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Sarkar R, Roychoudhury P, Kumar S, Dutta S, Konwar N, Subudhi PK, Dutta TK. Rapid detection of Actinobacillus pleuropneumoniae targeting the apxIVA gene for diagnosis of contagious porcine pleuropneumonia in pigs by Polymerase Spiral Reaction. Lett Appl Microbiol 2022; 75:442-449. [PMID: 35616177 DOI: 10.1111/lam.13749] [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: 03/20/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022]
Abstract
Actinobacillus pleuropneumoniae is the primary etiological agent of contagious porcine pleuropneumonia associated with serious economic impact on pig husbandry worldwide. Diagnosis of the disease by existing techniques including isolation and identification bacteria followed by serotyping, serological techniques, conventional PCR, real-time PCR and LAMP assays are cumbersome, time consuming, costly and not suitable for rapid field application. A novel isothermal polymerase chain reaction (PSR) technique is standardized for all the reagents, incubation time and incubation temperature against A. pleuropneumoniae. Sensitivity of the assay was determined against various dilutions of purified DNA and total bacterial count. Specificity of the assay was determined against 11 closely related bacterial isolates. The relative sensitivity and specificity was compared with bacterial isolation, conventional PCR and real-time PCR assays. The PSR assay for specific detection was standardized at 64o C for 30 minutes incubation in a water bath. The result was visible by the naked eye after centrifugation of the reaction mixture or after incorporation of SYBR Green dye as yellow-green fluorescence. The technique was found to be 100% specific and equally sensitive with real-time PCR and 10 times more sensitive than conventional PCR. The PSR assay could be applicable in detection of the organisms in porcine nasal swabs spiked with A. pleuropneumoniae. This is the first ever report on development of PSR for specific detection of A. pleuropneumoniae and can be applied for early diagnosis at field level.
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Affiliation(s)
- R Sarkar
- Department of Veterinary Microbiology, Central Agricultural University, Selesih, Aizawl, Mizoram-796 014, India
| | - P Roychoudhury
- Department of Veterinary Microbiology, Central Agricultural University, Selesih, Aizawl, Mizoram-796 014, India
| | - S Kumar
- Department of Veterinary Microbiology, Central Agricultural University, Selesih, Aizawl, Mizoram-796 014, India
| | - S Dutta
- Department of Veterinary Microbiology, Central Agricultural University, Selesih, Aizawl, Mizoram-796 014, India
| | - N Konwar
- Department of Veterinary Microbiology, Central Agricultural University, Selesih, Aizawl, Mizoram-796 014, India
| | - P K Subudhi
- Department of Veterinary Microbiology, Central Agricultural University, Selesih, Aizawl, Mizoram-796 014, India
| | - T K Dutta
- Department of Veterinary Microbiology, Central Agricultural University, Selesih, Aizawl, Mizoram-796 014, India
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Jangra S, Ghosh A, Mukherjee S, Baranwal VK, Dietzgen RG. Development of a Polymerase Spiral Reaction-Based Isothermal Assay for Rapid Identification of Thrips palmi. Front Mol Biosci 2022; 9:853339. [PMID: 35586189 PMCID: PMC9108268 DOI: 10.3389/fmolb.2022.853339] [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: 01/12/2022] [Accepted: 03/23/2022] [Indexed: 12/03/2022] Open
Abstract
Thrips cause considerable economic losses to a wide range of food, feed, and forest crops. They also transmit several plant viruses. Being cryptic, it is often difficult to distinguish thrips species in crops and large consignments by conventional methods. Melon thrips (Thrips palmi Karny, Thysanoptera: Thripidae) is an invasive insect pest of vegetables, legumes, and ornamentals besides being vector to several viruses. It poses a threat to domestic and international plant biosecurity and can invade and establish in new areas. Here, we report a polymerase spiral reaction (PSR)-based isothermal assay for rapid, sensitive, specific, low-cost, and on-site detection of T. palmi. To the best of our knowledge, this is the first application of PSR in the identification of any insect species. A primer pair designed based on 3′-polymorphism of mtCOIII region can specifically identify T. palmi without any cross-reactivity with predominant thrips species. The assay uses crude lysate of a single thrips saving time and reagents involved in nucleic acid extraction. The presence of T. palmi is visualized by the appearance of bright fluorescence under ultraviolet light or a change in reaction color thus avoiding gel electrophoresis steps. The entire process can be completed in 70 min on-site using only an ordinary water bath. The assay is sensitive to detecting as little as 50 attograms of T. palmi template. The assay was validated with known thrips specimens and found to be efficient in diagnosing T. palmi under natural conditions. The described method will be useful for non-expert personnel to detect an early infestation, accidental introduction to a new area, restrict the spread of diseases and formulate appropriate management strategies.
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Affiliation(s)
- Sumit Jangra
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Amalendu Ghosh
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Amalendu Ghosh, , orcid.org/0000-0001-6634-5771
| | - Sunil Mukherjee
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Virendra Kumar Baranwal
- Insect Vector Laboratory, Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Saint Lucia, QLD, Australia
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Wu X, Chen Q, Yang C, Ning Q, Liu Z. An enhanced visual detection assay for Listeria monocytogenes in food based on isothermal amplified peroxidase-mimicking catalytic beacon. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Ashmi M, Kumar B, Agrawal RK, Prakash C, Abhishek, Singh KP. Development of BruAb2_0168 based isothermal Polymerase Spiral Reaction assay for specific detection of Brucella abortus in clinical samples. Mol Cell Probes 2021; 59:101761. [PMID: 34400303 DOI: 10.1016/j.mcp.2021.101761] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 07/15/2021] [Accepted: 08/12/2021] [Indexed: 11/24/2022]
Abstract
Bovine brucellosis, predominantly caused by Brucella abortus is one of the most neglected zoonotic diseases causing severe economic losses in the dairy industry. The early and precise diagnosis of the disease is required to reduce the transmission of infection in humans as well as animals. In the current study, a rapid and novel isothermal amplification-based polymerase spiral reaction (PSR) was developed for the specific detection of Brucella abortus by targeting the BruAb2_0168 gene. The assay could be conducted at 65 °C in a water bath and results can be obtained after 60 min. The detection limit of the PSR assay was found to be 1.33fg. The sensitivity of the assay was found to be 104 fold higher than conventional PCR and equivalent to real-time PCR (RT-PCR). The assay didn't exhibit cross-reaction with selected pathogenic non-Brucella bacteria and Brucella spp. other than B. abortus. Forty clinical samples were also tested using this novel assay and it was able to detect 25 samples as positive, however, conventional PCR could detect the targeted organism in 22 samples only. To the extent of our knowledge, this is the first report towards the development of a PSR assay for specific detection of B. abortus. The assay can be used as a quick, sensitive and accurate test for the diagnosis of bovine brucellosis in the field setting. Relatively one of the paradigm-shifting aspects of this assay would be it does not require any expensive equipment and the results can be easily visualized by the unaided eye, therefore making PSR a valuable diagnostic tool in field conditions.
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Affiliation(s)
- Marcia Ashmi
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India
| | - Bablu Kumar
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Bareilly, UP, India.
| | - Ravi Kant Agrawal
- Division of Livestock Products Technology, ICAR- Indian Veterinary Research Institute, Bareilly, UP, India
| | - Chandan Prakash
- Centre for Animal Disease Research and Diagnosis, ICAR- Indian Veterinary Research Institute, Bareilly, UP, India
| | - Abhishek
- Division of Bacteriology and Mycology, ICAR- Indian Veterinary Research Institute, Bareilly, UP, India
| | - Karam Pal Singh
- Centre for Animal Disease Research and Diagnosis, ICAR- Indian Veterinary Research Institute, Bareilly, UP, India
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Tomar PS, Kumar JS, Patel S, Sharma S. Polymerase Spiral Reaction Assay for Rapid and Real Time Detection of West Nile Virus From Clinical Samples. Front Cell Infect Microbiol 2020; 10:426. [PMID: 32984063 PMCID: PMC7492713 DOI: 10.3389/fcimb.2020.00426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 07/13/2020] [Indexed: 12/02/2022] Open
Abstract
West Nile virus (WNV) is a mosquito-borne virus of public health importance. Currently, there is no FDA approved vaccine available against WNV infection in humans. Therefore, the early diagnosis of the WNV infection is important for epidemiologic control and timely clinical management in areas where multiple Flaviviruses are endemic. The present study aimed to develop reverse transcription polymerase spiral reaction (RT-PSR) assay that rapidly and accurately detects the envelope (env) gene of WNV. RT-PSR assay was optimized at 63°C for 60 min using real-time turbidimeter or visual detection by the addition of SYBR Green I dye. The standard curve for RT-PSR assay was generated using the 10-fold serial dilutions of in vitro transcribed WNV RNA. To determine the detection limit of RT-PSR assay, an amplified product of conventional RT-PCR was in vitro transcribed as per standard protocol. The detection limit of the newly developed RT-PSR assay was compared with that of conventional RT-PCR and CDC reported TaqMan real-time RT-PCR using a serial 10-fold dilution of IVT WNV RNA. The detection limit of RT-PSR was found to be 1 RNA copy, which is 100-fold higher than that of conventional RT-PCR (100 copies). This suggests that RT-PSR assay is a valuable diagnostic tool for rapid and real-time detection of WNV in acute-phase serum samples. The assay was validated with a panel of 107 WNV suspected human clinical samples with signs of acute posterior uveitis and onset of febrile illness. Out of 107 samples, 30 were found positive by RT-PSR assay. The specificities of the selected primer sets were established by the absence of cross-reactivity with other closely related members viruses of the Flaviviruses, Alphaviruses, and Morbilliviruses groups. No cross-reactivity was observed with other viruses. To best of our knowledge, this is the first report describing the RT-PSR assay for the detection of RNA virus (WNV) in clinical samples. RT-PSR is a high throughput method and more than 30 reactions can be run at once in real-time turbidimeter. PSR assay has potential to be used for a rapid screening of large number of clinical samples in endemic areas during an outbreak.
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Affiliation(s)
- Priyanka Singh Tomar
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
| | - Jyoti S Kumar
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
| | - Sapan Patel
- School of Studies in Botany, Jiwaji University, Gwalior, India
| | - Shashi Sharma
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
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Development of magnetic bead based sample extraction coupled polymerase spiral reaction for rapid on-site detection of Chikungunya virus. Sci Rep 2020; 10:11651. [PMID: 32669639 PMCID: PMC7363856 DOI: 10.1038/s41598-020-68469-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 06/25/2020] [Indexed: 11/25/2022] Open
Abstract
The molecular detection system has evolved over last two decades and is rapidly replacing the conventional confirmatory techniques in diagnostic virology. However the major limitation in implementation of available molecular detection assays is the non availability of field deployable nucleic acid isolation platform coupled with gene amplification technique. The rapid and early molecular detection is crucial for employing effective measure against many viral infections. The re-emergence of chikungunya virus (CHIKV) has led to epidemics since 2004 in several parts of the world including India. The main association of CHIKV with severe arthritis and long-lasting arthralgia and closely mimics symptoms of Dengue and Zika virus infection requiring laboratory confirmation. In this study, a simple magnetic bead based ribonucleic acid extraction method was optimized, which was coupled with isothermal polymerase spiral reaction (PSR) technique for early and rapid detection. Subsequently, the polymerase spiral reaction reagents were converted to dry down format that led to a rapid user friendly field compatible sample processing to answer method for rapid and onsite detection of Chikungunya virus. Both the methods were evaluated with a panel of clinical samples. The sensitivity of the assays were compared with available commercial viral RNA extraction platform and qRT-PCR. The in-house nucleic acid extraction system based on magnetic bead followed by dry down RT-Polymerase Spiral Reaction assay was found to be highly sensitive with 10 copies of RNA as limit of detection in CHIKV clinical specimens. With respect to other closely related viruses no cross reactivity was observed. This novel methodology has the potential to revolutionize the diagnosis of infectious agents in resource limited settings around the world.
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He S, Huang Y, Zhao Y, Pang B, Wang L, Sun L, Yu H, Wang J, Li J, Song X, Li H. A Reverse Transcription-Polymerase Spiral Reaction (RT-PSR)-Based Rapid Coxsackievirus A16 Detection Method and Its Application in the Clinical Diagnosis of Hand, Foot, and Mouth Disease. Front Microbiol 2020; 11:734. [PMID: 32477283 PMCID: PMC7236501 DOI: 10.3389/fmicb.2020.00734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Hand, foot, and mouth disease (HFMD) is a common viral illness affecting infants and children that is usually caused by Coxsackievirus A16 (CVA-16). To diagnose HFMD, we developed a method for rapid detection of CVA-16 based on reverse transcription-polymerase spiral reaction (RT-PSR). We used two pairs of primers that specifically recognize the conserved sequences of VP1 coding region of CVA-16, and template RNA was reverse transcribed and amplified in a single tube under isothermal conditions, total reaction time could be reduced to less than 40 min. The detection limit of this method was between 2.4 × 102 and 2.4 × 101 copies/μl with excellent specificity. To test the clinical applicability of the method, 40 clinical stool samples were analyzed using RT-PSR and quantitative reverse transcription-polymerase chain reaction, and comparison showed that the coincidence rate was 100%. Compared with other similar detection methods, RT-PSR requires less time, simpler operation, and lower cost. These results prove that our novel, simple, and reliable isothermal nucleic acid testing assay has potential application for clinical detection of CVA-16.
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Affiliation(s)
- Shiyu He
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, China
| | - Yanzhi Huang
- Research Laboratory, Changchun Children's Hospital, Changchun, China
| | - Yanling Zhao
- Research Laboratory, Changchun Children's Hospital, Changchun, China
| | - Bo Pang
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, China
| | - Lixue Wang
- Research Laboratory, Changchun Children's Hospital, Changchun, China
| | - Liwei Sun
- Research Laboratory, Changchun Children's Hospital, Changchun, China
| | - Haoyan Yu
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, China
| | - Juan Wang
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, China
| | - Juan Li
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, China
| | - Xiuling Song
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, China
| | - Hui Li
- Department of Hygienic Inspection, School of Public Health, Jilin University, Changchun, China
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Garcia LF, Silvio Batista Rodrigues E, Rocha Lino de Souza G, Jubé Wastowski I, Mota de Oliveira F, Torres Pio dos Santos W, Souza Gil E. Impedimetric Biosensor for Bovine Herpesvirus Type 1‐Antigen Detection. ELECTROANAL 2020. [DOI: 10.1002/elan.201900606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | | | | | - Wallans Torres Pio dos Santos
- Pharmacy Department Federal University of Jequitinhonha and Mucuri Valleys, Diamantina Minas Gerais 39803-371 Brazil
| | - Eric Souza Gil
- Faculty of Pharmacy Federal University of Goiás, Goiânia 74605-170 Goiás Brazil
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Momin KM, Milton AAP, Ghatak S, Thomas SC, Priya GB, Das S, Shakuntala I, Sanjukta R, Puro KU, Sen A. Development of a novel and rapid polymerase spiral reaction (PSR) assay to detect Salmonella in pork and pork products. Mol Cell Probes 2020; 50:101510. [DOI: 10.1016/j.mcp.2020.101510] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/30/2019] [Accepted: 01/13/2020] [Indexed: 02/08/2023]
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Sun W, Du Y, Li X, Du B. Rapid and Sensitive Detection of Hepatitis C Virus in Clinical Blood Samples Using Reverse Transcriptase Polymerase Spiral Reaction. J Microbiol Biotechnol 2020; 30:459-468. [PMID: 31893596 PMCID: PMC9728396 DOI: 10.4014/jmb.1910.10041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This study established a new polymerase spiral reaction (PSR) that combines with reverse transcription reactions for HCV detection targeting 5'UTR gene. To avoid cross-contamination of aerosols, an isothermal amplification tube (IAT), as a separate containment control, was used to judge the result. After optimizing the RT-PSR reaction system, its effectiveness and specificity were tested against 15 different virus strains which included 8 that were HCV positive and 7 as non-HCV controls. The results showed that the RT-PSR assay effectively detected all 8 HCV strains, and no false positives were found among the 7 non-HCV strains. The detection limit of our RT-PSR assay is comparable to the real-time RT-PCR, but is more sensitive than the RT-LAMP. The established RT-PSR assay was further evaluated for detection of HCV in clinical blood samples, and the resulting 80.25% detection rate demonstrated better or similar effectiveness compared to the RT-LAMP (79.63%) and real-time RT-PCR (80.25%). Overall, the results showed that the RT-PSR assay offers high specificity and sensitivity for HCV detection with great potential for screening HCV in clinical blood samples.
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Affiliation(s)
- Wenying Sun
- Clinical Laboratory, the Second Affiliated Hospital of Harbin Medical University, Harbin, 50086, P.R. China,Corresponding author Phone/Fax: +86-13845081362 E-mail:
| | - Ying Du
- Department of Experimental Diagnosis, Heilongjiang Provincial Hospital, Harbin, 150036, P.R. China
| | - Xingku Li
- Experimental Research Center, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, P.R. China
| | - Bo Du
- Experimental Research Center, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, P.R. China
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Wu Q, Xu X, Chen Q, Zuo K, Zhou Y, Zhang Z, Kan Y, Yao L, Ji J, Bi Y, Xie Q. Rapid and visible detection of Mycoplasma synoviae using a novel polymerase spiral reaction assay. Poult Sci 2020; 98:5355-5360. [PMID: 31222371 DOI: 10.3382/ps/pez356] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/01/2019] [Indexed: 12/19/2022] Open
Abstract
In this study, a rapid, specific, and sensitive detection assay for Mycoplasma synoviae (MS) was established using a polymerase spiral reaction (PSR) method. A pair of primers were designed according to the conserved region of the vlhA gene of MS, and PSR results were assessed using agarose gel electrophoresis and color rendering with a dye indicator. The optimum reaction temperature and time for PSR using the specific primers were 62°C and 40 min in a water bath, respectively. The sensitivity of the PSR assay for MS detection was 100 times more than that of the polymerase chain reaction assay based on agarose gel electrophoresis results and color change detected by the naked eye. Further experiments demonstrated that the primers specifically detected MS and showed no cross-reaction with other prevalent avian pathogens. Clinical sample testing confirmed that the MS-PSR assay is simple, rapid, specific, and sensitive, and thereby very suitable for application and promotion in the field and laboratories of grassroots units.
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Affiliation(s)
- Qianqian Wu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, PR China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, PR China
| | - Qinxi Chen
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, PR China
| | - Kejing Zuo
- Veterinary Laboratory, Guangzhou Zoo, Guangzhou 510642, PR China
| | - Yiting Zhou
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, PR China
| | - Zhibin Zhang
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, PR China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, PR China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, PR China
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang 473061, PR China
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
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Malik YS, Verma A, Kumar N, Deol P, Kumar D, Ghosh S, Dhama K. Biotechnological innovations in farm and pet animal disease diagnosis. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7150312 DOI: 10.1016/b978-0-12-816352-8.00013-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The application of innovative diagnostic technologies for the detection of animal pathogens at an early stage is essential in restricting the economic loss incurred due to emerging infectious animal diseases. The desirable characteristics of such diagnostic methods are easy to use, cost-effective, highly sensitive, and specific, coupled with the high-throughput detection capabilities. The enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are still the most common assays used for the detection of animal pathogens across the globe. However, utilizing the principles of ELISA and PCR, several serological and molecular technologies have been developed to achieve higher sensitivity, rapid, and point-of-care (POC) detection such as lateral flow assays, biosensors, loop-mediated isothermal amplification, recombinase polymerase amplification, and molecular platforms for field-level detection of animal pathogens. Furthermore, animal disease diagnostics need to be updated regularly to capture new, emerging and divergent infectious pathogens, and biotechnological innovations are helpful in fulfilling the rising demand for such diagnostics for the welfare of the society. Therefore, this chapter primarily describes and discusses in detail the serological, molecular, novel high-throughput, and POC assays to detect pathogens affecting farm and companion animals.
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Ji J, Xu X, Wang X, Zuo K, Li Z, Leng C, Kan Y, Yao L, Bi Y. Novel polymerase spiral reaction assay for the visible molecular detection of porcine circovirus type 3. BMC Vet Res 2019; 15:322. [PMID: 31492192 PMCID: PMC6731610 DOI: 10.1186/s12917-019-2072-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 09/02/2019] [Indexed: 03/21/2023] Open
Abstract
Background Porcine circovirus type 3 (PCV3) is a newly emerging circovirus that might be associated with porcine dermatitis and nephropathy syndrome, reproductive failure, and cardiac and multisystemic inflammation. To aid the prevention and control of the infectious disease caused by PCV3, we developed a novel isothermal amplification assay using polymerase spiral reaction (PSR), which allows the visual detection of preserved strains and clinical samples. Results This assay precisely amplified the PCV3 genome with the use of a water bath at 62 °C for 50 min. The detection limit was found to be 1.13 × 102 copies/μL by gel electrophoresis or with the use of a visible dye (an indicator comprising phenol red and cresol red). No cross-reaction with other porcine infectious viruses was observed. The detection results for 23 PCV3-positive samples by PSR were in accordance with loop-mediated isothermal amplification (LAMP) assay. The detection rate of the PSR assay for PCV3 positivity of clinical samples was 68/97, which was higher than LAMP assay (67/97). Conclusions These results indicated that the PSR assay provides an accurate and rapid method for the detection of PCV3 with high sensitivity and specificity. It is particularly suited for use in a simple laboratory setting without a thermal cycler or gel electrophoresis equipment.
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Affiliation(s)
- Jun Ji
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China.
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China
| | - Xueyu Wang
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China
| | - Kejing Zuo
- Veterinary Laboratory, Guangzhou Zoo, Guangzhou, 510642, People's Republic of China
| | - Zhili Li
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Chaoliang Leng
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China.
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China
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Wang X, Xu X, Hu W, Zuo K, Li Z, Kan Y, Yao L, Ji J, Bi Y. Visual detection of porcine epidemic diarrhea virus using a novel reverse transcription polymerase spiral reaction method. BMC Vet Res 2019; 15:116. [PMID: 30987635 PMCID: PMC6466714 DOI: 10.1186/s12917-019-1851-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Porcine epidemic diarrhea virus (PEDV) is a major etiological agent of porcine epidemic diarrhea around the world. Point-of-care testing in the field is lacking owing to the requirement for a simple, robust field applicable test that does not require professional laboratory equipment. The aim of this study was to establish a novel reverse transcription polymerase spiral reaction (RT-PSR) assay for the rapid detection of porcine epidemic diarrhea virus (PEDV). For the assay, a specific RT-PSR primer pair was designed against a conserved region in PEDV ORF3. RESULTS The RT-PSR was optimized, and PEDV could be detected after a 50 min incubation at 62 °C, in addition to the 15 min required for reverse transcription. No cross-reaction with other porcine infectious viruses was observed. This new method for PEDV detection was 10 times more sensitive than the conventional reverse transcription-polymerase chain reaction (RT-PCR) assay. The positive rates for 65 clinical samples using the new RT-PSR assay and the conventional RT-PCR assay were 58.46% (38/65) and 53.84% (35/65), respectively. In the RT-PSR assay, the addition of a mixture of dyes allowed a positive reaction to be directly observed by the naked eye. CONCLUSIONS These results indicate that this RT-PSR assay is capable of accurately detecting PEDV, and has the advantages of high specificity and sensitivity for the detection of PEDV.
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Affiliation(s)
- Xueyu Wang
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Wolong Road 1638, Nanyang, 473061, People's Republic of China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Wolong Road 1638, Nanyang, 473061, People's Republic of China
| | - Wen Hu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Wolong Road 1638, Nanyang, 473061, People's Republic of China
| | - Kejing Zuo
- Veterinary Laboratory, Guangzhou Zoo, Guangzhou, 510642, People's Republic of China
| | - Zhili Li
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Wolong Road 1638, Nanyang, 473061, People's Republic of China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Wolong Road 1638, Nanyang, 473061, People's Republic of China.
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Wolong Road 1638, Nanyang, 473061, People's Republic of China.
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China
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15
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Das A, Kumar B, Chakravarti S, Prakash C, Singh RP, Gupta V, Singh KP, Agrawal RK, Chaturvedi VK, Abhishek, Shrinet G. Rapid visual isothermal nucleic acid-based detection assay of Brucella species by polymerase spiral reaction. J Appl Microbiol 2018; 125:646-654. [PMID: 30152897 DOI: 10.1111/jam.13882] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 12/28/2022]
Abstract
AIM The aim of this study was to develop polymerase spiral reaction (PSR) for rapid, sensitive and specific detection of Brucella sp. METHODS AND RESULTS Polymerase spiral reaction assay was developed using specifically designed primers targeting the conserved multicopy IS711 gene of Brucella sp. The assay could be performed within 60 min at an isothermal temperature of 64°C. The lower limit of detection of PSR was 11·8 fg and conventional PCR was 1·18 pg of Brucella abortus genomic DNA. Thus, PSR was found to be 100-fold more sensitive than conventional PCR and was comparable to real-time PCR. The specificity of PSR was tested with other non-Brucella bacteria and also with some bacterial and viral pathogens causing abortions. The assay was found to be specific as it did not detect any putative pathogens other than Brucella sp. Fifty-six clinical samples suspected for brucellosis (aborted fetal stomach content) were screened with PSR to validate the applicability of the test to detect Brucella DNA. The same samples were also screened with conventional PCR and real-time PCR. Of 56 samples, 25 samples were found to be positive with both PSR as well as real-time PCR, whereas only 20 samples were found positive with conventional PCR. CONCLUSIONS The results of this study indicated that the PSR assay is a simple, rapid, sensitive and specific method for the detection of Brucella sp. that may improve diagnostic potential in clinical laboratories or can be used at diagnostic laboratories with minimal infrastructure. SIGNIFICANCE AND IMPACT OF THE STUDY The PSR assay, because of its simplicity and low cost, can be preferred to other molecular methods in the diagnosis of infectious diseases.
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Affiliation(s)
- A Das
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - B Kumar
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - S Chakravarti
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - C Prakash
- Centre for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - R P Singh
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - V Gupta
- Centre for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - K P Singh
- Centre for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - R K Agrawal
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - V K Chaturvedi
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Abhishek
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - G Shrinet
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
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