1
|
Liu Y, Chen L, Zhang Z, Zhang R, Xu J, Yang P, Sun Y, Chen Y, Xie C, Lin M, Zheng Y. Development and application of a novel recombinase polymerase amplification-Pyrococcus furiosus argonaute system for rapid detection of goose parvovirus. Poult Sci 2024; 103:104141. [PMID: 39137501 PMCID: PMC11372586 DOI: 10.1016/j.psj.2024.104141] [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: 04/07/2024] [Revised: 07/09/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
Rapid and accurate detection of goose parvovirus (GPV) is crucial for controlling outbreaks and mitigating their economic impact on the poultry industry. This study introduces recombinase polymerase amplification combined with the Pyrococcus furiosus argonaute (RPA-PfAgo) system, a novel diagnostic platform designed to address the limitations of traditional GPV detection methods. Capitalizing on the rapid DNA amplification of RPA and stringent nucleic acid cleavage by the PfAgo protein, the RPA-PfAgo system offers high specificity and sensitivity in detecting GPV. Our optimization efforts included primer and probe configurations, reaction parameters, and guided DNA selection, culminating in a detection threshold of 102 GPV DNA copies per microlitre. The specificity of the proposed method was rigorously validated against a spectrum of avian pathogens. Clinical application to lung tissues from GPV-infected geese yielded a detection concordance of 100%, surpassing that of qPCR and PCR in both rapidity and operational simplicity. The RPA-PfAgo system has emerged as a revolutionary diagnostic modality for managing this disease, as it is a promising rapid, economical, and onsite GPV detection method amenable to integration into broad-scale disease surveillance frameworks. Future explorations will extend the applicability of this method to diverse avian diseases and assess its field utility across various epidemiological landscapes.
Collapse
Affiliation(s)
- Yaqun Liu
- Guangdong Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products, Hanshan Normal University, Chaozhou 521041, China; Shantou University Medical College, Shantou 515000, China; Guangdong Taiantang Pharmaceutical Co., Ltd. Shantou 515000, China
| | - Lianghui Chen
- Industrial College of Biomedicine and Health Industry, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Zhenxia Zhang
- Guangdong Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products, Hanshan Normal University, Chaozhou 521041, China
| | - Rong Zhang
- Guangdong Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products, Hanshan Normal University, Chaozhou 521041, China
| | - Jinyu Xu
- Guangdong Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products, Hanshan Normal University, Chaozhou 521041, China
| | - Peikui Yang
- Guangdong Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products, Hanshan Normal University, Chaozhou 521041, China
| | - Yanjie Sun
- Guangdong Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products, Hanshan Normal University, Chaozhou 521041, China
| | - Yicun Chen
- Shantou University Medical College, Shantou 515000, China
| | - Chengsong Xie
- Guangdong Taiantang Pharmaceutical Co., Ltd. Shantou 515000, China
| | - Min Lin
- Guangdong Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products, Hanshan Normal University, Chaozhou 521041, China; Industrial College of Biomedicine and Health Industry, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Yuzhong Zheng
- Guangdong Key Laboratory of Functional Substances in Medicinal Edible Resources and Healthcare Products, Hanshan Normal University, Chaozhou 521041, China; Industrial College of Biomedicine and Health Industry, Youjiang Medical University for Nationalities, Baise 533000, China.
| |
Collapse
|
2
|
Fan Q, Xie Z, Zhao J, Hua J, Wei Y, Li X, Li D, Luo S, Li M, Xie L, Zhang Y, Zhang M, Wang S, Ren H, Wan L. Simultaneous differential detection of H5, H7 and H9 subtypes of avian influenza viruses by a triplex fluorescence loop-mediated isothermal amplification assay. Front Vet Sci 2024; 11:1419312. [PMID: 39015104 PMCID: PMC11250583 DOI: 10.3389/fvets.2024.1419312] [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: 04/18/2024] [Accepted: 06/21/2024] [Indexed: 07/18/2024] Open
Abstract
H5, H7, and H9 are pivotal avian influenza virus (AIV) subtypes that cause substantial economic losses and pose potential threats to public health worldwide. In this study, a novel triplex fluorescence reverse transcription-loop-mediated isothermal amplification (TLAMP) assay was developed in which traditional LAMP techniques were combined with probes for detection. Through this innovative approach, H5, H7, and H9 subtypes of AIV can be simultaneously identified and differentiated, thereby offering crucial technical support for prevention and control efforts. Three primer sets and composite probes were designed based on conserved regions of the haemagglutinin gene for each subtype. The probes were labelled with distinct fluorophores at their 3' ends, which were detached to release the fluorescence signal during the amplification process. The detection results were interpreted based on the colour of the TLAMP products. Then, the reaction conditions were optimized, and three primer sets and probes were combined in the same reaction system, resulting in a TLAMP detection assay for the differential diagnosis of AIV subtypes. Sensitivity testing with in vitro-transcribed RNA revealed that the detection limit of the TLAMP assay was 205 copies per reaction for H5, 360 copies for H7, and 545 copies for H9. The TLAMP assay demonstrated excellent specificity, no cross-reactivity with related avian viruses, and 100% consistency with a previously published quantitative polymerase chain reaction (qPCR) assay. Therefore, due to its simplicity, rapidity, sensitivity, and specificity, this TLAMP assay is suitable for epidemiological investigations and is a valuable tool for detecting and distinguishing H5, H7, and H9 subtypes of AIV in clinical samples.
Collapse
Affiliation(s)
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China (Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Tsuchida S, Himi N, Miura Y, Kodama S, Shindo T, Nakagawa K, Aoki T. Photoinduced electron transfer detection method for identifying UGT1A1*28 microsatellites. PLoS One 2023; 18:e0289506. [PMID: 37535593 PMCID: PMC10399816 DOI: 10.1371/journal.pone.0289506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
During development of a novel detection method for the UDP-glucuronosyl transferase 1A1 (UGT1A1)*28, the fluorescence intensity of a dye conjugated to cytosine (C) at the end of a DNA strand decreased upon hybridization with guanine (G). This phenomenon is referred to as photoinduced electron transfer (PeT). Using this phenomenon, we devised a method for the naked-eye detection of UGT1A1*28 (thymine-adenine (TA)-repeat polymorphism). Fluorescently labeled single-stranded DNA (ssDNA) oligonucleotides (probes) were designed and hybridized with complementary strand DNAs (target DNAs). Base pair formation at the blunt end between fluorescently labeled C (probe side) and G (target side), induced dramatic fluorescence quenching. Additionally, when the labeled-CG pair formed near the TA-repeat sequence, different TA-repeat numbers were discriminated. However, obtaining enough target DNA for this probe by typical polymerase chain reaction (PCR) was difficult. To enable the practical use of the probe, producing sufficient target DNA remains problematic.
Collapse
Affiliation(s)
- Shirou Tsuchida
- Division of Biochemistry, Department of Molecular Biosciences, School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu-cho, Ishikari-gun, Hokkaido, Japan
| | - Noriaki Himi
- Division of Biochemistry, Department of Molecular Biosciences, School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu-cho, Ishikari-gun, Hokkaido, Japan
| | - Yuuki Miura
- Division of Biochemistry, Department of Molecular Biosciences, School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu-cho, Ishikari-gun, Hokkaido, Japan
| | - Suzune Kodama
- Division of Biochemistry, Department of Molecular Biosciences, School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu-cho, Ishikari-gun, Hokkaido, Japan
| | - Tsugumi Shindo
- Division of Biochemistry, Department of Molecular Biosciences, School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu-cho, Ishikari-gun, Hokkaido, Japan
| | - Koji Nakagawa
- Division of Biochemistry, Department of Molecular Biosciences, School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu-cho, Ishikari-gun, Hokkaido, Japan
| | - Takashi Aoki
- Division of Biochemistry, Department of Molecular Biosciences, School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu-cho, Ishikari-gun, Hokkaido, Japan
| |
Collapse
|
4
|
Wu L, Wang W, Zhang J, Wu X, Chen Y, Gu X, Shao H, Li H, Liu W. Detection of Five Types of HPV Genotypes Causing Anogenital Warts (Condyloma Acuminatum) Using PCR-Tm Analysis Technology. Front Microbiol 2022; 13:857410. [PMID: 35655998 PMCID: PMC9152731 DOI: 10.3389/fmicb.2022.857410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Condyloma acuminatum (CA) is a common sexually transmitted disease caused by human papillomavirus (HPV) infection. We established a high-throughput, simple, low-cost, and accurate HPV-typing assay (polymerase chain reaction-melting temperature [PCR-Tm] analysis) to detect HPV in CA. Materials and Methods We detected 280 cervical scraping samples, including positive samples of HPV-6 (26), HPV-11 (12), HPV-16 (22), HPV-42 (18), HPV-43 (25), HPV-multiple (19), HPV- other type (58), and HPV-negative samples (100). All samples were compared by PCR-Tm analysis and a flow fluorescence hybridization assay. Sequencing was used to confirm the results of the PCR-Tm analysis. Results PCR-Tm analysis was specific for each genotype (HPV-6, HPV-11, HPV-16, HPV-42, and HPV-43). The sensitivity of the PCR-Tm analysis assay for each genotype was 103, 103, 103, 103, and 102 copies/reaction, respectively. Most of the 158 samples, including 58 HPV-other type positive and 100 HPV-negative samples tested by the flow fluorescence hybridization assay, were tested negative by PCR-Tm analysis. For the 122 remaining samples, 26 HPV-6, 12 HPV-11, 22 HPV-16, 18 HPV-42, 25 HPV-43, and 19 multiple HPV infections were detected through PCR-Tm analysis. In total, 25 HPV-6, 12 HPV-11, 21 HPV-16, 18 HPV-42, 25 HPV-43, and only 10 multiple HPV infections were detected by the flow fluorescence hybridization assay. The kappa coefficient for the analysis of PCR-Tm analysis and flow fluorescence hybridization assay was 0.940 (P < 0.0001), and the 95% confidence interval of the kappa coefficient was 90.3–97.7%. Conclusion PCR-Tm analysis enabled the detection of HPV-6, HPV-11, HPV-16, HPV-42, and HPV-43, including single and multiple infections.
Collapse
Affiliation(s)
- Lixia Wu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Laboratory Medicine, Children's Hospital of Soochow University, Medical College of Soochow University, Soochow, China
| | - Weifeng Wang
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Laboratory Medicine, Central Laboratory, Shanghai Tenth People's Hospital, Tongji University of Medicine, Shanghai, China
| | - Jie Zhang
- Department of Laboratory Medicine, Central Laboratory, Shanghai Tenth People's Hospital, Tongji University of Medicine, Shanghai, China
| | - Xuan Wu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Laboratory Medicine, Central Laboratory, Shanghai Tenth People's Hospital, Tongji University of Medicine, Shanghai, China
| | - Yan Chen
- Department of Laboratory Medicine, Central Laboratory, Shanghai Tenth People's Hospital, Tongji University of Medicine, Shanghai, China
| | - Xiaoping Gu
- Department of Laboratory Medicine, Shanghai Skin Disease Hospital, Tongji University of Medicine, Shanghai, China
| | - Huaqing Shao
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongsheng Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Weiwei Liu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Laboratory Medicine, Central Laboratory, Shanghai Tenth People's Hospital, Tongji University of Medicine, Shanghai, China.,Department of Laboratory Medicine, Shanghai Skin Disease Hospital, Tongji University of Medicine, Shanghai, China
| |
Collapse
|
5
|
Zhan Y, Zhang J, Yao S, Luo G. High-Throughput Two-Dimensional Polymerase Chain Reaction Technology. Anal Chem 2020; 92:674-682. [PMID: 31820952 DOI: 10.1021/acs.analchem.9b02030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polymerase chain reaction (PCR) is a very powerful tool for clinical gene detection. Multiplex PCR especially improves the throughput of this technology. However, it is often necessary to employ techniques such as electrophoresis, mass spectrometry, or sequencing after multiplex PCR amplification for product identification, which requires additional equipment and has high risks of contamination. In this work, we developed a high-throughput two-dimensional (2D) PCR technology that can identify multiple target genes simultaneously in just one closed tube and within a relatively short time by using both fluorescence and the melting temperature (Tm). As an example, a method detecting 9 human papillomavirus (HPV) subtypes and reference genes in a single tube was successfully established using 2D PCR. If designed properly, 2D PCR is believed to have the capability to identify more than 30 genes in one closed tube at a time. This method is particularly suitable for distinguishing microorganisms, single-nucleotide polymorphisms, and the methylation of genes and will be of great help to clinical work.
Collapse
Affiliation(s)
- Yuxia Zhan
- Comprehensive Laboratory , The Third Affiliated Hospital of Soochow University , Changzhou , Jiangsu 213003 , China.,Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research , Changzhou , Jiangsu 213003 , China
| | - Jun Zhang
- Comprehensive Laboratory , The Third Affiliated Hospital of Soochow University , Changzhou , Jiangsu 213003 , China.,Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research , Changzhou , Jiangsu 213003 , China
| | - Shuang Yao
- Comprehensive Laboratory , The Third Affiliated Hospital of Soochow University , Changzhou , Jiangsu 213003 , China.,Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research , Changzhou , Jiangsu 213003 , China
| | - Guanghua Luo
- Comprehensive Laboratory , The Third Affiliated Hospital of Soochow University , Changzhou , Jiangsu 213003 , China.,Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research , Changzhou , Jiangsu 213003 , China
| |
Collapse
|
6
|
Zhan YX, Luo GH. DNA methylation detection methods used in colorectal cancer. World J Clin Cases 2019; 7:2916-2929. [PMID: 31624740 PMCID: PMC6795732 DOI: 10.12998/wjcc.v7.i19.2916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/22/2019] [Accepted: 09/09/2019] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) remains a major contributor to the number of cancer-related deaths that occur annually worldwide. With the development of molecular biology methods, an increasing number of molecular biomarkers have been identified and investigated. CRC is believed to result from an accumulation of epigenetic changes, and detecting aberrant DNA methylation patterns is useful for both the early diagnosis and prognosis of CRC. Numerous studies are focusing on the development of DNA methylation detection methods or DNA methylation panels. Thus, this review will discuss the commonly used techniques and technologies to evaluate DNA methylation, their merits and deficiencies as well as the prospects for new methods.
Collapse
Affiliation(s)
- Yu-Xia Zhan
- Comprehensive Laboratory, Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research, the Third Affiliated Hospital of Soochow University, Changzhou 213003, Jiangsu Province, China
| | - Guang-Hua Luo
- Comprehensive Laboratory, Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research, the Third Affiliated Hospital of Soochow University, Changzhou 213003, Jiangsu Province, China
| |
Collapse
|
7
|
Mao H, Luo G, Zhan Y, Zhang J, Yao S, Yu Y. The mechanism and regularity of quenching the effect of bases on fluorophores: the base-quenched probe method. Analyst 2018; 143:3292-3301. [PMID: 29708557 DOI: 10.1039/c8an00116b] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The base-quenched probe method for detecting single nucleotide polymorphisms (SNPs) relies on real-time PCR and melting-curve analysis, which might require only one pair of primers and one probe.
Collapse
Affiliation(s)
- Huihui Mao
- Comprehensive Laboratory
- Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research
- the Third Affiliated Hospital of Soochow University
- Changzhou 213003
- China
| | - Guanghua Luo
- Comprehensive Laboratory
- Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research
- the Third Affiliated Hospital of Soochow University
- Changzhou 213003
- China
| | - Yuxia Zhan
- Comprehensive Laboratory
- Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research
- the Third Affiliated Hospital of Soochow University
- Changzhou 213003
- China
| | - Jun Zhang
- Comprehensive Laboratory
- Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research
- the Third Affiliated Hospital of Soochow University
- Changzhou 213003
- China
| | - Shuang Yao
- Comprehensive Laboratory
- Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research
- the Third Affiliated Hospital of Soochow University
- Changzhou 213003
- China
| | - Yang Yu
- Comprehensive Laboratory
- Changzhou Key Lab of Individualized Diagnosis and Treatment Associated with High Technology Research
- the Third Affiliated Hospital of Soochow University
- Changzhou 213003
- China
| |
Collapse
|