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Zhao Y, Zhou C, Guo B, Yang X, Wang H. Pyrococcus furiosus Argonaute-mediated porcine epidemic diarrhea virus detection. Appl Microbiol Biotechnol 2024; 108:137. [PMID: 38229331 DOI: 10.1007/s00253-023-12919-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024]
Abstract
Porcine epidemic diarrhea virus (PEDV), an enteric coronavirus, induces severe vomiting and acute watery diarrhea in unweaned piglets. The pig industry has suffered tremendous financial losses due to the high mortality rate of piglets caused by PEDV. Consequently, a simple and rapid on-site diagnostic technology is crucial for preventing and controlling PEDV. This study established a detection method for PEDV using recombinase-aided amplification (RAA) and Pyrococcus furiosus Argonaute (PfAgo), which can detect 100 copies of PEDV without cross-reactivity with other pathogens. The entire reaction of RAA and PfAgo to detect PEDV does not require sophisticated instruments, and the reaction results can be observed with the naked eye. Overall, this integrated RAA-PfAgo cleavage assay is a practical tool for accurately and quickly detecting PEDV. KEY POINTS: • PfAgo has the potential to serve as a viable molecular diagnostic tool for the detection and diagnosis of viral genomes • The RAA-PfAgo detection technique has a remarkable level of sensitivity and specificity • The RAA-PfAgo detection system can identify PEDV without needing advanced equipment.
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Affiliation(s)
- Yu Zhao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Boyan Guo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xin Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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Zhang T, Tang J, Zhang Y, Jin Y, Lin Z, Chen J, Huang J, Mo M. Establishment of a rapid real-time fluorescence-based recombinase-aided amplification method for detection of avian infectious bronchitis virus. J Virol Methods 2024; 328:114955. [PMID: 38768869 DOI: 10.1016/j.jviromet.2024.114955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
Infectious bronchitis (IB) is an acute, highly contagious contact respiratory disease of chickens caused by infectious bronchitis virus (IBV). IBV is very prone to mutation, which brings great difficulties to the prevention and control of the disease. Therefore, there is a pressing need for a method that is fast, sensitive, specific, and convenient for detecting IBV. In this study, a real-time fluorescence-based recombinase-aided amplification (RF-RAA) method was established. Primers and probe were designed based on the conserved regions of the IBV M gene and the reaction concentrations were optimized, then the specificity, sensitivity, and reproducibility of this assay were tested. The results showed that the RF-RAA method could be completed at 39℃ within 20 min, during which the results could be interpreted visually in real-time. The RF-RAA method had good specificity, no cross-reaction with common poultry pathogens, and it detected a minimum concentration of template of 2 copies/μL for IBV. Besides, its reproducibility was stable. A total of 144 clinical samples were tested by RF-RAA and real-time quantitative PCR (qPCR), 132 samples of which were positive and 12 samples were negative, and the coincidence rate of the two methods was 100 %. In conclusion, the developed RF-RAA detection method is rapid, specific, sensitive, reproducible, and convenient, which can be utilized for laboratory detection and clinical diagnosis of IBV.
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Affiliation(s)
- Taoni Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jinwen Tang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yu Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yinghao Jin
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Zixue Lin
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jiming Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jianni Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Meilan Mo
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China; Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning 530004, China; Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning 530004, China.
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3
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Luo T, Li K, Li C, Xia C, Gao C. Development of a triplex quantitative reverse transcription-polymerase chain reaction for the detection of porcine epidemic diarrhea virus, porcine transmissible gastroenteritis virus, and porcine rotavirus A. Front Microbiol 2024; 15:1390328. [PMID: 38800746 PMCID: PMC11117717 DOI: 10.3389/fmicb.2024.1390328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
Porcine viral diarrhea is caused by many pathogens and can result in watery diarrhea, dehydration and death. Various detection methods, such as polymerase chain reaction (PCR) and real-time quantitative PCR (qPCR), have been widely used for molecular diagnosis. We developed a triplex real-time quantitative reverse transcription PCR (qRT-PCR) for the simultaneous detection of three RNA viruses potentially associated with porcine viral diarrhea: porcine epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), and porcine rotavirus A (PoRVA). The triplex qRT-PCR had R2 values of 0.999 for the standard curves of PEDV, TGEV and PoRVA. Importantly, the limits of detection for PEDV, TGEV and PoRVA were 10 copies/μL. The specificity test showed that the triplex qRT-PCR detected these three pathogens specifically, without cross-reaction with other pathogens. In addition, the approach had good repeatability and reproducibility, with intra-and inter-assay coefficients of variation <1%. Finally, this approach was evaluated for its practicality in the field using 256 anal swab samples. The positive rates of PEDV, TGEV and PoRVA were 2.73% (7/256), 3.91% (10/256) and 19.14% (49/256), respectively. The co-infection rate of two or more pathogens was 2.73% (7/256). The new triplex qRT-PCR was compared with the triplex RT-PCR recommended by the Chinese national standard (GB/T 36871-2018) and showed 100% agreement for PEDV and TGEV and 95.70% for PoRVA. Therefore, the triplex qRT-PCR provided an accurate and sensitive method for identifying three potential RNA viruses for porcine viral diarrhea that could be applied to diagnosis, surveillance and epidemiological investigation.
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Affiliation(s)
| | | | | | - Changyou Xia
- State Key Laboratory for Animal Disease Control and Prevention, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Caixia Gao
- State Key Laboratory for Animal Disease Control and Prevention, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Xu S, Man Y, Xu X, Ji J, Wang Y, Yao L, Xie Q, Bi Y. The Development of a Multienzyme Isothermal Rapid Amplification Assay to Visually Detect Duck Hepatitis B Virus. Vet Sci 2024; 11:191. [PMID: 38787163 PMCID: PMC11126061 DOI: 10.3390/vetsci11050191] [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: 02/28/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Duck hepatitis B virus (DHBV) is widely prevalent in global ducks and has been identified in Chinese geese with a high prevalence; the available detection techniques are time-consuming and require sophisticated equipment. In this study, an assay combining multienzyme isothermal rapid amplification (MIRA) and lateral flow dipstick (LFD) was developed for the efficient and rapid detection of DHBV. The primary reaction condition of the MIRA assay for DHBV detection was 10 min at 38 °C without a temperature cycler. Combined with the LFD assay, the complete procedure of the newly developed MIRA assay for DHBV detection required only 15 min, which is about one-fourth of the reaction time for routine polymerase chain reaction assay. And electrophoresis and gel imaging equipment were not required for detection and to read the results. Furthermore, the detection limit of MIRA was 45.6 copies per reaction, which is approximately 10 times lower than that of a routine polymerase chain reaction assay. The primer set and probe had much simpler designs than loop-mediated isothermal amplification, and they were only specific to DHBV, with no cross-reactivity with duck hepatitis A virus subtype 1 and duck hepatitis A virus subtype 3, goose parvovirus, duck enteritis virus, duck circovirus, or Riemerella anatipestifer. In this study, we offer a simple, fast, and accurate assay method to identify DHBV in clinical serum samples of ducks and geese, which would be suitable for widespread application in field clinics.
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Affiliation(s)
- Shuqi Xu
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China; (S.X.); (Y.M.); (X.X.); (Y.W.); (L.Y.)
| | - Yuanzhuo Man
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China; (S.X.); (Y.M.); (X.X.); (Y.W.); (L.Y.)
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China; (S.X.); (Y.M.); (X.X.); (Y.W.); (L.Y.)
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China; (S.X.); (Y.M.); (X.X.); (Y.W.); (L.Y.)
| | - Yan Wang
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China; (S.X.); (Y.M.); (X.X.); (Y.W.); (L.Y.)
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang 473061, China; (S.X.); (Y.M.); (X.X.); (Y.W.); (L.Y.)
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.X.); (Y.B.)
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.X.); (Y.B.)
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Ren J, Zu C, Li Y, Li M, Gu J, Chen F, Li X. Establishment and application of a TaqMan-based multiplex real-time PCR for simultaneous detection of three porcine diarrhea viruses. Front Microbiol 2024; 15:1380849. [PMID: 38690365 PMCID: PMC11058560 DOI: 10.3389/fmicb.2024.1380849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction Porcine viral diarrhea is a common clinical disease, which results in high mortality and economic losses in the pig industry. Porcine epidemic diarrhea virus (PEDV), porcine rotavirus (PoRV), and porcine deltacoronavirus (PDCoV) are important diarrhea viruses in pig herds. The similarities of their clinical symptoms and pathological changes make it difficult to distinguish these three viruses clinically. Therefore, there is a need for a highly sensitive and specific method to simultaneously detect and differentiate these viruses. Methods A multiplex real-time PCR assay using TaqMan probes was developed to simultaneously detect PEDV, PoRV, and PDCoV. To assess the efficacy of the established assay, 30 clinical samples with diarrhea symptoms were used to compare the results obtained from the multiplex real-time PCR assay with those obtained from commercial singleplex real-time PCR kit. Importantly, a total of 4,800 diarrhea samples were tested and analyzed to validate the utility of the assay. Results This multiplex real-time PCR assay showed high sensitivity, specificity, and excellent repeatability with a detection limit of 1 × 102 copies/μL. Comparing the results of the commercial singleplex real-time PCR kit and the multiplex real-time PCR method for detecting PEDV, PoRV, and PDCoV, there was complete agreement between the two approaches. Clinical data revealed single infection rates of 6.56% for PEDV, 21.69% for PoRV, and 6.65% for PDCoV. The co-infection rates were 11.83% for PEDV + PoRV, 0.29% for PEDV + PDCoV, 5.71% for PoRV + PDCoV, and 1.29% for PEDV + PDCoV + PoRV, respectively. Discussion The multiplex real-time PCR method established in this study is a valuable diagnostic tool for simultaneously differentiating PEDV, PoRV, and PDCoV. This method is expected to significantly contribute to prevent and control the spread of infectious diseases, as well as aid in conducting epidemiological investigations.
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Affiliation(s)
- Jing Ren
- Shandong Engineering Research Center of Swine Health Data and Intelligent Monitoring, Dezhou University, Dezhou, China
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Congcong Zu
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, China
| | - Yang Li
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, China
| | - Meng Li
- Shandong Engineering Research Center of Swine Health Data and Intelligent Monitoring, Dezhou University, Dezhou, China
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Jinyuan Gu
- Shandong Engineering Research Center of Swine Health Data and Intelligent Monitoring, Dezhou University, Dezhou, China
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Fengling Chen
- Shandong Engineering Research Center of Swine Health Data and Intelligent Monitoring, Dezhou University, Dezhou, China
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Xiaowen Li
- Shandong Engineering Research Center of Swine Health Data and Intelligent Monitoring, Dezhou University, Dezhou, China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd. (NHLH Academy of Swine Research), Dezhou, China
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Wang F, Liang Q, Lv R, Ahmad S, Bano M, Weng G, Wen R. Optimization and Validation of Reverse Transcription Recombinase-Aided Amplification (RT-RAA) for Sorghum Mosaic Virus Detection in Sugarcane. Pathogens 2023; 12:1055. [PMID: 37624015 PMCID: PMC10457762 DOI: 10.3390/pathogens12081055] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Sorghum mosaic virus (SrMV) causes sugarcane mosaic disease and has significant adverse economic impacts on the cultivation of sugarcane. This study aimed to develop a rapid isotherm nucleic acid amplification method for detecting SrMV. Specific primers were designed to target the conserved region of the P3 gene of SrMV. The reverse transcription recombinase-aided amplification (RT-RAA) method was developed by screening primers and optimizing reaction conditions. Comparative analyses with RT-PCR demonstrated that the RT-RAA method exhibited superior specificity, sensitivity, and reliability for SrMV detection. Notably, using a standard plasmid diluted 10-fold continuously as a template, the sensitivity of RT-RAA was 100-fold higher than that of RT-PCR. Moreover, the RT-RAA reaction displayed flexibility in a temperature range of 24-49 °C, eliminating the need for expensive and complex temperature control equipment. Thus, this method could be utilized at ambient or even human body temperature. Within a short duration of 10 min at 39 °C, the target sequence of SrMV could be effectively amplified. Specificity analysis revealed no cross-reactivity between SrMV and other common sugarcane viruses detected via the RT-RAA. With its high sensitivity, rapid reaction time, and minimal equipment requirements, this method presents a promising diagnostic tool for the reliable and expedited detection of SrMV. Furthermore, it indicates broad applicability for successfully detecting other sugarcane viruses.
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Affiliation(s)
| | | | | | | | | | | | - Ronghui Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Ministry and Province Co-Sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; (F.W.); (Q.L.); (R.L.); (S.A.); (M.B.); (G.W.)
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Special Issue "State-of-the-Art Porcine Virus Research in China". Viruses 2023; 15:v15020412. [PMID: 36851626 PMCID: PMC9964372 DOI: 10.3390/v15020412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 01/23/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
China is one of the major countries involved in pig production and pork consumption [...].
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Cui H, Zhang C, Tu F, Zhao K, Kong Y, Pu J, Zhang L, Chen Z, Sun Y, Wei Y, Liang C, Liu J, Liu J, Guo Z. Rapid detection of influenza A viruses using a real-time reverse transcription recombinase-aided amplification assay. Front Cell Infect Microbiol 2023; 12:1071288. [PMID: 36683681 PMCID: PMC9849684 DOI: 10.3389/fcimb.2022.1071288] [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: 10/16/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction Influenza A viruses (IAVs) are important pathogens of respiratory infections, causing not only seasonal influenza but also influenza pandemics and posing a global threat to public health. IAVs infection spreads rapidly, widely, and across species, causing huge losses, especially zoonotic IAVs infections that are more harmful. Fast and sensitive detection of IAVs is critical for controlling the spread of this disease. Methods Here, a real-time reverse transcription recombinase-aided amplification (real-time RT-RAA) assay targeting conserved positions in the matrix protein gene (M gene) of IAVs, is successfully established to detect IAVs. The assay can be completed within 20 min at 42°C. Results The sensitivity of the real-time RT-RAA assay was 142 copies per reaction at 95% probability, which was comparable to the sensitivity of the RT-qPCR assay. The specificity assay showed that the real-time RT-RAA assay was specific to IAVs, and there was no cross-reactivity with other important viruses. In addition, 100%concordance between the real-time RT-RAA and RT-qPCR assays was achieved after testing 120 clinical specimens. Discussion The results suggested that the real-time RT-RAA assay we developed was a specific, sensitive and reliable diagnostic tool for the rapid detection of IAVs.
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Affiliation(s)
- Huan Cui
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
- College of Animal Medicine, Jilin University, Changchun, China
| | - Cheng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Fei Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
| | - Kui Zhao
- College of Animal Medicine, Jilin University, Changchun, China
| | - Yunyi Kong
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
| | - Jie Pu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
| | - Lei Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
| | - Zhaoliang Chen
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Yuanyuan Sun
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Yujie Wei
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Chuncai Liang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Juxiang Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
| | - Zhendong Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun, China
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Xu H, Peng L, Wu J, Khan A, Sun Y, Shen H, Li Z. Clustered Regularly Interspaced Short Palindromic Repeats-Associated Proteins13a combined with magnetic beads, chemiluminescence and reverse transcription-recombinase aided amplification for detection of avian influenza a (H7N9) virus. Front Bioeng Biotechnol 2023; 10:1094028. [PMID: 36686235 PMCID: PMC9849363 DOI: 10.3389/fbioe.2022.1094028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/02/2022] [Indexed: 01/06/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Clustered Regularly Interspaced Short Palindromic Repeats-Associated Proteins (CRISPR-Cas) have promising prospects in the field of nucleic acid molecular diagnostics. However, Clustered Regularly Interspaced Short Palindromic Repeats-based fluorescence detection technology is mainly hindered by proteins with conjugated double bonds and autofluorescence, resulting in high fluorescence background, low sensitivity and incompatible reaction systems, which are not conducive to automatic clinical testing. Chemiluminescence (CL) detection technology has been applied mainly owing to its greatly high sensitivity, as well as low background and rapid response. Therefore, we developed a rapid, ultrasensitive and economical detection system based on Clustered Regularly Interspaced Short Palindromic Repeats-Clustered Regularly Interspaced Short Palindromic Repeats-Associated Proteins 13a combined with magnetic beads (MBs) and chemiluminescence (CL) (Cas13a-MB-CL) to detect Influenza A (H7N9), an acute respiratory tract infectious disease. The carboxyl functionalized magnetic beads (MBs-COOH) were covalently coupled with aminated RNA probe while the other end of the RNA probe was modified with biotin. Alkaline phosphatase labeled streptavidin (SA-ALP) binds with biotin to form magnetic beads composites. In presence of target RNA, the collateral cleavage activity of Cas13a was activated to degrade the RNA probes on MBs and released Alkaline phosphatase from the composites. The composites were then magnetically separated followed by addition of ALP substrate Disodium 2-chloro-5-{4-methoxyspiro [1,2-dioxetane-3,2'-(5'-chloro) tricyclo (3.3.1.13,7) decan]-4-yl}-1-phenyl phosphate (CDP-star), to generate the chemiluminescence signal. The activity of Associated Proteins 13a and presence of target RNA was quantified by measuring the chemiluminescence intensity. The proposed method accomplished the detection of H7N9 within 30 min at 25°C. When combined with Reverse Transcription- Recombinase Aides Amplification (RT-RAA), the low detection limit limit of detection was as low as 19.7 fM (3S/N). Our proposed MB-Associated Proteins 13a-chemiluminescence was further evaluated to test H7N9 clinical samples, showing superior sensitivity and specificity.
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Affiliation(s)
- Hongpan Xu
- Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, China
| | - Lijun Peng
- Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, China,Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jie Wu
- Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, China
| | - Adeel Khan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), Southeast University, Nanjing, China
| | - Yifan Sun
- Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, China
| | - Han Shen
- Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, China,*Correspondence: Han Shen, ; Zhiyang Li,
| | - Zhiyang Li
- Nanjing Drum Tower Hospital Clinical College of Jiangsu University, Nanjing, China,*Correspondence: Han Shen, ; Zhiyang Li,
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Niu TM, Yu LJ, Zhao JH, Zhang RR, Ata EB, Wang N, Zhang D, Yang YL, Qian JH, Chen QD, Yang GL, Huang HB, Shi CW, Jiang YL, Wang JZ, Cao X, Zeng Y, Wang N, Yang WT, Wang CF. Characterization and pathogenicity of the porcine epidemic diarrhea virus isolated in China. Microb Pathog 2023; 174:105924. [PMID: 36473667 DOI: 10.1016/j.micpath.2022.105924] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Piglet diarrhea caused by the porcine epidemic diarrhea virus (PEDV) is a common problem on pig farms in China associated with high morbidity and mortality rates. In this study, three PEDV isolates were successfully detected after the fourth blind passage in Vero cells. The samples were obtained from infected piglet farms in Jilin (Changchun), and Shandong (Qingdao) Provinces of China and were designated as CH/CC-1/2018, CH/CC-2/2018, and CH/QD/2018. According to the analysis of the complete S protein gene sequence, the CH/CC-1/2018 and CH/CC-2/2018 were allocated to the G2b branch, while CH/QD/2018 was located in the G1a interval and was closer to the vaccine strain CV777. Successful detection and identification of the isolated strains were carried out using electron microscopy and indirect immunofluorescence. Meanwhile, animal challenge experiments and viral RNA copies determination were used to compare the pathogenicity. The results showed that CH/CC-1/2018 in Changchun was more pathogenic than CH/QD/2018 in Qingdao. In conclusion, the discovery of these new strains is conducive to the development of vaccines to prevent the pandemic of PEDV, especially that the CH/CC-1/2018, and CH/CC-2/2018 were not related to the classical vaccine strain CV777.
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Affiliation(s)
- Tian-Ming Niu
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Ling-Jiao Yu
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jin-Hui Zhao
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Rong-Rong Zhang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Emad Beshir Ata
- Parasitology and Animal Diseases Dep, Vet. Res. Institute, National Research Centre, 12622, Dokki, Cairo, Egypt
| | - Nan Wang
- Jilin Province Animal Disease Prevention and Control Center, Changchun, China
| | - Di Zhang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yong-Lei Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jia-Hao Qian
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Qiao-Dan Chen
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Gui-Lian Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Hai-Bin Huang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chun-Wei Shi
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yan-Long Jiang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jian-Zhong Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xin Cao
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yan Zeng
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Nan Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Wen-Tao Yang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China.
| | - Chun-Feng Wang
- College of Veterinary Medicine, College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of the Ministry of Education, Jilin Agricultural University, Changchun, China.
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11
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Pang L, Pi X, Yang X, Song D, Qin X, Wang L, Man C, Zhang Y, Jiang Y. Nucleic acid amplification-based strategy to detect foodborne pathogens in milk: a review. Crit Rev Food Sci Nutr 2022; 64:5398-5413. [PMID: 36476145 DOI: 10.1080/10408398.2022.2154073] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Milk contaminated with trace amounts of foodborne pathogens can considerably threaten food safety and public health. Therefore, rapid and accurate detection techniques for foodborne pathogens in milk are essential. Nucleic acid amplification (NAA)-based strategies are widely used to detect foodborne pathogens in milk. This review article covers the mechanisms of the NAA-based detection of foodborne pathogens in milk, including polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), rolling circle amplification (RCA), and enzyme-free amplification, among others. Key factors affecting detection efficiency and the advantages and disadvantages of the above techniques are analyzed. Potential on-site detection tools based on NAA are outlined. We found that NAA-based strategies were effective in detecting foodborne pathogens in milk. Among them, PCR was the most reliable. LAMP showed high specificity, whereas RPA and RCA were most suitable for on-site and in-situ detection, respectively, and enzyme-free amplification was more economical. However, factors such as sample separation, nucleic acid target conversion, and signal transduction affected efficiency of NAA-based strategies. The lack of simple and effective sample separation methods to reduce the effect of milk matrices on detection efficiency was noteworthy. Further research should focus on simplifying, integrating, and miniaturizing microfluidic on-site detection platforms.
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Affiliation(s)
- Lidong Pang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xiaowen Pi
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Danliangmin Song
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xue Qin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Lihan Wang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yu Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
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12
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Cui H, Tu F, Zhang C, Zhang C, Zhao K, Liu J, Dong S, Chen L, Liu J, Guo Z. Real-Time Reverse Transcription Recombinase-Aided Amplification Assay for Rapid Amplification of the N Gene of SARS-CoV-2. Int J Mol Sci 2022; 23:ijms232315269. [PMID: 36499594 PMCID: PMC9736922 DOI: 10.3390/ijms232315269] [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: 10/16/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/08/2022] Open
Abstract
COVID-19 was officially declared a global pandemic disease on 11 March 2020, with severe implications for healthcare systems, economic activity, and human life worldwide. Fast and sensitive amplification of the severe acute respiratory syndrome virus 2 (SARS-CoV-2) nucleic acids is critical for controlling the spread of this disease. Here, a real-time reverse transcription recombinase-aided amplification (RT-RAA) assay, targeting conserved positions in the nucleocapsid protein gene (N gene) of SARS-CoV-2, was successfully established for SARS-CoV-2. The assay was specific to SARS-CoV-2, and there was no cross-reaction with other important viruses. The sensitivity of the real-time RT-RAA assay was 142 copies per reaction at 95% probability. Furthermore, 100% concordance between the real-time RT-RAA and RT-qPCR assays was achieved after testing 72 clinical specimens. Further linear regression analysis indicated a significant correlation between the real-time RT-RAA and RT-qPCR assays with an R2 value of 0.8149 (p < 0.0001). In addition, the amplicons of the real-time RT-RAA assay could be directly visualized by a portable blue light instrument, making it suitable for the rapid amplification of SARS-CoV-2 in resource-limited settings. Therefore, the real-time RT-RAA method allows the specific, sensitive, simple, rapid, and reliable detection of SARS-CoV-2.
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Affiliation(s)
- Huan Cui
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
- College of Animal Medicine, Jilin University, Changchun 130062, China
| | - Fei Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
| | - Cheng Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Chunmao Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
| | - Kui Zhao
- College of Animal Medicine, Jilin University, Changchun 130062, China
| | - Juxiang Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Shishan Dong
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Ligong Chen
- College of Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
- Correspondence: (J.L.); (Z.G.); Tel.: +86-431-86985932 (J.L.); +86-431-86985975 (Z.G.)
| | - Zhendong Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Changchun 130122, China
- Correspondence: (J.L.); (Z.G.); Tel.: +86-431-86985932 (J.L.); +86-431-86985975 (Z.G.)
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13
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Xia W, Chen Y, Ding X, Liu X, Lu H, Guo C, Zhang H, Wu Z, Huang J, Fan Z, Yu S, Sun H, Zhu S, Wu Z. Rapid and Visual Detection of Type 2 Porcine Reproductive and Respiratory Syndrome Virus by Real-Time Fluorescence-Based Reverse Transcription Recombinase-Aided Amplification. Viruses 2022; 14:v14112526. [PMID: 36423135 PMCID: PMC9699348 DOI: 10.3390/v14112526] [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: 10/16/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is one of the most important diseases that has brought significant economic losses to the swine industry worldwide. Rapid and accurate PRRS virus (PRRSV) detection is one of the key factors for PRRS prevention and control. This study developed a real-time fluorescence-based reverse transcription recombinase-aided amplification (RF-RT-RAA) method for type 2 PRRSV (PRRSV-2) detection. The RF-RT-RAA assay could be performed at 42 °C for 20 min with the optimal primers and a probe. RF-RT-RAA results could be monitored using real-time fluorescence read-out or visually observed with the naked eye using a portable blue light transilluminator. The method had a strong specificity; no cross-reaction was identified with the detected common swine viruses. Moreover, the technique yielded high sensitivity with the lowest detection limit of 101 copies/μL and exhibited good repeatability and reproductively with the coefficients of variation (CV) less than 10%. Eighty-seven clinical samples were tested using RF-RT-RAA and a commercial PRRSV-2 RT-qPCR detection kit. The coincidence rate was 100% between RF-RT-RAA (real-time fluorescence read-out) and RT-qPCR, and 97.7% between RF-RT-RAA (visually observed) and RT-qPCR. The RF-RT-RAA assay provides a new method for rapid and visual detection of PRRSV-2.
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Affiliation(s)
- Wenlong Xia
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224007, China
- Correspondence: (W.X.); (Z.W.)
| | - Yao Chen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224007, China
| | - Xue Ding
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224007, China
| | - Xiaoming Liu
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Huipeng Lu
- Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China
| | - Changming Guo
- Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China
| | - Hua Zhang
- School of Pharmacy, Yancheng Teachers University, Yancheng 224007, China
- Jiangsu Province Engineering Research Center of Tumor Targeted Nano Diagnostic and Therapeutic Materials, Yancheng Teachers University, Yancheng 224007, China
| | - Zhijun Wu
- School of Pharmacy, Yancheng Teachers University, Yancheng 224007, China
- Jiangsu Province Engineering Research Center of Tumor Targeted Nano Diagnostic and Therapeutic Materials, Yancheng Teachers University, Yancheng 224007, China
| | - Jing Huang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224007, China
| | - Zhongjun Fan
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224007, China
| | - Shupei Yu
- Yancheng Animal Husbandry and Veterinary Station, Yancheng 224001, China
| | - Huaichang Sun
- College of Veterinary Medicine, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Shanyuan Zhu
- Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China
| | - Zhi Wu
- Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China
- Correspondence: (W.X.); (Z.W.)
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14
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Wu X, Kong J, Yao Z, Sun H, Liu Y, Wu Z, Liu J, Zhang H, Huang H, Wang J, Chen M, Zeng Y, Huang Y, Chen F, Xie Q, Zhang X. A new rapid and sensitive method for detecting chicken infectious anemia virus. Front Microbiol 2022; 13:994651. [PMID: 36246275 PMCID: PMC9558101 DOI: 10.3389/fmicb.2022.994651] [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: 07/15/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Since the chicken infectious anemia virus (CIAV) was discovered in 1979, which has been reported as an economically significant and immunosuppressive poultry disease in the world. A novel clinical detection method for the prevention and control of CIAV in the poultry sector is urgently needed. Here, we established a real-time recombinase-aided amplification assay (RAA) for CIAV on-site with a rapid, highly sensitive, strongly specific, low-cost, and simple operational molecular diagnosis detection method. The primers and probe were developed using the CIAV VP2 gene sequence, which has a 117-bp specific band. This assay, which could be carried out at 41°C and completed in 30 min without cross-reactivity with other viruses, had the lowest detection limit of 10 copies of CIAV DNA molecules per reaction. Furthermore, the kappa value of this assay was 0.947, the sensitivity was 93.33%, and the specificity was 100% when compared to the real-time quantitative polymerase chain reaction assay (real-time qPCR). These results indicate that using a real-time RAA assay to detect CIAV on-site could be beneficial. In the future, the real-time RAA test may be a regular assay for the prevention and control of CIAV, as well as help the reduction of economic losses in the poultry business.
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Affiliation(s)
- Xiuhong Wu
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Jie Kong
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Ziqi Yao
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Hejing Sun
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Yuanjia Liu
- Department of Veterinary Medicine, College of Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Zhiqiang Wu
- Wen’s Group Academy, Wen’s Foodstuffs Group Co., Ltd, Yunfu, Xinxing, China
| | - Jiajia Liu
- Wen’s Group Academy, Wen’s Foodstuffs Group Co., Ltd, Yunfu, Xinxing, China
| | - Hao Zhang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Haohua Huang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Jin Wang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Mengjun Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Yichen Zeng
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Yinpeng Huang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Feng Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Qingmei Xie
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
- *Correspondence: Qingmei Xie,
| | - Xinheng Zhang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
- Xinheng Zhang,
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15
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Wu X, Chu F, Zhang L, Chen S, Gao L, Zhang H, Huang H, Wang J, Chen M, Xie Z, Chen F, Zhang X, Xie Q. New rapid detection by using a constant temperature method for avian leukosis viruses. Front Microbiol 2022; 13:968559. [PMID: 36060773 PMCID: PMC9433894 DOI: 10.3389/fmicb.2022.968559] [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: 06/14/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
The avian leukemia virus causes avian leukemia (AL), a severe immunosuppressive disease in chickens (ALV). Since the 1990s, the diversity of ALV subpopulations caused by ALV genome variation and recombination, and the complexity of the infection and transmission, with currently no effective commercial vaccine and therapeutic for ALV, has resulted in severe economic losses to the chicken business in various parts of the world. Therefore, as a key means of prevention and control, an effective, rapid, and accurate detection method is imperative. A new real-time reverse transcription recombinase-aided amplification (RT-RAA) assay for ALV with rapid, highly specific, low-cost, and simple operational characteristics have been developed in this study. Based on the amplification of 114 base pairs from the ALV P12 gene, real-time RT-RAA primers and a probe were designed for this study. The lowest detection line was 10 copies of ALV RNA molecules per response, which could be carried out at 39°C in as fastest as 5 min and completed in 30 min, with no cross-reactivity with Marek's disease virus, avian reticuloendothelial virus, Newcastle disease virus, infectious bronchitis virus, infectious bursal disease virus, infectious laryngotracheitis virus, and avian influenza virus. Furthermore, the kappa value of 0.91 (>0.81) was compared with reverse transcription–polymerase chain reaction (RT-PCR) for 44 clinical samples, and the coefficients of variation were within 5.18% of the repeated assays with three low-level concentration gradients. These results indicate that using a real-time RT-RAA assay to detect ALV could be a valuable method.
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Affiliation(s)
- Xiuhong Wu
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Fengsheng Chu
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Luxuan Zhang
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou, China
| | - Sheng Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Liguo Gao
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Hao Zhang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Haohua Huang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Jin Wang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Mengjun Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
| | - Zi Xie
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Feng Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
| | - Xinheng Zhang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
- *Correspondence: Xinheng Zhang
| | - Qingmei Xie
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, China
- Qingmei Xie
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16
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Abstract
INTRODUCTION Recombinase polymerase amplification (RPA) is a promising and emerging technology for rapidly amplifying target nucleic acid from minimally processed samples and through small portable instruments. RPA is suitable for point-of-care testing (POCT) and on-site field testing, and it is compatible with microfluidic devices. Several detection assays have been developed, but limited research has dug deeper into the chemistry of RPA to understand its kinetics and fix its shortcomings. AREAS COVERED This review provides a detailed introduction of RPA molecular mechanism, kits formats, optimization, application, pros, and cons. Moreover, this critical review discusses the nonspecificity issue of RPA, highlights its consequences, and emphasizes the need for more research to resolve it. This review discusses the reaction kinetics of RPA in relation to target length, product quantity, and sensitivity. This critical review also questions the novelty of recombinase-aided amplification (RAA). In short, this review discusses many aspects of RPA technology that have not been discussed previously and provides a deeper insight and new perspectives of the technology. EXPERT OPINION RPA is an excellent choice for pathogen detection, especially in low-resource settings. It has a potential to replace PCR for all purposes, provided its shortcomings are fixed and its reagent accessibility is improved.
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Affiliation(s)
- Mustafa Ahmad Munawar
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
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