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Liao K, Peng W, Qian B, Nan W, Shan Y, Zeng D, Tang F, Wu X, Chen Y, Xue F, Dai J. A highly adaptable platform powered by CRISPR-Cas12a to diagnose lumpy skin disease in cattle. Anal Chim Acta 2022; 1221:340079. [PMID: 35934339 DOI: 10.1016/j.aca.2022.340079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 12/24/2022]
Abstract
Lumpy skin disease (LSD) in cattle, a transboundary viral disease of cattle once restricted to Africa, has been spreading to many European and Asian countries in the past decade with huge economic losses. This emerging worldwide threat to cattle warrants the development of diagnostic methods for accurate disease screening of suspected samples to effectively control the spread of LSD. In this study, we integrated pre-amplification and three kinds of sensor systems with CRISPR and therefore established an LSD diagnosis platform with highly adaptable and ultra-sensitive advantages. It was the first CRISPR-powered platform that could identify lumpy skin disease virus from vaccine strains of goat pox virus and sheep pox virus. Its limit of detection (LOD) was one copy/reaction after introducing PCR or recombinase-aided amplification (RAA). Moreover, this platform achieved a satisfactory overall agreement in clinical diagnoses of 50 samples and its reproducibility and accuracy were superior to other qPCR methods we tested. The whole diagnostic procedure, from DNA extraction to the results, could complete in 5 h with a total cost of 1.7-9.6 $/test. Overall, this CRISPR-powered platform provided a novel diagnostic tool for portable, ultra-sensitive, rapid, and highly adaptable disease screening of LSD and may be an effective method to control this transboundary disease's spread.
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Affiliation(s)
- Kai Liao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanqing Peng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingxu Qian
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenlong Nan
- Laboratory of Diagnostics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China
| | - Yuping Shan
- Lianyungang Animal Husbandry and Veterinary Station, Lianyungang, Jiangsu, 222003, China
| | - Dexin Zeng
- Technology Center of Hefei Customs, Hefei, 230022, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaodong Wu
- Laboratory of Diagnostics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China
| | - Yiping Chen
- Laboratory of Diagnostics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China.
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; China Pharmaceutical University, Nanjing, 211198, China
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Jiang C, Tao D, Geng Y, Yang H, Xu B, Chen Y, Hu C, Chen H, Xie S, Guo A. Sensitive and Specific Detection of Lumpy Skin Disease Virus in Cattle by CRISPR-Cas12a Fluorescent Assay Coupled with Recombinase Polymerase Amplification. Genes (Basel) 2022; 13:genes13050734. [PMID: 35627121 PMCID: PMC9141258 DOI: 10.3390/genes13050734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023] Open
Abstract
Lumpy skin disease (LSD) is a severe and highly infectious pox disease of cattle caused by the lumpy skin disease virus (LSDV). To facilitate early control of LSD, this study aimed to develop a new rapid on-site LSDV detection method using an orf068 gene-based recombinase polymerase amplification assay (RPA) coupled with a CRISPR-Cas12a-based fluorescence assay (RPA-Cas12a-fluorescence assay). The results showed that the sensitivity of our RPA-Cas12a-fluorescence assay for detecting LSDV orf068 gene reached 5 copies/μL with plasmid as a template, and 102 TCID50/mL with viral genomic DNA as a template. No cross-reaction with other common bovine viruses was observed. Further, an on-site RPA-Cas12a-fluorescence assay of 40 clinical samples from cattle with or without LSD showed a diagnostic sensitivity of 96.3% (95% CI: 81.0-99.9%) and specificity of 92.31% (95% CI: 62.1-99.6%), which was close to those of the quantitative PCR assay. Therefore, our RPA-Cas12a-fluorescence assay has promising prospects in on-site rapid LSDV detection.
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Affiliation(s)
- Chuanwen Jiang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
| | - Dagang Tao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
| | - Yuanchen Geng
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
| | - Hao Yang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
| | - Bingrong Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan 430070, China
| | - Changmin Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan 430070, China
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan 430070, China
| | - Shengsong Xie
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Correspondence: (S.X.); (A.G.); Tel.: +86-2787-2871-15 (A.G.)
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (C.J.); (Y.G.); (H.Y.); (Y.C.); (H.C.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (D.T.); (C.H.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan 430070, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of China Agriculture and Rural Affairs, Wuhan 430070, China
- Correspondence: (S.X.); (A.G.); Tel.: +86-2787-2871-15 (A.G.)
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Agianniotaki EI, Chaintoutis SC, Haegeman A, De Clercq K, Chondrokouki E, Dovas CI. A TaqMan probe-based multiplex real-time PCR method for the specific detection of wild type lumpy skin disease virus with beta-actin as internal amplification control. Mol Cell Probes 2021; 60:101778. [PMID: 34774743 DOI: 10.1016/j.mcp.2021.101778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/22/2021] [Accepted: 11/09/2021] [Indexed: 11/28/2022]
Abstract
Lumpy skin disease (LSD) is a transboundary disease of economic importance affecting cattle and buffaloes. In South-Eastern Europe, immunization of cattle with homologous live attenuated vaccines for LSD control has prevented outbreaks since 2017, but has been associated with adverse reactions resembling disease symptoms. Thus, a diagnostic method suitable for disease surveillance in farms during vaccination campaigns with Neethling (Onderstepoort) and SIS type (Lumpyvax) live attenuated LSDV vaccines in Europe should be able to detect the wild type (WT) LSDV in animals with adverse reactions to the vaccines and samples with potentially high titers of the vaccine LSDV. To this end, a real-time PCR method targeting the EEV gene of LSDV was developed for the specific detection of WT strains, along with the use of beta-actin gene as an internal amplification control (IAC). Amplification efficiency of the WT virus target was 99.0% and 98.6%, in the presence and in the absence of high loads of vaccine LSDV, respectively. In the presence of 105.6 vaccine LSDV DNA copies, the limit of detection for WT LSDV was 12.6 DNA copies per reaction. The inter-assay CV was 0.04% for WT LSDV and 0.13% for beta-actin. The method can confirm diagnosis in suspect cases irrespective of the presence of the vaccine LSDV DNA by overcoming the masking effect of the WT LSDV. The simultaneous amplification of the beta-actin gene further assures the quality of diagnostic testing. The new method is a surveillance tool, complementing the DIVA real-time PCR during vaccination campaigns and can provide rapid insight on the targeted EEV gene in countries with novel and recombinant LSDV strains.
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Affiliation(s)
- Eirini I Agianniotaki
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece; National Reference Laboratory for Capripoxviruses, Department of Molecular Diagnostics, FMD, Virological, Rickettsial & Exotic Diseases, Directorate of Athens Veterinary Center, Ministry of Rural Development and Food, Athens, Greece
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andy Haegeman
- Exotic Viruses and Particular Diseases Unit, Sciensano, Ukkel, Belgium
| | - Kris De Clercq
- Exotic Viruses and Particular Diseases Unit, Sciensano, Ukkel, Belgium
| | - Eleni Chondrokouki
- National Reference Laboratory for Capripoxviruses, Department of Molecular Diagnostics, FMD, Virological, Rickettsial & Exotic Diseases, Directorate of Athens Veterinary Center, Ministry of Rural Development and Food, Athens, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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Das A, Wang Y, Babiuk S, Bai J, Dodd K, Jia W. Development of multiplex real-time PCR assays for differential detection of capripoxvirus, parapoxvirus and foot-and-mouth disease virus. Transbound Emerg Dis 2021; 69:1326-1337. [PMID: 33837669 DOI: 10.1111/tbed.14099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
This study reports the development of multiplex real-time PCR assays for differential detection of capripoxvirus (CaPV), parapoxvirus (PaPV) and foot-and-mouth disease virus (FMDV) in sheep, goats and cattle. Three multiplex assays were developed, a capripox (CaP) rule-out assay for simultaneous detection and differentiation of CaPV and PaPV, a FMD rule-out assay for simultaneous detection and differentiation of FMDV and PaPV, and a FMD/CaP rule-out assay for simultaneous detection and differentiation of CaPV, PaPV and FMDV. All multiplex assays included β-actin gene ACTB as an internal positive control to monitor PCR inhibition and accuracy of nucleic acid extractions. The optimized assays were highly specific to the target viruses (CaPV, PaPV and FMDV) with no cross-reactivity against other viruses that cause similar clinical signs. Using positive control plasmids as template, the limit of detection (LOD) of the multiplex assays were estimated as 2 CaPV, 7 PaPV and 15 FMDV copies per assay. The amplification efficiency (AE) and correlation coefficient (R2 ), estimated from the standard curves (Ct vs. log10 template dilution), were 94%-106% and >0.99, respectively, for CaP and FMD rule-out assays, 96%-116% (AE) and >0.98 (R2 ), respectively, for CaP/FMD rule-out assays and 91%-102% and >0.99, respectively, for the corresponding singleplex assays. The diagnostic sensitivity (DSe) of the multiplex assays was assessed on 35 CaPV and 39 FMDV clinical specimens from experimentally infected (CS-E) animals, and 29 CaPV (LSDV), 28 FMDV and 36 PaPV clinical specimens from naturally infected (CS-N) animals; all tested positive (DSe 100%) except two CS-E FMDV specimens that were tested negative by FMD rule-out and the corresponding singleplex (FMDV) assays (37/39; DSe 95%). The newly developed multiplex assays offer a valuable tool for differential detection of clinically indistinguishable CaPV, PaPV and FMDV in suspected animals and animals with mixed infections.
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Affiliation(s)
- Amaresh Das
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
| | - Yin Wang
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Kimberly Dodd
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
| | - Wei Jia
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
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