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研究生: 凌偉碩
Ling, Wei-Shuo
論文名稱: 病毒偵測的先導型研究
A pilot study of virus detection methods
指導教授: 王憲威
Wang, Shainn-Wei
學位類別: 碩士
Master
系所名稱: 醫學院 - 分子醫學研究所
Institute of Molecular Medicine
論文出版年: 2012
畢業學年度: 101
語文別: 中文
論文頁數: 92
中文關鍵詞: 人類免疫缺失病毒後天性免疫不全症候群核酸篩檢方法自動核酸擴增
外文關鍵詞: Human immunodeficiency virus (HIV), acquired immunodeficiency syndrome (AIDS), nucleic acid testing (NAT), autocycling amplification
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  • 後天性免疫不全症候群(AIDS;acquired immunodeficiency syndrome),於西元1981年發現首例病例,且截至西元2010年為止,全球約有三千四百萬人正感染愛滋病病毒。對於病患之投藥、治療時程甚至於此疾病之監控,皆取決於是否能夠精準地檢測感染以及監控病患體內之病毒數。近年來,以愛滋病病毒之核酸為偵測目標的檢測方式(NAT;nucleic acid testing)逐漸發展成熟,諸如反轉錄聚合酶鏈鎖反應(RT-PCR;reverse transcription polymerase chain reaction)、標的核酸序列擴增法(NASBA;nucleic acid sequence based amplification)等,因此我們希望研發一套以自動核酸擴增技術為基礎的高靈敏性檢測套組,並針對台灣分佈比例最高之B亞型愛滋病病毒其gag基因進行檢測。在本篇研究中,我們嘗試以兩種(X與Y型)自動核酸擴增檢測法針對愛滋病病毒標準質體(pHXB2)進行靈敏性、專一性等可行性測試。實驗結果顯示Y型自動核酸擴增檢測法對於快速以及準確地檢測HIV具有其許多優勢。首先,此檢測方法之靈敏度相當地高,目前已可以偵測到10個分子的HIV DNA 質體,且可於加熱後之血液中偵測到1個感染之T細胞。其次,此檢測方法非常省時且價廉,因為不需要經由抽取HIV RNA以及反轉錄等步驟,可以直接偵測HIV DNA,大幅降低額外反應所衍生之影響以及檢測所需之時間。再者,此檢測方法之專一性亦相當地高,因為只有當目標序列存在時,擴增反應才會進行。最後,偵測結果之判讀相當地簡便,因為有別於以往傳統膠體電泳分析方法,可以於反應最終產物中直接加入核酸染劑,即可以肉眼或紫外光影像系統直接觀察。綜觀本篇研究實驗結果,本檢測套組有相當大的潛力可以成為一套快速、價廉以及高精準度之HIV檢測套組。另外,透過設計、整合更多的專一性引子對,可以促使此檢測套組在臨床醫學亦或是商業套組中,對於全世界各種HIV基因型患者之檢測以及篩選提供更大的應用。

    Human immunodeficiency virus (HIV) has resulted in more than 25 million deaths worldwide since its discovery. Currently, approximately 34 million people are living with AIDS (UNAIDS, 2011 Global Report). To effectively track the disease, tools developed for highly sensitive HIV detection that are rapid, cost-friendly, and static of accuracy in diagnosing HIV early infection and screening of clinical/donor specimens are necessary. In this study, we developed two autocycling amplification-based detection methods (X and Y types) for detecting HIV-1 B subtype virus that is predominantly circulating in Taiwan region (42.2%). The results showed that the Y-type autocycling amplification based assay possess many advantages for fast and accurate detection of HIV infection. First, this detection assay is sensitive because it can stably detect at least 10 copies of HIV nucleic acids and 1 infected Jurkat T reporter cell in boiled human blood. Second, the detection assay is time and cost effective because it can detect HIV DNA without complicated procedures such as extraction and reverse transcription of HIV RNA. Third, the detection is specific because it can amplify signals only when target sequences exist. Fourth, the interpretation of HIV positive/negative result does not require sophisticated tool because DNA staining dye can be simply added in the reaction product to distinguish amplified products by naked eyes or with UV light imaging system. Our data collectively indicated that the Y-type detection method has great potential to be a rapid, cost effective, and highly sensitive HIV detection kit. By designing and integrating more specific primers, the assay may have better clinical usage and commercial application in detecting and screening different HIV genotypes in HIV-1 infected specimens around the world.

    考試合格證明....................................................................................................................... I 中文摘要.............................................................................................................................. II 英文摘要.............................................................................................................................III 致謝.......................................................................................................................................V 目錄.....................................................................................................................................VI 表目錄...................................................................................................................................X 圖目錄.................................................................................................................................XI 附錄...................................................................................................................................XII 符號及縮寫......................................................................................................................XIII 緒論........................................................................................................................................1 一. 研究動機................................................................................................................1 二. 現行偵測方式以及其改善目標............................................................................3 1. RT-PCR technology...........................................................................................4 2. NASBA technology............................................................................................4 3. bDNA technology...............................................................................................4 三. X型扣鎖探針的原理與應用................................................................................6 1. 單核酸多型性分析與原位雜合........................................................................8 2. 微矩陣與多重檢測............................................................................................9 3. RNA分析.........................................................................................................10 4. 感染性致病源的檢測......................................................................................10 四. Y型恆溫套環式核酸擴增反應的原理與應用..................................................12 1. Bst DNA polymerase........................................................................................13 2. 引子對數目......................................................................................................13 3. 作用溫度..........................................................................................................13 五. 實驗目標..............................................................................................................16 實驗材料與方法..................................................................................................................17 一. 愛滋病病毒核酸序列資料收集與比對..............................................................17 二. 辨識目標序列挑選以及PLP扣鎖探針設計.....................................................17 三. 辨識目標序列挑選以及LAMP引子對設計.....................................................18 四. 磷酸激酶反應......................................................................................................19 五. X型扣鎖探針最佳使用量調整.............. ...........................................................19 六. X型扣鎖探針檢測..............................................................................................20 1. 黏合反應 (ligation) ........................................................................................20 (1) T4 DNA ligase中溫黏合反應................................................................20 (2) Ampligase DNA ligase循環溫度黏合反應...........................................21 (3) Taq DNA ligase循環溫度黏合反應......................................................22 2. 外切酶反應 (Exonuclease reaction) ..............................................................22 3. 滾式環形擴增反應 (RCA;rolling circle amplification) .............................23 七. Y型恆溫套環式核酸擴增反應..........................................................................23 1. 評估反應適用溫度..........................................................................................25 2. 測試反應作用時間..........................................................................................25 3. 偵測靈敏度測試..............................................................................................26 4. 偵測專一性測試..............................................................................................27 5. 偵測感染細胞株測試......................................................................................28 6. 模擬感染血液偵測測試..................................................................................29 八. 一般PCR聚合酶鏈鎖反應................................................................................30 九. DNA 電泳分析...................................................................................................30 十. DNA顯色劑呈色反應........................................................................................31 十一. 試劑......................................................................................................................32 結果......................................................................................................................................33 一. X型扣鎖探針及滾式環形擴增反應..................................................................33 1. 第一型愛滋病B亞型病毒各基因保守序列區域之分析.............................33 2. 扣鎖探針之檢測流程......................................................................................33 3. 扣鎖探針適用量之探討..................................................................................34 4. 探討不同黏合酶對於扣鎖探針檢測之適用性………………….................34 二. Y型恆溫套環式核酸擴增反應..........................................................................35 1. 第一型愛滋病B亞型病毒各基因保守序列區域之分析.............................35 2. 探討gag-specific LAMP assay與vpr-specific LAMP assay 最佳反應溫度..................................................................................................36 3. 探討gag-specific LAMP assay與vpr-specific LAMP assay 反應所需時間..................................................................................................37 4. 探討gag-specific LAMP assay與vpr-specific LAMP assay 偵測之靈敏度..................................................................................................37 5. 探討gag-specific LAMP assay與vpr-specific LAMP assay 偵測之專一性..................................................................................................39 6. 評估gag-specific LAMP assay檢測結果判讀之簡便性..............................39 7. 探討gag-specific LAMP assay與vpr-specific LAMP assay 於感染細胞模式下之偵測能力......................................................................39 8. 探討gag-specific LAMP assay於模擬感染血液模式下之偵測能力.........40 討論.....................................................................................................................................42 參考文獻.............................................................................................................................51 圖.........................................................................................................................................66 表.........................................................................................................................................83 附錄.....................................................................................................................................86 自述.....................................................................................................................................92

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