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Zhang X, Zhao Y, Zhu X, Tian W, Zhang C. Rapid detection of four major HFMD-associated enteroviruses by multiplex HiFi-LAMP assays. Anal Bioanal Chem 2024; 416:1971-1982. [PMID: 38358534 DOI: 10.1007/s00216-024-05197-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/19/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Hand, foot, and mouth disease (HFMD) caused by various enteroviruses is a major public health concern globally. Human enterovirus 71(EVA71), coxsackievirus A16 (CVA16), coxsackievirus A6 (CVA6), and coxsackievirus A10 (CVA10) are four major enteroviruses responsible for HFMD. Rapid, accurate, and specific point-of-care (POC) detection of the four enteroviruses is crucial for the prevention and control of HFMD. Here, we developed two multiplex high-fidelity DNA polymerase loop-mediated isothermal amplification (mHiFi-LAMP) assays for simultaneous detection of EVA71, CVA16, CVA6, and CVA10. The assays have good specificity and exhibit high sensitivity, with limits of detection (LOD) of 11.2, 49.6, 11.4, and 20.5 copies per 25 μL reaction for EVA71, CVA16, CVA6, and CVA10, respectively. The mHiFi-LAMP assays showed an excellent clinical performance (sensitivity 100.0%, specificity 83.3%, n = 47) when compared with four singleplex RT-qPCR assays (sensitivity 93.1%, specificity 100%). In particular, the HiFi-LAMP assays exhibited better performance (sensitivity 100.0%, specificity 100%) for CVA16 and CVA6 than the RT-qPCR assays (sensitivity 75.0-92.3%, specificity 100%). Furthermore, the mHiFi-LAMP assays detected all clinical samples positive for the four enteroviruses within 30 min, obviously shorter than about 1-1.5 h by the RT-qPCR assays. The new mHiFi-LAMP assays can be used as a robust point-of-care testing (POCT) tool to facilitate surveillance of HFMD at rural and remote communities and resource-limited settings.
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Affiliation(s)
- Xiaoling Zhang
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China
| | - Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China
| | - Xiaoyi Zhu
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China
| | - Weimin Tian
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China.
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China.
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2
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Chen X, Du C, Zhao Q, Zhao Q, Wan Y, He J, Yuan W. Rapid and visual identification of HIV-1 using reverse transcription loop-mediated isothermal amplification integrated with a gold nanoparticle-based lateral flow assay platform. Front Microbiol 2023; 14:1230533. [PMID: 37502395 PMCID: PMC10368893 DOI: 10.3389/fmicb.2023.1230533] [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: 05/29/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Human immunodeficiency virus type one (HIV-1) infection remains a major public health problem worldwide. Early diagnosis of HIV-1 is crucial to treat and control this infection effectively. Here, for the first time, we reported a novel molecular diagnostic assay called reverse transcription loop-mediated isothermal amplification combined with a visual gold nanoparticle-based lateral flow assay (RT-LAMP-AuNPs-LFA), which we devised for rapid, specific, sensitive, and visual identification of HIV-1. The unique LAMP primers were successfully designed based on the pol gene from the major HIV-1 genotypes CRF01_AE, CRF07_BC, CRF08_BC, and subtype B, which are prevalent in China. The optimal HIV-1-RT-LAMP-AuNPs-LFA reaction conditions were determined to be 68°C for 35 min. The detection procedure, including crude genomic RNA isolation (approximately 5 min), RT-LAMP amplification (35 min), and visual result readout (<2 min), can be completed within 45 min. Our assay has a detection limit of 20 copies per test, and we did not observe any cross-reactivity with any other pathogen in our testing. Hence, our preliminary results indicated that the HIV-1-RT-LAMP-AuNPs-LFA assay can potentially serve as a useful point-of-care diagnostic tool for HIV-1 detection in a clinical setting.
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Affiliation(s)
- Xu Chen
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
- Clinical Medical Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Cheng Du
- Department of Anesthesiology, The Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Qiang Zhao
- Clinical Laboratory, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
| | - Qi Zhao
- Gastroenterology of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Yonghu Wan
- Experiment Center, Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, Guizhou, China
| | - Jun He
- Clinical Laboratory, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
| | - Wei Yuan
- Department of Quality Control, Guizhou Provincial Center for Clinical Laboratory, Guiyang, Guizhou, China
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3
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Zhang X, Zhao Y, Zeng Y, Zhang C. Evolution of the Probe-Based Loop-Mediated Isothermal Amplification (LAMP) Assays in Pathogen Detection. Diagnostics (Basel) 2023; 13:diagnostics13091530. [PMID: 37174922 PMCID: PMC10177487 DOI: 10.3390/diagnostics13091530] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/19/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP), as the rank one alternative to a polymerase chain reaction (PCR), has been widely applied in point-of-care testing (POCT) due to its rapid, simple, and cost-effective characteristics. However, it is difficult to achieve real-time monitoring and multiplex detection with the traditional LAMP method. In addition, these approaches that use turbidimetry, sequence-independent intercalating dyes, or pH-sensitive indicators to indirectly reflect amplification can result in false-positive results if non-specific amplification occurs. To fulfill the needs of specific target detection and one-pot multiplex detection, a variety of probe-based LAMP assays have been developed. This review focuses on the principles of these assays, summarizes their applications in pathogen detection, and discusses their features and advantages over the traditional LAMP methods.
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Affiliation(s)
- Xiaoling Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yi Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
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4
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Qin L, Lou F, Wang Y, Zhang Y, Liu S, Hun X. CRISPR/Cas12a Coupled with Enzyme-DNA Molecular Switch Photoelectrochemical Assay for HIV Nucleic Acid. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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5
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Sivakumar R, Park SY, Lee NY. Quercetin-Mediated Silver Nanoparticle Formation for the Colorimetric Detection of Infectious Pathogens Coupled with Loop-Mediated Isothermal Amplification. ACS Sens 2023; 8:1422-1430. [PMID: 36952605 DOI: 10.1021/acssensors.2c02054] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Here, quercetin-mediated silver nanoparticle (AgNP) formation combined with loop-mediated isothermal amplification (LAMP) was introduced to colorimetrically detect two major infectious pathogens, SARS-CoV-2 and Enterococcus faecium, using a foldable PMMA microdevice. The nitrogenous bases of LAMP amplicons can readily form a complex with Ag+ ions, and the catechol moiety in quercetin, which acted as a reducing agent, could be chelated with Ag+ ions, resulting in the easy electron transfer from the oxidant to the reductant and producing brown-colored AgNPs within 5 min. The introduced method exhibited higher sensitivity than agarose gel electrophoresis due to more active redox centers in quercetin. The detection limit was attained at 101 copies μL-1 and 101 CFU mL-1 for SARS-CoV-2 RNA and E. faecium, respectively. A foldable microdevice made of two pieces of PMMA that fully integrates DNA extraction, amplification, and detection processes was fabricated to establish practical applicability. On one PMMA, DNA extraction was performed in a reaction chamber inserted with an FTA card, and then LAMP reagents were added for amplification. Silver nitrate was added to the reaction chamber after LAMP. On the other PMMA, quercetin-soaked paper discs loaded in the detection chamber were folded toward the reaction chamber for colorimetric detection. An intense brown color was produced within 5 min when heated at 65 °C. The introduced colorimetric assay, which is highly favorable for laboratory and on-site applications, could be a valuable alternative to conventional methods for detecting infectious diseases, given its unique principle, simplicity, and naked-eye detection.
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Affiliation(s)
- Rajamanickam Sivakumar
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, South Korea
| | - So Yeon Park
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, South Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, South Korea
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Gulinaizhaer A, Zou M, Ma S, Yao Y, Fan X, Wu G. Isothermal nucleic acid amplification technology in HIV detection. Analyst 2023; 148:1189-1208. [PMID: 36825492 DOI: 10.1039/d2an01813f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nucleic acid testing for HIV plays an important role in the early diagnosis and monitoring of antiretroviral therapy outcomes in HIV patients and HIV-infected infants. Currently, the main molecular diagnostic methods employed are complex, time-consuming, and expensive to operate in resource-limited areas. Isothermal nucleic acid amplification technology overcomes some of the shortcomings of traditional assays and makes it possible to use point-of-care tests for molecular HIV detection. Here, we summarize and discuss the latest technological advances in isothermal nucleic acid amplification for HIV detection, with the intent of providing guidance for the development of subsequent HIV assays with high sensitivity and specificity.
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Affiliation(s)
- Abudushalamu Gulinaizhaer
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Mingyuan Zou
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Shuo Ma
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Yuming Yao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Xiaobo Fan
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China. .,Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing 210009, Jiangsu, China
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7
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Zhao Y, Zeng Y, Lu R, Wang Z, Zhang X, Wu N, Zhu T, Wang Y, Zhang C. Rapid point-of-care detection of BK virus in urine by an HFman probe-based loop-mediated isothermal amplification assay and a finger-driven microfluidic chip. PeerJ 2023; 11:e14943. [PMID: 36915661 PMCID: PMC10007963 DOI: 10.7717/peerj.14943] [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: 10/11/2022] [Accepted: 02/01/2023] [Indexed: 03/16/2023] Open
Abstract
Background BK virus (BKV)-associated nephropathy (BKVN) is one of the leading causes of renal dysfunction and graft loss in renal transplant recipients. Early monitoring of BKV in urine is crucial to minimize the deleterious effects caused by this virus on preservation of graft function. Methods We report a simple, rapid, sensitive loop-mediated isothermal amplification (LAMP) assay using an HFman probe for detecting BKV in urine. To evaluate the performance of the assay, a comparison of the HFman probe-based LAMP (HF-LAMP) assay with two qPCR assays was performed using urine samples from 132 HIV-1 infected individuals. We further evaluated the performance of HF-LAMP directly using the urine samples from these HIV-1 infected individuals and 30 kidney transplant recipients without DNA extraction. Furthermore, we combined the HF-LAMP assay with a portable finger-driven microfluidic chip for point-of-care testing (POCT). Results The assay has high specificity and sensitivity with a limit of detection (LOD) of 12 copies/reaction and can be completed within 30 min. When the DNA was extracted, the HF-LAMP assay showed an equivalent and potentially even higher sensitivity (93.5%) than the qPCR assays (74.2-87.1%) for 132 urine samples from HIV-1 infected individuals. The HF-LAMP assay can be applied in an extraction-free format and can be completed within 45 min using a simple heat block. Although some decreased performance was seen on urine samples from HIV-1 infected individuals, the sensitivity, specificity, and accuracy of the extraction-free BKV HF-LAMP assay were 95%, 100%, and 96.7% for 30 clinical urine samples from kidney transplant recipients, respectively. Conclusion The assay has high specificity and sensitivity. Combined with a portable finger-driven microfluidic chip for easy detection, this method shows great potential for POCT detection of BKV.
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Affiliation(s)
- Yongjuan Zhao
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Yi Zeng
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Renfei Lu
- Nantong Third Hospital Affiliated to Nantong University, Nantong, China
| | - Zhiying Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology, School of Engineering Medicine, Beihang University, Beijing, China
| | | | - Nannan Wu
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Tongyu Zhu
- Shanghai Medical College, Shanghai, China.,Zhongshan Hospital, Shanghai, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology, School of Engineering Medicine, Beihang University, Beijing, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Shanghai, China
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8
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Ye M, Chen X, Duo L, Ma J, Cao L, Zhang C, Zheng YT. Identification of two novel HIV-1 circulating recombinant forms of CRF111_01C and CRF116_0108 in southwestern Yunnan, China. Virulence 2022; 13:19-29. [PMID: 34951549 PMCID: PMC9794008 DOI: 10.1080/21505594.2021.2010399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Yunnan, the region hardest hit by HIV/AIDS in China, is also an area with the most abundant HIV-1 genetic diversity. A large number of novel HIV-1 circulating recombinant forms (CRFs) and unique recombinants were identified among injection drug users in Yunnan; however, few were found among sexual contacts. Here, we obtained 15 near full-length genome sequences (NFLGs) from HIV-1 seropositive heterosexual contacts in Yunnan who received antiretroviral therapy during the period from 2014 to 2016. Phylogenetic analysis showed that six NFLGs belonged to CRF01_AE (n = 3) and CRF106_cpx (n = 3), and the other nine sequences were novel inter-subtype recombinants. Of the recombinants, two novel CRFs (CRF111_01 C (n = 4) and CRF116_0108 (n = 4)) and one CRF106_cpx variant (n = 1) were identified. CRF111_01 C had a CRF01_AE backbone with seven subtype C fragments inserted into the gag, pol, vif, env, nef and 3'LTR regions. CRF116_0108 had a CRF08_BC backbone with a CRF01_AE fragment inserted into the pol, tat, rev, vif, vpr, vpu and env regions. Phylogeographic analyses estimated that CRF111_01 C and CRF116_0108 originated approximately 1995.7-1998.6 and 1991.7-1993.7, respectively. These identifications of two novel HIV-1 CRFs highlighted the importance of continuous surveillance in heterosexual contacts and other high-risk groups in this region and the surrounding regions.
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Affiliation(s)
- Mei Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kiz-cuhk Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xin Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kiz-cuhk Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Lin Duo
- Yunnan Fuwai Cardiovascular Hospital, Kunming, Yunnan, China
| | - Jin Ma
- Cangyuan Va Autonomous County People’s Hospital, Lincang, Yunnan, China
| | - Le Cao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China,Chiyu Zhang
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kiz-cuhk Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China,CONTACT Yong-Tang Zheng
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Zeng Y, Feng Y, Zhao Y, Zhang X, Yang L, Wang J, Gao Z, Zhang C. An HFman Probe-Based Multiplex Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Simultaneous Detection of Hantaan and Seoul Viruses. Diagnostics (Basel) 2022; 12:diagnostics12081925. [PMID: 36010275 PMCID: PMC9406646 DOI: 10.3390/diagnostics12081925] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022] Open
Abstract
Hantaviruses are zoonotic pathogens that are widely distributed worldwide. Hantaan virus (HTNV) and Seoul virus (SEOV) are two most common hantaviruses that infect humans and cause hemorrhagic fever with renal syndrome (HFRS). Rapid and sensitive detection of HTNV and SEOV are crucial for surveillance, clinical treatment and management of HFRS. This study aimed to develop a rapid HFman probe-based mulstiplex reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to simultaneously detect HTNV and SEOV. A novel multiplex RT-LAMP assay was developed, and 46 serum samples obtained from clinically suspected patients were used for evaluation. The novel RT-LAMP assay can detect as low as 3 copies/reaction of hantaviruses with a detection limit of 41 and 73 copies per reaction for HTNV and SEOV, respectively. A clinical evaluation showed that the consistencies of the multiplex RT-LAMP with RT-qPCR assay were 100% and 97.8% for HTNV and SEOV, respectively. In view of the high prevalence of HTNV and SEOV in rural areas with high rodent density, a colorimetric visual determination method was also developed for point-of-care testing (POCT) for the diagnosis of the two viruses. The novel multiplex RT-LAMP assay is a sensitive, specific, and efficient method for simultaneously detecting HTNV and SEOV.
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Affiliation(s)
- Yi Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yun Feng
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Diseases Control and Prevention, Dali 671000, China
| | - Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Xiaoling Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Lifen Yang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Diseases Control and Prevention, Dali 671000, China
| | - Juan Wang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Diseases Control and Prevention, Dali 671000, China
| | - Zihou Gao
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Diseases Control and Prevention, Dali 671000, China
- Correspondence: (Z.G.); or (C.Z.)
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Correspondence: (Z.G.); or (C.Z.)
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10
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Lin M, Li Z, Lin Q, Wang P, Liu W, Yuan J, Hong Z, Chen Y. Development and Clinical Application of a Rapid and Visual Loop-Mediated Isothermal Amplification Test for tetM gene in Clostridioides difficile Strains Cultured from Feces. Int J Infect Dis 2022; 122:676-684. [PMID: 35843495 DOI: 10.1016/j.ijid.2022.07.032] [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: 01/20/2022] [Revised: 04/23/2022] [Accepted: 07/09/2022] [Indexed: 10/17/2022] Open
Abstract
OBJECTIVES To develop a rapid and visual loop-mediated isothermal amplification (LAMP) assay targeting the tetM gene in Clostridioides difficile (C. difficile) strains cultured from feces. METHODS Primers were designed to recognize the tetM gene in C. difficile by LAMP, using turbidity and visual detection. The sensitivity and specificity of LAMP primers was determined. Besides, We conducted both LAMP and polymerase chain reaction (PCR) for the tcdA, tcdB, cdtA, cdtB, ermB, tetM genes in 300 toxigenic C. difficile strains cultured from feces. RESULTS The target DNA was amplified and visualized within 60 minutes at a temperature of 62°C. A total of 26 bacterial strains were found negative for tetM, which manifested high specificity of the primers. The detection limit of LAMP was 36.1 pg/µl, which was 100-fold more sensitive than PCR. The positive rate of tetM in toxigenic C. difficile strains cultured from feces was 93.3% by both LAMP and PCR. The proportion of toxin types in those C. difficile strains was 95.7% for A+B+CDT-, 4% for A-B+CDT-, and 0.3% for A+B+CDT+, respectively. CONCLUSIONS This is the first study examining tetM gene in C. difficile strains cultured from feces by LAMP. Its high specificity and sensitivity, as well as visual detection, make the new assay a powerful diagnostic tool for rapid testing.
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Affiliation(s)
- Minyi Lin
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-Sen University, 52 East Meihua Road, Zhuhai, 519000, China
| | - Zitong Li
- Department of Gastroenterology, Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave. Guangzhou, China
| | - Qianyun Lin
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, No. 95, Yong An Road, Xi Cheng District, Beijing, 100050, China
| | - Pu Wang
- Department of Gastroenterology, Guangdong Provincial Key Laboratory of Gastroenterology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave. Guangzhou, China
| | - Wei Liu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 20 Dongda Street, Fengtai District, Beijing, 100071, China
| | - Zhongsi Hong
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-Sen University, 52 East Meihua Road, Zhuhai, 519000, China.
| | - Ye Chen
- Department of Gastroenterology, Integrative Microecology Center, Shenzhen Hospital, Southern Medical University, 1333 New Lake Road, Shenzhen, 518100, China.
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11
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Loop mediated isothermal amplification for detection of foodborne parasites: A journey from lab to lab-on-a-chip. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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12
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Zhang X, Li H, Liu Z, Zhao Y, Zeng Y, Dong Y, Li L, Zhang C. An HFman probe-based reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for HIV-1 detection. Mol Cell Probes 2022; 64:101834. [PMID: 35732248 DOI: 10.1016/j.mcp.2022.101834] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is suitable for the development of a rapid and cost-effective nucleic acid technique for point of care (POC) applications. However, LAMP methods often generate non-specific amplification, therefore inevitably resulting in false positive results especially when sequence-independent dyes are used to indirectly reflect the results. In this study, we established and optimized a reverse transcription LAMP (RT-LAMP) assay with a high-fidelity DNA polymerase-mediated fluorescent probe (HFman probe) for human immunodeficiency virus-1 (HIV-1) detection. The assay showed high sensitivity and specificity. Using 101 plasma samples with different HIV-1 viral load, we demonstrated that our assay can detect the major HIV-1 subtypes circulating in China, including CRF01_AE, CRF07_BC, CRF08_BC, CRF55_01B, and unique recombinant forms (URFs). We also compared our assay with an approved commercial real-time quantitative polymerase chain reaction (RT-qPCR) kit and found the sensitivity, specificity and consistency was 88.8%, 100% and 89.1%, respectively. The HFman probe-based RT-LAMP assay is a high specific detection method that is rapid, variant-tolerant and simple to operate, and thus is of great significance for timely disclosure of HIV status and rapid POC diagnosis.
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Affiliation(s)
- Xiaoling Zhang
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Hanping Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ziwei Liu
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yongjuan Zhao
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yi Zeng
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yajuan Dong
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Center for Pathogen Research, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Lin Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Chiyu Zhang
- Shanghai Clinical Research Center for Infectious Disease (HIV/AIDS), Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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Dong Y, Zhao Y, Li S, Wan Z, Lu R, Yang X, Yu G, Reboud J, Cooper JM, Tian Z, Zhang C. Multiplex, Real-Time, Point-of-care RT-LAMP for SARS-CoV-2 Detection Using the HFman Probe. ACS Sens 2022; 7:730-739. [PMID: 35192340 PMCID: PMC8887655 DOI: 10.1021/acssensors.1c02079] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/08/2022] [Indexed: 12/11/2022]
Abstract
Viral evolution impacts diagnostic test performance through the emergence of variants with sequences affecting the efficiency of primer binding. Such variants that evade detection by nucleic acid-based tests are subject to selective pressure, enabling them to spread more efficiently. Here, we report a variant-tolerant diagnostic test for SARS-CoV-2 using a loop-mediated isothermal nucleic acid-based amplification (LAMP) assay containing high-fidelity DNA polymerase and a high-fidelity DNA polymerase-medicated probe (HFman probe). In addition to demonstrating a high tolerance to variable SARS-CoV-2 viral sequences, the mechanism also overcomes frequently observed limitations of LAMP assays arising from non-specific amplification within multiplexed reactions performed in a single "pot". Results showed excellent clinical performance (sensitivity 94.5%, specificity 100%, n = 190) when compared directly to a commercial gold standard reverse transcription quantitative polymerase chain reaction assay for the extracted RNA from nasopharyngeal samples and the capability of detecting a wide range of sequences containing at least alpha and delta variants. To further validate the test with no sample processing, directly from nasopharyngeal swabs, we also detected SARS-CoV-2 in positive clinical samples (n = 49), opening up the possibility for the assay's use in decentralized testing.
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Affiliation(s)
- Yajuan Dong
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yongjuan Zhao
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Shenwei Li
- Shanghai
International Travel Healthcare Center, Shanghai 200335, China
| | - Zhenzhou Wan
- Medical
Laboratory of Taizhou Fourth People’s Hospital, Taizhou 225300, China
| | - Renfei Lu
- Clinical
Laboratory, Nantong Third Hospital Affiliated
to Nantong University, Nantong 226006, China
| | - Xianguang Yang
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Guoying Yu
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Julien Reboud
- Division
of Biomedical Engineering, University of
Glasgow, G12 8LT Glasgow, U.K.
| | - Jonathan M. Cooper
- Division
of Biomedical Engineering, University of
Glasgow, G12 8LT Glasgow, U.K.
| | - Zhengan Tian
- Shanghai
International Travel Healthcare Center, Shanghai 200335, China
| | - Chiyu Zhang
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
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