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Flores-Contreras EA, González-González E, Trujillo-Rodríguez GDJ, Rodríguez-Sánchez IP, Ancer-Rodríguez J, Pérez-Maya AA, Alvarez-Cuevas S, Martinez-Fierro ML, Marino-Martínez IA, Garza-Veloz I. Isothermal Technologies for HPV Detection: Current Trends and Future Perspectives. Pathogens 2024; 13:653. [PMID: 39204253 PMCID: PMC11357395 DOI: 10.3390/pathogens13080653] [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: 06/16/2024] [Revised: 07/12/2024] [Accepted: 07/25/2024] [Indexed: 09/03/2024] Open
Abstract
The human papillomavirus (HPV) is a non-enveloped DNA virus transmitted through skin-to-skin contact that infects epithelial and mucosal tissue. It has over 200 known genotypes, classified by their pathogenicity as high-risk and low-risk categories. High-risk HPV genotypes are associated with the development of different types of cancers, including cervical cancer, which is a leading cause of mortality in women. In clinical practice and the market, the principal tests used to detect HPV are based on cytology, hybrid detection, and qPCR. However, these methodologies may not be ideal for the required timely diagnosis. Tests have been developed based on isothermal nucleic acid amplification tests (INAATs) as alternatives. These tests offer multiple advantages over the qPCR, such as not requiring specialized laboratories, highly trained personnel, or expensive equipment like thermocyclers. This review analyzes the different INAATs applied for the detection of HPV, considering the specific characteristics of each test, including the HPV genotypes, gene target, the limit of detection (LOD), detection methods, and detection time. Additionally, we discuss the tests available on the market that are approved by the Food and Drug Administration (FDA). Finally, we address the challenges and potential solutions for the large-scale implementation of INAATs, particularly in rural or underserved areas.
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Affiliation(s)
- Elda A. Flores-Contreras
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Everardo González-González
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
| | - Gerardo de Jesús Trujillo-Rodríguez
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
| | - Iram P. Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico;
| | - Jesús Ancer-Rodríguez
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Antonio Alí Pérez-Maya
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico;
| | - Salomon Alvarez-Cuevas
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Margarita L. Martinez-Fierro
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
| | - Iván A. Marino-Martínez
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
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2
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Srivastava P, Prasad D. Isothermal nucleic acid amplification and its uses in modern diagnostic technologies. 3 Biotech 2023; 13:200. [PMID: 37215369 PMCID: PMC10193355 DOI: 10.1007/s13205-023-03628-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Nucleic acids are prominent biomarkers for diagnosing infectious pathogens using nucleic acid amplification techniques (NAATs). PCR, a gold standard technique for amplifying nucleic acids, is widely used in scientific research and diagnosis. Efficient pathogen detection is a key to adequate food safety and hygiene. However, using bulky thermal cyclers and costly laboratory setup limits its uses in developing countries, including India. The isothermal amplification methods are exploited to develop miniaturized sensors against viruses, bacteria, fungi and other pathogenic organisms and have been applied for in situ diagnosis. Isothermal amplification techniques have been found suitable for POC techniques and follow WHO's ASSURED criteria. LAMP, NASBA, SDA, RCA and RPA are some of the isothermal amplification techniques which are preferable for POC diagnostics. Furthermore, methods such as WGA, CPA, HDA, EXPAR, SMART, SPIA and DAMP were introduced for even more accuracy and robustness. Using recombinant polymerases and other nucleic acid-modifying enzymes has dramatically broadened the detection range of target pathogens under the scanner. The coupling of isothermal amplification methods with advanced technologies such as CRISPR/Cas systems, fluorescence-based chemistries, microfluidics and paper-based sensors has significantly influenced the biosensing and diagnosis field. This review comprehensively analyzed isothermal nucleic acid amplification methods, emphasizing their advantages, disadvantages and limitations.
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Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
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3
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Zhang L, Ju Y, Hu H, Ma C, Huang Y, Gong L, Liu Y, Bian L. Preliminary establishment and validation of a loop-mediated isothermal amplification assay for convenient screening of 13 types of high-risk human papillomaviruses in cervical secretions. J Virol Methods 2022; 303:114501. [PMID: 35217104 DOI: 10.1016/j.jviromet.2022.114501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The detection of human papillomaviruses (HPV) is a well-recognized strategy in early screening and prevention of cervical cancer. However, it's hard to carry out in undeveloped area because the sophisticated equipment that required in traditional methods is usually unavailable. To overcome this situation, we aim to establish a loop-mediated isothermal amplification (LAMP) method, which is simple and reliable for on-site detection of HPV. METHODS At least 3 sets of LAMP primers for each of the 13 types of high risk HPV were designed. After preliminary validation, the candidate primers were used in the detection of clinical samples and the results were head-to-head compared with a clinically approved real-time PCR assay. The performance of the LAMP method was assessed by kappa concordance test. RESULTS Cervical secretions samples from 1412 patients were included, with 224 samples were used in the preliminary screening of the LAMP primers and the other 1188 samples were used in the verification. Compared with real-time PCR method, the specificity of our LAMP method for each type of HPV were 100 %, and 11 of the 13 types had a sensitivity greater than 80 %. Among them, HPV 31 and 52 demonstrated the best performance, both with Kappa value of 0.913 (P < 0.0001). Besides, HPV 18, 35 and 56 only achieved a Kappa value less than 0.7, indicating their primers or reaction conditions may need further optimization. In general, the sensitivity, specificity, positive predictive value, negative predictive value and agreement of the LAMP assay in all HPV types was 86.9 %, 100 %, 100 %, 71.4 %, and 90.2 %, respectively (Kappa = 0.766, P < 0.0001). CONCLUSION In present study, we preliminary established and validated a LAMP method for HPV detection. This method could combine with self-sampling, thermostatic device, and appropriate dyes to form a simple and effective assay in the future, which would has good prospect and practical value in cervical cancer prevention, especially in undeveloped area.
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Affiliation(s)
- Lijuan Zhang
- The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Yan Ju
- The Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100027, China
| | - Haixu Hu
- The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Chunhui Ma
- The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China; School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
| | - Yan Huang
- The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Lili Gong
- The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Yi Liu
- The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China.
| | - Lihong Bian
- The Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100027, China.
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4
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Vo DT, Story MD. Facile and direct detection of human papillomavirus (HPV) DNA in cells using loop-mediated isothermal amplification (LAMP). Mol Cell Probes 2021; 59:101760. [PMID: 34364994 DOI: 10.1016/j.mcp.2021.101760] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 02/07/2023]
Abstract
Human papillomavirus (HPV)-mediated cancers, particularly cervical and oropharyngeal cancer, lead to hundreds of thousands of deaths worldwide each year. Simple, straightforward, and cost-effective detection of HPV DNA from patients with these malignancies or at risk for developing cancer can improve outcomes for patients, serving as a tool for early detection, monitoring treatment response, and assessment of cancer recurrence. Loop-mediated isothermal amplification (LAMP) is a simple and robust method for the detection and amplification of DNA in a single tube, utilizing the Bst strand-displacing DNA polymerase. We developed a workflow utilizing LAMP for the visual detection of HPV DNA in oral rinses. We demonstrate that LAMP is able to easily discriminate between two of the high-risk HPV subtypes, HPV16 and HPV18. We then utilized LAMP to visually detect HPV DNA directly from cells in oral rinses, mimicking a clinical inspired scenario of detecting HPV DNA in clinical samples. Our results suggest that LAMP is a robust, colorimetric assay method for the detection of HPV DNA in complex cellular samples, and further development is warranted to bring LAMP into the clinic.
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Affiliation(s)
- Dat T Vo
- Department of Radiation Oncology, Division of Clinical Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Michael D Story
- Department of Radiation Oncology, Division of Molecular Radiation Biology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
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5
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Zamani M, Robson JM, Fan A, Bono MS, Furst AL, Klapperich CM. Electrochemical Strategy for Low-Cost Viral Detection. ACS CENTRAL SCIENCE 2021; 7:963-972. [PMID: 34235257 PMCID: PMC8227598 DOI: 10.1021/acscentsci.1c00186] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 05/08/2023]
Abstract
Sexually transmitted infections, including the human immunodeficiency virus (HIV) and the human papillomavirus (HPV), disproportionally impact those in low-resource settings. Early diagnosis is essential for managing HIV. Similarly, HPV causes nearly all cases of cervical cancer, the majority (90%) of which occur in low-resource settings. Importantly, infection with HPV is six times more likely to progress to cervical cancer in women who are HIV-positive. An inexpensive, adaptable point-of-care test for viral infections would make screening for these viruses more accessible to a broader set of the population. Here, we report a novel, cost-effective electrochemical platform using gold leaf electrodes to detect clinically relevant viral loads. We have combined this platform with loop-mediated isothermal amplification and a CRISPR-based recognition assay to detect HPV. Lower limits of detection were demonstrated down to 104 total copies of input nucleic acids, which is a clinically relevant viral load for HPV DNA. Further, proof-of-concept experiments with cervical swab samples, extracted using standard extraction protocols, demonstrated that the strategy is extendable to complex human samples. This adaptable technology could be applied to detect any viral infection rapidly and cost-effectively.
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Affiliation(s)
- Marjon Zamani
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - James M. Robson
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Andy Fan
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Michael S. Bono
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Ariel L. Furst
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- (A.L.F.)
| | - Catherine M. Klapperich
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- (C.M.K.)
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6
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Rafiq A, Ali WR, Asif M, Ahmed N, Khan WS, Mansoor S, Bajwa SZ, Amin I. Development of a LAMP assay using a portable device for the real-time detection of cotton leaf curl disease in field conditions. Biol Methods Protoc 2021; 6:bpab010. [PMID: 34084942 PMCID: PMC8164779 DOI: 10.1093/biomethods/bpab010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 11/22/2022] Open
Abstract
Cotton production is seriously affected by the prevalent cotton leaf curl disease (CLCuD) that originated from Nigeria (Africa) to various parts of Asia including Pakistan, India, China and Philippines. Due to CLCuD, Pakistan suffers heavy losses approximately 2 billion USD per annum. Numerous reports showed that CLCuD is associated with multiple species of begomoviruses, alphasatellites and a single species of betasatellite, that is ‘Cotton leaf curl Multan betasatellite’ (CLCuMuB). The most prevalent form of CLCuD is the combination of ‘Cotton leaf curl Kokhran virus’-Burewala strain (CLCuKoV-Bur) and CLCuMuB. Thus, the availability of an in-field assay for the timely detection of CLCuD is important for the control and management of the disease. In this study, a robust method using the loop-mediated isothermal amplification (LAMP) assay was developed for the detection of CLCuD. Multiple sets of six primers were designed based on the conserved regions of CLCuKoV-Bur and CLCuMuB-βC1 genes. The results showed that the primer set targeting the CLCuMuB-βC1 gene performed best when the LAMP assay was performed at 58°C using 100 ng of total plant tissue DNA as a template in a 25 µl reaction volume. The limit of detection for the assay was as low as 22 copies of total purified DNA template per reaction. This assay was further adapted to perform as a colorimetric and real-time LAMP assay which proved to be advantageously applied for the rapid and early point-of-care detection of CLCuD in the field. Application of the assay could help to prevent the huge economic losses caused by the disease and contribute to the socio-economic development of underdeveloped countries.
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Affiliation(s)
- Amna Rafiq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 44000, Pakistan
| | - Waqas Rafique Ali
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Nasim Ahmed
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 44000, Pakistan
| | - Waheed S Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Sadia Zafar Bajwa
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box No. 577, Jhang Road, Faisalabad 38000, Pakistan
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7
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Wang J, Staheli JP, Wu A, Kreutz JE, Hu Q, Wang J, Schneider T, Fujimoto BS, Qin Y, Yen GS, Weng B, Shibley K, Haynes H, Winer RL, Feng Q, Chiu DT. Detection of 14 High-Risk Human Papillomaviruses Using Digital LAMP Assays on a Self-Digitization Chip. Anal Chem 2021; 93:3266-3272. [PMID: 33534543 DOI: 10.1021/acs.analchem.0c04973] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cervical cancer is the fourth-leading cause of cancer deaths among women worldwide and most cases occur in developing countries. Detection of high-risk (HR) HPV, the etiologic agent of cervical cancer, is a primary screening method for cervical cancer. However, the current gold standard for HPV detection, real-time PCR, is expensive, time-consuming, and instrumentation-intensive. A rapid, low-cost HPV detection method is needed for cervical cancer screening in low-resource settings. We previously developed a digital loop-mediated isothermal amplification (dLAMP) assay for rapid, quantitative detection of nucleic acids without the need for thermocycling. This assay employs a microfluidic self-digitization chip to automatically digitize a sample into an array of nanoliter wells in a simple assay format. Here we evaluate the dLAMP assay and self-digitization chip for detection of the commonly tested 14 high-risk HPVs in clinical samples. The dLAMP platform provided reliable genotyping and quantitative detection of the 14 high-risk HPVs with high sensitivity, demonstrating its potential for simple, rapid, and low-cost diagnosis of HPV infection.
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Affiliation(s)
- Jiasi Wang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jeannette P Staheli
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98105, United States
| | - Andrew Wu
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98105, United States
| | - Jason E Kreutz
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Qiongzheng Hu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jingang Wang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Thomas Schneider
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bryant S Fujimoto
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yuling Qin
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gloria S Yen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bob Weng
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Kara Shibley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Halia Haynes
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rachel L Winer
- Department of Epidemiology, University of Washington, Seattle, Washington 98195, United States
| | - Qinghua Feng
- FIDALAB, Seattle, Washington 98199, United States
| | - Daniel T Chiu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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8
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Daskou M, Tsakogiannis D, Alexopoulou DS, Dimitriou TG, Mossialos D, Amoutzias GD, Kottaridi C, Markoulatos P. A colorimetric IsoPCR for the rapid and sensitive visual detection of high-risk HPV16 in clinical samples with hydroxynaphthol blue. J Virol Methods 2021; 290:114072. [PMID: 33485938 DOI: 10.1016/j.jviromet.2021.114072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/04/2020] [Accepted: 01/16/2021] [Indexed: 01/06/2023]
Abstract
HPV16 infection is found in more than 50 % of cervical cancer cases worldwide, triggering the development of numerous molecular techniques for viral diagnosis. The present study focuses on the development of a colorimetric IsoPCR for HPV16 DNA detection. The methodology combines the advantages of PCR and LAMP, while the most significant aspect of the new established methodology is the visual detection of amplification products through hydroxynapthol blue dye, thus minimizing the time and labor needed. An experimental cut-off value was tested through reconstitution experiments, while the specificity was evaluated by assessing clinical samples. The analytical sensitivity of the new colorimetric IsoPCR was found to be 0.1 viral DNA copy per reaction, while the specificity was 100 % for the detection of HPV16 DNA. The assay enabled the amplification of viral DNA in cases with viral load lower than 1 copy. In conclusion, the new established colorimetric IsoPCR can be regarded as an attractive molecular tool that facilitates the specific, rapid and highly sensitive visual detection of HPV16 DNA even at the very early stages of viral infection.
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Affiliation(s)
- M Daskou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece
| | - D Tsakogiannis
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece.
| | - D S Alexopoulou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece
| | - T G Dimitriou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece
| | - D Mossialos
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece
| | - G D Amoutzias
- Bioinformatics Laboratory, University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Biopolis, Larissa, Greece
| | - C Kottaridi
- Second Department of Pathology, Attikon University Hospital, National and Kapodistrian University of Athens, Chaidari, Athens, 12462, Greece; Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, GR, 54124, Greece
| | - P Markoulatos
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece
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9
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Fauzi FH, Hamzan NI, Rahman NA, Suraiya S, Mohamad S. Detection of human papillomavirus in oropharyngeal squamous cell carcinoma. J Zhejiang Univ Sci B 2020; 21:961-976. [PMID: 33843162 DOI: 10.1631/jzus.b2000161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Worldwide there has been a significant increase in the incidence of oropharyngeal squamous cell carcinoma (OPSCC) etiologically attributed to oncogenic human papillomavirus (HPV). Reliable and accurate identification and detection tools are important as the incidence of HPV-related cancer is on the rise. Several HPV detection methods for OPSCC have been developed and each has its own advantages and disadvantages in regard to sensitivity, specificity, and technical difficulty. This review summarizes our current knowledge of molecular methods for detecting HPV in OPSCC, including HPV DNA/RNA polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), p16 immunohistochemistry (IHC), and DNA/RNA in situ hybridization (ISH) assays. This summary may facilitate the selection of a suitable method for detecting HPV infection, and therefore may help in the early diagnosis of HPV-related carcinoma to reduce its mortality, incidence, and morbidity.
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Affiliation(s)
- Fatin Hazwani Fauzi
- School of Dental Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Nurul Izzati Hamzan
- School of Dental Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Nurhayu Ab Rahman
- School of Dental Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Siti Suraiya
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Suharni Mohamad
- School of Dental Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
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10
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Rungkamoltip P, Temisak S, Piboonprai K, Japrung D, Thangsunan P, Chanpanitkitchot S, Chaowawanit W, Chandeying N, Tangjitgamol S, Iempridee T. Rapid and ultrasensitive detection of circulating human papillomavirus E7 cell-free DNA as a cervical cancer biomarker. Exp Biol Med (Maywood) 2020; 246:654-666. [PMID: 33307803 DOI: 10.1177/1535370220978899] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has attracted attention as a non-invasive biomarker for diagnosing and monitoring various cancers. Given that human papillomavirus (HPV) DNA integration and overexpression of E6/E7 oncogenes are pivotal events for carcinogenesis, we sought to determine if HPV E7 cfDNA could serve as a specific biomarker for cervical cancer detection. We applied droplet digital PCR (ddPCR) to quantify HPV16/18 E7 cfDNA from the serum of patients with cervical cancer, cervical intraepithelial neoplasia, and controls. HPV16/18 E7 cfDNA was highly specific for cervical cancer, displaying 30.77% sensitivity, 100% specificity, and an area under the curve of 0.65. Furthermore, we developed a sensitive isothermal detection of HPV16/18 E7 and the PIK3CA WT reference gene based on recombinase polymerase amplification combined with a lateral flow strip (RPA-LF). The assay took less than 30 min and the detection limit was 5-10 copies. RPA-LF exhibited 100% sensitivity and 88.24% specificity towards HPV16/18 E7 cfDNA in clinical samples. The agreement between RPA-LF and ddPCR was 83.33% (κ = 0.67) for HPV16 E7 and 100% (κ = 1.0) for HPV18 E7, indicating a good correlation between both tests. Therefore, we conclude that HPV E7 cfDNA represents a potential tumor marker with excellent specificity and moderate sensitivity for minimally invasive cervical cancer monitoring. Moreover, the RPA-LF assay provides an affordable, rapid, and ultrasensitive tool for detecting HPV cfDNA in resource-limited settings.
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Affiliation(s)
- Phetploy Rungkamoltip
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Sasithon Temisak
- Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani 12120, Thailand
| | - Kitiya Piboonprai
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand.,Laboratory of Host Defense, The World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pattanapong Thangsunan
- Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani 12120, Thailand
| | - Saranya Chanpanitkitchot
- Department of Obstetrics and Gynecology, Rajavithi Hospital, College of Medicine, Rangsit University, Bangkok 10400, Thailand
| | - Woraphot Chaowawanit
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand
| | - Nutthaporn Chandeying
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand
| | - Siriwan Tangjitgamol
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand.,Obstetrics and Gynecology Section, MedPark Hospital, Bangkok 10110, Thailand
| | - Tawin Iempridee
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
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11
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Wang J, Liu J, Song G, Cao Z, Pan J, Li X, Gao Y, Qi J, Chen Z, Fan G, Bai X, Zhang R, Wang R, Duan Q, Li L, Shen X, Ma X. Internally controlled recombinase-aided amplification (IC-RAA) assays for the detection of human papillomavirus genotypes 16 and 18 using extracted DNA and samples treated with nucleic acid releasing agent. Arch Virol 2020; 165:2241-2247. [PMID: 32681408 DOI: 10.1007/s00705-020-04722-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/25/2020] [Indexed: 10/23/2022]
Abstract
Cervical cancer is primarily caused by persistent infection with high-risk human papillomavirus (HPV), and 70% of cases are associated with HPV16 and 18 infections. The objective of this study was to establish rapid, simple, and sensitive internally controlled recombinase-aided amplification (IC-RAA) assays for the detection of HPV16 and 18. The assays were performed at 39 ℃ and were completed within 30 min. A total of 277 clinical samples of exfoliated cervical cells were tested by IC-RAA assays and commercial HPV real-time fluorescent PCR kits using extracted DNA and samples treated with nucleic acid releasing agent. The analytical sensitivity of the IC-RAA assay was found to be 10 copies/μL for the detection of HPV16 and 18 when using recombinant plasmids as targets. The optimal concentration of the internal control (IC) plasmid and 18 was 1000 copies/μL for HPV16 and 100 copies/μL for HPV18. The clinical sensitivity of the IC-RAA assays for HPV16 using extracted DNA and samples treated with nucleic acid releasing agent was 98.73% and 97.47%, respectively, with kappa values of 0.977 (P < 0.01) and 0.955 (P < 0.01), respectively, and 100% The specificity in both cases. For HPV18, the sensitivity and specificity were 100%, and the kappa value was 1 for both samples (P < 0.01). The IC-RAA assay is a promising tool for the detection of HPV16 and HPV18, especially in resource-constrained settings.
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Affiliation(s)
- Jinrong Wang
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, 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, No. 155, Changbai Street, Changping District, Beijing, 102206, China.,Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China
| | - Jianli Liu
- General Administration of Customs (Beijing) International Travel Healthcare Centre, No. 20 Heping Li North Street, Dongcheng District, Beijing, 100013, China
| | - Guowei Song
- Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China
| | - Zhi Cao
- Beijing Chaoyang Maternal and Child Health Hospital, No. 25 Huaweili, Chaoyang District, Beijing, China
| | - Jing Pan
- Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, 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, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Yuan Gao
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, 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, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Juju Qi
- Myasthenia Gravis Research Institute, The First Hospital of Shijiazhuang, 36 Fanxi Road, Shijiazhuang, 050011, Hebei, China
| | - Ziwei 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, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Guohao 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
| | - 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, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Ruiqing Zhang
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, 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, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Ruihuan Wang
- 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
| | - Qingxia Duan
- Hebei Medical University, 361 East Zhongshan Road, Shijiazhuang, 050031, 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, No. 155, Changbai Street, 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.
| | - 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, No. 155, Changbai Street, Changping District, Beijing, 102206, 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, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
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12
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Yin K, Ding X, Li Z, Zhao H, Cooper K, Liu C. Dynamic Aqueous Multiphase Reaction System for One-Pot CRISPR-Cas12a-Based Ultrasensitive and Quantitative Molecular Diagnosis. Anal Chem 2020; 92:8561-8568. [PMID: 32390420 DOI: 10.1021/acs.analchem.0c01459] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recently, CRISPR-Cas technology has opened a new era of nucleic acid-based molecular diagnostics. However, current CRISPR-Cas-based nucleic acid biosensing has a lack of the quantitative detection ability and typically requires separate manual operations. Herein, we reported a dynamic aqueous multiphase reaction (DAMR) system for simple, sensitive and quantitative one-pot CRISPR-Cas12a based molecular diagnosis by taking advantage of density difference of sucrose concentration. In the DAMR system, recombinase polymerase amplification (RPA) and CRISPR-Cas12a derived fluorescent detection occurred in spatially separated but connected aqueous phases. Our DAMR system was utilized to quantitatively detect human papillomavirus (HPV) 16 and 18 DNAs with sensitivities of 10 and 100 copies within less than 1 h. Multiplex detection of HPV16/18 in clinical human swab samples were successfully achieved in the DAMR system using 3D-printed microfluidic device. Furthermore, we demonstrated that target DNA in real human plasma samples can be directly amplified and detected in the DAMR system without complicated sample pretreatment. As demonstrated, the DAMR system has shown great potential for development of next-generation point-of-care molecular diagnostics.
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Affiliation(s)
- Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030, United States
| | - Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030, United States
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030, United States
| | - Hui Zhao
- Department of Mechanical Engineering, University of Nevada, Las Vegas, Las Vegas, Nevada 89154, United States
| | - Kumarasen Cooper
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce St. Philadelphia, Pennsylvania 19104, United States
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030, United States
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13
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Shah UJ, Nasiruddin M, Dar SA, Khan MKA, Akhter MR, Singh N, Rabaan AA, Haque S. Emerging biomarkers and clinical significance of HPV genotyping in prevention and management of cervical cancer. Microb Pathog 2020; 143:104131. [PMID: 32169490 DOI: 10.1016/j.micpath.2020.104131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/10/2020] [Accepted: 03/06/2020] [Indexed: 12/15/2022]
Abstract
Cervical cancer is a growing and serious problem world-wide in women, but more acute in developing countries especially in Indian subcontinent. The main causative agent for the disease is Human Papilloma Virus (HPV). The history of the cervical cancer goes back to eighteenth century as the HPV infection is reported since 1800s. Presently, the genetic structure of HPV is well defined. Several screening tests including cytology and visual based screening and high risk HPV testing are available. Also available are various clinical and commercial diagnostic tests. However due to the lack of awareness and population-based screening programs, the morbidity and mortality rate is alarmingly high. There are new emerging biomarkers including E6/E7 mRNA, p16ink4a, markers of aberrant S-phase induction, chromosomal abnormalities and miRNAs along with advanced genotyping methods. These markers have clinical significance and are helpful in disease prevention and management. Further, recent advancement in the field of metagenomics has increased the prospects of identifying newer microbes, viruses hitherto reported thus far in the context of HPV infection. Analysis of HPV cases using modern tools including genotyping using more powerful biomarkers is envisaged to enhance the prospects of early diagnosis, better prognosis, more reliable treatment and eventual management of the disease.
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Affiliation(s)
- Ushma Jaykamal Shah
- MedGenome Labs Ltd., Kailash Cancer Hospital and Research Center, Muni Seva Ashram, P.O. Goraj, Tal. Waghodia, Dist. Vadodara, 391760, Gujarat, India
| | - Mohammad Nasiruddin
- Anand Diagnostic Laboratory (A Neuberg Associate), Neuberg Anand Reference Laboratory, Anand Tower, 54, Bowring Hospital Road, Shivajinagar, Bangalore - 560001, India.
| | - Sajad Ahmad Dar
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Md Khurshid Alam Khan
- School of Life Sciences, BS Abdur Rahman Crescent Institute of Science and Technology, Chennai, 600048, Tamil Nadu, India
| | - Mohammad Riyaz Akhter
- MedGenome Labs Ltd., 3rd Floor, Narayana Nethralaya Building, Narayana Health City, # 258/A, Bommasandra, Hosur Road, Bangalore, 560099, Karnataka, India
| | - Nidhi Singh
- Department of Obstetrics and Gynecology, Prasad Institute of Medical Sciences, Lucknow, 226401, Uttar Pradesh, India
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Saudi Aramco, Dhahran, 31311, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia.
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14
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Yang X, Qi YJ, Al-Attala MN, Gao ZH, Yi XK, Zhang AF, Zang HY, Gu CY, Gao TC, Chen Y. Rapid Detection of Alternaria Species Involved in Pear Black Spot Using Loop-Mediated Isothermal Amplification. PLANT DISEASE 2019; 103:3002-3008. [PMID: 31573432 DOI: 10.1094/pdis-01-19-0149-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Alternaria species are the most important fungal pathogens that attack various crops as well as fruit trees such as pear and cause black spot disease. Here, a loop-mediated isothermal amplification (LAMP) assay is developed for the detection of Alternaria species. A. alternata cytochrome b (cyt-b) gene was used to design two pairs of primers and amplified a 229-bp segment of Aacyt-b gene. The results showed that LAMP assay is faster and simpler than polymerase chain reaction (PCR). LAMP assay is highly sensitive method for the detection of about 1 pg of genomic DNA of A. alternata by using optimized concentration of MgCl2 (4 mM) in final LAMP reaction. In contrast, the limit of detection was 1 ng of target DNA via conventional PCR. Among the genomic DNA of 46 fungal species, only the tubes containing DNA of Alternaria spp. except A. porri, A. solani, and A. infectoria changed color from orange to yellowish green with SYBR Green I including the main pathogens of pear black spot. The yellowish green color was indicative of DNA amplification. Moreover, LAMP assay was used for testing infected tissues among 22 healthy and diseased pear tissues; the orange color changed to yellowish green for infected tissues only. Altogether, we conclude that cyt-b gene can be used for the detection of Alternaria spp. via LAMP assay, which is involved in pear black spot disease.
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Affiliation(s)
- Xue Yang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
| | - Yong-Jie Qi
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Anhui Province, China
| | - Mohamed N Al-Attala
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Plant Pathology Unit, Plant Protection Department, Desert Research Center, Cairo 11753, Egypt
| | - Zheng-Hui Gao
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Anhui Province, China
| | - Xing-Kai Yi
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Anhui Province, China
| | - Ai-Fang Zhang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
| | - Hao-Yu Zang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
| | - Chun-Yan Gu
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
| | - Tong-Chun Gao
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
| | - Yu Chen
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China
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15
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Daskou M, Tsakogiannis D, Dimitriou TG, Amoutzias GD, Mossialos D, Kottaridi C, Gartzonika C, Markoulatos P. WarmStart colorimetric LAMP for the specific and rapid detection of HPV16 and HPV18 DNA. J Virol Methods 2019; 270:87-94. [PMID: 31042552 DOI: 10.1016/j.jviromet.2019.04.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 04/15/2019] [Accepted: 04/26/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND AND OBJECTIVES Persistent infection with High-Risk HPV genotypes is the principal cause for the development of cervical cancer with HPV16 and HPV18 to be the most frequently identified HPV genotypes observed in approximately 70% of cervical cancer cases worldwide. The present study focused on the development of a simple molecular methodology based on WarmStart colorimetric LAMP for the specific identification of HPV16 and HPV18. METHODS The method was developed by designing LAMP type-specific primer sets that target the E6 gene. The assay was applied using HPV-positive clinical samples along with control cases in order to evaluate the specificity of the newly designed isothermal protocol. In addition, an experimental cutoff value was estimated through reconstitution experiments with HPV-DNA plasmids. LAMP amplicons were visualized by color changes, thus eliminating the requirement for post-amplification processing steps. RESULTS The WarmStart colorimetric LAMP facilitates the isothermal amplification of 10 copies per reaction of both HPV16 and HPV18 DNA, while it exhibits 100% specificity for the detection of the corresponding genotypes in LSIL and HSIL cases. Moreover, the assay demonstrates 100% PPV and 100% NPV. Finally, the sensitivity of conventional PCR with the type-specific LAMP primer sets (B3/F3) for the HPV16, HPV18 DNA detection was 100 copies/reaction and 10 copies/reaction, respectively. CONCLUSIONS The newly established WarmStart colorimetric LAMP can be considered as a powerful molecular tool that it can be easily implemented in small clinical and research laboratories for a rapid and efficient identification of the most tumorigenic HPV genotypes.
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Affiliation(s)
- M Daskou
- Microbiology-Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - D Tsakogiannis
- Microbiology-Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500, Larissa, Greece.
| | - T G Dimitriou
- Microbiology-Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - G D Amoutzias
- Bioinformatics Laboratory, University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, BIOPOLIS, Larissa, Greece
| | - D Mossialos
- Microbiology-Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - C Kottaridi
- Department of Cytopathology, National and Kapodistrian University of Athens, Medical School, "ATTIKON" University Hospital, 1 Rimini, Haidari, 12462, Athens, Greece
| | - C Gartzonika
- Department of Microbiology, University of Ioannina, Medical School, Ioannina, Greece
| | - P Markoulatos
- Microbiology-Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Biopolis, 41500, Larissa, Greece
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16
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Mudhigeti N, Kalawat U, Hulikal N, Kante M. Evaluation of loop-mediated isothermal amplification assay for detection and typing of human papilloma virus 16 and 18 from endocervical samples. Indian J Med Microbiol 2019; 37:241-247. [PMID: 31745026 DOI: 10.4103/ijmm.ijmm_19_58] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Many human papillomavirus (HPV) types are associated with cervical cancer (CC). Therefore, HPV genotyping has both clinical and epidemiological importance. HPV 16 and 18 are two principal high-risk types responsible for more than 70% of all CC cases. Although several commercial and non-commercial genotyping assays are available, there is a need for a cost-effective and sensitive genotyping method for low- and middle-income countries. Methods The study was aimed at evaluation of loop-mediated isothermal amplification (LAMP) assay for HPV genotyping in cervical samples. A total of six primer sets for each HPV type were selected for the assay. The LAMP assay was standardised and validated with HPV control panel. Cervical biopsies were subjected to nested multiplex polymerase chain reaction (NM-PCR; as a part of routine diagnostic workup) and LAMP (HPV 16 and 18) simultaneously. Results A total of 225 clinical samples were processed during the study period. The sensitivity of the assay was determined using the 10-fold dilutions of positive controls. Both the HPV 16-LAMP and HPV 18-LAMP assays were shown to detect as low as 10 viral copies per reaction, which is similar to that of NM-PCR. The LAMP assay had a good agreement (new cases; 92%, post-chemoradiotherapy [post-CRT]; 89.1%) with NM-PCR for the detection of both HPV 16 and 18. As compared to histology (new cases; 79.8%, post-CRT; 51.3%), LAMP had better agreement with NM-PCR for detection of HPV from post-CRT cases. Conclusions We evaluated the LAMP assay for simultaneous detection and typing of HPV 16 and 18. The assay had good agreement with NM-PCR for detection of both HPV 16 and 18. The LAMP assay is a promising tool for HPV genotyping along with routine cervical cytology, especially in resource-constrained settings.
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Affiliation(s)
- Nagaraja Mudhigeti
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - Usha Kalawat
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - Narendra Hulikal
- Department of Surgical Oncology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - Meenakshi Kante
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
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17
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Kreutz JE, Wang J, Sheen AM, Thompson AM, Staheli JP, Dyen MR, Feng Q, Chiu DT. Self-digitization chip for quantitative detection of human papillomavirus gene using digital LAMP. LAB ON A CHIP 2019; 19:1035-1040. [PMID: 30734822 PMCID: PMC6420227 DOI: 10.1039/c8lc01223g] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Digital nucleic acid amplification and detection methods provide excellent sensitivity and specificity and allow absolute quantification of target nucleic acids. Isothermal methods such as digital loop-mediated isothermal amplification (digital LAMP) have potential for use in rapid disease diagnosis in low-resource settings due to their speed and lack of thermal cycling. We previously developed a self-digitization (SD) chip, a simple microfluidics device that automatically digitizes a sample into an array of nanoliter wells, for use in digital LAMP. In this work, we improve the SD chip design to increase sample loading efficiency, speed, and completeness, and test a range of well volumes and numbers. We demonstrate the diagnostic capability of this platform by applying it to quantifying human papillomavirus 18 gene.
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Affiliation(s)
- Jason E Kreutz
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA.
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18
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Genomagnetic LAMP-based electrochemical test for determination of high-risk HPV16 and HPV18 in clinical samples. Anal Chim Acta 2018; 1042:37-43. [DOI: 10.1016/j.aca.2018.08.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/06/2018] [Accepted: 08/10/2018] [Indexed: 12/29/2022]
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19
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Zhang Q, Shavalier M, Standish I, Glenney GW, Loch TP, Faisal M. Development of a loop-mediated isothermal amplification assay for the detection and quantification of epizootic epitheliotropic disease virus (salmonid herpesvirus-3). J Virol Methods 2018; 264:44-50. [PMID: 30444983 PMCID: PMC7119762 DOI: 10.1016/j.jviromet.2018.11.006] [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: 04/12/2018] [Revised: 10/02/2018] [Accepted: 11/12/2018] [Indexed: 11/25/2022]
Abstract
A quantitative LAMP method for identification of EEDV has been developed. Analytical sensitivity of the qLAMP is as low as 78 pg extracted DNA from tissue. The method is highly specific for EEDV. The EEDV qLAMP method was evaluated against the qPCR method.
Epizootic Epitheliotropic Disease Virus (EEDV; Salmonid Herpesvirus-3) causes a serious disease hatchery-reared lake trout (Salvelinus namaycush), threatening restoration efforts of this species in North America. The current inability to replicate EEDV in vitro necessitates the search for a reproducible, sensitive, and specific assay that allows for its detection and quantitation in a time- and cost-effective manner. Herein, we describe a loop-mediated isothermal amplification (LAMP) assay that was developed for the quantitative detection of EEDV in infected fish tissues. The newly developed LAMP reaction was optimized in the presence of calcein, and the best results were produced using 2 mM MgCl2, 1.8 mM dNTPs and at an incubation temperature of 67.1 °C. This method was highly specific to EEDV, as it showed no cross-reactivity with several fish viruses, including Salmonid Herpesvirus-1, -2, -4, and -5, Infectious Pancreatic Necrosis Virus, Spring Viremia of Carp Virus, Infectious Hematopoietic Necrosis Virus, Golden Shiner Reovirus, Fathead Minnow Nidovirus, and Viral Hemorrhagic Septicemia Virus. The analytical sensitivity of the EEDV-LAMP method was estimated to be as low as 16 copies of plasmid per reaction. When infected fish tissue was used, a positive reaction could be obtained when an infected gill tissue sample that contained 430 viral copies/μg was diluted up to five orders of magnitude. The sensitivity and specificity of the newly developed LAMP assay compared to the SYBR Green qPCR assay were 84.3% and 93.3%, respectively. The quantitative LAMP for EEDV had a correlation coefficient (R2 = 0.980), and did not differ significantly from the SYBR Green quantitative PCR assay (p > 0.05). Given its cost- and time-effectiveness, this quantitative LAMP assay is suitable for screening lake trout populations and for the initial diagnosis of clinical cases.
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Affiliation(s)
- Qingli Zhang
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China; Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48824, USA
| | - Megan Shavalier
- Comparative Medicine and Integrative Biology, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Isaac Standish
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48824, USA
| | - Gavin W Glenney
- U.S. Fish and Wildlife Service, Lamar Fish Health Center, Lamar, PA 16848, USA
| | - Thomas P Loch
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48824, USA; Department of Fisheries and Wildlife, College of Agriculture and Natural Resources,Michigan State University, East Lansing, MI 48824, USA
| | - Mohamed Faisal
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48824, USA; Comparative Medicine and Integrative Biology, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; Department of Fisheries and Wildlife, College of Agriculture and Natural Resources,Michigan State University, East Lansing, MI 48824, USA.
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20
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Draz MS, Kochehbyoki KM, Vasan A, Battalapalli D, Sreeram A, Kanakasabapathy MK, Kallakuri S, Tsibris A, Kuritzkes DR, Shafiee H. DNA engineered micromotors powered by metal nanoparticles for motion based cellphone diagnostics. Nat Commun 2018; 9:4282. [PMID: 30327456 PMCID: PMC6191441 DOI: 10.1038/s41467-018-06727-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/24/2018] [Indexed: 12/29/2022] Open
Abstract
HIV-1 infection is a major health threat in both developed and developing countries. The integration of mobile health approaches and bioengineered catalytic motors can allow the development of sensitive and portable technologies for HIV-1 management. Here, we report a platform that integrates cellphone-based optical sensing, loop-mediated isothermal DNA amplification and micromotor motion for molecular detection of HIV-1. The presence of HIV-1 RNA in a sample results in the formation of large-sized amplicons that reduce the motion of motors. The change in the motors motion can be accurately measured using a cellphone system as the biomarker for target nucleic acid detection. The presented platform allows the qualitative detection of HIV-1 (n = 54) with 99.1% specificity and 94.6% sensitivity at a clinically relevant threshold value of 1000 virus particles/ml. The cellphone system has the potential to enable the development of rapid and low-cost diagnostics for viruses and other infectious diseases.
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Affiliation(s)
- Mohamed Shehata Draz
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, 02139, MA, USA
- Department of Medicine, Harvard Medical School, Boston, 02115, MA, USA
- Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Kamyar Mehrabi Kochehbyoki
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, 02139, MA, USA
| | - Anish Vasan
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, 02139, MA, USA
| | - Dheerendranath Battalapalli
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, 02139, MA, USA
| | - Aparna Sreeram
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, 02139, MA, USA
| | - Manoj Kumar Kanakasabapathy
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, 02139, MA, USA
| | - Shantanu Kallakuri
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, 02139, MA, USA
| | - Athe Tsibris
- Department of Medicine, Harvard Medical School, Boston, 02115, MA, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, 02139, MA, USA
| | - Daniel R Kuritzkes
- Department of Medicine, Harvard Medical School, Boston, 02115, MA, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, 02139, MA, USA
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, 02139, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, 02115, MA, USA.
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21
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Yang X, Al-Attala MN, Zhang Y, Zhang AF, Zang HY, Gu CY, Gao TC, Chen Y, Al-Attala MN, Ali F, Li YF, Yao J, Zhu JG. Rapid Detection of Ustilaginoidea virens from Rice using Loop-Mediated Isothermal Amplification Assay. PLANT DISEASE 2018; 102:1741-1747. [PMID: 30125168 DOI: 10.1094/pdis-01-18-0065-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ustilaginoidea virens is an important fungus that causes rice false smut disease. This disease significantly reduces both grain yield and quality. Various methods have been developed for the detection of U. virens but most of these methods need sophisticated equipment such as a thermal cycler. Here, we present a loop-mediated isothermal amplification (LAMP) assay for the specific detection of U. virens. This assay used a specific region of the UvG-β1 gene (212-bp region) to design six LAMP primers. The LAMP assay was optimized by the combination of rapidity, simplicity, and high sensitivity for the detection of about 1 pg of target genomic DNA in the reaction whereas, with polymerase chain reaction (PCR), there was no amplification of DNA with concentrations less than 1 ng. Among the genomic DNA of 22 fungus species and two strains of U. virens, only the tube containing the DNA of U. virens changed to yellowish green with SYBR Green I. The color change was indicative of DNA amplification. No DNA was amplified from either the other 22 fungus species or the negative control. Moreover, 20 spikelets and 22 rice seed samples were used for the detection of rice false smut via LAMP. The results were comparable with conventional PCR. We conclude that gene UvG-β1 coupled with LAMP assay, can be used for the detection and identification of U. virens gene via LAMP.
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Affiliation(s)
- Xue Yang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Mohamed N Al-Attala
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Yong Zhang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Ai-Fang Zhang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Hao-Yu Zang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Chun-Yan Gu
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Tong-Chun Gao
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Yu Chen
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China; and Laboratory of Quality & Safety Risk Assessment for Agro-Products, Hefei, Ministry of Agriculture, China; and Key Laboratory of Anhui Agricultural Sciences
| | - Mohamed N Al-Attala
- Plant Pathology Unit, Plant Protection Department, Desert Research Center, Cairo 11753, Egypt
| | - Farman Ali
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences; and Department of Agriculture, Abdul Wali Khan University Mardan, Pakistan
| | - Yun-Fei Li
- Anhui Entry-Exit Inspection and Quarantine Bureau, Hefei 230022, China
| | - Jian Yao
- Anhui Entry-Exit Inspection and Quarantine Bureau, Hefei 230022, China
| | - Jin-Guo Zhu
- Hunan Entry-Exit Inspection and Quarantine Bureau, Changsha 410004, China
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22
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Draz MS, Moazeni M, Venkataramani M, Lakshminarayanan H, Saygili E, Lakshminaraasimulu NK, Kochehbyoki KM, Kanakasabapathy MK, Shabahang S, Vasan A, Bijarchi MA, Memic A, Shafiee H. Hybrid Paper-Plastic Microchip for Flexible and High-Performance Point-of-Care Diagnostics. ADVANCED FUNCTIONAL MATERIALS 2018; 28:1707161. [PMID: 30416415 PMCID: PMC6223320 DOI: 10.1002/adfm.201707161] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A low-cost and easy-to-fabricate microchip remains a key challenge for the development of true point-of-care (POC) diagnostics. Cellulose paper and plastic are thin, light, flexible, and abundant raw materials, which make them excellent substrates for mass production of POC devices. Herein, a hybrid paper-plastic microchip (PPMC) is developed, which can be used for both single and multiplexed detection of different targets, providing flexibility in the design and fabrication of the microchip. The developed PPMC with printed electronics is evaluated for sensitive and reliable detection of a broad range of targets, such as liver and colon cancer protein biomarkers, intact Zika virus, and human papillomavirus nucleic acid amplicons. The presented approach allows a highly specific detection of the tested targets with detection limits as low as 102 ng mL-1 for protein biomarkers, 103 particle per milliliter for virus particles, and 102 copies per microliter for a target nucleic acid. This approach can potentially be considered for the development of inexpensive and stable POC microchip diagnostics and is suitable for the detection of a wide range of microbial infections and cancer biomarkers.
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Affiliation(s)
- Mohamed Shehata Draz
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Maryam Moazeni
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Manasa Venkataramani
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Harini Lakshminarayanan
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ecem Saygili
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nivethitha Kota Lakshminaraasimulu
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kamyar Mehrabi Kochehbyoki
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Manoj Kumar Kanakasabapathy
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shirin Shabahang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anish Vasan
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mohamad Ali Bijarchi
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Adnan Memic
- Center for Nanotechnology, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's, Hospital, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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23
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Assessing the performance of a Loop Mediated Isothermal Amplification (LAMP) assay for the detection and subtyping of high-risk suptypes of Human Papilloma Virus (HPV) for Oropharyngeal Squamous Cell Carcinoma (OPSCC) without DNA purification. BMC Cancer 2018; 18:166. [PMID: 29422018 PMCID: PMC5806493 DOI: 10.1186/s12885-018-4087-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 01/31/2018] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Oropharyngeal Squamous Cell Carcinoma (OPSCC) is increasing in incidence despite a decline in traditional risk factors. Human Papilloma Virus (HPV), specifically subtypes 16, 18, 31 and 35, has been implicated as the high-risk etiologic agent. HPV positive cancers have a significantly better prognosis than HPV negative cancers of comparable stage, and may benefit from different treatment regimens. Currently, HPV related carcinogenesis is established indirectly through Immunohistochemistry (IHC) staining for p16, a tumour suppressor gene, or polymerase chain reaction (PCR) that directly tests for HPV DNA in biopsied tissue. Loop mediated isothermal amplification (LAMP) is more accurate than IHC, more rapid than PCR and is significantly less costly. In previous work we showed that a subtype specific HPV LAMP assay performed similar to PCR on purified DNA. In this study we examined the performance of this LAMP assay without DNA purification. METHODS We used LAMP assays using established primers for HPV 16 and 18, and new primers for HPV 31 and 35. LAMP reaction conditions were tested on serial dilutions of plasmid HPV DNA to confirm minimum viral copy number detection thresholds. LAMP was then performed directly on different human cell line samples without DNA purification. RESULTS Our LAMP assays could detect 105, 103, 104, and 105 copies of plasmid DNA for HPV 16, 18, 31, and 35, respectively. All primer sets were subtype specific, with no cross-amplification. Our LAMP assays also reliably amplified subtype specific HPV DNA from samples without requiring DNA isolation and purification. CONCLUSIONS The high risk OPSCC HPV subtype specific LAMP primer sets demonstrated, excellent clinically relevant, minimum copy number detection thresholds with an easy readout system. Amplification directly from samples without purification illustrated the robust nature of the assay, and the primers used. This lends further support HPV type specific LAMP assays, and these specific primer sets and assays can be further developed to test for HPV in OPSCC in resource and lab limited settings, or even bedside testing.
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24
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Leow CH, Fischer K, Leow CY, Cheng Q, Chuah C, McCarthy J. Single Domain Antibodies as New Biomarker Detectors. Diagnostics (Basel) 2017; 7:diagnostics7040052. [PMID: 29039819 PMCID: PMC5745390 DOI: 10.3390/diagnostics7040052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 01/02/2023] Open
Abstract
Biomarkers are defined as indicators of biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. Biomarkers have been widely used for early detection, prediction of response after treatment, and for monitoring the progression of diseases. Antibodies represent promising tools for recognition of biomarkers, and are widely deployed as analytical tools in clinical settings. For immunodiagnostics, antibodies are now exploited as binders for antigens of interest across a range of platforms. More recently, the discovery of antibody surface display and combinatorial chemistry techniques has allowed the exploration of new binders from a range of animals, for instance variable domains of new antigen receptors (VNAR) from shark and variable heavy chain domains (VHH) or nanobodies from camelids. These single domain antibodies (sdAbs) have some advantages over conventional murine immunoglobulin owing to the lack of a light chain, making them the smallest natural biomarker binders thus far identified. In this review, we will discuss several biomarkers used as a means to validate diseases progress. The potential functionality of modern singe domain antigen binders derived from phylogenetically early animals as new biomarker detectors for current diagnostic and research platforms development will be described.
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Affiliation(s)
- Chiuan Herng Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Katja Fischer
- Bacterial Pathogenesis and Scabies Laboratory, QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia.
| | - Chiuan Yee Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kelantan 16150, Malaysia.
| | - Qin Cheng
- Department of Drug Resistance and Diagnostics, Australian Army Malaria Institute, Brisbane 4051, Australia.
| | - Candy Chuah
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan 16150, Malaysia.
| | - James McCarthy
- Clinical Tropical Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane 4029, Australia.
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25
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Kumvongpin R, Jearanaikoon P, Wilailuckana C, Sae-Ung N, Prasongdee P, Daduang S, Wongsena M, Boonsiri P, Kiatpathomchai W, Swangvaree SS, Sandee A, Daduang J. Detection assay for HPV16 and HPV18 by loop-mediated isothermal amplification with lateral flow dipstick tests. Mol Med Rep 2017; 15:3203-3209. [DOI: 10.3892/mmr.2017.6370] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 01/27/2017] [Indexed: 11/06/2022] Open
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26
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Kumvongpin R, Jearanaikool P, Wilailuckana C, Sae-ung N, Prasongdee P, Daduang S, Wongsena M, Boonsiri P, Kiatpathomchai W, Swangvaree SS, Sandee A, Daduang J. High sensitivity, loop-mediated isothermal amplification combined with colorimetric gold-nanoparticle probes for visual detection of high risk human papillomavirus genotypes 16 and 18. J Virol Methods 2016; 234:90-5. [DOI: 10.1016/j.jviromet.2016.04.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 03/08/2016] [Accepted: 04/12/2016] [Indexed: 10/21/2022]
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27
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Yang JF, Zhao CZ, Lu KX. Development and application of a rapid detection system for human papillomavirus and Herpes simplex virus-2 by loop-mediated isothermal amplification assay. Microb Pathog 2016; 97:178-82. [PMID: 27287497 DOI: 10.1016/j.micpath.2016.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 05/31/2016] [Accepted: 06/06/2016] [Indexed: 11/26/2022]
Abstract
Human papillomavirus (HPV) infection is an important factor that causes cervical cancer and non-melanoma skin cancer (NMSC), while HSV-2 plays an important role when HR-HPV triggers the cancer. Thus, a quick and convenient assay in the detection of HPV and HSV-2in the screening of HPV and HSV-2 infection is required. Two respective HPV and HSV-2 detection methods were established based on loop-mediated isothermal amplification (LAMP) assay. Specific outer primers, inner primers, and loop primers were designed according to the conserved domains of HPV and HSV-2 genomes, respectively, while degenerate primers were used for HPV assay. After optimizing the reaction conditions, the results were observed by LAMP Tubidimeter real-time LA-320. Standard plasmids HPV-L-P and HSV-2-L-P were cloned and used in sensitivity tests of HPV LAMP and HSV-2 LAMP, respectively. Fifty samples of actinic keratosis (AK), 20 samples of squamous cell carcinoma (SCC), 50 samples of basal cell carcinoma (BCC) and 20 samples of seborrheic keratosis (SK) were detected by HPV assay. Seventy three clinical samples of vaginitis, chronic cervicitis, cervical intraepithelial neoplasias and cervical cancer level positive were detected with HPV and HSV-2 assays. The reaction conditions of two assays were the same with a reaction temperature of 63 °C and a reaction time of 45 min. The sensitivity of HPV LAMP assay was 10 copies/μL, while that of the HSV-2 LAMP assay was 100 copies/μL. No cross-reactivity was observed. The HPV positive rates of AK, SCC, BCC and SK samples were 80% (40/50), 75% (15/20), 44% (22/50) and 21% (15/72), respectively. As an economic and quick diagnostic tool, LAMP assay is conducive to the extensive screening of HPV and HSV-2 and has huge potential to be promoted in resource-limited hospitals.
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Affiliation(s)
- Jin-Fang Yang
- Department of Gynaecology and Obstetrics, Binzhou People's Hospital, Binzhou 256610, China
| | - Chang-Zhen Zhao
- Department of Gynaecology and Obstetrics, Binzhou People's Hospital, Binzhou 256610, China
| | - Ke-Xin Lu
- Department of Gynaecology and Obstetrics, Binzhou Medical University Hospital, Binzhou 256610, China.
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28
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Jearanaikoon P, Prakrankamanant P, Leelayuwat C, Wanram S, Limpaiboon T, Promptmas C. The evaluation of loop-mediated isothermal amplification-quartz crystal microbalance (LAMP-QCM) biosensor as a real-time measurement of HPV16 DNA. J Virol Methods 2016; 229:8-11. [DOI: 10.1016/j.jviromet.2015.12.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 11/25/2022]
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29
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Livingstone DM, Rohatensky M, Mintchev P, Nakoneshny SC, Demetrick DJ, van Marle G, Dort JC. Loop mediated isothermal amplification (LAMP) for the detection and subtyping of human papillomaviruses (HPV) in oropharyngeal squamous cell carcinoma (OPSCC). J Clin Virol 2016; 75:37-41. [PMID: 26780110 DOI: 10.1016/j.jcv.2016.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 12/08/2015] [Accepted: 01/05/2016] [Indexed: 01/12/2023]
Abstract
BACKGROUND Human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma (OPSCC) is a growing problem that presents a significant challenge to Otolaryngologist-Head and Neck Surgeons. Knowledge of HPV status yields critical prognostic information, with potential for treatment selection based on tumour HPV status. The current gold standard of diagnosis, PCR, is expensive, demanding and time consuming. Alternatives such as p16 immunohistochemistry are subjective and potentially inaccurate. Loop-mediated isothermal amplification (LAMP) is a rapid, robust and inexpensive molecular diagnostic technique. OBJECTIVES Our aim was to verify LAMP as a potential bedside diagnostic assay for subtyping of HPV in OPSCC. STUDY DESIGN DNA from 72 formalin-fixed paraffin embedded (FFPE) OPSCC patient samples was tested. PCR and LAMP were then performed to specifically identify HPV 16, 18, 31, 33 and 35. RESULTS AND CONCLUSIONS For these high-risk subtypes, LAMP had an overall sensitivity of 99.4% and specificity of 93.2% relative to PCR. LAMP is a promising technology that can accurately diagnose high-risk HPV infection.
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Affiliation(s)
- D M Livingstone
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
| | - M Rohatensky
- Undergraduate Medical Education, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - P Mintchev
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - S C Nakoneshny
- Ohlson Research Initiative, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - D J Demetrick
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary and Calgary Laboratory Services, Calgary, Alberta, Canada
| | - G van Marle
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - J C Dort
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Ohlson Research Initiative, Southern Alberta Cancer Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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30
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The development of DNA-based quartz crystal microbalance integrated with isothermal DNA amplification system for human papillomavirus type 58 detection. Biosens Bioelectron 2013; 40:252-7. [DOI: 10.1016/j.bios.2012.07.033] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 06/29/2012] [Accepted: 07/19/2012] [Indexed: 11/23/2022]
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31
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Satoh T, Matsumoto K, Fujii T, Sato O, Gemma N, Onuki M, Saito H, Aoki D, Hirai Y, Yoshikawa H. Rapid genotyping of carcinogenic human papillomavirus by loop-mediated isothermal amplification using a new automated DNA test (Clinichip HPV™). J Virol Methods 2012; 188:83-93. [PMID: 23219807 DOI: 10.1016/j.jviromet.2012.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 10/22/2012] [Accepted: 10/30/2012] [Indexed: 10/27/2022]
Abstract
This study was designed to evaluate the Clinichip HPV test, a new DNA test that detects carcinogenic human papillomavirus (HPV) rapidly by loop-mediated isothermal amplification and performs genotyping of all 13 carcinogenic types using automated DNA chip technology with an assay time 2.5h. Using this test, 247 Japanese women (109 with normal cytology, 43 with cervical intraepithelial neoplasia grade 1, 60 with cervical intraepithelial neoplasia grade 2/3 and 35 with invasive cervical cancer) were tested for carcinogenic HPV genotypes. The results were compared to those obtained by the polymerase chain reaction-amplified DNA sequencing using 13 type-specific primers. Overall, there was very good agreement for the detection of carcinogenic HPV between the Clinichip test and direct sequencing, with 95.5% total agreement and a kappa value of 0.91. Comparison of the detection of individual HPV types shows that the overall agreement was also high (range: 96.8-100%). In women with cervical intraepithelial neoplasia grade 2 or worse, the detection rate of carcinogenic HPV was 95.7% by both the Clinichip test and the direct-sequencing method, indicating complete agreement between the two methods. In conclusion, it was found that the Clinichip test is a promising new laboratory method for genotyping of carcinogenic HPV.
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Affiliation(s)
- Toyomi Satoh
- Department of Obstetrics and Gynecology, University of Tsukuba, Japan
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32
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Kittiloespaisan E, Ojida A, Hamachi I, Seetang-Nun Y, Kiatpathomchai W, Wongkongkatep J. Label-free Fluorescent Detection of Loop-mediated Isothermal Amplification of Nucleic Acid Using Pyrophosphate-selective Xanthene-based Zn(II)-coordination Chemosensor. CHEM LETT 2012. [DOI: 10.1246/cl.2012.1666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ekkachai Kittiloespaisan
- Department of Biotechnology, Faculty of Science, Mahidol University
- CENTEX Shrimp, Faculty of Science, Mahidol University
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Yortyot Seetang-Nun
- CENTEX Shrimp, Faculty of Science, Mahidol University
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
| | - Wansika Kiatpathomchai
- CENTEX Shrimp, Faculty of Science, Mahidol University
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency
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Ravindran A, Levy J, Pierson E, Gross DC. Development of a loop-mediated isothermal amplification procedure as a sensitive and rapid method for detection of 'candidatus Liberibacter solanacearum' in potatoes and Psyllids. PHYTOPATHOLOGY 2012; 102:899-907. [PMID: 22881872 DOI: 10.1094/phyto-03-12-0055-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This study reports the development of a loop-mediated isothermal amplification procedure (LAMP) for polymerase chain reaction (PCR)-based detection of 'Candidatus Liberibacter solanacearum', the bacterial causal agent of potato zebra chip (ZC) disease. The 16S rDNA gene of 'Ca. Liberibacter solanacearum' was used to design a set of six primers for LAMP PCR detection of the bacterial pathogen in potato plants and the psyllid vector. The advantage of the LAMP method is that it does not require a thermocycler for amplification or agarose gel electrophoresis for resolution. Positive LAMP results can be visualized directly as a precipitate. The LAMP strategy reported here reliably detected 'Ca. Liberibacter solanacearum' and the closely related species 'Ca. Liberibacter asiaticus', the causative agent of huanglongbing disease of citrus, in plant DNA extracts. Although not as sensitive as quantitative real-time PCR, LAMP detection was equivalent to conventional PCR in tests of ZC-infected potato plants from the field. Thus, the LAMP method shows strong promise as a reliable, rapid, and cost-effective method of detecting 'Ca. Liberibacter' pathogens in psyllids and field-grown potato plants and tubers.
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Affiliation(s)
- Aravind Ravindran
- Department of Palnt Pathology and Microbiology, Texas A&M University, College Station 77843, USA
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