TWI261618B - Method for detecting and differentiating enteroviruses and the primers and probes therefor - Google Patents
Method for detecting and differentiating enteroviruses and the primers and probes therefor Download PDFInfo
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- TWI261618B TWI261618B TW89125306A TW89125306A TWI261618B TW I261618 B TWI261618 B TW I261618B TW 89125306 A TW89125306 A TW 89125306A TW 89125306 A TW89125306 A TW 89125306A TW I261618 B TWI261618 B TW I261618B
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Abstract
Description
1261618 A7 _____ B7 五、發明說明(,) 經濟部智慧財產局員工消費合作社印製 發明背景 腸病毒屬於小RNA病毒科而e)。該病毒科 在成員數量上代表非常大的RNA病毒家族,但在病毒顆粒 尺寸及複雜程度上倶爲最小之一。腸病毒之病毒體包括由 60個次單元所組成,每個次單元由四種蛋白質(VP1-VP4) 以正二十面體對稱方式圍繞由單股正意義RNA形成之基因 體。腸病毒短暫棲於人類消化道,也可以從腸道後段或喉嚨 分離。人類來源之腸病毒包括小兒麻痺病毒(血淸型1至 3),克沙奇病毒A群(CAV,血淸型1至22及24)及克沙奇 病毒B群(CBV,血淸型1至6),腸道細胞病變孤獨病毒(血 淸型1至9, 11至27及29至33)及腸病毒(血淸型68-71)。 人類腸病毒感染可導致大範圍渉及神經,皮膚及黏膜,心臟 及肌肉,眼,呼吸道及胃腸道疾病的急性症狀,以及無明顯 特徵之熱病,廣泛之嬰兒疾病及糖尿病。在非小兒麻痺之腸 病毒中,一些未分類之血淸型所造成的感染特別在夏季及初 秋盛行於一些國家及地區,例如腸病毒70型及71型。腸病 毒71型曾由罹患腦膜炎、腦炎及類似小兒麻痺脊髓炎之麻 痺患者身上分離,仍爲世界上時而致命之中樞神經系統疾病 之主要原因。再者,此型病毒在一些地區引起人類手足口疾 病之爆發,例如在日本,瑞典及台灣。 腸病毒的一般診斷通常包括病毒收穫及血淸學試驗。病 毒的單離可包含自漱喉水、喉嚨棉拭、糞便、直腸棉拭中分 離病毒,有時可從腦脊髓液(在無菌性腦膜炎的情形)中分離 病毒。將經分離之病毒樣品接種至組織培養物或乳鼠(後者 請 先 閱 讀 背 意1261618 A7 _____ B7 V. INSTRUCTIONS (,) Printed by the Ministry of Economic Affairs, Intellectual Property Office, Staff Consumer Cooperatives Background of the Invention Enterovirus belongs to the picornavirus family and e). The Virology family represents a very large family of RNA viruses in terms of number of members, but is one of the smallest in terms of virus particle size and complexity. The virion of enterovirus consists of 60 subunits, each subunit consisting of four proteins (VP1-VP4) in a icosahedral symmetrical manner around a genome formed by a single positive sense RNA. The enterovirus temporarily inhabits the human digestive tract and can also be isolated from the posterior segment of the intestine or from the throat. Enteroviruses of human origin include poliovirus (blood type 1 to 3), soxavirus group A (CAV, blood type 1 to 22 and 24) and soxavirus group B (CBV, blood type 1) To 6), intestinal cytopathic diseases of autism virus (blood type 1 to 9, 11 to 27 and 29 to 33) and enterovirus (blood type 68-71). Human enterovirus infection can cause a wide range of sputum and nerves, skin and mucous membranes, acute symptoms of heart and muscle, eye, respiratory and gastrointestinal diseases, as well as fever without obvious characteristics, a wide range of infant diseases and diabetes. In non-polioviruses, infections caused by some unclassified blood stasis types are particularly prevalent in some countries and regions in summer and early autumn, such as enterovirus types 70 and 71. Enterovirus type 71 has been isolated from patients with meningitis, encephalitis, and polio-like myelitis, and remains the leading cause of the world's deadly central nervous system disease. Furthermore, this type of virus causes human hand, foot and mouth disease outbreaks in some areas, such as in Japan, Sweden and Taiwan. The general diagnosis of enterovirus usually involves viral harvesting and blood sputum testing. The isolation of the virus may include the isolation of the virus from the throat water, the throat swab, the stool, the rectal cotton swab, and sometimes the virus from the cerebrospinal fluid (in the case of aseptic meningitis). Inoculate the isolated virus sample into tissue culture or suckling mice (the latter please read the back)
頁 I I I I I 訂 4 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) 1261618 經濟部智慧財產局員工消費合作社印製 A7 B7 五、發明說明(>) 專門爲克沙奇病毒)中繁殖及鑑定。此種病毒收穫程序每次 耗費一至二星期才能完成。另外,亦需合格技術人員參與才 得以完成。 血淸學試驗方面通常進行中和試驗以偵測對感染病毒 具專一性之中和性抗體。對於一些腸道細胞病變孤獨病毒而 言,血球凝集抑制試驗可指出血淸型專一性感染。血淸抗體 亦能經由免疫螢光技術在蓋玻片上使用被感染細胞培養物 作爲抗原來進行偵測及滴定。然而,血淸學試驗難以用於評 估,因爲血淸型的種類很多,除非所用的抗原是由特定個人 分離或在典型臨床疾病流行性爆發時分離。在所有的血淸學 試驗中,熟習本技術之人員必須從結果讀數去判斷何者爲決 定値(cut-off values)。同時,在這些試驗中所使用的抗原通 常需要特別的技術及一段時間來製備以降低異質型反應或 交叉反應的發生率。 病毒收穫及血淸學試驗倶不能提供一個快速的診斷工 具。然而,與腸病毒相關的急性症狀可發展甚速,在有些案 例中可能在數天內發展成爲致命性。因此對於在實際上能快 速且簡易偵測腸病毒的方法有殷切需求。 發明總論 本發明相關於新穎之寡核苷對以用於偵測腸病毒在檢 體中存在與否。本發明之個別引子對包括第一引子及第二引 子,其有利於經由核酸增幅試驗(如聚合酶鏈反應)快速診斷 出與腸病毒相關之疾病或症狀。 本發明令人驚異地發現一些核苷酸序列係相關於腸病 4 本紙張尺度適用中國國家標準(CNS)A4規格(210 χ 297公釐) _ ϋ n I n n an ϋ 一:eJ n ·ϋ ϋ I _1 in I (請先閱讀背面之注咅?事項寫本頁) 1261618 A7 B7 經濟部智慧財產局員工消費合作社印製 五、發明說明(h) 毒核酸中的保守性區域。因此,本發明進而提供合成性核芽 酸序列,其能夠專一性與腸病毒核酸之意義股或相關於該意 義股之核酸進行雜交。 在另一方面,本發明相關於一種偵測腸病毒核酸在檢體 中存在與否的方法。本發明之方法包含(a)在一增幅方法中 將該檢體與本發明之一寡核苷引子對接觸;及(b)經由偵測增 幅產物之存在與否以決定腸病毒之存在與否。 較佳的是,在本發明之方法中,該檢體於增幅方法中可 同時接觸除了第一對引子以外之第二對本發明之寡核苷酸 引子。在第二對中的引子與第一對中的引子不同。在第二對 中的引子可具有與第一對中相對應引子不同之第一引子或 第二引子。較佳的是,第二對中兩個引子皆與第一對的引子 不同。進而,該檢體於增幅方法中可同時接觸除了第一對及 第二對引子以外之第三對本發明之寡核苷酸引子。同樣的, 在第三對中的引子與第一對或第二對中的引子皆不同。 在另一方面,本發明之方法可進而包含在一增幅方法中 將該步驟(a)之產物與本發明之第二寡核苷引子對接觸。第 二對引子經選擇而能在一增幅方法中被用於增幅一序列,該 序列相同於或被包含於使用第一對引子之增幅方法中可得 到之序列。 在本發明方法之另一方面,可將在步驟(b)偵測到的增 幅產物與本發明之至少一個合成性核苷酸序列進行專一性 雜交反應。 在另一方面,本發明相關於一種在檢體中偵測及鑑別腸 5 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) I Μ··· Μ·· η··· I Μ·· · SMI ΒΜ» * ΗΒΗ I I ·ι^ (請先閱讀背面之注意事項寫本頁) 1261618 A7 B7 經濟部智慧財產局員工消費合作社印製 五、發明說明(4) 病毒71型的方法。該方法包含(a)在一增幅方法中將該檢體 與本發明之至少一對寡核苷引子接觸;(b)經由偵測增幅產物 之存在與否以決定腸病毒71型之存在與否;及(c〇將在步驟 (b) 偵測到的增幅產物與本發明之含有序列SEQIDNO:12或 SEQ ID Ν0··13之合成性核苷酸序列進行專一性雜交反應。 較佳的是,所偵測到的增幅產物係與本發明之含有序列SEQ ID NO: 12及SEQ ID NO: 13之合成性核苷酸序列進行專一性 雜交反應。 在另一方面,本發明相關於一種在檢體中偵測及鑑別克 沙奇病毒A16型的方法。該方法包含(a)在一增幅方法中將 該檢體與本發明之至少一對寡核苷引子接觸;(b)經由偵測增 幅產物之存在與否以決定克沙奇病毒A16型之存在與否;及 (c) 將在步驟(b)偵測到的增幅產物與本發明之含有序列SEQ ID NO: 14或SEQ ID NO: 15之合成性核苷酸序列進行專一性 雜交反應。較佳的是,所偵測到的增幅產物係與本發明之含 有序列SEQ ID N0:14及SEQ ID Ν0··15之合成性核苷酸序 列進行專一性雜交反應。 在另一方面,本發明相關於一種在檢體中偵測及鑑別腸 病毒71型及/或克沙奇病毒Α16型的方法。該方法包含(a) 在一增幅方法中將該檢體與本發明之至少一對寡核苷引子 接觸;(b)經由偵測增幅產物之存在與否以決定腸病毒71型 及/或克沙奇病毒A16型之存在與否;及(c)將在步驟(b)偵測 到的增幅產物與本發明之至少一個含有序列SEQ ID NO:12 或SEQ ID N0:13之合成性核苷酸序列及至少一個含有序列 6 (請先閱讀背面之注咅?事項寫本頁)Page IIIII Book 4 This paper scale applies to China National Standard (CNS) A4 specification (210 X 297 mm) 1261618 Ministry of Economic Affairs Intellectual Property Office Staff Consumer Cooperative Printed A7 B7 V. Invention Description (>) Dedicated to Keshaqi Virus ) breeding and identification. This virus harvesting process takes one to two weeks to complete. In addition, qualified technicians are required to participate in the process. In the blood sputum test, a neutralization test is usually performed to detect a specific neutralizing antibody against a virus. For some intestinal cytopathic solitary viruses, the hemagglutination inhibition test may indicate a blood-stasis-specific infection. Blood sputum antibodies can also be detected and titrated by immunofluorescence using an infected cell culture as an antigen on a coverslip. However, hemorrhagic trials are difficult to assess because there are many types of blood stasis, unless the antigen used is isolated by a particular individual or isolated in the event of a typical clinical outbreak. In all blood tests, those skilled in the art must determine from the result readings which are cut-off values. At the same time, the antigens used in these assays typically require special techniques and a period of time to prepare to reduce the incidence of heterogeneous or cross-reactive reactions. Viral harvesting and blood tests do not provide a quick diagnostic tool. However, acute symptoms associated with enterovirus can develop very rapidly, and in some cases may develop into fatality within a few days. Therefore, there is a strong demand for a method for rapidly and easily detecting enterovirus in practice. SUMMARY OF THE INVENTION The present invention relates to novel oligonucleoside pairs for detecting the presence or absence of enteroviruses in a sample. The individual primer pairs of the present invention include a first primer and a second primer which facilitate rapid diagnosis of diseases or symptoms associated with enteroviruses via nucleic acid amplification assays such as polymerase chain reaction. The present inventors have surprisingly found that some nucleotide sequences are associated with enteric disease. This paper scale applies to the Chinese National Standard (CNS) A4 specification (210 297 297 mm) _ ϋ n I nn an ϋ one: eJ n · ϋ ϋ I _1 in I (Please read the note on the back? Write this page) 1261618 A7 B7 Ministry of Economic Affairs Intellectual Property Bureau Employees Consumption Cooperative Printed 5, Inventions (h) Conservative areas in toxic nucleic acids. Accordingly, the present invention further provides a synthetic nucleotide sequence which is capable of hybridizing specifically to a sense strand of enterovirus nucleic acid or a nucleic acid associated with the sense strand. In another aspect, the invention relates to a method of detecting the presence or absence of enterovirus nucleic acid in a sample. The method of the present invention comprises (a) contacting the sample with one of the oligonucleoside primer pairs of the present invention in an amplification method; and (b) determining the presence or absence of the enterovirus by detecting the presence or absence of the amplification product; . Preferably, in the method of the present invention, the sample is simultaneously contacted with a second pair of oligonucleotide primers of the present invention in addition to the first pair of primers in the amplification method. The primers in the second pair are different from the ones in the first pair. The primers in the second pair may have a first primer or a second primer that is different from the corresponding primer in the first pair. Preferably, both of the second pair of primers are different from the first pair of primers. Further, the sample may simultaneously contact a third pair of oligonucleotide primers of the present invention other than the first pair and the second pair of primers in the amplification method. Similarly, the primers in the third pair are different from the ones in the first pair or the second pair. In another aspect, the method of the invention can further comprise contacting the product of step (a) with a second oligonucleoside primer pair of the invention in an amplification method. The second pair of primers is selected for use in an amplification method for an amplification sequence which is identical to or is included in the sequence obtainable by the amplification method using the first pair of primers. In another aspect of the method of the invention, the amplified product detected in step (b) can be specifically hybridized with at least one synthetic nucleotide sequence of the invention. In another aspect, the present invention relates to detecting and identifying intestines in a specimen. The paper size is applicable to the Chinese National Standard (CNS) A4 specification (210 X 297 mm). I Μ··· Μ·· η·· · I Μ·· · SMI ΒΜ» * ΗΒΗ II · ι^ (Please read the note on the back to write this page) 1261618 A7 B7 Ministry of Economic Affairs Intellectual Property Bureau Employees Consumption Cooperative Printed 5, Invention Description (4) Virus Type 71 Methods. The method comprises (a) contacting the sample with at least one pair of oligonucleoside primers of the invention in an amplification method; (b) determining the presence or absence of enterovirus 71 by detecting the presence or absence of the amplification product; And (c) performing the specific hybridization reaction of the amplified product detected in the step (b) with the synthetic nucleotide sequence of the present invention comprising the sequence of SEQ ID NO: 12 or SEQ ID Ν 0··13. The detected amplification product is subjected to a specific hybridization reaction with the synthetic nucleotide sequence of the present invention comprising the sequences of SEQ ID NO: 12 and SEQ ID NO: 13. In another aspect, the present invention relates to A method for detecting and identifying a Crohn's virus A16 in a sample, the method comprising: (a) contacting the sample with at least one pair of oligonucleoside primers of the invention in an amplification method; (b) detecting The presence or absence of the amplification product to determine the presence or absence of the Crox virus A16 type; and (c) the amplification product detected in step (b) and the sequence of the invention comprising SEQ ID NO: 14 or SEQ ID NO : 15 synthetic nucleotide sequence for specific hybridization reaction. Preferably, the detected increase in yield The system is subjected to a specific hybridization reaction with the synthetic nucleotide sequence of the present invention comprising the sequences SEQ ID NO: 14 and SEQ ID Ν 0··15. In another aspect, the present invention relates to a detection in a sample and A method of identifying Enterovirus 71 and/or Croxvirus Α16. The method comprises (a) contacting the sample with at least one pair of oligonucleoside primers of the invention in an amplification method; (b) detecting Detecting the presence or absence of the amplification product to determine the presence or absence of Enterovirus 71 and/or Croxvirus A16; and (c) including the amplification product detected in step (b) with at least one of the present invention The synthetic nucleotide sequence of SEQ ID NO: 12 or SEQ ID NO: 13 and at least one containing sequence 6 (please read the back of the note first).
-I I I I I 丨—訂 — I I I I I-I I I I I 丨—订 — I I I I I
J · 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) 1261618 A7 B7 五、發明說明(<) SEQ ID NO:14或SEQ ID N0:15之合成性核苷酸序列進行專 一性雜交反應。較佳的是,所偵測到的增幅產物係與本發明 之含有序列 SEQ ID NO:12、SEQ ID NO:13、SEQ ID NO:14 及SEQ ID NO:15之合成性核苷酸序列進行專一性雜交反 應。 在另一方面,本發明提供在檢體中偵測腸病毒之套組, 其包含至少一對本發明寡核苷酸引子。較佳的是,本發明之 套組包含超過一對之本發明寡核苷酸引子。在本發明另一方 面,該套組可進而包含至少一個本發明合成性核苷酸序列。 在另一方面,本發明提供在檢體中偵測及鑑別腸病毒 71型之套組,其包含至少一對本發明寡核苷酸引子及至少 一個含有序列SEQ ID N0:12或SEQ ID NO:13之合成性核 苷酸序列。較佳的是,本發明之套組包含超過一對之本發明 寡核苷酸引子。在本發明較佳的具體事實中,該套組係包含 含有序列SEQ ID N0:12或SEQ ID N0:13之合成性核苷酸 序列。 在另一方面,本發明提供在檢體中偵測及鑑別克沙奇病 毒A16型之套組,其包含至少一對本發明寡核苷酸引子及 至少一個含有序列SEQ ID N0:14或SEQ ID NO:15之合成 性核苷酸序列。較佳的是,本發明之套組包含超過一對之本 發明寡核苷酸引子。在本發明較佳的具體事實中,該套組係 包含含有序列SEQ ID N0:14或SEQ ID N0:15之合成性核 苷酸序列。 在另一方面,本發明提供在檢體中偵測及鑑別腸病毒 7 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) (請先閱讀背面之注意事項寫本頁) 訂--------- 碑 經濟部智慧財產局員工消費合作社印製 1261618 A7 B7 經濟部智慧財產局員工消費合作社印製 五、發明說明(") 圖4爲腸病毒71型,克沙奇病毒A16型及腸道細胞病 變孤獨病毒第3型之核酸分別經多樣化聚合酶鏈反應 (multiplex PCR)增幅後,與腸病毒共通型探針(p卜p2, p3 )及腸病毒71型,克沙奇病毒A16型專一性探針(71-2, 71-3,16-1,16-2)雜交之結果。聚合酶鏈反應使用之引子配 對爲f5/rl及f7/r4,固定在尼龍膜探針之分佈位置如下:將 此6x6點陣十字等分爲4個3x3的等分,其中左上方區塊屬 腸病毒共通型探針區塊,每一排各爲3個探針之3重複,右 上區塊爲腸病毒71型區,由兩個專一性探針交錯排列,左 下區塊爲克沙奇病毒A16型區,由兩個專一性探針交錯排 列。 較佳具體事實之詳細說明 專有名詞”專一性雜交”或”專一性雜交反應’’意指寡核 苷酸與目標序列之間的互補性雜交。專有名詞”專一性”或" 專一性地π意指該互補性雜交所顯示之專一性,其允許在該 寡核苷酸與該目標序列之間有少許不相符(mismatch)但不 會負面影響偵測雜交訊號之黏合(annealing)。 專有名詞"檢體”意指包括任何含有核酸之生物性物質 之檢體。較佳地,專有名詞’’檢體’’意指包括全血’血淸’尿 液,唾液,腦脊髓液,精液,淚水,喉嚨棉拭,直腸棉拭, 排洩物等之生物性檢體。 專有名詞’’增幅方法”意指增幅核酸序列之試驗或方 法。例如,該”增幅方法"包括聚合酶鏈反應(PCR)試驗’連 接酶鏈反應(LCR)試驗,Qfl-複製酶增幅法,活體外轉錄法’ 9 I---- (請先閱讀背面之注咅?事項^$寫本頁) I: 訂-------- 4 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) 1261618 A7 B7 五、發明說明(?) 活體外反轉錄法及自持性序列複製。 專有名詞”高度嚴格條件”意指所選擇之雜交條件就特 定序列及既定的離子強度與pH値下約較熱融點(Tm)低5 °C。熱融點溫度時(在既定的離子強度與pH値下)50%之目 標序列可與完全相配對之探針雜交。典型上,高度嚴格條件 下,鹽濃度在pH 7約爲0.2M且溫度至少高於60°C。 在此所用的鹽基代號包括代表在天然DNA分子中可發 現之天然來源嘌呤及嘧啶的代號(即,A,G,T及C),以及 熟習該項技術者在合成寡核苷酸所習知之代表混合鹽基的 代號(如R,Y,S,H)。關於本案說明書所使用的代號,A(或 a)表示腺嘌呤,G(或g)表示鳥糞嘌呤,T(或t)表示胸腺嘧 啶,C(或c)表示胞嘧啶,R(或r)表示腺嘌呤或鳥糞嘌呤,Y(或 y)表示胸腺嘧啶或胞嘧啶,S(或s)表示鳥糞嘌呤或胞嘧啶, 且Η(或h)表示腺嘌呤,胸腺嘧啶或胞嘧啶。 本發明有利於偵測衍生自腸病毒之核酸。本發明提供快 速及靈敏的方法以偵測衍生自腸病毒之核酸之存在與否。在 本發明較佳的具體事實中,本發明之方法爲基於聚合酶鏈反 應(PCR)之試驗。在另一方面,本發明提供非常專一之PCR 引子對,其可用於偵測及/或確認特定腸病毒血淸型,如腸 病毒71型及克沙奇病毒A16型。在另一方面,本發明提供 專一性核苷酸序列,其能夠與自使用本發明引子對之增幅方 法可得到的核酸片段進行專一性雜交反應。 有一些增幅方法皆可使用,但基於PCR的方法爲較佳 的。PCR方法在相關技藝中所知甚詳,因此在此僅作簡 10 (請先閱讀背面之注意事項寫本頁)J · This paper size applies to the Chinese National Standard (CNS) A4 specification (210 X 297 mm) 1261618 A7 B7 V. Inventive Note (<) Synthetic nucleotide sequence of SEQ ID NO: 14 or SEQ ID NO: 15. Perform a specific hybridization reaction. Preferably, the detected amplification product is carried out with the synthetic nucleotide sequence of the invention comprising the sequences SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14 and SEQ ID NO: 15. Specific hybridization reaction. In another aspect, the invention provides a kit for detecting enterovirus in a sample comprising at least one pair of oligonucleotide primers of the invention. Preferably, the kit of the invention comprises more than one pair of oligonucleotide primers of the invention. In another aspect of the invention, the kit can further comprise at least one synthetic nucleotide sequence of the invention. In another aspect, the invention provides a kit for detecting and identifying an enterovirus 71 type in a sample comprising at least one pair of oligonucleotide primers of the invention and at least one comprising the sequence of SEQ ID NO: 12 or SEQ ID NO: A synthetic nucleotide sequence of 13. Preferably, the kit of the invention comprises more than one pair of oligonucleotide primers of the invention. In a preferred specific aspect of the invention, the kit comprises a synthetic nucleotide sequence comprising the sequence SEQ ID NO: 12 or SEQ ID NO: 13. In another aspect, the invention provides a kit for detecting and identifying a Croxvirus A16 type in a sample comprising at least one pair of oligonucleotide primers of the invention and at least one comprising the sequence SEQ ID NO: 14 or SEQ ID NO: A synthetic nucleotide sequence of 15. Preferably, the kit of the invention comprises more than one pair of oligonucleotide primers of the invention. In a preferred specific aspect of the invention, the kit comprises a synthetic nucleotide sequence comprising the sequence SEQ ID NO: 14 or SEQ ID NO: 15. In another aspect, the present invention provides for detecting and identifying enterovirus in a sample. 7 The paper size is applicable to the Chinese National Standard (CNS) A4 specification (210 X 297 mm) (please read the back note before writing this page) Order --------- Monument Ministry of Economic Affairs Intellectual Property Bureau employee consumption cooperative printing 1261618 A7 B7 Ministry of Economic Affairs Intellectual Property Bureau employee consumption cooperative printing 5, invention description (") Figure 4 is enterovirus 71, The nucleic acid of the Crohn's virus A16 type and the intestinal cytopathic autism virus type 3 is amplified by multiplex PCR, and is combined with the enterovirus common probe (p, p2, p3) and enterovirus. Type 71, the result of hybridization of the Croxvirus A16-specific probe (71-2, 71-3, 16-1, 16-2). The primers used in the polymerase chain reaction were paired with f5/rl and f7/r4, and the position of the probe attached to the nylon membrane probe was as follows: this 6x6 lattice cross was equally divided into four 3x3 aliquots, of which the upper left block belongs to Enterovirus common probe block, each row is 3 repeats of 3 probes, the upper right block is enterovirus 71 type region, which is staggered by two specific probes, and the lower left block is saxag virus The A16 type region is staggered by two specific probes. DETAILED DESCRIPTION OF THE PREFERRED DETAILS The proper noun "specific hybridization" or "specific hybridization" means hybridization between an oligonucleotide and a target sequence. The proper noun "specificity" or "speciality" Sexually π means the specificity exhibited by the complementary hybridization, which allows for a slight mismatch between the oligonucleotide and the target sequence without adversely affecting the detection of hybridization signal binding (annealing) The proper noun "sample" means a sample including any biological substance containing nucleic acid. Preferably, the proper noun ''sample'' means biological examination including whole blood 'blood sputum' urine, saliva, cerebrospinal fluid, semen, tears, throat swab, rectal cotton swab, excrement, etc. body. The proper noun ''amplification method'' means a test or method for amplifying a nucleic acid sequence. For example, the "amplification method" includes a polymerase chain reaction (PCR) test, a ligase chain reaction (LCR) test, and an increase in Qfl-replicase. Law, In Vitro Transcription Method ' 9 I---- (Please read the note on the back first? Matters ^$ write this page) I: Order --- 4 This paper scale applies to Chinese national standards (CNS A4 size (210 X 297 mm) 1261618 A7 B7 V. Description of invention (?) In vitro reverse transcription and self-sustaining sequence replication. The proper noun "highly stringent conditions" means that the selected hybridization conditions are about 5 ° C lower than the thermal melting point (Tm) for a particular sequence and a given ionic strength at pH 。. At the point of hot melt (at a given ionic strength and pH )), 50% of the target sequence can hybridize to the fully matched probe. Typically, under highly stringent conditions, the salt concentration is about 0.2 M at pH 7 and the temperature is at least above 60 °C. As used herein, a salt-based designation includes the symbols (i.e., A, G, T, and C) representing natural sources of purines and pyrimidines that are found in natural DNA molecules, as well as those skilled in the art of synthesizing oligonucleotides. Known to represent the code of the mixed base (such as R, Y, S, H). For the code used in the present specification, A (or a) means adenine, G (or g) means guano, T (or t) means thymine, C (or c) means cytosine, R (or r) Represents adenine or guano, Y (or y) represents thymine or cytosine, S (or s) represents guanosine or cytosine, and Η (or h) represents adenine, thymine or cytosine. The invention facilitates the detection of nucleic acids derived from enteroviruses. The present invention provides a rapid and sensitive method for detecting the presence or absence of nucleic acids derived from enteroviruses. In a preferred embodiment of the invention, the method of the invention is based on a polymerase chain reaction (PCR) assay. In another aspect, the invention provides a very specific pair of PCR primers that can be used to detect and/or confirm a particular enterovirus blood sputum type, such as enterovirus 71 and oxavirus A16. In another aspect, the invention provides a specific nucleotide sequence which is capable of undergoing a specific hybridization reaction with a nucleic acid fragment obtainable by the amplification method using the primer of the present invention. Some amplification methods are available, but a PCR based method is preferred. The PCR method is well known in the relevant art, so it is only used here as a simple 10 (please read the note on the back first to write this page)
一 * ΜΒΒ ΗΜ I ΜΒ» · I I Ml· MM MM AIBIM 4 經濟部智慧財產局員工消費合作社印製 本紙張尺度適用中國國家標準(CNS)A4規格(210 χ 297公釐) 1261618 A7 B7 五、發明說明(4 ) 述。對於PCR方法及步驟程序的綜覽,可參考例如,u.S. 專利 Nos. 4,683,195 及 4,683,202; 4,965,188;及 Innis寺人所編者之PCR步驟程序“A Guide to Methods and Application” (Academic Press, Inc·, San Diego, CA· 1990)。PCR反應劑及方法程序亦爲商業化可得者。 因爲腸病毒爲RNA病毒,增幅方法的第一步爲針對欲 複製的區域製造DNA拷貝(cDNA)。反轉錄方法可以分開的 方式進行,或以均質性反轉錄-聚合酶鏈反應(RT-PCR)的方 式進行,後者爲用於增幅RNA之聚合酶鏈反應改良方法。 適合將腸病毒核酸進行PCR增幅的方法見述於Romero及 Rotbart 之 “Diagnostic Molecular Biology: Principles and Applications” pp.401-406, Persing 等人編著(Mayo Foundation,Rochester,MN 1993); Rotbart 等人 U.S.專 利 No· 5,075,212 及 Egger 等人,J· Clin· Microbiol· 33:1442-1447 (1995)。 本發明提供新穎的寡核苷酸引子對以用於在檢體中偵 測腸病毒存在與否。本發明之個別引子對包括第一引子及第 二引子,其有利於經由核酸增幅試驗(例如聚合酶鏈反應)快 速診斷與腸病毒相關之疾病或症狀。本發明之引子尋標至編 碼特定保守性區域之意義股或反義股。單一引子對或複數引 子對之特定組合得到陣列式增幅產物,其可用於偵測在檢體 中存在之腸病毒。在本發明較佳的組合中,第一引子包含選 自包括下列之群組之序列 Π: TTGTRCGCCTGTTTTA (SEQ ID NO: 1), 11 本紙張尺度適用中國國家標準(CNS)A4規格(210 χ 297公釐) f (請先閱讀背面之注意事項^填寫本頁) 裝-------訂·--— 1 — 經濟部智慧財產局員工消費合作社印製 1261618 Α7 Β7 五、發明說明(,。) 〇: CAAGCACTTCTGTHHCCCCGG (SEQ ID NO: 2), 〇: TACTTCGAGAARCCYAGTA (SEQ ID NO: 3), f5: AAGAGYCTATTGAGCTA (SEQ ID NO: 4)及 f7: GGI TGG TRS TGG AAR TTI CC (SEQ ID NO: 5)。 第二引子包含選自包括下列之群組之序列 Rl: CACYGGATGGCCAATCCAA (SEQ ID NO: 6), R2: ATTGTCACCATAAGCAGCCA (SEQ ID NO: 7),及 R4: AR RTTIAT CCA YTG RTGIGG (SEQ ID NO: 8)。 本發明引子之序列相關於如圖1所示在框中之習知腸 病毒cDNA序列。設計這些引子時,對相關病毒CDNA序列 進行鹼基修正以增進引子黏合之效率並擴大使用這些引子 可偵測之序列歧異範圍。 包含本發明序列SEQ ID N0s:5及8之引子相關於腸病 毒基因體之編碼區域。相關於腸病毒基因體之編碼區域之引 子係意欲涵蓋包含與序列SEQ ID N0s:5及8有關之退化性 序列之引子。上列序列SEQ ID NOs:5及8係根據該等序列 所相關的密碼子而以適當的三連子(triplet)方式示意性描 繪。 在本發明中,更較佳之組合包含一對或多對下列引子: F1(SEQ ID NO: l)/rl(SEQ ID NO: 6); f2(SEQ ID NO: 2)/rl(SEQ ID NO: 6); F3(SEQ ID NO: 3)/rl(SEQ ID NO: 6); f5(SEQ ID NO: 4)/rl(SEQ ID NO: 6); F1(SEQ ID NO: l)/r2(SEQ ID NO: 7); C(SEQ ID NO: 2)/r2(SEQ ID NO: 7); F3(SEQ ID NO: 3)/r2(SEQ ID NO: 7); f5(SEQ ID NO: 4)/r2(SEQ ID NO: 7);及 F7(SEQ ID NO: 5)/r2(SEQ ID NO:7)。I* ΜΒΒ ΗΜ I ΜΒ» · II Ml· MM MM AIBIM 4 Ministry of Economic Affairs Intellectual Property Bureau Staff Consumer Cooperative Printed This paper scale applies China National Standard (CNS) A4 specification (210 297 297 mm) 1261618 A7 B7 V. Invention Description (4). For an overview of the PCR method and procedure, see, for example, uS Patent Nos. 4,683,195 and 4,683,202; 4,965,188; and the PCR procedure of the editor of Innis Temple "A Guide to Methods and Application" (Academic Press, Inc., San Diego, CA. 1990). PCR reagents and method programs are also commercially available. Since enterovirus is an RNA virus, the first step in the amplification method is to make a DNA copy (cDNA) for the region to be replicated. The reverse transcription method can be carried out in a separate manner or by homogenous reverse transcription-polymerase chain reaction (RT-PCR), which is an improved method for polymerase chain reaction for amplifying RNA. Methods suitable for PCR amplification of enterovirus nucleic acids are described in "Diagnostic Molecular Biology: Principles and Applications" by Romero and Rotbart, pp. 401-406, edited by Persing et al. (Mayo Foundation, Rochester, MN 1993); Rotbart et al. Patent No. 5,075,212 and Egger et al, J. Clin. Microbiol, 33: 1442-1447 (1995). The present invention provides novel pairs of oligonucleotide primers for detecting the presence or absence of enterovirus in a specimen. The individual primer pairs of the present invention include a first primer and a second primer which facilitate rapid diagnosis of a disease or symptom associated with enterovirus via a nucleic acid amplification assay (e.g., polymerase chain reaction). The primers of the present invention are searched to encode significant or antisense strands of a particular conservative region. A single primer pair or a combination of a plurality of primer pairs results in an array amplification product that can be used to detect enteroviruses present in the sample. In a preferred combination of the invention, the first primer comprises a sequence selected from the group consisting of: TTGTRCGCCTGTTTTA (SEQ ID NO: 1), 11 This paper scale applies to the Chinese National Standard (CNS) A4 specification (210 χ 297 f) (Please read the note on the back ^ fill out this page) Pack ------- book ·-- 1 - Ministry of Economic Affairs Intellectual Property Bureau employee consumption cooperative printing 1261618 Α7 Β7 5, invention description ( , ): CAAGCACTTCTGTHHCCCCGG (SEQ ID NO: 2), 〇: TACTTCGAGAARCCYAGTA (SEQ ID NO: 3), f5: AAGAGYCTATTGAGCTA (SEQ ID NO: 4) and f7: GGI TGG TRS TGG AAR TTI CC (SEQ ID NO: 5). The second primer comprises a sequence R1 selected from the group consisting of: CACYGGATGGCCAATCCAA (SEQ ID NO: 6), R2: ATTGTCACCATAAGCAGCCA (SEQ ID NO: 7), and R4: AR RTTIAT CCA YTG RTGIGG (SEQ ID NO: 8) . The sequence of the primer of the present invention is related to the conventional enterovirus cDNA sequence shown in Figure 1 in the box. When these primers are designed, base modifications are performed on the relevant viral CDNA sequences to increase the efficiency of primer binding and to expand the range of sequence discrimination detectable using these primers. The primers comprising the sequences of the present invention SEQ ID NOs: 5 and 8 are related to the coding region of the enterovirus genome. Primers relating to the coding region of the enterovirus genome are intended to encompass primers comprising degenerate sequences associated with the sequences SEQ ID NOs: 5 and 8. The above listed sequences SEQ ID NOs: 5 and 8 are schematically depicted in a suitable triplet based on the codons associated with the sequences. In the present invention, a more preferred combination comprises one or more pairs of the following primers: F1 (SEQ ID NO: l) / rl (SEQ ID NO: 6); f2 (SEQ ID NO: 2) / rl (SEQ ID NO) : 6); F3 (SEQ ID NO: 3) / rl (SEQ ID NO: 6); f5 (SEQ ID NO: 4) / rl (SEQ ID NO: 6); F1 (SEQ ID NO: l) / r2 (SEQ ID NO: 7); C (SEQ ID NO: 2) / r2 (SEQ ID NO: 7); F3 (SEQ ID NO: 3) / r2 (SEQ ID NO: 7); f5 (SEQ ID NO: 4) /r2 (SEQ ID NO: 7); and F7 (SEQ ID NO: 5) / r2 (SEQ ID NO: 7).
在本發明較佳的方面,引子對f7(SEQ IDNO:5)/r4(SEQ ID ΝΟ··8)特別適用於增幅方法中偵側腸病毒71型(EV71)及 12 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) (請先閱讀背面之注意事項¾填寫本頁) β 訂--------- 經濟部智慧財產局員工消費合作社印製 1261618 A7 B7 五、發明說明(0 ) 克沙奇病毒A16型(Cox A16)。 根據圖1,熟習該項技術者可瞭解如何選擇適合偵測及 /或增幅腸病毒基因體中所欲片段之至少一對本發明引子, 並因此容易決定欲使用之本發明引子對。如圖1所示,當第 一引子包含序列SEQ ID N0:5或其退化性序列則第二引子 應包含序列SEQ ID N0:8或其退化性序列。 爲了經由PCR去增幅在檢體中之目標核酸序列,該序 列必須能夠與增幅系統中元件接觸(accessible)。通常,此接 觸性經由將核酸自該檢體中單離而予以確認。在相關技藝中 已知相異之自生物性檢體中抽取核酸之技術,特別是核糖核 酸。或者,若該檢體係相當易於破壞,則核酸經由PCR技 術增幅前毋需純化。亦即若該檢體包括細胞(特別是周邊血 液淋巴細胞或單核細胞),細胞內成份之溶解及分散可經由 將細胞懸浮於低張性溶液中而輕易達成。 經濟部智慧財產局員工消費合作社印製 每個PCR周期的第一步係有關將引子延長作用所得之 核酸雙股加以分離。當雙股分離後,PCR中下一步係有關 將已分離之核酸股與目標序列兩側之引子進行雜交(即黏 合)。該引子隨後被延長而形成目標序列之互補性拷貝。爲 了成功的PCR增幅,考慮每個引子沿著雙股序列進行雜交 的位置來設計該引子,使得從一引子合成所得的延伸產物自 模版分離後,作爲另一引子之延伸作用的模版。變性,雜交, 及延長之周期依需要重覆多次以獲得增幅核酸之需要份 量。 在PCR方法之較佳具體事實中,股分離之達成係經由 13 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) ' 1261618 經濟部智慧財產局員工消費合作社印製 A7 B7 五、發明說明(士) 將反應物加熱至充份高的溫度達充份時間,造成雙股之變性 但不會造成聚合酶不可逆之變性。在PCR中引子對之模版 依賴性延長作用係經由聚合性物質在適量之四種去氧核糖 核苷三磷酸(典型上爲dATP,dGTP,dCTP及dTTP)存在下 於包含合適鹽類,金屬離子及pH緩衝性系統之培育液體內 進行催化而成。合適的聚合性物質爲已知可催化模版-依賴 性DNA合成之酵素。在本發明中,引子延長作用之最初模 版典型上爲RNA。適於自RNA模版合成cDNA之反轉錄酶 (RTs)爲習知的。 PCR最通常以自動化方法使用熱安定酵素進行。在此 方法中,反應混合物的溫度自動經由變性範圍、引子黏合範 圍及延長反應範圍進行循環。 如上所述,本發明之較佳具體事實倂含RT-PCR增幅反 應。然而,熟習該項技術者將認知到目標序列在檢體中的增 幅可用任何習知方法完成,如連接酶鏈反應(LCR),Qfi-複 製酶增幅,活體外轉錄,及子持性序列複製,以上皆可提供 充份的增幅。 本發明方法所生產之被增幅片段增幅產物")之大小 典型上足以決定腸病毒之存在與否。因此,在本發明之一些 具體事實中,在檢體中所產出之被增幅片段之大小區分(例 如凝膠電泳分析)可用於決定在檢體中腸病毒之存在與否。 此典型上經由將含有已知核酸之對照組以和用於增幅目標 檢體所用者相同的引子進行增幅。根據習知方法將被增幅的 序列在瓊脂糖凝膠上電泳並以溴化乙啶標示後,將檢體及對 14 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) ' -- π 裝--------訂---------. (請先閱讀背面之注意事項¾填寫本頁)In a preferred aspect of the invention, the primer pair f7 (SEQ ID NO: 5) / r4 (SEQ ID ΝΟ · 8) is particularly suitable for use in an amplification method for detection of enterovirus 71 (EV71) and 12 paper scales for Chinese countries. Standard (CNS) A4 specification (210 X 297 mm) (Please read the note on the back 3⁄4 to fill out this page) β 订--------- Ministry of Economic Affairs Intellectual Property Bureau Staff Consumer Cooperative Printed 1261618 A7 B7 V. INSTRUCTIONS (0) Croxvirus A16 (Cox A16). According to Fig. 1, those skilled in the art will know how to select at least one pair of primers of the present invention suitable for detecting and/or amplifying a desired fragment of the enterovirus genome, and thus easily determine the pair of primers of the present invention to be used. As shown in Figure 1, when the first primer comprises the sequence SEQ ID NO: 5 or its degenerate sequence then the second primer should comprise the sequence SEQ ID NO: 8 or its degenerate sequence. In order to increase the target nucleic acid sequence in the sample via PCR, the sequence must be accessible to the elements in the amplification system. Typically, this contact is confirmed by detaching the nucleic acid from the sample. Techniques for extracting nucleic acids from biological samples, such as ribonucleotides, are known in the related art. Alternatively, if the assay system is relatively susceptible to disruption, the nucleic acid will need to be purified prior to amplification by PCR techniques. That is, if the specimen includes cells (especially peripheral blood lymphocytes or monocytes), the dissolution and dispersion of intracellular components can be easily achieved by suspending the cells in a low-tension solution. Printed by the Intellectual Property Office of the Ministry of Economic Affairs, the Consumer Cooperatives. The first step in each PCR cycle is to separate the double strands of nucleic acid from the extension of the primer. When the double strands are separated, the next step in the PCR is to hybridize (i.e., bind) the separated nucleic acid strands to primers flanking the target sequence. The primer is then extended to form a complementary copy of the target sequence. For successful PCR amplification, the primers are designed in such a way that each primer is hybridized along the double-stranded sequence, so that the extension product synthesized from one primer is separated from the template and used as a template for extension of another primer. The period of denaturation, hybridization, and elongation is repeated as many times as necessary to obtain the desired amount of amplified nucleic acid. In the better specific case of the PCR method, the completion of the stock separation is based on the 13-sheet paper scale applicable to the Chinese National Standard (CNS) A4 specification (210 X 297 mm) ' 1261618 Ministry of Economic Affairs Intellectual Property Bureau Staff Consumer Cooperative Printed A7 B7 V. INSTRUCTIONS (S) The reaction is heated to a high temperature for a sufficient period of time to cause denaturation of the double strands without causing irreversible denaturation of the polymerase. In the PCR, the template-dependent extension of the primer is based on the presence of a suitable amount of metal ions in the presence of a suitable amount of four deoxyribonucleoside triphosphates (typically dATP, dGTP, dCTP and dTTP). And catalyzed by the incubation liquid of the pH buffering system. Suitable polymeric materials are those known to catalyze stencil-dependent DNA synthesis. In the present invention, the initial template for the elongation of the primer is typically RNA. Reverse transcriptases (RTs) suitable for the synthesis of cDNA from RNA templates are conventional. PCR is most commonly carried out using automated methods using thermal stability enzymes. In this method, the temperature of the reaction mixture is automatically circulated through the denaturation range, the primer adhesion range, and the extended reaction range. As described above, the preferred specific fact of the present invention contains an RT-PCR amplification reaction. However, those skilled in the art will recognize that the increase in the target sequence in the sample can be accomplished by any conventional method, such as ligase chain reaction (LCR), Qfi-replicase amplification, in vitro transcription, and daughter-holding sequence replication, All of the above can provide sufficient increase. The size of the amplified fragment amplification product ") produced by the method of the invention is typically sufficient to determine the presence or absence of enterovirus. Thus, in some specific instances of the invention, the size of the amplified fragments produced in the specimen (e. g., gel electrophoresis analysis) can be used to determine the presence or absence of enterovirus in the specimen. This is typically augmented by introducing the control group containing the known nucleic acid with the same primer used for the amplification of the target sample. After the amplified sequence was electrophoresed on an agarose gel and labeled with ethidium bromide according to the conventional method, the sample and the 14-sheet paper size were applied to the Chinese National Standard (CNS) A4 specification (210 X 297 mm). ' -- π 装 -------- set --- ------. (Please read the notes on the back 3⁄4 fill out this page)
I 1261618 A7 B7 經濟部智慧財產局員工消費合作社印製 五、發明說明(、'Ί ) 照組之條帶型態進行比較。檢體結果與對照組比較出現之相 異或額外的條帶指出腸病毒之存在。 爲了確定PCR增幅結果之正確性,可以在一增幅方法 中使用一對以上的引子。在本發明之方法中’彼此不同的引 子對可以同時或先後使用。在一個增幅方法中同時使用本發 明一對以上引子之情形下,一對引子與另一對引子的不同可 爲第一個引子或第二個引子,或第一個引子或第二個引子皆 有不同。在另一種情形,若在一增幅方法中連續使用本發明 之兩對引子,第二對引子能用於增幅之序列’相等於使用第 一對引子在增幅方法中推想可獲得之序列或在該可獲得序 列範圍之內。根據圖1,實施者可以經由輕易決定同時使用 或先後使用之一對以上的引子來進行本發明方法。 或者,本發明之增幅產物可使用對目標核酸具專一性之 寡核苷酸探針進行偵測。探針通常選自對單一目標序列具有 專一^丨生之腸病毒基因體區域。 序列_專一性探針雜交反應爲一種習知甚詳之在檢體中 偵測所欲核酸之方法。在充份嚴格之雜交反應條件下’探針 僅與實質上互補性序列發生專一性雜交反應。雜交反應條件 的嚴格性可以放寬以容忍不同程度之序列不相符性。被增幅 產物之偵測使用此序列-專一性雜交反應以確定偵測到正確 之被增幅目標,藉此減少因來自其他生物或其他污染序列之 相似性序列存在之故造成僞陽性的機會。 本發明令人驚異地發現一些核苷酸序列相關於腸病毒 核酸之保守性區域。因此,本發明進而提供該等合成性核苷 15 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) >裝--------訂--------- (請先閱讀背面之注意事項Λ1填寫本頁) f 1261618 經濟部智慧財產局員工消費合作社印製 A7 B7 五、發明說明(A ) (antiligand)或抗體結合。或者,探針可直接與如螢光發生基 團,化學發光劑或酵素之標定進行共軛結合。標定方式的選 擇取決於所需之靈敏度,與探針共軛結合之容易性,安定性 需求及可用的儀器而定。 本發明探針及引子可使用傳統習知方法進行合成及標 定。作爲探針及引子之寡核苷酸可根據Beaucage,S.L.及 Caruthers,Μ·Η·(1981,Tetrahedron Letts·,22(20):1859-1862) 首先描述之固體相亞胺基磷酸酯三酯方法使用自動化合成 儀進行化學合成,如Needham-VanDevanter,D.R·等人在 1984,Nucleic Acid Res·,12:6159-6168 中所述。寡核苦酸 之純化或可經由天然丙烯醯胺凝膠電泳法或經由陰離子-交 換樹脂 HPLC 進行,如 Pearson,J.D·及 Regnier,F.E.在 1983, J. Chrom.,255:137-149 中所述者。 上述引子及試驗係用於偵測檢體中的腸病毒,診斷腸病 毒相關疾病及症狀及確定特定症狀或症狀組合與特定腸病 毒存在之間的關聯性(或切斷此種關聯)。診斷上的應用可用 病史及受試個體的特徵加以補充及確認。經由本發明方法診 斷之腸病毒疾病,症候群及症狀包含所有在本文及科學文g 中已報告與腸病毒相關之疾病,症候群及症狀,特別包含無 菌性腦膜炎,腸病毒糖尿病,腸病毒結膜炎,急性軟弱性g 庳,急性良性心包炎,發疹,內皮疹,擴張性心肌病變,□ 足病,慢性疲憊症狀,熱病及上呼吸道感染。腸病毒感染及 其與症候群的關聯性之偵測使得發展疫苗及治療方法成胃 可能。 18 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) ^ n n ϋ ϋ ϋ ϋ· ^1 一I ϋ ϋ 1_1 11 n ·ϋ I (請先閱讀背面之注音?事項巧填寫本頁)I 1261618 A7 B7 Ministry of Economic Affairs Intellectual Property Bureau employee consumption cooperative printing 5, invention description (, 'Ί) according to the strip type of the group. Differences in the results of the specimens compared with the control group or additional bands indicate the presence of enterovirus. To determine the correctness of the PCR amplification results, more than one pair of primers can be used in an amplification method. In the method of the present invention, pairs of primers different from each other can be used simultaneously or sequentially. In the case where one or more primers of the present invention are simultaneously used in one amplification method, the difference between a pair of primers and another pair of primers may be the first primer or the second primer, or the first primer or the second primer There are different. In another case, if two pairs of primers of the present invention are continuously used in an amplification method, the second pair of primers can be used for the sequence of amplifications, which is equivalent to the sequence that can be obtained by using the first pair of primers in the amplification method or Available within the sequence range. According to Fig. 1, the practitioner can carry out the method of the invention by easily determining whether to use one or more of the primers simultaneously or sequentially. Alternatively, the amplification products of the invention can be detected using oligonucleotide probes specific for the target nucleic acid. The probe is typically selected from a region of the enterovirus genome that has a specific target sequence. The sequence-specific probe hybridization reaction is a well-known method for detecting a desired nucleic acid in a sample. Under sufficient stringent hybridization reaction conditions, the probe only undergoes a specific hybridization reaction with a substantially complementary sequence. The stringency of hybridization reaction conditions can be relaxed to tolerate varying degrees of sequence inconsistency. Detection of the amplified product uses this sequence-specific hybridization reaction to determine that the correct amplified target is detected, thereby reducing the chance of false positives due to the presence of similar sequences from other organisms or other contaminating sequences. The present inventors have surprisingly found that some nucleotide sequences are associated with conserved regions of enterovirus nucleic acid. Therefore, the present invention further provides such synthetic nucleosides 15 The paper size is applicable to the Chinese National Standard (CNS) A4 specification (210 X 297 mm) > --- (Please read the notes on the back first 填写1 fill out this page) f 1261618 Ministry of Economic Affairs Intellectual Property Bureau employee consumption cooperative printed A7 B7 V. Invention description (A) (antiligand) or antibody binding. Alternatively, the probe can be directly conjugated to a calibration such as a fluorescent generating group, a chemiluminescent agent or an enzyme. The choice of calibration method depends on the sensitivity required, the ease with which the probe is conjugated, the stability requirements, and the instrument available. The probes and primers of the present invention can be synthesized and calibrated using conventional methods. Oligonucleotides as probes and primers can be described in accordance with Beaucage, SL and Caruthers, 1981·Η· (1981, Tetrahedron Letts, 22(20): 1859-1862). Methods Chemical synthesis was performed using an automated synthesizer as described by Needham-Van Devanter, DR et al., 1984, Nucleic Acid Res., 12: 6159-6168. Purification of oligonucleotides can be carried out by natural acrylamide gel electrophoresis or via anion-exchange resin HPLC, as described by Pearson, JD. and Regnier, FE, 1983, J. Chrom., 255: 137-149. Narrator. The above primers and tests are used to detect enteroviruses in specimens, to diagnose diseases and symptoms associated with enteroviruses, and to determine (or cut off) the association between specific symptoms or combinations of symptoms and the presence of specific enteric viruses. Diagnostic applications can be supplemented and confirmed with a history and characteristics of the individual being tested. Enterovirus diseases, syndromes and symptoms diagnosed by the method of the present invention include all diseases, syndromes and symptoms which have been reported in this and the scientific literature, including aseptic meningitis, enterovirus diabetes, enterovirus conjunctivitis, Acute weakness g 庳, acute benign pericarditis, rash, endothelial rash, dilated cardiomyopathy, □ foot disease, chronic fatigue symptoms, fever and upper respiratory tract infection. The detection of enterovirus infection and its association with syndromes makes it possible to develop vaccines and treatments. 18 The paper size applies to the Chinese National Standard (CNS) A4 specification (210 X 297 mm) ^ nn ϋ ϋ ϋ ϋ · ^1 I I ϋ ϋ 1_1 11 n · ϋ I (Please read the phonetic on the back first? This page)
II
1261618 A7 B7 五、發明說明(J ) 本發明亦提供套組,其爲多容器單位而包括有利於實施 本發明方法之成份。有利的套組可包括用於偵測意欲目標核 酸之探針。在一些情況下,該探針可固著於合適的支持膜 上。該套組將亦可包含本發明所提供之引子。該套組中其他 選擇性成份包含,例如,反轉錄酶或聚合酶,基質核苷三磷 酸,用於標定的物質(例如,當標定物爲生物素時,含卵白 素(avidin)-酵素共軛物及酵素基質及發色原)及用於反轉 錄,PCR,或雜交反應之合適緩衝液。除了上述成份以外, 該套組亦可包含進行本發明方法之指示。 在本發明說明中所引述之文獻均以參考資料的方式倂 入本案。 本發明其他的特徵及優點將可明顯見於下列偏好具體 事實及申請專利範圍。 實例 下列實施例用於示範說明本發明。這些實施例不以任何 方式意欲限制本發明之範圍,但用於指示如何實施本發明的 材料及方法。 實例1:腸病毒之偵測 經濟部智慧財產局員工消費合作社印製 1.1.病毒 所使用的59個腸病毒樣本(見表1)或自臨床收集之檢 體中單離或得自美國標準菌種中心(ATCC)。腸病毒經由中 和試驗使用匯合之免疫血淸加以鑑定,接著以單型中和性多 株抗體確認其血淸型。如結果所示,59個樣本包括不同的 腸病毒血淸型(見表1)。病毒於MRC5單層細胞培養物中繁 19 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) 1261618 A7 B7 經濟部智慧財產局員工消費合作社印製 五、發明說明(J)1261618 A7 B7 V. INSTRUCTIONS (J) The present invention also provides kits that are multi-container units and include ingredients that facilitate the performance of the methods of the present invention. An advantageous kit can include a probe for detecting the desired target nucleic acid. In some cases, the probe can be attached to a suitable support membrane. The kit will also include the primers provided by the present invention. Other optional components of the kit include, for example, reverse transcriptase or polymerase, matrix nucleoside triphosphates, for calibration purposes (eg, when the calibration is biotin, avidin-enzyme is present) Conjugates and enzyme matrices and chromogens) and suitable buffers for reverse transcription, PCR, or hybridization reactions. In addition to the above ingredients, the kit may also include instructions for performing the methods of the invention. The documents cited in the description of the present invention are incorporated herein by reference. Other features and advantages of the present invention will be apparent from the following description of the specific facts and claims. EXAMPLES The following examples are intended to illustrate the invention. The examples are not intended to limit the scope of the invention in any way, but are intended to indicate how to practice the materials and methods of the invention. Example 1: Detection of Enteroviruses Ministry of Economic Affairs Intellectual Property Bureau Staff Consumer Cooperatives Printed 1.1. 59 enterovirus samples used in the virus (see Table 1) or isolated from clinically collected samples. Kind of Center (ATCC). The enterovirus was identified by a neutralization test using confluent immune blood clots, and then the blood type was confirmed by a single-type neutralizing multi-drug antibody. As shown by the results, 59 samples included different enterovirus blood sputum types (see Table 1). Virus in MRC5 monolayer cell culture 19 This paper scale applies Chinese National Standard (CNS) A4 specification (210 X 297 mm) 1261618 A7 B7 Ministry of Economic Affairs Intellectual Property Bureau employee consumption cooperative printing 5, invention description (J)
1.2. 抽取 RNA1.2. Extracting RNA
病毒RNAs係經由將總核酸自經感染單層細胞培養物 之離心沉澱物單離而得。約4-6 xlO6個細胞(每毫升)於溶 解緩衝液(5〇mMNaC卜 20mM Tris HC1 (pH 7.5) ’ 50 mM EDTA,1%硫酸十二烷酯鈉)中溶解,以酚-氯仿萃取三次 並以氯仿萃取一次,且隨後自2.5M含乙醇之乙酸銨中沉 澱。將核酸離心沉澱物以75%乙醇淸洗,進行乾燥並懸浮於 100微升之無菌蒸餾水中。:RNA製備物被貯於-80°C。 1.3. PCR增幅試驗 增幅試驗之第一步爲合成將被增幅之腸病毒RNA基因 體部份之DNA拷貝(cDNA)(即反轉錄步驟)。經由聚合酶鏈 反應進行之反轉錄作用於20μ1之反應混合物(Ιμΐ之個別 總 RNA,20 mM Tr*is-HCl (pH 8.4),50 mM Κα,5 mM MgCl2,10 mM DTT,各爲 0.5 mM 之 dATP,dCTP,dGTP 及dTTP,以及50奈克之隨意六元體)中進行。將檢體培育 於65°C5分鐘,隨後置於冰上1分鐘。加入50單位之反轉 錄酶並將該混合物於42°C培育50分鐘。該反應藉由在70 °C培育15分鐘而終止。所得的cDNA產物被貯於-20°C。 經由PCR之DNA增幅作用於25 1反應混合物[12 1 之 cDNA,20 mM Tris-HCl (pH 8.0),0· 1 mM EDTA,1 mM DTT,1.0% triton X-100,50% 甘油,1.5 mM MgCl2,各 150 M 之 dATP,dCTP,dGTP 及 dTTP,各 10 pmol 之 各個別引子及2·5 U之Taq DNA聚合酶]中進行。在增幅反 20 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) (請先閱讀背面之注意事項再填寫本頁)Viral RNAs are obtained by singulating total nucleic acids from centrifuged pellets of infected monolayer cell cultures. About 4-6 x 10 6 cells (per ml) were dissolved in lysis buffer (5 mM NaOH, 20 mM Tris HCl (pH 7.5) '50 mM EDTA, 1% sodium dodecyl sulfate), and extracted three times with phenol-chloroform. It was extracted once with chloroform and then precipitated from 2.5 M ammonium acetate containing ethanol. The nucleic acid pellet was washed with 75% ethanol, dried and suspended in 100 μl of sterile distilled water. : RNA preparations were stored at -80 °C. 1.3. PCR Amplification Assay The first step in the amplification assay is the synthesis of a DNA copy (cDNA) of the portion of the enterovirus RNA gene to be amplified (ie, the reverse transcription step). Reverse transcription by polymerase chain reaction on 20 μl of reaction mixture (Ιμΐ of individual total RNA, 20 mM Tr*is-HCl (pH 8.4), 50 mM Κα, 5 mM MgCl 2 , 10 mM DTT, each 0.5 mM It is carried out in dATP, dCTP, dGTP and dTTP, and 50 ng of random hexamed body. The samples were incubated at 65 ° C for 5 minutes and then placed on ice for 1 minute. 50 units of the reversed enzyme was added and the mixture was incubated at 42 ° C for 50 minutes. The reaction was terminated by incubation at 70 °C for 15 minutes. The resulting cDNA product was stored at -20 °C. DNA amplification via PCR was applied to the 25 1 reaction mixture [12 1 cDNA, 20 mM Tris-HCl (pH 8.0), 0·1 mM EDTA, 1 mM DTT, 1.0% triton X-100, 50% glycerol, 1.5 mM MgCl2 was carried out in 150 M of each of dATP, dCTP, dGTP and dTTP, each of 10 pmol of each primer and 2·5 U of Taq DNA polymerase. Applicable to China National Standard (CNS) A4 specification (210 X 297 mm) in the increase of 20 paper scales (please read the notes on the back and fill out this page)
一· ϋ n an _1 n I ϋ I n I— n .^1 I ϋ ϋ I· n an _1 n I ϋ I n I— n .^1 I ϋ ϋ I
1261618 A7 _ B7_ 五、發明說明() 應中所使用的引子對爲包含下列序列之引子: fl(SEQ ID NO: l)/rl(SEQ ID NO: 6) » G(SEQ ID NO: 2)/rl(SEQ ID NO: 6), C(SEQ ID NO: 3)/rl(SEQ ID NO: 6); f5(SEQ ID NO: 4)/rl(SEQ ID NO: 6), fl(SEQ ID NO: l)/r2(SEQ ID NO: 7), C(SEQ ID NO: 2)/r2(SEQ ID NO: 7), fi(SEQ ID NO: 3)/r2(SEQ ID NO: 7) R f5(SEQ ID NO: 4)/r2(SEQ ID NO: 7)。 引子rl及r2以生物素在5’端標定供後續偵測步驟使 用。每個增幅反應進行40個溫度周期(於94°C變性4分鐘, 於55°C進行引子對黏合1分鐘,及於72°C延長1分鐘)。 1.4. DNA產物之分離 將PCR產物之少量(每個10μ1)於1.5%瓊脂糖凝膠於 0·5χΤΒΕ 緩衝液(0.045Μ Tris_硼酸鹽,0.001M EDTA)中 於100伏特下進行電泳30分鐘。電泳後,將凝膠染以溴化 乙啶並於UV光源下觀察。所有病毒樣本使用本發明引子之 增幅反應於UV光源下觀察皆顯示陽性結果。使用引子對 f5/rl針對59個病毒樣本進行之PCR增幅數據示於表1。 表1 血淸型 樣本數 顯示陽性PCR結果之 樣本數 EV71 17 17 CA7 2 2 CA9 1 1 CA10 1 1 CA 11 1 1 CA16 14 14 CA 24 1 1 CB 1 1 1 CB2 1 1 CB3 1 1 21 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) 1261618 A7 B7 五、發明說明(/) CB4 1 1 CB5 5 5 CB6 1 1 Echo 1 1 1 Echo 2 1 1 Echo 3 1 1 Echo 4 1 1 Echo 5 1 1 Echo 6 1 1 Echo 7 3 3 Echo 9 1 1 Echo 11 1 1 Echo 14 1 1 總計 59 59 以不同引子之組合,利用聚合酶鏈反應增幅腸病毒71 型核酸之電泳分析圖示於圖2。a至h行各使用之引子對 爲:a:fl/rl,b:f2/rl,c:f3/rl,d:f5/rl,e:fl/r2,f: f2/r2, g:f3/rl,h:f5/r2。m爲核酸大小標記,1至5分別爲:1: 600 bp,2: 500 bp,3: 400 bp,4: 300 bp,5: 200 bp 〇 上述結果證明本發明引子,可廣泛用於偵測腸病毒之核 酸存在與否,藉此診斷腸病毒之存在與否。 1.5.雜交反應分析 將三個腸病毒-專一性探針(pl,p2及p3)用於偵測經增 幅之DNA片段,其分別包含序列SEQ ID ΝΟ_·9,SEQ ID NO:10 及 SEQ ID ΝΟ:11。 將探針進行加熱以變性(95°C,5分鐘)並快速於冰上驟 冷2分鐘,接著將這些探針(每個ΙΟμΜ)固著於尼龍膜(來自 BoehringerManngeim)上。三個探針(每個1 1)被施用及曝露 22 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) (請先閱讀背面之注咅?事項再填寫本頁)1261618 A7 _ B7_ V. INSTRUCTIONS () The primer pairs used in the application are primers containing the following sequences: fl(SEQ ID NO: l)/rl(SEQ ID NO: 6) » G(SEQ ID NO: 2) /rl (SEQ ID NO: 6), C (SEQ ID NO: 3) / rl (SEQ ID NO: 6); f5 (SEQ ID NO: 4) / rl (SEQ ID NO: 6), fl (SEQ ID NO: l) / r2 (SEQ ID NO: 7), C (SEQ ID NO: 2) / r2 (SEQ ID NO: 7), fi (SEQ ID NO: 3) / r2 (SEQ ID NO: 7) R F5 (SEQ ID NO: 4) / r2 (SEQ ID NO: 7). The primers rl and r2 are labeled with biotin at the 5' end for subsequent detection steps. Each amplification reaction was carried out for 40 temperature cycles (denaturation at 94 ° C for 4 minutes, adhesion at 55 ° C for 1 minute, and extension at 72 ° C for 1 minute). 1.4. Isolation of DNA product A small amount of PCR product (10 μl each) was electrophoresed on a 1.5% agarose gel in 0.5 μM buffer (0.045 Μ Tris-borate, 0.001 M EDTA) at 100 volts for 30 minutes. . After electrophoresis, the gel was stained with ethidium bromide and observed under a UV light source. All virus samples showed positive results using the amplification of the primers of the present invention under UV light source. The PCR amplification data for the 59 virus samples using the primer pair f5/rl is shown in Table 1. Table 1 Number of bloody samples shows the number of positive PCR results EV71 17 17 CA7 2 2 CA9 1 1 CA10 1 1 CA 11 1 1 CA16 14 14 CA 24 1 1 CB 1 1 1 CB2 1 1 CB3 1 1 21 This paper The scale applies to China National Standard (CNS) A4 specification (210 X 297 mm) 1261618 A7 B7 V. Invention description (/) CB4 1 1 CB5 5 5 CB6 1 1 Echo 1 1 1 Echo 2 1 1 Echo 3 1 1 Echo 4 1 1 Echo 5 1 1 Echo 6 1 1 Echo 7 3 3 Echo 9 1 1 Echo 11 1 1 Echo 14 1 1 Total 59 59 Electrophoretic analysis of the amplification of enterovirus 71 nucleic acid by polymerase chain reaction using a combination of different primers Shown in Figure 2. The pair of primers used in each of the a to h lines are: a: fl/rl, b: f2/rl, c: f3/rl, d: f5/rl, e: fl/r2, f: f2/r2, g: f3 /rl,h:f5/r2. m is a nucleic acid size marker, and 1 to 5 are: 1:600 bp, 2: 500 bp, 3: 400 bp, 4: 300 bp, 5: 200 bp. The above results prove that the primer of the present invention can be widely used for detection. The presence or absence of nucleic acid of enterovirus, thereby diagnosing the presence or absence of enterovirus. 1.5. Hybridization Analysis Three enterovirus-specific probes (pl, p2 and p3) were used to detect amplified DNA fragments comprising the sequences SEQ ID ΝΟ_·9, SEQ ID NO: 10 and SEQ ID, respectively. Hey: 11. The probes were heated to denature (95 ° C, 5 minutes) and quenched rapidly on ice for 2 minutes, and then these probes (each ΙΟμΜ) were fixed to a nylon membrane (from Boehringer Manngeim). Three probes (each 1 1) are applied and exposed 22 This paper size applies to the Chinese National Standard (CNS) A4 specification (210 X 297 mm) (please read the notes on the back side and then fill out this page)
▼ * .1· n 1· ammt ί I 1 一- n ϋ 1 ·ϋ 1 a—· I▼ * .1· n 1· ammt ί I 1 a- n ϋ 1 ·ϋ 1 a—· I
經濟部智慧財產局員工消費合作社印製 1261618 A7 五、發明說明(^) 於紫外線幅射(254nm,0.15 J/cm2)之下。 將生物素標定之PCR產物(每個8μ1)在95°C加熱5分鐘 進行變性並於冰上驟冷2分鐘,並加入雜交反應溶液[5x標 準檸檬酸鹽(SSC),0.1%(w/v)N-月桂醯基肉豆蔻酸’ 0.1%(w/v)硫酸十二烷酯鈉(SDS),lx阻斷緩衝液(來自 BoehringerManngeim,20ml/100cm2)]中。含有 PCR 產物之 雜交反應溶液隨後與尼龍膜及經標定之探針共同培育。於 5〇t:培育1小時以後,將該等膜於室溫使用淸洗緩充液 (2xSSC及0.1%SDS)淸洗五次,隨後加入鏈卵白素鹼性磷酸 酶(2μ1/20ιη1 lx阻斷緩衝液)。將膜置於室溫下30分鐘並於 室溫下以順丁烯二酸緩衝液(0.1M順丁烯二酸,0.15M NaCl,Ph 7.5)淸洗五次。將膜於偵測緩衝液(〇.1!4丁1^-HC1;0.1M NaCl;50Mm MgCl2,pH 9.5)中平衡 5 分鐘並與新 鮮製備之顏色-基質溶液(45μ1 NBT溶液混合35μ1 X-磷酸溶 液),並用偵測緩衝液加到1〇毫升)在黑暗中培育1〇分鐘。 最後將膜以lxTE緩衝液淸洗以終止反應並於室溫下晾乾。 將雜交反應訊號進行偵測及記錄。結果示於表2。 (請先閱讀背面之注意事項再填寫本頁) 經濟部智慧財產局員工消費合作社印製 表2 血淸型 受試樣本之 數目 顯示可偵測之雜交反應訊號 之受試樣本之數目 P1 P2 P3 CA16 6 6 6 6 CA21 1 1 1 1 CA 24 1 1 1 1 23 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐) 1261618 經濟部智慧財產局員工消費合作社印製 A7 B7 五、發明說明(,) CB 1 1 1 1 1 CB2 2 2 2 2 CB3 1 1 1 1 CB4 1 1 1 1 CB5 1 1 1 1 CB6 1 1 1 1 Echo 3 3 3 3 3 Echo 5 1 1 1 1 Echo 6 1 1 1 1 Echo 9 2 2 2 2 Echo 11 3 3 3 3 Echo 14 1 1 1 1 Echo 21 3 3 3 3 Echo 24 1 1 1 1 Echo 30 2 2 2 2 Echo 31 2 2 2 2 EV71 7 7 7 7 Polio 1 2 2 2 2 Polio 2 2 2 2 2 Polio 3 2 2 2 2 腸病毒71型及克沙奇病毒A16型之核酸經聚合酶鏈反 應放大後與腸病毒共通型探針(pi,p2,p3)雜交之結果示 於圖3。聚合酶鏈反應使用之引子配對爲f5/rl,固定在尼龍 膜探針之分部位置如下:最上面一列及最下面一列爲雜交控 制組,使用之探針爲豬流產及呼吸道症候群病毒(porcine reproductive and respiratory syndrome virus,PRRSV ) ORF 7 的一段核酸序列,由於雜交液中含有與此探針互補之核酸序 列,故雜交反應順利完成時,此兩列會有訊號產生。左邊第 一排之第2至4點:探針pi,中間排之第2至4點:探針 p2,右邊第一排之第2至4點:探針p3。1及2:腸病毒71 24 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐)Ministry of Economic Affairs Intellectual Property Bureau employee consumption cooperative printing 1261618 A7 V. Invention description (^) Under ultraviolet radiation (254nm, 0.15 J/cm2). The biotin-labeled PCR products (each 8 μl) were denatured by heating at 95 ° C for 5 minutes and quenched on ice for 2 minutes, and a hybridization reaction solution [5x standard citrate (SSC), 0.1% (w/) was added. v) N-laurosyl myristic acid '0.1% (w/v) sodium dodecyl sulfate (SDS), lx blocking buffer (from Boehringer Manngeim, 20 ml/100 cm2). The hybridization reaction solution containing the PCR product is then incubated with a nylon membrane and a calibrated probe. After 5 hours of incubation: 1 hour after incubation, the membranes were rinsed five times with rinsing buffer (2xSSC and 0.1% SDS) at room temperature, followed by the addition of streptavidin alkaline phosphatase (2μ1/20ιη1 lx resistance). Broken buffer). The membrane was left at room temperature for 30 minutes and rinsed five times with maleic acid buffer (0.1 M maleic acid, 0.15 M NaCl, Ph 7.5) at room temperature. The membrane was equilibrated in detection buffer (〇.1!4丁1^-HC1; 0.1M NaCl; 50Mm MgCl2, pH 9.5) for 5 minutes and mixed with freshly prepared color-matrix solution (45μ1 NBT solution 35μ1 X- Phosphoric acid solution), and added to the test solution with 1 ml of detection buffer for 1 minute in the dark. The membrane was finally rinsed with lxTE buffer to stop the reaction and allowed to air dry at room temperature. The hybridization reaction signal is detected and recorded. The results are shown in Table 2. (Please read the precautions on the back and fill out this page.) Ministry of Economic Affairs Intellectual Property Office Staff Consumer Cooperatives Printed Table 2 The number of blood samples received by the sample shows the number of samples of the detectable hybridization signal. P2 P3 CA16 6 6 6 6 CA21 1 1 1 1 CA 24 1 1 1 1 23 This paper scale applies to China National Standard (CNS) A4 specification (210 X 297 mm) 1261618 Ministry of Economic Affairs Intellectual Property Bureau employee consumption cooperative prints A7 B7 V. INSTRUCTIONS (,) CB 1 1 1 1 1 CB2 2 2 2 2 CB3 1 1 1 1 CB4 1 1 1 1 CB5 1 1 1 1 CB6 1 1 1 1 Echo 3 3 3 3 3 Echo 5 1 1 1 1 Echo 6 1 1 1 1 Echo 9 2 2 2 2 Echo 11 3 3 3 3 Echo 14 1 1 1 1 Echo 21 3 3 3 3 Echo 24 1 1 1 1 Echo 30 2 2 2 2 Echo 31 2 2 2 2 EV71 7 7 7 7 Polio 1 2 2 2 2 Polio 2 2 2 2 2 Polio 3 2 2 2 2 Enterovirus 71 and oxacin A16 nucleic acids are amplified by polymerase chain reaction and enterovirus-conjugated probes ( The results of the hybridization of pi, p2, p3) are shown in Fig. 3. The primers used in the polymerase chain reaction were paired with f5/rl, and the positions of the probes fixed in the nylon membrane probe were as follows: the uppermost column and the lowermost column were the hybridization control group, and the probes used were porcine abortion and respiratory syndrome virus (porcine). Reproductive and respiratory syndrome virus (PRRSV) A nucleic acid sequence of ORF 7 that has a nucleic acid sequence complementary to the probe in the hybridization solution, so that the two columns will generate a signal when the hybridization reaction is successfully completed. Point 2 to 4 of the first row on the left: probe pi, point 2 to 4 in the middle row: probe p2, point 2 to 4 in the first row on the right: probe p3. 1 and 2: Enterovirus 71 24 This paper size applies to the Chinese National Standard (CNS) A4 specification (210 X 297 mm)
1261618 A7 B7 五、發明說明(# ) 型與克沙奇病毒A16型於雜交控制點及腸病毒共通型探針 位置均有訊號。3:爲不含核酸之控制組,僅於雜交控制探針 有訊號。 實例2:偵測及鑑別腸病毒71型(EV71)與克沙奇病毒 A16 型(Cox A16) 2.1. PCR增幅試驗 RNA抽取及反轉錄步驟在實例1中所述之相同條件下 進行。在此試驗中所使用的PCR引子爲包含序列f7(SEQID NO:5)/r4(SEQ ID N0:8)之引子對。 PCR反應混合物及溫度周期條件如實例1中所述加以 調整。 2.2. 雜交反應試驗 用於偵測EV71之探針爲含有序列SEQ ID NO:12(71-2) 及SEQ ID NO:13(71-3)之探針。用於偵測Cox A16之探針 爲含有序列 SEQ ID NO: 14(16-1)及 SEQ ID NO: 15(16-2)之探 針。雜交反應試驗如實例1中所述條件進行。 經濟部智慧財產局員工消費合作社印製 結果顯示使用引子對f7/r4及探針71-2與71-3之本發 明方法能專一性偵測及鑑別EV71及非-EV71腸病毒。結果 顯示使用引子對f7/r4及探針16-1與16-2之本發明方法能 專一性偵測及鑑別Cox A16及非-Cox A16腸病毒。 實例3:偵測及鑑別EV71,Cox A16,非-EV71腸病毒 及非-Cox A16腸病毒之套組 25 氏張尺度適用中國國家標準(CNS)A4規格(210 X 297公羞) ~ ' 1261618 A7 ____ B7____ 五、發明說明(/ ) 使用本發明之套組同時對EV71及CoxA16進行偵測。 該套組提供材料及步驟程序使得實施者能夠進行多樣化 PCR試驗。病毒RNA抽取及反轉錄步驟在實例1中所述之 相同條件下進行。多樣化PCR於25 1反應混合物(每單位 含有 12 1 之 cDNA,50mM THs-HCl(pH 8.3),70mM KC卜 2.5mMMgCl2,各爲 200 M 之 dATP,dCTP,dGTP 及 dTTP, 10 pmol 之引子 f5/rl,20 pmol 之引子 f7/r4 及 3U 之 Taq DNA 聚合酶)中進行。每個增幅反應進行4〇溫度周期(於94°C變 性4分鐘,於55°C進行引子對黏合1分鐘,及於72°C延長1 分鐘)。經該多樣化PCR增幅後,所得之PCR產物與固著探 針之膜(pi,p2及p3針對腸病毒,71-2及71-3專一針對 EV71,且16-1及16_2專一針對Cox A16)共同培育。雜交 反應試驗的所有條件均與實例1中所述者相同。結果顯示該 套組(提供包括多樣化PCR及多樣化雜交反應偵測之系統) 可偵測及鑑別EV71,Cox A16,非-EV71腸病毒及非_c〇x A16腸病毒。使用本發明不同探針之雜交反應試驗數據示於 表3。 3 表 經濟部智慧財產局員工消費合作社印製 腸病毒之 血淸型 受試樣 本之數 顯示可偵測之雜交反應訊號之受試 _K之數目 本i 缓明探針 pi p2 p3 71-2 71-3 16-1 16-2 CA16 6 6 6 6 0 0 6 6 CA21 1 1 1 1 0 0 0 0 CA 24 1 1 1 1 0 0 0 0 CB 1 1 1 1 1 0 0 0 0 CB2 2 2 2 2 0 0 0 0 26 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公着) 1261618 A7 B7 五、發明說明( CB3 0 CB4 0 0 0 0 CB5 0 0 0 0 CB6 01261618 A7 B7 V. INSTRUCTION DESCRIPTION (#) The type and the Croxvirus A16 have signals at the hybrid control point and the enterovirus common probe position. 3: For the control group containing no nucleic acid, only the hybridization control probe has a signal. Example 2: Detection and identification of Enterovirus 71 (EV71) and Croxvirus A16 (Cox A16) 2.1. PCR amplification assay The RNA extraction and reverse transcription steps were carried out under the same conditions as described in Example 1. The PCR primer used in this assay is a primer pair comprising the sequence f7 (SEQ ID NO: 5) / r4 (SEQ ID NO: 8). The PCR reaction mixture and temperature cycle conditions were adjusted as described in Example 1. 2.2. Hybridization reaction assay The probe for detecting EV71 is a probe containing the sequences of SEQ ID NO: 12 (71-2) and SEQ ID NO: 13 (71-3). The probe for detecting Cox A16 is a probe containing the sequences SEQ ID NO: 14 (16-1) and SEQ ID NO: 15 (16-2). The hybridization reaction assay was carried out as described in Example 1. Printed by the Intellectual Property Office of the Ministry of Economic Affairs, the Consumers' Cooperatives show that the method of using the primers for f7/r4 and probes 71-2 and 71-3 can specifically detect and identify EV71 and non-EV71 enteroviruses. The results show that the method of the present invention using primer pair f7/r4 and probes 16-1 and 16-2 can specifically detect and identify Cox A16 and non-Cox A16 enterovirus. Example 3: Detection and identification of EV71, Cox A16, non-EV71 enterovirus and non-Cox A16 enterovirus sets 25-point scale applicable to China National Standard (CNS) A4 specification (210 X 297 shy) ~ ' 1261618 A7 ____ B7____ V. INSTRUCTIONS (/) The EV71 and CoxA16 are simultaneously detected using the kit of the present invention. The kit provides materials and procedures to enable the practitioner to perform a variety of PCR tests. The viral RNA extraction and reverse transcription steps were carried out under the same conditions as described in Example 1. Diversified PCR in 25 1 reaction mixture (12 1 cDNA per unit, 50 mM THs-HCl (pH 8.3), 70 mM KC b 2.5 mMMgCl2, each 200 M DATP, dCTP, dGTP and dTTP, 10 pmol primer f5 /rl, 20 pmol of primer f7/r4 and 3U of Taq DNA polymerase). Each amplification reaction was carried out for 4 Torr (4 minutes at 94 °C, 1 minute at 55 °C, and 1 minute at 72 °C). After the amplification of the diversified PCR, the obtained PCR product and the membrane of the immobilized probe (pi, p2 and p3 are directed against enterovirus, 71-2 and 71-3 are specific to EV71, and 16-1 and 16_2 are specific to Cox A16). ) Co-cultivation. All conditions of the hybridization reaction test were the same as those described in Example 1. The results show that the kit (providing a system including diversified PCR and diverse hybridization detection) can detect and identify EV71, Cox A16, non-EV71 enterovirus and non-c〇x A16 enterovirus. The hybridization reaction test data using the different probes of the present invention are shown in Table 3. 3 The Ministry of Economic Affairs, Intellectual Property Office, Staff and Consumer Cooperatives, the blood-type type of enterovirus-printed samples, the number of samples showing the detectable hybridization reaction signal, the number of _K, the i-promoting probe pi p2 p3 71- 2 71-3 16-1 16-2 CA16 6 6 6 6 0 0 6 6 CA21 1 1 1 1 0 0 0 0 CA 24 1 1 1 1 0 0 0 0 CB 1 1 1 1 1 0 0 0 0 CB2 2 2 2 2 0 0 0 0 26 This paper scale applies to China National Standard (CNS) A4 specification (210 X 297 public) 1261618 A7 B7 V. Invention description ( CB3 0 CB4 0 0 0 0 CB5 0 0 0 0 CB6 0
Echo 3 0 0Echo 3 0 0
Echo 5 0Echo 5 0
Echo 6 0 0 0Echo 6 0 0 0
Echo 9 2 2 2 2Echo 9 2 2 2 2
Echo 11Echo 11
Echo 14 0Echo 14 0
Echo 21 0Echo 21 0
Echo 24Echo 24
Echo 30 2 2 2 2Echo 30 2 2 2 2
Echo 31 2 2 2 2 EV71 7 7 7Echo 31 2 2 2 2 EV71 7 7 7
Polio 1 2 2 2 2Polio 1 2 2 2 2
Polio 2 2 2 2 2Polio 2 2 2 2 2
Polio 3 2 2 2 2 經濟部智慧財產局員工消費合作社印製 腸病毒71型,克沙奇病毒A16型及ECHO病毒第3型 之核酸分別經多樣化聚合酶鏈反應(multiplex PCR)增幅 後,與腸病毒共通型探針(pi,p2,p3)及腸病毒71型, 克沙奇病毒A16型專一性探針(71-2,71-3,16-1及16-2) 雜交之結果示於圖4。聚合酶鏈反應使用之引子配對爲f5/rl 及f7/r4,固定在尼龍膜探針之分部位置如下:此爲6x6點 分部的探針點陣,以十字將此6x6點陣等分爲4個3x3的等 分,其中左上方區塊屬腸病毒共通型探針區塊,每一排各爲 3個探針之3重複,右上區塊爲腸病毒71型區,由兩個專 一性探針交錯排列,左下區塊爲克沙奇病毒A16型區,由 兩個專一性探針交錯排列。1:共通型與腸病毒Η型探針位 置均有訊5虎,2:共通型與克沙奇病毒A16型探針位置均有言只 27 、紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐)Polio 3 2 2 2 2 Ministry of Economic Affairs, Intellectual Property Office, Staff Consumer Cooperative, Printing Enterovirus 71, Crohn's virus A16 and ECHO virus type 3 nucleic acids were amplified by multiplex PCR, respectively. Hybridization results with enterovirus common probes (pi, p2, p3) and enterovirus 71, and oxacinvirus A16 specific probes (71-2, 71-3, 16-1 and 16-2) Shown in Figure 4. The primers used in the polymerase chain reaction were paired with f5/rl and f7/r4, and the positions of the nylon membrane probes were fixed as follows: This is a 6x6 point probe array, which is equally divided by a 6x6 dot matrix. There are 4 3x3 aliquots, wherein the upper left block belongs to the enterovirus common probe block, each row has 3 replicates of 3 probes, and the upper right block is EV71 type region, which consists of two specific ones. The sexual probes are staggered, and the lower left block is a Crohn's virus A16 type region, which is staggered by two specific probes. 1: Common and enterovirus sputum probe positions are all 5 tigers, 2: common type and saxag virus A16 type probe position is only 27, the paper scale is applicable to China National Standard (CNS) A4 specification ( 210 X 297 mm)
1261618 A7 ___B7__ 五、發明說明(A ) 號;3:只有共通型區域探針有訊號。 根據本發明可作之不同修正及變化對於熟習該項技術 者而言均顯然不會偏離本發明的範圍與精神。雖然本發明已 敘述特定的偏好具體事實,必須瞭解的是本發明不應被不當 地限制於該等特定具體事實上。事實上,在實施本發明之已 述模式方面,對於熟習該項技術者而言顯而易知之不同修正 亦被涵蓋於下列申請專利範圍之內。 經濟部智慧財產局員工消費合作社印製 28 本紙張尺度適用中國國家標準(CNS)A4規格(210 X 297公釐)1261618 A7 ___B7__ V. Invention Description (A); 3: Only common area probes have signals. It is apparent to those skilled in the art that various modifications and variations can be made without departing from the scope and spirit of the invention. Although the present invention has been described with respect to specific specific facts, it must be understood that the present invention should not be unduly limited to the specific details. In fact, the various modifications that are apparent to those skilled in the art are also within the scope of the following claims. Printed by the Intellectual Property Office of the Ministry of Economic Affairs, the Consumers' Cooperatives. 28 This paper scale applies the Chinese National Standard (CNS) A4 specification (210 X 297 mm).
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