453. [PMID: 31038274 DOI: 10.1111/tbed.13215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/18/2022]
Abstract
We investigated Seneca Valley virus (SVV) contamination in pig feed and feed ingredients. Twenty-seven samples were collected from two Brazilian feed mills and subjected to conventional RT-nested-PCR and qRT-PCR assays. Seven samples were SVV-positive with viral loads of 3.94-4.33 log10 genomic copies/g of feed. The study reveals SVV feed and feed ingredient contamination under natural conditions in Brazil.
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Affiliation(s)
- Raquel Arruda Leme
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Paraná, Brazil.,Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Flavia Megumi Miyabe
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Paraná, Brazil.,Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Alais Maria Dall Agnol
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Paraná, Brazil.,Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Alice Fernandes Alfieri
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Paraná, Brazil.,Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Paraná, Brazil
| | - Amauri Alcindo Alfieri
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Paraná, Brazil.,Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Paraná, Brazil
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16
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Pinheiro-de-Oliveira TF, Fonseca-Júnior AA, Camargos MF, Laguardia-Nascimento M, Giannattasio-Ferraz S, Cottorello ACP, de Oliveira AM, Góes-Neto A, Barbosa-Stancioli EF. Reverse transcriptase droplet digital PCR to identify the emerging vesicular virus Senecavirus A in biological samples. Transbound Emerg Dis 2019; 66:1360-1369. [PMID: 30864242 DOI: 10.1111/tbed.13168] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 12/13/2022]
Abstract
Senecavirus A (SVA) belonging to the family Picornaviridae, genus Senecavirus was incidentally isolated in 2002 from the PER.C6 (transformed foetal retinoblast) cell line. However, currently, this virus is associated with vesicular disease in swine and it has been reported in countries such as the United States of America, Canada, China, Thailand and Colombia. In Brazil, the SVA was firstly reported in 2015 in outbreaks of vesicular disease in swine, clinically indistinguishable of Foot-and-mouth disease, a contagious viral disease that generates substantial economic losses. In the present work, it was standardized a diagnostic tool for SVA based on RNA reverse transcriptase droplet digital PCR (RT-ddPCR) using one-step and two-step approaches. Analytical sensitivity and specificity were done in parallel with real-time PCR, RT-qPCR (one-step and two-step) for comparison of sensitivity and specificity of both methods. In the standardization of RT-ddPCR, the double-quenched probe and the temperature gradient were crucial to reduce background and improve amplitude between positive and negative droplets. The limit of detection and analytical specificity of techniques of one-step techniques showed superior performance than two-step methods described here. Additionally, the results showed 94.2% concordance (p < 0.001) for RT-ddPCR and RT-qPCR using the one-step assay approach and biological samples from Brazilian outbreaks of Senecavirus A. However, ddRT-PCR had a better performance than RT-PCR when swine serum pools were tested. According to the results, the one-step RT-ddPCR and RT-qPCR is highlighted to be used as an auxiliary diagnostic tool for Senecavirus A and for viral RNA absolute quantification in biological samples (RT-ddPCR), being a useful tool for vesicular diseases control programs.
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Affiliation(s)
| | - A A Fonseca-Júnior
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - M F Camargos
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - M Laguardia-Nascimento
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | | | - A C P Cottorello
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - A M de Oliveira
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - A Góes-Neto
- Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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17
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Leme RA, Miyabe FM, Dall Agnol AM, Alfieri AF, Alfieri AA. A new wave of Seneca Valley virus outbreaks in Brazil. Transbound Emerg Dis 2019; 66:1101-1104. [DOI: 10.1111/tbed.13151] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/07/2019] [Accepted: 02/12/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Raquel A. Leme
- Laboratory of Animal VirologyDepartment of Veterinary Preventive MedicineUniversidade Estadual de Londrina Londrina Paraná Brazil
- Multi‐User Animal Health LaboratoryMolecular Biology UnitDepartment of Veterinary Preventive MedicineUniversidade Estadual de Londrina Londrina Paraná Brazil
| | - Flavia M. Miyabe
- Laboratory of Animal VirologyDepartment of Veterinary Preventive MedicineUniversidade Estadual de Londrina Londrina Paraná Brazil
- Multi‐User Animal Health LaboratoryMolecular Biology UnitDepartment of Veterinary Preventive MedicineUniversidade Estadual de Londrina Londrina Paraná Brazil
| | - Alais M. Dall Agnol
- Laboratory of Animal VirologyDepartment of Veterinary Preventive MedicineUniversidade Estadual de Londrina Londrina Paraná Brazil
- Center for Agroveterinary SciencesUniversidade do Estado de Santa Catarina Lages Santa Catarina Brazil
| | - Alice F. Alfieri
- Laboratory of Animal VirologyDepartment of Veterinary Preventive MedicineUniversidade Estadual de Londrina Londrina Paraná Brazil
- Multi‐User Animal Health LaboratoryMolecular Biology UnitDepartment of Veterinary Preventive MedicineUniversidade Estadual de Londrina Londrina Paraná Brazil
| | - Amauri A. Alfieri
- Laboratory of Animal VirologyDepartment of Veterinary Preventive MedicineUniversidade Estadual de Londrina Londrina Paraná Brazil
- Multi‐User Animal Health LaboratoryMolecular Biology UnitDepartment of Veterinary Preventive MedicineUniversidade Estadual de Londrina Londrina Paraná Brazil
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18
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Zhang Z, Zhang Y, Lin X, Chen Z, Wu S. Development of a novel reverse transcription droplet digital PCR assay for the sensitive detection of Senecavirus A. Transbound Emerg Dis 2018; 66:517-525. [PMID: 30375741 DOI: 10.1111/tbed.13056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/08/2018] [Accepted: 10/24/2018] [Indexed: 12/27/2022]
Abstract
In pigs, Senecavirus A (SVA) causes a vesicular disease that is clinically indistinguishable from foot-and-mouth disease, vesicular stomatitis and swine vesicular disease. Sensitive and specific detection of SVA is critical for controlling this emerging disease. In this study, a novel reverse transcription droplet digital PCR (RT-ddPCR) assay, targeting the conserved viral polymerase 3D gene, was established for the detection of SVA. This assay exhibited good linearity, repeatability and reproducibility, and maintained linearity at extremely low concentrations of SVA nucleic acid templates. The detection limit of RT-ddPCR was 1.53 ± 0.22 copies of SVA RNA per reaction (n = 8), and the assay showed approximately 10-fold greater sensitivity than a reverse transcription real-time PCR (RT-rPCR) assay. Moreover, specificity analysis showed that the RT-ddPCR for SVA had no cross-reactivity with other important swine pathogens. In clinical diagnosis of 134 pig serum and tissue samples, 26 and 21 samples were identified as positive by RT-ddPCR and RT-rPCR, respectively. The overall agreement between the two assays was 96.27% (129/134). Further linear regression analysis showed a significant correlation between the RT-ddPCR and RT-rPCR assays with an R2 value of 0.9761. Our results indicate that the RT-ddPCR assay is a robust diagnostic tool for the sensitive detection of SVA, even in samples with a low viral load.
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Affiliation(s)
- Zhou Zhang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Yongning Zhang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Xiangmei Lin
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University, Jiangsu, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Jiangsu, China
| | - Shaoqiang Wu
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
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19
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Lin J, Chen L, Jiang W, Zhang H, Shi Y, Cai W. Rapid detection of low-level HeLa cell contamination in cell culture using nested PCR. J Cell Mol Med 2018; 23:227-236. [PMID: 30353657 PMCID: PMC6307787 DOI: 10.1111/jcmm.13923] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 08/26/2018] [Indexed: 01/08/2023] Open
Abstract
HeLa cells are a commonly used cell line in many biological research areas. They are not picky for culture medium and proliferate rapidly. HeLa cells are a notorious source of cell cross‐contamination and have been found to be able to contaminate a wide range of cell lines in cell culture. In this study, we reported a simple and efficient method for detecting the presence of HeLa cell contamination in cell culture. HPV‐18 was used as a biomarker. The cell culture supernatant was used directly as the template for nested PCR without extracting nucleic acid. By PCR amplification of the cell culture supernatant with the designed primers, we were able to detect the presence of HeLa cells in the culture. The sensitivity of this method can reach 1%, which is 10‐fold higher than Short tandem repeat sequence (STR) profiling. This simple, rapid, and “noninvasive” quality checking method should find applications in routine cell culture practice.
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Affiliation(s)
- Jun Lin
- Institute of Apply Genomics, Fuzhou University, Fuzhou, China.,School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Lin Chen
- Institute of Apply Genomics, Fuzhou University, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Wenqian Jiang
- Institute of Apply Genomics, Fuzhou University, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Huilian Zhang
- Institute of Apply Genomics, Fuzhou University, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Yang Shi
- Institute of Apply Genomics, Fuzhou University, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Weiwen Cai
- Institute of Apply Genomics, Fuzhou University, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
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20
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Zeng F, Cong F, Liu X, Lian Y, Wu M, Xiao L, Yuan W, Huang R, Ma J, Guo P, Luo M. Development of a real time loop-mediated isothermal amplification method for detection of Senecavirus A. J Virol Methods 2018; 261:98-103. [PMID: 30096349 DOI: 10.1016/j.jviromet.2018.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/04/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
Abstract
Senecavirus A (SVA), formerly known as Seneca Valley Virus (SVV), is one of causative agents of vesicular diseases in swine. Recently, the outbreaks associated with vesicular disease caused by SVA infection in pig herds have been reported in Brazil, USA, China, Thailand and Canada. Several molecular detection methods have been established to determine the infection of SVA, including real time reverse transcription PCR assay, nested PCR, a TaqMan-based qRT-PCR assay and RNA-based in situ hybridization method. In our study, an assay for the identification of SVA in pig herds using real time reverse transcription loop-mediated isothermal amplification (real time RT-LAMP) was developed. The limit of detection for the assay was 1 TCID50/ml. One hundred and eighteen field samples from pigs were used to validate the assay for clinical application. Our result demonstrated that real time RT-LAMP assay is a cost-effective and highly specific and sensitive alternative for the rapid detection of SVA in clinical samples.
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Affiliation(s)
- Fanwen Zeng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
| | - Feng Cong
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
| | - Xiangnan Liu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
| | - Yuexiao Lian
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China; Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
| | - Miaoli Wu
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
| | - Li Xiao
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
| | - Wen Yuan
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
| | - Ren Huang
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
| | - Jingyun Ma
- College of Animal Science, South China Agricultural University, Wushan Road 483, Tianhe District, Guangzhou 510642, China.
| | - Pengju Guo
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
| | - Manlin Luo
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China.
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