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Li X, Zhu S, Zhang X, Ren Y, He J, Zhou J, Yin L, Wang G, Zhong T, Wang L, Xiao Y, Zhu C, Yin C, Yu X. Advances in the application of recombinase-aided amplification combined with CRISPR-Cas technology in quick detection of pathogenic microbes. Front Bioeng Biotechnol 2023; 11:1215466. [PMID: 37720320 PMCID: PMC10502170 DOI: 10.3389/fbioe.2023.1215466] [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: 05/02/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
The rapid diagnosis of pathogenic infections plays a vital role in disease prevention, control, and public health safety. Recombinase-aided amplification (RAA) is an innovative isothermal nucleic acid amplification technology capable of fast DNA or RNA amplification at low temperatures. RAA offers advantages such as simplicity, speed, precision, energy efficiency, and convenient operation. This technology relies on four essential components: recombinase, single-stranded DNA-binding protein (SSB), DNA polymerase, and deoxyribonucleoside triphosphates, which collectively replace the laborious thermal cycling process of traditional polymerase chain reaction (PCR). In recent years, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated proteins) system, a groundbreaking genome engineering tool, has garnered widespread attention across biotechnology, agriculture, and medicine. Increasingly, researchers have integrated the recombinase polymerase amplification system (or RAA system) with CRISPR technology, enabling more convenient and intuitive determination of detection results. This integration has significantly expanded the application of RAA in pathogen detection. The step-by-step operation of these two systems has been successfully employed for molecular diagnosis of pathogenic microbes, while the single-tube one-step method holds promise for efficient pathogen detection. This paper provides a comprehensive review of RAA combined with CRISPR-Cas and its applications in pathogen detection, aiming to serve as a valuable reference for further research in related fields.
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Affiliation(s)
- Xiaoping Li
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Shuying Zhu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Xinling Zhang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Yanli Ren
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Jing He
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Jiawei Zhou
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Liliang Yin
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Gang Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Tian Zhong
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Ling Wang
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Ying Xiao
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Guangdong-Hong Kong-Macau Joint Laboratory for Contaminants Exposure and Health, Guangzhou, Guangdong Province, 510006, China
| | - Chunying Zhu
- Clinical Psychology Department, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang Province, 310005, China
| | - Chengliang Yin
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Xi Yu
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Guangdong-Hong Kong-Macau Joint Laboratory for Contaminants Exposure and Health, Guangzhou, Guangdong Province, 510006, China
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Li FY, Guo YH, Sun ZL, Liu H, Zhao MC, Cui J, Jiang Y, Shen XX, Ma XJ, Feng ZS. Rapid two-stage amplification in a single tube for simultaneous detection of norovirus GII and group a rotavirus. J Clin Lab Anal 2023; 37:e24858. [PMID: 36916770 PMCID: PMC10098066 DOI: 10.1002/jcla.24858] [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: 10/11/2022] [Revised: 02/06/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
The most prevalent viruses currently causing diarrhea are norovirus and rotavirus, and rapid and sensitive detection methods are essential for the early diagnosis of disease. The purpose of this study was to establish a sensitive single-tube two-stage nucleic acid amplification method-reverse transcription recombinase-assisted PCR (RT-RAP)-for simultaneous detection of norovirus GII and group A Rotavirus, with the first stage consisting of isothermal reverse transcription recombinase-aided amplification (RT-RAA) and the second stage consisting of qPCR (quantitative PCR). RT-RAP is more sensitive than either RT-RAA or qRT-PCR (quantitative RT-PCR) alone. And the addition of a barrier that can be disassembled after heating enabled the detection of samples within 1 h in a single closed tube. Sensitivity was 10 copies/reaction of norovirus (Novs) GII and group A rotavirus (RVA). In parallel, two hundred fecal specimens were used to evaluate the method and compare it with a commercial fluorescent quantitative RT-PCR. The data showed kappa values of 0.957 and 0.98 (p < 0.05) for detecting Novs GII and RVA by the two methods, indicating the potential of the newly established assay to be applied to clinical and laboratory testing.
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Affiliation(s)
- Feng-Yu Li
- Hebei Medical University, Shijiazhuang, Hebei, China.,Hebei General Hospital, Shijiazhuang, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying-Hui Guo
- Department of Clinical Laboratory, Children's Hospital of Hebei Province, Shijiazhuang, Hebei, China
| | - Zhen-Lu Sun
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong Liu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong, China
| | - Meng-Chuan Zhao
- Department of Clinical Laboratory, Children's Hospital of Hebei Province, Shijiazhuang, Hebei, China
| | - Jia Cui
- Hebei General Hospital, Shijiazhuang, Hebei, China
| | - Yue Jiang
- The Third Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhi-Shan Feng
- Hebei Medical University, Shijiazhuang, Hebei, China.,Hebei General Hospital, Shijiazhuang, Hebei, China.,Hebei Medical Laboratory Clinical Medical Research Center, Shijiazhuang City, Hebei Province, China.,Hebei Key Laboratory of Molecular Medicine, Shijiazhuang City, Hebei Province, China
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3
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Jiao J, Qi Y, He P, Wan W, OuYang X, Yu Y, Wen B, Xiong X. Development of a Lateral Flow Strip-Based Recombinase-Aided Amplification for Active Chlamydia psittaci Infection. Front Microbiol 2022; 13:928025. [PMID: 35770169 PMCID: PMC9234530 DOI: 10.3389/fmicb.2022.928025] [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: 04/25/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Chlamydia psittaci is the causative agent of psittacosis, a worldwide zoonotic disease. A rapid, specific, and sensitive diagnostic assay would be benefit for C. psittaci infection control. In this study, an assay combining recombinase-aided amplification and a lateral flow strip (RAA-LF) for the detection of active C. psittaci infection was developed. The RAA-LF assay targeted the CPSIT_RS02830 gene of C. psittaci and could be accomplished in 15 min at a single temperature (39°C). The analytical sensitivity of the assay was as low as 1 × 100 copies/μl and no cross-reaction with some other intracellular pathogens was observed. Moreover, all feces samples from mice infected with C. psittaci at day-1 post-infection were positive in the RAA-LF assay. In conclusion, the RAA-LF assay provides a convenient, rapid, specific and sensitive method for detection of active C. psittaci infection and it is also suitable for C. psittaci detection in field.
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Affiliation(s)
- Jun Jiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yong Qi
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Peisheng He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Weiqiang Wan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xuan OuYang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yonghui Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bohai Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolu Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- *Correspondence: Xiaolu Xiong,
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Solid-phase recombinase polymerase amplification using ferrocene-labelled dNTPs for electrochemical detection of single nucleotide polymorphisms. Biosens Bioelectron 2022; 198:113825. [PMID: 34838372 DOI: 10.1016/j.bios.2021.113825] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/01/2021] [Accepted: 11/18/2021] [Indexed: 11/21/2022]
Abstract
Hypertrophic cardiomyopathies (HCM) are the principal cause of sudden cardiac death in young athletes and it is estimated that 1 in 500 people have HCM. The aim of this work was to develop an electrochemical platform for the detection of HCM-associated SNP in the Myosin Heavy Chain 7 (MYH7) gene, in fingerprick blood samples. The platform exploits isothermal solid-phase primer elongation using recombinase polymerase amplification with either individual or a combination of four ferrocene-labelled nucleoside triphosphates. Four thiolated reverse primers containing a variable base at their 3' end were immobilised on individual gold electrodes of an array. Following hybridisation with target DNA, solid phase recombinase polymerase amplification was carried out and primer elongation incorporating the ferrocene labelled oligonucleotides was only detected at one of the electrodes, thus facilitating identification of the SNP under interrogation. The assay was applied to the direct detection of the SNP in fingerprick blood samples from eight different individuals, with the results obtained corroborating with next generation sequencing. The ability to be able to robustly identify the SNP using a 10 μL fingerprick sample, demonstrates that SNP discrimination is achieved using low femtomolar (ca. 8 × 105 copies DNA) levels of DNA.
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Fan G, Zhang R, He X, Tian F, Nie M, Shen X, Ma X. RAP: A Novel Approach to the Rapid and Highly Sensitive Detection of Respiratory Viruses. Front Bioeng Biotechnol 2021; 9:766411. [PMID: 34805120 PMCID: PMC8602363 DOI: 10.3389/fbioe.2021.766411] [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: 08/29/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Recombinase aided amplification (RAA) is an emerging isothermal amplification method used for detecting various pathogens. However, RAA requires a complex and long probe to ensure high sensitivity during fluorescence assay. TaqMan probe used for quantitative PCR (qPCR) is simple and universal. Herein, we developed a new approach for detecting nucleic acids of pathogens, known as RAP (Recombinase aided PCR). The method combines RAA and qPCR to ensure a rapid and highly sensitive detection using a conventional qPCR device. RAP is a two-stage amplification process performed in a single tube within 1 hour. The method involves an RAA reaction for 10 min at 39°C (first stage) followed by 15 cycles of qPCR (second stage). Using human adenovirus 3 (HADV3) and human adenovirus 7 (HADV7) plasmids, the sensitivities of RAP assays for detecting HADV3 and HADV7 were 6 and 17 copies per reaction, respectively. The limit of RAP detection was at least 16-fold lower than the corresponding qPCR, and no-cross reaction with other respiratory viruses was observed. The results of RAP analysis revealed 100% consistency with qPCR assay. This study shows that RAP assay is a rapid, specific, and highly sensitive detection method with a potential for clinical and laboratory application.
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Affiliation(s)
- Guohao Fan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqing Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaozhou He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fengyu Tian
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mingzhu Nie
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinxin Shen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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Li J, Yang Z, Mao LF, Chen RH, Yu XF, Yang XH, Zhang GZ, Wang HQ, Chen SC, Zhao G. Reverse transcription recombinase-aided amplification assay for rapid detection of the influenza A(H1N1)pdm09 H275Y mutation that confers oseltamivir resistance. Mol Cell Probes 2021; 60:101771. [PMID: 34560257 DOI: 10.1016/j.mcp.2021.101771] [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: 02/05/2021] [Revised: 05/02/2021] [Accepted: 09/17/2021] [Indexed: 11/30/2022]
Abstract
The emergence of the influenza A(H1N1)pdm09 virus with the NA-H275Y mutation, which confers oseltamivir resistance, must be monitored, especially in patients undergoing neuraminidase inhibitor treatment. In this study, we developed a reverse transcription recombinase-aided amplification assay that has high sensitivity (detection limit: 1.0 × 101 copies/μL) and specificity for detecting the oseltamivir-resistant H275Y mutation; the assay is performed within 30 min at a constant temperature of 39° Celsius using an isothermal device. This method is suitable for the clinical application of targeted testing, thereby providing technical support for precision medicine in individual drug applications for patients with severe infection or immunosuppression.
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Affiliation(s)
- Jun Li
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Zi Yang
- Dali University, Yunnan, 671003, China
| | - Ling-Feng Mao
- Hangzhou Baocheng Biotechnology Co., Ltd., Zhejiang, 310052, China
| | - Ren-Hua Chen
- Department of Infectious Diseases, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Xin-Fen Yu
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Xu-Hui Yang
- Department of Infectious Diseases, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Guo-Zhong Zhang
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Hao-Qiu Wang
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Shu-Chang Chen
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China
| | - Gang Zhao
- Microbiology Laboratory, Hangzhou Centre for Disease Control and Prevention, Zhejiang, 310021, China.
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Chen Z, Shen X, Wang J, Zhao X, Gao Y, Zhang R, Wang J, Liu L, Nie X, Ma X. Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. China CDC Wkly 2021; 3:448-453. [PMID: 34594910 PMCID: PMC8392983 DOI: 10.46234/ccdcw2021.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/19/2021] [Indexed: 11/14/2022] Open
Abstract
Background: COVID-19 infection is a major public health problem worldwide, and the D614G mutation enhances the infectivity of COVID-19. Methods: A probe-directed recombinase amplification (PDRA) assay was discussed to detect the D614G mutation at 39 ℃ for 30 min. The sensitivity, specificity, and reproducibility of the PDRA were evaluated by D614 and G614 recombinant plasmids. The clinical performance of PDRA assay was validated by testing of 53 previously confirmed COVID-19 positive RNAs and 10 negative samples. Direct sequencing was carried out in parallel for comparison. Result: With good reproducibility and specificity, the PDRA assay worked well with the concentration in the range of 103-107 copies/reaction. Compared with direct sequencing as a reference, the recombinase-aided amplification (RAA) assay obtained 100% sensitivity and 100% specificity using clinical samples. Conclusions: A rapid, convenient, sensitive, and specific method to detect D614G mutation was developed, which offers a useful tool to monitor mutations in COVID-19 virus RNA.
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Affiliation(s)
- Ziwei Chen
- Department of Laboratory Medicine, Third Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinxin Shen
- Department of NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ji Wang
- Department of NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiang Zhao
- Department of NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuan Gao
- Department of NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqin Zhang
- Department of NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jinrong Wang
- Department of NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Leping Liu
- Department of Blood Transfusion, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinmin Nie
- Department of Laboratory Medicine, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xuejun Ma
- Department of NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
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Qin Z, Xue L, Cai W, Gao J, Jiang Y, Yang J, Liang Y, Wang L, Zhang J, Hu Y, Wu Q. Development of a recombinase-aided amplification assay for rapid detection of human norovirus GII.4. BMC Infect Dis 2021; 21:248. [PMID: 33750333 PMCID: PMC7941963 DOI: 10.1186/s12879-021-05942-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/28/2021] [Indexed: 12/28/2022] Open
Abstract
Background Human noroviruses are one of the main causes of foodborne illnesses and represent a serious public health concern. Rapid and sensitive assays for human norovirus detection are undoubtedly necessary for clinical diagnosis, especially in regions without more sophisticated equipment. Method The rapid reverse transcription recombinase-aided amplification (RT-RAA) is a fast, robust and isothermal nucleic acid detection method based on enzyme reaction. This method can complete the sample detection at 39 °C in 30 min. In this study, we successfully established a rapid reverse transcription recombinase-aided amplification (RT-RAA) assay for the detection of human norovirus GII.4 and applied this assay to clinical samples, as well as comparison with commercial reverse transcription real-time fluorescence quantitative PCR (RT-qPCR). Results At 95% probability, the detection sensitivity of RT-RAA was 3.425 log10 genomic copies (LGC)/reaction. Moreover, no cross-reaction was observed with other norovirus genogroups and other common foodborne viruses. Stool samples were examined by RT-RAA and reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). Compared of RT-qPCR, kappa values for human norovirus detection with RT-RAA were 0.894 (p < 0.001), indicating that both assays were in agreement. Conclusion This RT-RAA assay provides a rapid, specific, and sensitive assay for human norovirus detection and is suitable for clinical testing.
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Affiliation(s)
- Zhiwei Qin
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China.,Faculty Agriculture and Food, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Weicheng Cai
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Junshan Gao
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Yueting Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, People's Republic of China
| | - Jiale Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Yanhui Liang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Linping Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China
| | - Yongdan Hu
- Faculty Agriculture and Food, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China.
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, No. 100, Xianlie Zhong Road, Guangzhou, Guangdong, 510070, People's Republic of China.
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9
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Xie G, Zhou D, Zhao G, Feng X, Aguilar ZP, Xu H. Recombinase aided amplification with photoreactive DNA-binding dye for rapid detection of viable Staphylococcus aureus. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110249] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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10
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Duan Q, Li X, He X, Shen X, Cao Y, Zhang R, Bai X, Zhang J, Ma X. A duplex probe-directed recombinase amplification assay for detection of single nucleotide polymorphisms on 8q24 associated with prostate cancer. ACTA ACUST UNITED AC 2020; 54:e9549. [PMID: 33263645 PMCID: PMC7695445 DOI: 10.1590/1414-431x20209549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Single nucleotide polymorphisms (SNPs) have important application value in the research of population genetics, hereditary diseases, tumors, and drug development. Conventional methods for detecting SNPs are typically based on PCR or DNA sequencing, which is time-consuming, costly, and requires complex instrumentation. In this study, we present a duplex probe-directed recombinase amplification (duplex-PDRA) assay that can perform real-time detection of two SNPs (rs6983267 and rs1447295) in four reactions in two tubes at 39°C within 30 min. The sensitivity of duplex-PDRA was 2×103-104 copies per reaction and no cross-reactivity was observed. A total of 382 clinical samples (179 prostate cancer patients and 203 controls) from northern China were collected and tested by duplex-PDRA assay and direct sequencing. The genotyping results were completely identical. In addition, the association analysis of two SNPs with prostate cancer risk and bone metastasis was conducted. We found that the TT genotype of rs6983267 (OR: 0.42; 95%CI: 0.23-0.78; P=0.005) decreased the risk of prostate cancer, while the CA genotype of rs1447295 (OR: 1.89; 95%CI: 1.20-2.96; P=0.005) increased the risk of prostate cancer. However, no association between the two SNPs (rs6983267 and rs1447295) and bone metastasis in prostate cancer was found in this study (P>0.05). In conclusion, the duplex-PDRA assay is an effective method for the simultaneous detection of two SNPs and shows great potential for widespread use in research and clinical settings.
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Affiliation(s)
- Qingxia Duan
- Hebei Medical University, Shijiazhuang, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Xinna Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China.,Yangzhou Center for Disease Control and Prevention, Yangzhou, Jiangsu, China
| | - Xiaozhou He
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Xinxin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Yu Cao
- Hebei Medical University, Shijiazhuang, Hebei, China
| | - Ruiqing Zhang
- Hebei Medical University, Shijiazhuang, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Xueding Bai
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Jinyan Zhang
- Hebei Medical University Fourth Affiliated Hospital, Shijiazhuang, Hebei, China
| | - Xuejun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
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11
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Wang Y, Cui Y, Yu Z, Li Y, Bai C, Sun P, Zhu W, Li Y. Development of a recombinase-aided amplification assay for detection of orf virus. J Virol Methods 2020; 280:113861. [PMID: 32343981 DOI: 10.1016/j.jviromet.2020.113861] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/23/2022]
Abstract
Orf, caused by orf virus (ORFV), is an important zoonotic disease that infects goat and sheep, leading to huge economic losses. ORFV can also cause cutaneous lesions in people who come in close contact with the diseased animals. Although accurate diagnostic methods for ORFV infection exist, there is a need for a rapid, specific, and sensitive method for easy clinical application. Here, we successfully established a recombinase-aided amplification (RAA) assay for rapid detection of ORFV. The analytical sensitivity of the assay for ORFV detection is 1 × 101 copies per reaction. Moreover, no cross-reaction was observed with other common DNA viruses. A total of 45 archived suspected ORFV infected nasal scab skin samples were examined by RAA and SYBR Green-based real-time polymerase chain reaction (PCR). Compared with the real-time PCR assay, the kappa values of the RAA assay for ORFV detection was 0.845 (p <0.001), indicating that both assay results were fully in agreement. In conclusion, this detection assay provides a rapid, sensitive, and specific method for ORFV detection and is suitable for ORFV clinical testing.
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Affiliation(s)
- Yong Wang
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Yongqiu Cui
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Zhaorong Yu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Yeqiu Li
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Caixia Bai
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Pei Sun
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Wen Zhu
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, PR China
| | - Yongdong Li
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, PR China.
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12
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Wang RH, Zhang H, Zhang Y, Li XN, Shen XX, Qi JJ, Fan GH, Xiang XY, Zhan ZF, Chen ZW, Ma XJ. Development and evaluation of recombinase-aided amplification assays incorporating competitive internal controls for detection of human adenovirus serotypes 3 and 7. Virol J 2019; 16:86. [PMID: 31262315 PMCID: PMC6604330 DOI: 10.1186/s12985-019-1178-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/14/2019] [Indexed: 12/20/2022] Open
Abstract
Background Human adenoviruses are a common group of viruses that cause acute infectious diseases. Human adenovirus (HAdV) 3 and HAdV 7 cause major outbreaks of severe pneumonia. A reliable and practical method for HAdV typing in clinical laboratories is lacking. A simple, rapid and accurate molecular typing method for HAdV may facilitate clinical diagnosis and epidemiological control. Methods We developed and evaluated duplex real-time recombinase-aided amplification (RAA) assays incorporating competitive internal controls for detection of HAdV 3 and HAdV 7, respectively. The assays were performed in a one-step in a single tube reaction at 39° for 20 min. Results The analytical sensitivities of the duplex RAA assays for HAdV 3 and HAdV 7 were 5.0 and 14.8 copies per reaction, respectively (at 95% probability by probit regression analysis). No cross-reaction was observed with other types of HAdV or other common respiratory viruses. The duplex RAA assays were used to detect 152 previously-defined HAdV-positive samples. These results agreed with those obtained using a published triplex quantitative real-time PCR protocol. Conclusions We provide the first report of internally-controlled duplex RAA assays for the detection of HAdV 3 and HAdV 7. These assays effectively reduce the rate of false negative results and may be valuable for detection of HAdV 3 and HAdV 7 in clinical laboratories, especially in resource-poor settings.
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Affiliation(s)
- Rui-Huan Wang
- University of South China, College of Public Health, No. 28, West Changsheng Street, Hengyang, 421001, Hunan, China.,Hunan Provincial Center for Disease Control and Prevention, No. 450, Furong Street, Changsha, 410005, Hunan, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Hong Zhang
- University of South China, College of Public Health, No. 28, West Changsheng Street, Hengyang, 421001, Hunan, China. .,Hunan Provincial Center for Disease Control and Prevention, No. 450, Furong Street, Changsha, 410005, Hunan, China.
| | - Yi Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xin-Na Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Ju-Ju Qi
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Guo-Hao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xing-Yu Xiang
- Hunan Provincial Center for Disease Control and Prevention, No. 450, Furong Street, Changsha, 410005, Hunan, China
| | - Zhi-Fei Zhan
- Hunan Provincial Center for Disease Control and Prevention, No. 450, Furong Street, Changsha, 410005, Hunan, China
| | - Zi-Wei Chen
- The Third Xiangya Hospital of Central South University, 138 Tongzipo Road, Yuelu District, Changsha City, 410013, Hunan Province, China
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
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13
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Qi J, Li X, Zhang Y, Shen X, Song G, Pan J, Fan T, Wang R, Li L, Ma X. Development of a duplex reverse transcription recombinase-aided amplification assay for respiratory syncytial virus incorporating an internal control. Arch Virol 2019; 164:1843-1850. [PMID: 31053978 PMCID: PMC7086889 DOI: 10.1007/s00705-019-04230-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/06/2019] [Indexed: 01/09/2023]
Abstract
Human respiratory syncytial virus (RSV) is a common viral pathogen that causes lower respiratory tract infections in infants and children globally. In this study, we developed a duplex reverse transcription recombinase-aided amplification (duplex-rtRAA) assay containing an internal control in a single closed tube for the detection of human RSV. The internal control in the amplification effectively eliminated false-negative results and ensured the accuracy of the duplex-rtRAA system. We first developed and evaluated a universal singleplex-rtRAA assay for RSV. The sensitivity of this assay for RSV was determined as 4.4 copies per reaction, and the specificity was 100%. Next, a duplex-rtRAA assay with an internal control was established. The sensitivity of the duplex-rtRAA assay approached 5.0 copies per reaction, and no cross-reaction with other common respiratory viruses was observed. The two detection methods (singleplex-rtRAA and duplex-rtRAA) developed in this study were used to test 278 clinical specimens, and the results showed absolute consistency with RSV RT-qPCR analysis, demonstrating 100% diagnostic sensitivity and specificity. These data indicate that the duplex-rtRAA has great potential for the rapid detection of RSV with a high sensitivity.
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Affiliation(s)
- Juju Qi
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Xinna Li
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Yi Zhang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Xinxin Shen
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Guowei Song
- Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China
| | - Jing Pan
- Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China
| | - Tao Fan
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Ruihuan Wang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Road, Changping District, Beijing, 102206, China
| | - Lixin Li
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China. .,Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China.
| | - Xuejun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Road, Changping District, Beijing, 102206, China.
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14
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Shen XX, Qiu FZ, Shen LP, Yan TF, Zhao MC, Qi JJ, Chen C, Zhao L, Wang L, Feng ZS, Ma XJ. A rapid and sensitive recombinase aided amplification assay to detect hepatitis B virus without DNA extraction. BMC Infect Dis 2019; 19:229. [PMID: 30836947 PMCID: PMC6402085 DOI: 10.1186/s12879-019-3814-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/13/2019] [Indexed: 12/13/2022] Open
Abstract
Background Hepatitis B virus (HBV) infection is the major public health problem worldwide. In clinical practice, serological and molecular assays are the most commonly used diagnostic methods to detect HBV infection in clinical practices. Methods Here we present a rapid and sensitive recombinase aided amplification assay (RAA) to detect HBV at 39.0 °C for 30 min without DNA extraction from serum samples. The analytical sensitivity of RAA assay was 100 copies per reaction and showed no cross reaction with human immunodeficiency virus (HIV) and hepatitis C virus (HCV). The universality of RAA assay was validated by testing of 41 archived serum samples with predefined HBV genotypes (B, C and D). Results A total of 130 archived suspected HBV infected serum samples were detected by commercial qPCR with DNA extraction and RAA assay without DNA extraction (heat-treatment). Compared with qPCR assay as a reference, the RAA assay obtained 95.7% sensitivity and 100% specificity and a kappa value of 0.818. Conclusions We developed a rapid, convenient, highly sensitive and specific method to detect HBV without DNA extraction in clinical samples. This RAA method of HBV detection is very suitable for clinical testing.
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Affiliation(s)
- Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Fang-Zhou Qiu
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Hebei Medical University, Shijiazhuang, 050031, Hebei, China
| | - Li-Ping Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ten-Fei Yan
- Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, Shijiazhuang, 050011, Hebei, China
| | - Meng-Chuan Zhao
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Ju-Ju Qi
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Hebei Medical University, Shijiazhuang, 050031, Hebei, China
| | - Chen Chen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Li Zhao
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Hebei Medical University, Shijiazhuang, 050031, Hebei, China
| | - Le Wang
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Zhi-Shan Feng
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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15
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A look back at 2018. Biotechniques 2019; 66:12-13. [DOI: 10.2144/btn-2018-0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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