| 研究生: |
劉鵬雯 Liu, Peng-Wen |
|---|---|
| 論文名稱: |
應用商品化pH微小電極試片建立反轉錄恆溫式圈環型核酸增幅檢測平台進行登革熱第二型病毒繼代培養樣本之判別 Development of a Commercial Micro pH Electrode Strip-based Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) Platform for Determination of Subculture Sample of DENV-2 Virus |
| 指導教授: |
張憲彰
Chang, Hsien-Chang |
| 學位類別: |
碩士 Master |
| 系所名稱: |
工學院 - 生物醫學工程學系 Department of BioMedical Engineering |
| 論文出版年: | 2023 |
| 畢業學年度: | 111 |
| 語文別: | 英文 |
| 論文頁數: | 54 |
| 中文關鍵詞: | 登革熱 、反轉錄恆溫式圈環型核酸增幅法 、pH值檢測 |
| 外文關鍵詞: | Dengue fever, RT-LAMP, pH value detection |
| 相關次數: | 點閱:73 下載:0 |
| 分享至: |
| 查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報 |
登革熱是由埃及伊蚊傳播的病毒傳染疾病,主要流行於熱帶和亞熱帶地區。然而,隨著氣候變遷和都市化的影響,目前全球已有超過半數人口處於感染登革熱的風險當中,因此登革熱早期診斷平台的開發對於病患處置及疫情監控至關重要。恆溫式圈環型核酸增幅法(LAMP)是一具有潛力的新興核酸恆溫增幅技術,與傳統的登革熱檢測方法相較之下檢測效能更好且具成本效益,且現行已有若干使用 技術的診斷平台取得政府授權用於病毒感染的檢測。然而,現有的 檢測平台大多依賴於光學方法,因此常發生偽陰性結果,且需昂貴的光學儀器進行即時訊號變化檢測。雖然後續有研究團隊開發場效電晶體(FET)的感測晶片應用於 技術中,但由於臨床端需要使用拋棄式耗材進行檢測,因此未來產線的建立以及高價的單次檢測費用是必須面對的問題。為了避免這些困難,我們提出了一種新的 檢測平台,該平台為使用商品化的印刷 微電極試片,透過測量反轉錄恆溫式圈環型核酸增幅反應後的 差異來進行結果判讀。該試片設計為單次使用,無需校準步驟,量測僅需 分鐘。在測量當中僅需要少量樣本 μl),並且試片可以輕鬆放入常規 管中進行直接 值測量。在本研究中,我們使用登革熱第二型病毒的繼代培養樣本進行了平台的驗證,陽性樣本在61° 進行 反應 分鐘後, 值呈 單位(病毒數量相當於 PFU)的下降,而陰性樣本則僅出現的小於± 單位變化。總結來說,我們提出了一種應用商品化 微電極試片的 檢測平台,該平台有望成為高效且具成本效益的登革病毒檢測技術。其簡單操作的方式和應用彈性使其具有改變核酸檢測方法的潛力,將有助於登革熱的及時診斷和有效控制疫情爆發。
Dengue fever is a viral disease transmitted by Aedes mosquitoes, primarily found in tropical and sub-tropical regions. However, with climate change and urbanization, more than half of the world’s population is at risk of the infection. Therefore, the development of early and reliable diagnostic methods is crucial for patient managements and effective surveillance of the pandemics. Loop-mediated isothermal amplification (LAMP) is a promising nucleic acid amplification technique which is a compelling alternative to conventional diagnostic methods due to their limited effectiveness and affordability. Several LAMP-based diagnostic platforms have been authorized for viral infections. However, most existing LAMP detection platforms rely on optical methods, which is associated with frequent false negatives and the need for expensive real-time monitoring instruments. Some FET-based sensors were introduced in LAMP detection, but the requirement for single use in clinical practices leaves the concerns about establishment of mass production and high cost for each detection. To address these issues, we propose a novel LAMP detection platform that utilizes a commercially available screen-printed pH microelectrode strip. This chip is designed for single-use and waives the need for calibration steps and the pH measurement can be completed within around 1.5 min. It measures the pH difference after the RT-LAMP reaction. Only a small sample volume (<10 μl) is required and can easily fit in regular PCR tubes for direct pH measurement. In this study, the subculture samples of DENV-2 were tested for validation of the presented platform. For positive samples, a pH drops of 0.2-0.5 units (the detectable concentration ranges from 100 ~ 100000 PFU) is observed after the LAMP reaction at 61°C within 30 min, while negative samples show a minimal ±0.1 pH change. Overall, our proposed commercial micro pH electrode strip-based RT-LAMP platform offers a practical solution for efficient and cost-effective dengue virus detection. With its simplicity and scalability, it has the potential to revolutionize nucleic acid detection methods, facilitating timely diagnosis and effective control of dengue outbreaks.
1. Teoh, E.P., et al., The structural basis for serotype-specific neutralization of dengue virus by a human antibody. Sci Transl Med, 2012. 4(139): p. 139ra83.
2. Thomas, S.J., et al., Dengue virus infection: Clinical manifestations and diagnosis, in UpToDate, M.S. Hirsch, Editor.: UpToDate, Waltham, MA. (Access on July 02, 2023).
3. Guzman, M.G., M. Alvarez, and S.B. Halstead, Secondary infection as a risk factor for dengue hemorrhagic fever/dengue shock syndrome: an historical perspective and role of antibody-dependent enhancement of infection. Arch Virol, 2013. 158(7): p. 1445-59.
4. Montoya, M., et al., Symptomatic versus inapparent outcome in repeat dengue virus infections is influenced by the time interval between infections and study year. PLoS Negl Trop Dis, 2013. 7(8): p. e2357.
5. Alvarez, M., et al., Dengue Hemorrhagic Fever Caused by Sequential Dengue 1–3 Virus Infections over a Long Time Interval: Havana Epidemic, 2001–2002. Am. J. Trop. Med. Hyg., 2006. 75(6): p. 1113-1117.
6. Kalayanarooj, S., Clinical Manifestations and Management of Dengue/DHF/DSS. Trop Med Health, 2011. 39(4 Suppl): p. 83-7.
7. McCracken, M.K., et al., Enhanced dengue vaccine virus replication and neutralizing antibody responses in immune primed rhesus macaques. NPJ Vaccines, 2021. 6(1): p. 77.
8. Sridhar, S., et al., Effect of Dengue Serostatus on Dengue Vaccine Safety and Efficacy. N Engl J Med, 2018. 379(4): p. 327-340.
9. World Health Organization. Dengue and severe dengue. [cited 2023 July 02]; Available from: https://www.who.int/news-room/fact-sheets/detail/dengue-and-severe-dengue.
10. Rocklov, J. and Y. Tozan, Climate change and the rising infectiousness of dengue. Emerg Top Life Sci, 2019. 3(2): p. 133-142.
11. Bhatt, S., et al., The global distribution and burden of dengue. Nature, 2013. 496(7446): p. 504-7.
12. Messina, J.P., et al., The current and future global distribution and population at risk of dengue. Nat Microbiol, 2019. 4(9): p. 1508-1515.
13. Weaver, S.C., Urbanization and geographic expansion of zoonotic arboviral diseases: mechanisms and potential strategies for prevention. Trends Microbiol., 2013. 21(8): p. 360-363.
14. Rivera, A., et al., Travel-Associated and Locally Acquired Dengue Cases - United States, 2010-2017. MMWR Morb Mortal Wkly Rep, 2020. 69(6): p. 149-154.
15. Yang, X., et al., Global burden for dengue and the evolving pattern in the past 30 years. J Travel Med, 2021. 28(8).
16. Duong, V., et al., Asymptomatic humans transmit dengue virus to mosquitoes. Proc Natl Acad Sci U S A, 2015. 112(47): p. 14688-93.
17. Nguyet, M.N., et al., Host and viral features of human dengue cases shape the population of infected and infectious Aedes aegypti mosquitoes. Proc Natl Acad Sci U S A, 2013. 110(22): p. 9072-7.
18. Pang, J., et al., Progress and Challenges towards Point-of-Care Diagnostic Development for Dengue. J Clin Microbiol, 2017. 55(12): p. 3339-3349.
19. Storch, G.A., Diagnostic virology. Clin Infect Dis, 2000. 31(3): p. 739-51.
20. Walker, T., et al., Mosquito cell lines: history, isolation, availability and application to assess the threat of arboviral transmission in the United Kingdom. Parasit Vectors, 2014. 7: p. 382.
21. Hodinka, R.L., Point: is the era of viral culture over in the clinical microbiology laboratory? J Clin Microbiol, 2013. 51(1): p. 2-4.
22. Kohler, G. and C. Milstein, Continuous cultures of fused cells secreting antibody of predefined specificity. Nature, 1975. 256(5517): p. 495-7.
23. Datta, S. and C. Wattal, Dengue NS1 antigen detection: a useful tool in early diagnosis of dengue virus infection. Indian J Med Microbiol, 2010. 28(2): p. 107-10.
24. Shu, P.Y., et al., Application of the dengue virus NS1 antigen rapid test for on-site detection of imported dengue cases at airports. Clin Vaccine Immunol, 2009. 16(4): p. 589-91.
25. Huang, C.H., et al., Laboratory diagnostics of dengue fever: an emphasis on the role of commercial dengue virus nonstructural protein 1 antigen rapid test. J Microbiol Immunol Infect, 2013. 46(5): p. 358-65.
26. Gyurech, D., et al., False positive dengue NS1 antigen test in a traveller with an acute Zika virus infection imported into Switzerland. Swiss Med Wkly, 2016. 146: p. w14296.
27. Lukman, N., et al., Comparison of the Hemagglutination Inhibition Test and IgG ELISA in Categorizing Primary and Secondary Dengue Infections Based on the Plaque Reduction Neutralization Test. Biomed Res Int, 2016. 2016: p. 5253842.
28. Peeling, R.W., et al., Evaluation of diagnostic tests: dengue. Nat Rev Microbiol, 2010. 8(12 Suppl): p. S30-8.
29. Hunsperger, E.A., et al., Evaluation of commercially available anti-dengue virus immunoglobulin M tests. Emerg Infect Dis, 2009. 15(3): p. 436-40.
30. Vaughn, D.W., et al., Dengue in the early febrile phase: viremia and antibody responses. J Infect Dis, 1997. 176(2): p. 322-30.
31. Shu, P.Y. and J.H. Huang, Current advances in dengue diagnosis. Clin Diagn Lab Immunol, 2004. 11(4): p. 642-50.
32. Gurukumar, K.R., et al., Development of real time PCR for detection and quantitation of Dengue Viruses. Virol J, 2009. 6: p. 10.
33. Price, C.P., Point of care testing. BMJ, 2001. 322(7297): p. 1285-8.
34. Drain, P.K., et al., Diagnostic point-of-care tests in resource-limited settings. Lancet Infect Dis, 2014. 14(3): p. 239-49.
35. Peeling, R.W., et al., Rapid tests for sexually transmitted infections (STIs): the way forward. Sex Transm Infect, 2006. 82 Suppl 5(Suppl 5): p. v1-6.
36. Nichols, J.H., Point-of-care testing, in Contemporary Practice in Clinical Chemistry. 2020. p. 323-336.
37. Naseri, M., et al., ASSURED‐compliant point‐of‐care diagnostics for the detection of human viral infections. Rev. Med. Virol., 2021. 32(2).
38. Land, K.J., et al., REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes. Nat Microbiol, 2019. 4(1): p. 46-54.
39. Kozel, T.R. and A.R. Burnham-Marusich, Point-of-Care Testing for Infectious Diseases: Past, Present, and Future. J Clin Microbiol, 2017. 55(8): p. 2313-2320.
40. Esbin, M.N., et al., Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection. RNA, 2020. 26(7): p. 771-783.
41. Tanriverdi, S., L. Chen, and S. Chen, A rapid and automated sample-to-result HIV load test for near-patient application. J Infect Dis, 2010. 201 Suppl 1: p. S52-8.
42. Nie, S., et al., Evaluation of Alere i Influenza A&B for rapid detection of influenza viruses A and B. J Clin Microbiol, 2014. 52(9): p. 3339-44.
43. Notomi, T., et al., Loop-mediated isothermal amplification of DNA. Nucleic Acids Res, 2000. 28(12): p. E63.
44. Nagamine, K., T. Hase, and T. Notomi, Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol Cell Probes, 2002. 16(3): p. 223-9.
45. Toumazou, C., et al., Simultaneous DNA amplification and detection using a pH-sensing semiconductor system. Nat Methods, 2013. 10(7): p. 641-6.
46. Duarte-Guevara, C., et al., On-chip electrical detection of parallel loop-mediated isothermal amplification with DG-BioFETs for the detection of foodborne bacterial pathogens. RSC Advances, 2016. 6(106): p. 103872-103887.
47. Moser, N., et al., Quantitative detection of dengue serotypes using a smartphone-connected handheld lab-on-chip platform. Front Bioeng Biotechnol, 2022. 10: p. 892853.
48. Francois, P., et al., Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications. FEMS Immunol Med Microbiol, 2011. 62(1): p. 41-8.
49. World Health Organization, The use of loop-mediated isothermal amplification (TB-LAMP) for the diagnosis of pulmonary tuberculosis. 2016.
50. Becherer, L., et al., Loop-mediated isothermal amplification (LAMP) – review and classification of methods for sequence-specific detection. Anal. Methods, 2020. 12(6): p. 717-746.
51. Purushothaman, S., C. Toumazou, and C.-P. Ou, Protons and single nucleotide polymorphism detection: A simple use for the Ion Sensitive Field Effect Transistor. Sensors and Actuators B: Chemical, 2006. 114(2): p. 964-968.
52. C.K. Mathews, K.G.A., K.E. Van Holde, in: C.K. Mathews, K.E.Van Holde, K.G. Ahern (Eds.), Biochemistry, third ed. 2000: Benjamin Cummings, San Francisco, Harlow.
53. Steitz, T.A., DNA- and RNA-dependent DNA polymerases. Current Opinion in Structural Biology, 1993. 3(1): p. 31-38.
54. Castro, C., et al., Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases. Proc Natl Acad Sci U S A, 2007. 104(11): p. 4267-72.
55. Eid, J., et al., Real-time DNA sequencing from single polymerase molecules. Science, 2009. 323(5910): p. 133-8.
56. Tanner, N.A., Y. Zhang, and T.C. Evans, Jr., Visual detection of isothermal nucleic acid amplification using pH-sensitive dyes. BioTechniques, 2015. 58(2): p. 59-68.
57. Tanner, N.A., Y. Zhang, and T.C. Evans, Jr., Simultaneous multiple target detection in real-time loop-mediated isothermal amplification. BioTechniques, 2012. 53(2): p. 81-9.
58. Tanner, N.A. and T.C. Evans, Jr., Loop-mediated isothermal amplification for detection of nucleic acids. Curr Protoc Mol Biol, 2014. 105: p. Unit 15 14.
59. Poole, C.B., et al., Colorimetric tests for diagnosis of filarial infection and vector surveillance using non-instrumented nucleic acid loop-mediated isothermal amplification (NINA-LAMP). PLoS One, 2017. 12(2): p. e0169011.
60. Aoki, M.N., et al., Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load. Sci Rep, 2021. 11(1): p. 9026.
61. Dao Thi, V.L., et al., A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples. Sci Transl Med, 2020. 12(556).
62. Wu, S., et al., Colorimetric isothermal nucleic acid detection of SARS-CoV-2 with dye combination. Heliyon, 2021. 7(4): p. e06886.
63. van Pelt-Verkuil, E., A. van Belkum, and J.P. Hays, Principles and Technical Aspects of PCR Amplification. 2008: Springer Dordrecht.
64. Yang, L., et al., Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly. J Am Chem Soc, 2004. 126(27): p. 8441-53.
65. Lorenz, T.C., Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies. J Vis Exp, 2012(63): p. e3998.
66. Newcombe, R.G., Two-sided confidence intervals for the single proportion: comparison of seven methods. Stat. Med., 1998. 17(8): p. 857-872.
67. Wilson, E.B., Probable Inference, the Law of Succession, and Statistical Inference. J. Am. Stat. Assoc., 1927. 22(158).
68. Harris, A.R., et al., Impact of Protein Fouling on the Charge Injection Capacity, Impedance, and Effective Electrode Area of Platinum Electrodes for Bionic Devices. ChemElectroChem, 2021. 8(6): p. 1078-1090.
69. Xie, S., et al., Using the ubiquitous pH meter combined with a loop mediated isothermal amplification method for facile and sensitive detection of Nosema bombycis genomic DNA PTP1. Chem Commun (Camb), 2014. 50(100): p. 15932-5.
70. Salm, E., et al., Electrical detection of nucleic acid amplification using an on-chip quasi-reference electrode and a PVC REFET. Anal Chem, 2014. 86(14): p. 6968-75.
71. Kainz, P., The PCR plateau phase - towards an understanding of its limitations. Biochim Biophys Acta, 2000. 1494(1-2): p. 23-7.
72. Kainz, P., A. Schmiedlechner, and H.B. Strack, Specificity-enhanced hot-start PCR: addition of double-stranded DNA fragments adapted to the annealing temperature. BioTechniques, 2000. 28(2): p. 278-82.
73. Jansson, L. and J. Hedman, Challenging the proposed causes of the PCR plateau phase. Biomol Detect Quantif, 2019. 17: p. 100082.
校內:2028-08-28公開