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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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4
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Kidd SP, Burns D, Armson B, Beggs AD, Howson ELA, Williams A, Snell G, Wise EL, Goring A, Vincent-Mistiaen Z, Grippon S, Sawyer J, Cassar C, Cross D, Lewis T, Reid SM, Rivers S, James J, Skinner P, Banyard A, Davies K, Ptasinska A, Whalley C, Ferguson J, Bryer C, Poxon C, Bosworth A, Kidd M, Richter A, Burton J, Love H, Fouch S, Tillyer C, Sowood A, Patrick H, Moore N, Andreou M, Morant N, Houghton R, Parker J, Slater-Jefferies J, Brown I, Gretton C, Deans Z, Porter D, Cortes NJ, Douglas A, Hill SL, Godfrey KM, Fowler VL. Reverse-Transcription Loop-Mediated Isothermal Amplification Has High Accuracy for Detecting Severe Acute Respiratory Syndrome Coronavirus 2 in Saliva and Nasopharyngeal/Oropharyngeal Swabs from Asymptomatic and Symptomatic Individuals. J Mol Diagn 2022; 24:320-336. [PMID: 35121140 PMCID: PMC8806713 DOI: 10.1016/j.jmoldx.2021.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/02/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Previous studies have described reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal/oropharyngeal swab and saliva samples. This multisite clinical evaluation describes the validation of an improved sample preparation method for extraction-free RT-LAMP and reports clinical performance of four RT-LAMP assay formats for SARS-CoV-2 detection. Direct RT-LAMP was performed on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva samples from asymptomatic and symptomatic individuals across health care and community settings. For direct RT-LAMP, overall diagnostic sensitivity (DSe) was 70.35% (95% CI, 63.48%-76.60%) on swabs and 84.62% (95% CI, 79.50%-88.88%) on saliva, with diagnostic specificity of 100% (95% CI, 98.98%-100.00%) on swabs and 100% (95% CI, 99.72%-100.00%) on saliva, compared with quantitative RT-PCR (RT-qPCR); analyzing samples with RT-qPCR ORF1ab CT values of ≤25 and ≤33, DSe values were 100% (95% CI, 96.34%-100%) and 77.78% (95% CI, 70.99%-83.62%) for swabs, and 99.01% (95% CI, 94.61%-99.97%) and 87.61% (95% CI, 82.69%-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and diagnostic specificity were 96.06% (95% CI, 92.88%-98.12%) and 99.99% (95% CI, 99.95%-100%) for swabs, and 80.65% (95% CI, 73.54%-86.54%) and 99.99% (95% CI, 99.95%-100%) for saliva, respectively. These findings demonstrate that RT-LAMP is applicable to a variety of use cases, including frequent, interval-based direct RT-LAMP of saliva from asymptomatic individuals who may otherwise be missed using symptomatic testing alone.
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Affiliation(s)
- Stephen P Kidd
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Daniel Burns
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; School of Electronics and Computer Science, University of Southampton, Southampton, United Kingdom
| | - Bryony Armson
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom; vHive, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Andrew D Beggs
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | | | - Anthony Williams
- University of Southampton and Division of Specialist Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Gemma Snell
- University of Southampton and Division of Specialist Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Emma L Wise
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Alice Goring
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | | | - Seden Grippon
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Jason Sawyer
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Claire Cassar
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - David Cross
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Thomas Lewis
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Scott M Reid
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Samantha Rivers
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Joe James
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Paul Skinner
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Ashley Banyard
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Kerrie Davies
- Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, United Kingdom
| | - Anetta Ptasinska
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Celina Whalley
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Jack Ferguson
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Claire Bryer
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Charlie Poxon
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Andrew Bosworth
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Michael Kidd
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom; Public Health West Midlands Laboratory, Birmingham, United Kingdom
| | - Alex Richter
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Jane Burton
- High Containment Microbiology, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - Hannah Love
- High Containment Microbiology, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - Sarah Fouch
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Claire Tillyer
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Amy Sowood
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Helen Patrick
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Nathan Moore
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, United Kingdom
| | - Rebecca Houghton
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Joe Parker
- National Biofilms Innovation Centre, University of Southampton, Southampton, United Kingdom
| | | | - Ian Brown
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Cosima Gretton
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Zandra Deans
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Deborah Porter
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Nicholas J Cortes
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; Gibraltar Health Authority, Gibraltar, United Kingdom
| | - Angela Douglas
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Sue L Hill
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Keith M Godfrey
- National Institute for Health Research Southampton Biomedical Research Centre, University of Southampton and University Hospital, Southampton, United Kingdom; MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, United Kingdom.
| | - Veronica L Fowler
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
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5
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Wang H, Ding X, Sun W, Chen Z, Bai L, Liang H, Liu Y, Zhang W, Wang G, Yang G, Mauk MG, Cui Y, Chen L. Recombinase polymerase amplification assay for rapid detection of Seneca Valley Virus. Anal Biochem 2022; 642:114564. [DOI: 10.1016/j.ab.2022.114564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/02/2022] [Accepted: 01/17/2022] [Indexed: 11/01/2022]
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Wang W, Zhou L, Ge X, Han J, Guo X, Chen Y, Zhang Y, Yang H. Development of a VP2-based real-time fluorescent reverse transcription recombinase-aided amplification assay to rapidly detect Senecavirus A. Transbound Emerg Dis 2021; 69:2828-2839. [PMID: 34931455 DOI: 10.1111/tbed.14435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 01/28/2023]
Abstract
Senecavirus A (SVA), a newly emergent picornavirus correlated with sudden neonatal mortality and vesicular lesions in pigs, has had a considerable impact on the global pig farming industry. Timely and dependable detection of SVA is helpful in preventing the further spread of this pathogenic virus. In the current study, a real-time fluorescent reverse transcription recombinase-aided amplification (rRT-RAA) assay, which targets the most conserved region within the VP2 gene of SVA, was developed and evaluated for SVA detection. The detection limit for this assay was tested to be 1.185 50% tissue culture infective dose (TCID50 ) of SVA RNA per reaction at a 95% confidence interval, which is comparable to that of a previously published rRT-PCR assay for SVA. The testing results of the rRT-RAA assay were very reproducible and repeatable, with inter- and intra-assay coefficient of variation values less than 7.0%. In addition, the established rRT-RAA assay displayed excellent specificity for SVA detection without cross-reaction with other clinically important swine pathogenic viruses. The diagnostic performance of rRT-RAA was evaluated using 189 clinical swine samples, which were detected in parallel using the reference rRT-PCR assay. The results showed that 146 and 151 samples tested positive for SVA by rRT-RAA and rRT-PCR, respectively. The overall agreement between both assays was 97.4% (184/189) with a kappa value of 0.927 (p < .001). Further linear regression analysis demonstrated that the detection results between the two assays were significantly correlated (R2 = 0.9192, p < .0001). Taken together, our newly established rRT-RAA assay is a powerful and time-saving diagnostic tool for SVA detection in clinical samples. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wenlong Wang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Yanhong Chen
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Yongning Zhang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
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7
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Wanjala BW, Ateka EM, Miano DW, Fuentes S, Perez A, Low JW, Kreuze JF. Loop-Mediated Isothermal Amplification assays for on-site detection of the main sweetpotato infecting viruses. J Virol Methods 2021; 298:114301. [PMID: 34560111 PMCID: PMC8543070 DOI: 10.1016/j.jviromet.2021.114301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 11/22/2022]
Abstract
Globally, Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV) occur frequently and in combination cause sweetpotato virus disease (SPVD). Many viral diseases are economically important and negatively impact the production and movement of germplasm across regions. Rapid detection of viruses is critical for effective control. Detection and quantification of viruses directly from sweetpotato remains a challenge. Current diagnostic tests are not sensitive enough to reliably detect viruses directly from the plant or require expensive laboratory equipment and expertise to perform. We developed a simple and rapid loop-mediated isothermal amplification (LAMP) assay for the detection of SPFMV, SPCSV and begomoviruses related to sweet potato leaf curl virus (SPLCV). Laboratory validation recorded 100 % diagnostic sensitivity for all the three viruses. The LAMP assays were customized for field testing using a lyophilized thermostable isothermal master mix in a ready-to-use form that required no cold chain. The average time to positivity (TTP) was: SPFMV 5-30 min, SPCSV 15-43 min s and begomoviruses 28-45 mins. LAMP on-site testing results were comparable to PCR and RT-PCR confirmatory laboratory tests. The LAMP assay is a powerful tool for rapid sweetpotato virus detection at a reasonable cost and thus could serve as quality control systems for planting materials.
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Affiliation(s)
- Bramwel W Wanjala
- International Potato Center, SSA Regional Office, PO Box 25171, 00603, Nairobi, Kenya; Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, 00200, Nairobi, Kenya.
| | - Elijah M Ateka
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, 00200, Nairobi, Kenya.
| | - Douglas W Miano
- University of Nairobi, P.O. Box: 30197, 00100, Nairobi, Kenya.
| | - Segundo Fuentes
- International Potato Center, Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru.
| | - Ana Perez
- International Potato Center, Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru.
| | - Jan W Low
- International Potato Center, SSA Regional Office, PO Box 25171, 00603, Nairobi, Kenya.
| | - Jan F Kreuze
- International Potato Center, Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru.
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8
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Howson ELA, Kidd SP, Armson B, Goring A, Sawyer J, Cassar C, Cross D, Lewis T, Hockey J, Rivers S, Cawthraw S, Banyard A, Anderson P, Rahou S, Andreou M, Morant N, Clark D, Walsh C, Laxman S, Houghton R, Slater-Jefferies J, Costello P, Brown I, Cortes N, Godfrey KM, Fowler VL. Preliminary optimisation of a simplified sample preparation method to permit direct detection of SARS-CoV-2 within saliva samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 2021; 289:114048. [PMID: 33358911 PMCID: PMC7750029 DOI: 10.1016/j.jviromet.2020.114048] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/28/2020] [Accepted: 12/12/2020] [Indexed: 11/15/2022]
Abstract
We describe the optimisation of a simplified sample preparation method which permits rapid and direct detection of SARS-CoV-2 RNA within saliva, using reverse-transcription loop-mediated isothermal amplification (RT-LAMP). Treatment of saliva samples prior to RT-LAMP by dilution 1:1 in Mucolyse™, followed by dilution in 10 % (w/v) Chelex© 100 Resin and a 98 °C heat step for 2 min enabled detection of SARS-CoV-2 RNA in positive saliva samples. Using RT-LAMP, SARS-CoV-2 RNA was detected in as little as 05:43 min, with no amplification detected in 3097 real-time reverse transcription PCR (rRT-PCR) negative saliva samples from staff tested within a service evaluation study, or for other respiratory pathogens tested (n = 22). Saliva samples can be collected non-invasively, without the need for skilled staff and can be obtained from both healthcare and home settings. Critically, this approach overcomes the requirement for, and validation of, different swabs and the global bottleneck in obtaining access to extraction robots and reagents to enable molecular testing by rRT-PCR. Such testing opens the possibility of public health approaches for effective intervention during the COVID-19 pandemic through regular SARS-CoV-2 testing at a population scale, combined with isolation and contact tracing.
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Affiliation(s)
- Emma L A Howson
- GeneSys Biotech Limited, Camberley, Surrey, UK; The Pirbright Institute, Ash Road, Woking, Surrey, UK
| | - Stephen P Kidd
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK.
| | - Bryony Armson
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK; vHive, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Alice Goring
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK
| | - Jason Sawyer
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Claire Cassar
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - David Cross
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Tom Lewis
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Jess Hockey
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | | | | | - Paul Anderson
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Sabah Rahou
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, UK
| | | | | | | | - Rebecca Houghton
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK
| | | | - Paula Costello
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK
| | - Ian Brown
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Nicholas Cortes
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK; NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton, UK
| | - Veronica L Fowler
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK
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9
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Fowler VL, Armson B, Gonzales JL, Wise EL, Howson ELA, Vincent-Mistiaen Z, Fouch S, Maltby CJ, Grippon S, Munro S, Jones L, Holmes T, Tillyer C, Elwell J, Sowood A, de Peyer O, Dixon S, Hatcher T, Patrick H, Laxman S, Walsh C, Andreou M, Morant N, Clark D, Moore N, Houghton R, Cortes NJ, Kidd SP. A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection. J Infect 2021; 82:117-125. [PMID: 33271166 PMCID: PMC7703389 DOI: 10.1016/j.jinf.2020.10.039] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/04/2020] [Accepted: 10/07/2020] [Indexed: 12/23/2022]
Abstract
The COVID-19 pandemic has illustrated the importance of simple, rapid and accurate diagnostic testing. This study describes the validation of a new rapid SARS-CoV-2 RT-LAMP assay for use on extracted RNA or directly from swab offering an alternative diagnostic pathway that does not rely on traditional reagents that are often in short supply during a pandemic. Analytical specificity (ASp) of this new RT-LAMP assay was 100% and analytical sensitivity (ASe) was between 1 × 101 and 1 × 102 copies per reaction when using a synthetic DNA target. The overall diagnostic sensitivity (DSe) and specificity (DSp) of RNA RT-LAMP was 97% and 99% respectively, relative to the standard of care rRT-PCR. When a CT cut-off of 33 was employed, above which increasingly evidence suggests there is a low risk of patients shedding infectious virus, the diagnostic sensitivity was 100%. The DSe and DSp of Direct RT-LAMP (that does not require RNA extraction) was 67% and 97%, respectively. When setting CT cut-offs of ≤33 and ≤25, the DSe increased to 75% and 100%, respectively, time from swab-to-result, CT < 25, was < 15 min. We propose that RNA RT-LAMP could replace rRT-PCR where there is a need for increased sample throughput and Direct RT-LAMP as a near-patient screening tool to rapidly identify highly contagious individuals within emergency departments and care homes during times of increased disease prevalence ensuring negative results still get laboratory confirmation.
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Affiliation(s)
- Veronica L Fowler
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Eco Animal Health, The Grange, 100 The High Street, London, UK
| | - Bryony Armson
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Jose L Gonzales
- Wageningen Bioveterinary Research (WBVR), PO Box 65, 8200 AB Lelystad, the Netherlands
| | - Emma L Wise
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Emma L A Howson
- GeneSys Biotech Limited, Camberley, Surrey, UK; The Pirbright Institute, Ash Road, Pirbright, Woking, UK
| | - Zoe Vincent-Mistiaen
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Sarah Fouch
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Pharmacy and Biomedical Sciences, University of Portsmouth, UK
| | - Connor J Maltby
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Seden Grippon
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Simon Munro
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Lisa Jones
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Tom Holmes
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Claire Tillyer
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Joanne Elwell
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Amy Sowood
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Oliver de Peyer
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Sophie Dixon
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Thomas Hatcher
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Helen Patrick
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | | | | | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, UK
| | | | - Nathan Moore
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Rebecca Houghton
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Nicholas J Cortes
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Stephen P Kidd
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK.
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10
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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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11
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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: 16] [Impact Index Per Article: 3.2] [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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12
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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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13
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Li J, Liang W, Xu S, Shi J, Zhou X, Liu B, Yu L, Xiong J, Si G, He D. Rapid and sensitive detection of Senecavirus A by reverse transcription loop-mediated isothermal amplification combined with a lateral flow dipstick method. PLoS One 2019; 14:e0216245. [PMID: 31048910 PMCID: PMC6497277 DOI: 10.1371/journal.pone.0216245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/16/2019] [Indexed: 11/19/2022] Open
Abstract
Senecavirus A (SVA) is a critical pathogen causing vesicular lesions in sows and acute death of newborn piglets, resulting in very large economic losses in the pig industry. To restrict the transmission of SVA, an establishment of an effective diagnostic method is crucial for the prevention and control of the disease. However, traditional detection methods often have many drawbacks. In this study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) was combined with a lateral flow dipstick (LFD) to detect SVA. The resulting RT-LAMP-LFD assay was performed at 60°C for 50 min and then directly judged on an LFD visualization strip. This method shows high specificity and sensitivity to SVA. The detection limit of RT-LAMP was 4.56x10-8 ng/μL RNA, approximately 11 copies/μL RNA, and it was 10 times more sensitive than RT-PCR. This detection method’s positive rate for clinical samples is comparable to that of RT-PCR. This method is time saving and highly efficient and is thus expected to be used to diagnose SVA infections in this field.
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Affiliation(s)
- Jinhui Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Weifang Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Shuaifei Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jian Shi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xia Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bowen Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Li Yu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jingfeng Xiong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Guangbin Si
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Dongsheng He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, Guangzhou, China
- * E-mail:
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14
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Armson B, Walsh C, Morant N, Fowler V, Knowles NJ, Clark D. The development of two field-ready reverse transcription loop-mediated isothermal amplification assays for the rapid detection of Seneca Valley virus 1. Transbound Emerg Dis 2019; 66:497-504. [PMID: 30372584 PMCID: PMC6434928 DOI: 10.1111/tbed.13051] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 09/11/2018] [Accepted: 10/19/2018] [Indexed: 12/25/2022]
Abstract
Seneca Valley virus 1 (SVV-1) has been associated with vesicular disease in swine, with clinical signs indistinguishable from those of other notifiable vesicular diseases such as foot-and-mouth disease. Rapid and accurate detection of SVV-1 is central to confirm the disease causing agent, and to initiate the implementation of control processes. The development of rapid, cost-effective diagnostic assays that can be used at the point of sample collection has been identified as a gap in preparedness for the control of SVV-1. This study describes the development and bench validation of two reverse transcription loop-mediated amplification (RT-LAMP) assays targeting the 5'-untranslated region (5'-UTR) and the VP3-1 region for the detection of SVV-1 that may be performed at the point of sample collection. Both assays were able to demonstrate amplification of all neat samples diluted 1/100 in negative pig epithelium tissue suspension within 8 min, when RNA was extracted prior to the RT-LAMP assay, and no amplification was observed for the other viruses tested. Simple sample preparation methods using lyophilized reagents were investigated, to negate the requirement for RNA extraction. Only a small delay in the time to amplification was observed for these lyophilized reagents, with a time from sample receipt to amplification achieved within 12 min. Although diagnostic validation is recommended, these RT-LAMP assays are highly sensitive and specific, with the potential to be a useful tool in the rapid diagnosis of SVV-1 in the field.
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Affiliation(s)
- Bryony Armson
- The Pirbright InstitutePirbrightSurreyUK
- Institute of Biodiversity, Animal Health and Comparative MedicineCollege of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
- GeneSys Biotech LimitedCamberleySurreyUK
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