曲 夢(mèng) 江艷華 李風(fēng)鈴 姚 琳 逄鳳嬌 王聯(lián)珠 翟毓秀
裝甲R(shí)NA在牡蠣中諾如病毒4種RNA提取方法比較研究中的應(yīng)用*
曲 夢(mèng) 江艷華 李風(fēng)鈴 姚 琳①逄鳳嬌 王聯(lián)珠 翟毓秀
(中國(guó)水產(chǎn)科學(xué)研究院黃海水產(chǎn)研究所 農(nóng)業(yè)農(nóng)村部水產(chǎn)品質(zhì)量安全檢測(cè)與評(píng)價(jià)重點(diǎn)實(shí)驗(yàn)室 青島 266071)
RNA提取是諾如病毒檢測(cè)的關(guān)鍵步驟,而目前貝類中諾如病毒RNA提取、檢測(cè)方法的比較與評(píng)價(jià)常囿于缺乏量值明確、無(wú)生物安全隱患的標(biāo)準(zhǔn)樣品作為參考依據(jù)。本研究將前期制備的 GⅡ型諾如病毒裝甲R(shí)NA (3.0×1010拷貝)作為標(biāo)準(zhǔn)樣品,人工污染牡蠣()消化腺勻漿物,用4種常見RNA提取方法:TRIzol試劑、Viral RNA Kit、High Pure Viral Nucleic Acid Kit、柱式病毒RNAOUT試劑盒,分別提取RNA,經(jīng)實(shí)時(shí)熒光RT-PCR檢測(cè)后,利用標(biāo)準(zhǔn)曲線進(jìn)行定量分析,分別計(jì)算4種方法對(duì)裝甲R(shí)NA的回收率。結(jié)果顯示,對(duì)于勻漿樣本,TRIzol法對(duì)裝甲R(shí)NA的回收率最高(6.80±0.89)%,顯著高于Viral RNA Kit (4.51±2.28)%,二者的回收率又顯著高于High Pure Viral Nucleic Acid Kit (0.24±0.05)%與柱式病毒RNAOUT試劑盒(0.11±0.02)% (?0.05);對(duì)于凍干樣本,Viral RNA Kit對(duì)裝甲R(shí)NA的回收率最高(8.71±0.17)%,顯著高于TRIzol試劑(7.12±0.64)%,二者的回收率又顯著高于High Pure Viral Nucleic Acid Kit (0.33±0.12)%與柱式病毒RNAOUT試劑盒(0.06±0.01)% (?0.05)。研究表明,TRIzol試劑與Viral RNA Kit對(duì)牡蠣消化腺樣本中人工添加的裝甲R(shí)NA均有良好的回收效果,同時(shí)也提示裝甲R(shí)NA可作為一種良好的標(biāo)準(zhǔn)樣品用于不同RNA提取試劑盒方法的評(píng)價(jià)與比較研究。
諾如病毒;裝甲R(shí)NA;牡蠣;RNA提取方法;比較
人類各年齡段的非菌性胃腸炎中約有95%是由諾如病毒(Norovirus, NoVs)引起的(Ma, 2014)。我國(guó)是全球15個(gè)腹瀉病高負(fù)擔(dān)國(guó)家之一,NoVs在我國(guó)腹瀉病例中的檢出率在11.6%~59.52%之間(閻巖等, 2013; 余建興等, 2015; 陳莉莉等, 2018),食物污染是NoVs傳播的最主要途徑,NoVs成為影響我國(guó)食品安全與公共衛(wèi)生的重要病原。研究表明,多數(shù)NoVs疫情的暴發(fā)都與生食受污染牡蠣等貝類有關(guān)(Westrell, 2010)。牡蠣屬于雙殼濾食性生物,其內(nèi)臟中存在NoVs受體及其合成酶(Le, 2006; 姜薇等, 2014; 姚琳等, 2016),牡蠣濾食海水中有機(jī)碎屑、微藻(任黎華等, 2013),極易將水體中污染的NoVs特異性富集于體內(nèi),因此被認(rèn)為是引起NoVs食源性感染的高風(fēng)險(xiǎn)食品之一(Persson, 2018)。
實(shí)時(shí)熒光RT-PCR目前是NoVs檢測(cè)的主要方法,而RNA提取是NoVs檢測(cè)的基礎(chǔ),RNA的純度、濃度及RT-PCR抑制物的多少對(duì)檢測(cè)結(jié)果影響很大,如何提取高質(zhì)量的RNA是檢測(cè)的關(guān)鍵(Tan, 2009)。不同方法在RNA提取效率及對(duì)抑制物的去除效果方面有所差別,并最終影響檢測(cè)結(jié)果(江濤等, 2017)。選擇合適的提取方法,可從源頭上最大程度避免NoVs檢測(cè)結(jié)果的假陰性,確保檢測(cè)結(jié)果的科學(xué)性和可靠性。由于NoVs無(wú)法按照傳統(tǒng)方法進(jìn)行體外培養(yǎng),因此在比較或評(píng)價(jià)不同提取方法時(shí),多數(shù)研究者用陽(yáng)性NoVs腹瀉樣本或替代病毒—鼠諾如病毒添加到空白樣本中(Uhrbrand, 2017; Kanwar, 2018)模擬實(shí)際樣本,前者病毒含量不一且存在嚴(yán)重生物安全隱患,后者要經(jīng)過繁瑣的細(xì)胞培養(yǎng)與病毒含量測(cè)定。針對(duì)上述問題,近年來有研究開發(fā)出裝甲R(shí)NA技術(shù),即將檢測(cè)靶標(biāo)RNA包裝在噬菌體病毒樣顆粒內(nèi),一方面利用噬菌體衣殼蛋白保護(hù)易降解的RNA,另一方面病毒樣顆粒高度模擬了病毒粒子結(jié)構(gòu),在提取、裂解等環(huán)節(jié)展示出與天然病毒的相似性(Pan, 2012),成為目前廣泛應(yīng)用的RNA病毒檢測(cè)質(zhì)控品。
本課題組前期建立了基于Qβ噬菌體的裝甲R(shí)NA制備平臺(tái)(張奇等, 2017),制備了多批內(nèi)含NoVs檢測(cè)靶標(biāo)的裝甲R(shí)NA。本研究將上述裝甲R(shí)NA作為量值明確的標(biāo)準(zhǔn)樣品添加到牡蠣內(nèi)臟勻漿物中,以此模擬污染樣本來比較TRIzol試劑等4種主要RNA提取方法對(duì)內(nèi)臟勻漿物中裝甲R(shí)NA的回收率,旨在篩選一種適合牡蠣中NoVs RNA提取的方法,同時(shí)探討裝甲R(shí)NA作為量值明確的標(biāo)準(zhǔn)樣品用于方法比較研究的可行性。
RNA提取試劑TRIzol?購(gòu)自Life公司;RNA 提取試劑盒Viral RNA Kit 購(gòu)自O(shè)MEGA公司,High Pure Viral Nucleic Acid Kit購(gòu)自Roche公司,柱式病毒RNAOUT購(gòu)自北京TIANDZ基因科技有限公司;One Step PrimeScriptTMRT-PCR Kit購(gòu)自寶生物工程(大連)有限公司;無(wú)水乙醇、異丙醇、氯仿等試劑均為分析純。GⅡ型諾如病毒裝甲R(shí)NA由本實(shí)驗(yàn)室制備、定量(3.0×108拷貝/μl)。參照GB 4789.42-2016《食品安全國(guó)家標(biāo)準(zhǔn)食品微生物學(xué)檢驗(yàn)諾如病毒檢驗(yàn)》,由生工生物工程(上海)股份有限公司合成檢測(cè)GⅡ型NoVs所需的引物、探針,名稱及序列見表1。實(shí)時(shí)熒光定量PCR儀為美國(guó)Roche公司LightCycler 2.0。
表1 引物、探針信息
Tab.1 Information of primers and probe
注:R=A/G;W=A/T;FAM=羧基熒光素;TAMARA=羧基四甲基羅丹明
Note: R=A/G; W=A/T; FAM=Carboxyfluorescein; TAMARA= Carboxytetramethylrhodamine
將實(shí)驗(yàn)室收集的、經(jīng)實(shí)時(shí)熒光RT-PCR檢測(cè)GⅡ型諾如病毒呈陰性的牡蠣消化腺樣品混合并勻漿,分裝至48支15 ml無(wú)酶離心管中,每管2.0 g,分別添加3.0×1010拷貝的裝甲R(shí)NA,充分混勻,室溫放置1 h,制成牡蠣消化腺人工污染勻漿樣品;從中隨機(jī)取24管樣品逐一稱重后真空冷凍干燥,制成消化腺人工污染凍干樣品,凍干后再次逐一稱重,檢測(cè)前根據(jù)每管失水的量加入相應(yīng)重量的RNase-free H2O復(fù)水,渦旋混勻。
按照說明書分別用TRIzol試劑、High Pure Viral Nucleic Acid Kit、柱式病毒RNAOUT、Viral RNA Kit提取1.2中制備的人工污染樣品。每種樣品提取5次。
用TaKaRa One Step PrimescriptTMRT-PCR kit 對(duì)提取的RNA進(jìn)行實(shí)時(shí)熒光RT-PCR檢測(cè),反應(yīng)體系和循環(huán)參數(shù)如下:2×one step RT-PCR Buffer Ⅲ 10 μl,TaKaRa ExHS(5 U/μl) 0.4 μl,PrimeScript RT EnzymeMix Ⅱ 0.4 μl, QNIF2(10 μmol/L)、COG2R(10 μmol/L)各0.3 μl, QNIFs(10 μmol/L)0.4 μl,RNA 2.0 μl,RNase- free H2O 6.2 μl;以RNase-free H2O為模板設(shè)置空白對(duì)照,以諾如病毒檢測(cè)陰性且未添加裝甲R(shí)NA的牡蠣內(nèi)臟作為陰性對(duì)照。循環(huán)參數(shù)為42℃5 min,95℃ 10 sec;95℃ 5 sec,60℃ 20 sec,40個(gè)循環(huán)。每份樣品的RNA平行測(cè)3次,記錄t值。
利用本實(shí)驗(yàn)室前期建立的GⅡ型諾如病毒裝甲R(shí)NA定量用標(biāo)準(zhǔn)曲線=-3.562+37.938 (張奇等, 2017),計(jì)算各樣品中裝甲R(shí)NA的拷貝數(shù)。根據(jù)不同的提取方法與樣本類型,分別計(jì)算裝甲R(shí)NA的回收率。計(jì)算公式:裝甲R(shí)NA回收率=提取出的裝甲R(shí)NA拷貝數(shù)/添加到樣品中的裝甲R(shí)NA拷貝數(shù)×100%。
將勻漿樣品與凍干樣品經(jīng)4種不同提取方法提取RNA檢測(cè)得到的t值和裝甲R(shí)NA回收率采用SPSS 20.0進(jìn)行單因素方差分析(One-way ANOVA),<0.05為差異顯著。t值和回收率的分布用GraphPad Prism 6.0分析與繪圖。
在牡蠣內(nèi)臟勻漿物中添加3.0×1010拷貝GⅡ型諾如病毒裝甲R(shí)NA,經(jīng)4種方法提取后的RNA進(jìn)行實(shí)時(shí)熒光RT-PCR檢測(cè),所得t值統(tǒng)計(jì)后見表2,t值分布經(jīng)GraphPad Prism 6.0處理,見圖1。對(duì)于勻漿樣品,TRIzol法所提取的RNA得到的t值最小,其次是Viral RNA Kit,二者差異性顯著(?0.05),High Pure Viral Nucleic Acid Kit與柱式病毒RNAOUT試劑盒的t值較大,二者之間差異不顯著,但與TRIzol法與Viral RNA Kit相比,差異顯著(?0.05)。對(duì)于凍干樣品,TRIzol法與Viral RNA Kit的t值均很小,二者差異性不顯著(?0.05),High Pure Viral Nucleic Acid Kit與柱式病毒RNAOUT試劑盒的t值仍較大,二者之間差異不顯著,但與TRIzol法與Viral RNA Kit相比,差異顯著(?0.05)。
表2 實(shí)時(shí)熒光RT-PCR分析4種提取方法所得RNA的t值(X±SD)
Tab.2 Ct values of RNA obtained from 4 extraction methods analyzed with realtime RT-PCR (X±SD)
注:同列數(shù)據(jù)中相同上標(biāo)字母表示差異不顯著(> 0.05),下同
Note: Values in the same column with same superscrips are not significantly different (>0.05), the same as below
圖1 4種RNA提取方法對(duì)應(yīng)Ct值的分布
將4種RNA提取方法所得t值代入標(biāo)準(zhǔn)曲線計(jì)算出2.0 μl RNA所含的裝甲R(shí)NA拷貝數(shù),再根據(jù)不同試劑盒的提取流程,最終計(jì)算出4種提取方法對(duì)添加的裝甲R(shí)NA的回收率,結(jié)果見表3。所得裝甲R(shí)NA的回收率經(jīng)GraphPad Prism 6.0分析后,結(jié)果見圖2。對(duì)于勻漿樣品,TRIzol法的回收率最高,其次是Viral RNA Kit,二者差異性顯著(?0.05),但均能達(dá)到GB 4789.42-2016中關(guān)于回收率應(yīng)大于1%的要求,High Pure Viral Nucleic Acid Kit與柱式病毒RNAOUT試劑盒的回收率均很低,二者之間差異不顯著,但與TRIzol法與Viral RNA Kit相比,差異顯著(?0.05)。對(duì)于凍干樣品,Viral RNA Kit的回收率最高,其次是TRIzol法均超過2%,二者差異性不顯著(?0.05),High Pure Viral Nucleic Acid Kit與柱式病毒RNAOUT試劑盒的回收率很低,二者之間差異不顯著,但與Viral RNA Kit與TRIzol法相比,差異顯著(?0.05)。
表3 4種RNA提取方法對(duì)裝甲R(shí)NA的回收率(X±SD,=5, %)
Tab.3 Recovery of 4 RNA extraction methods for armored RNA (X±SD, n=5, %)
圖2 4種RNA提取方法對(duì)裝甲R(shí)NA的回收率
NoVs是世界范圍內(nèi)的一種重要食源性病毒,是引起人類急性胃腸炎的主要病原。牡蠣因其自身生物學(xué)特性成為NoVs傳播的重要載體之一,實(shí)時(shí)熒光RT- PCR目前是檢測(cè)NoVs的“金標(biāo)準(zhǔn)”,然而受污染牡蠣自身存在大量RT-PCR抑制物、NoVs含量低、基因分型多等因素影響,其檢測(cè)難度高于常見RNA病毒,提高檢測(cè)方法的靈敏度和病毒回收率是各國(guó)學(xué)者一直關(guān)注的問題(Francoise, 2009)。部分提取方法對(duì)目標(biāo)RNA的提取效率低、對(duì)樣本中存在的RT-PCR抑制物去除效果不好、擴(kuò)增前RNA出現(xiàn)降解等問題往往造成檢測(cè)結(jié)果的假陰性(Das, 2011)。因此,比較病毒RNA提取方法成為優(yōu)化、篩選NoVs檢測(cè)方法的重點(diǎn)之一。雖然NoVs目前已可以基于干細(xì)胞轉(zhuǎn)化出的腸上皮細(xì)胞進(jìn)行人工培養(yǎng)(Ettayebi, 2016),但對(duì)實(shí)驗(yàn)條件與經(jīng)驗(yàn)有嚴(yán)格的要求,短期內(nèi)很難在大多從事應(yīng)用性基礎(chǔ)研究的實(shí)驗(yàn)室開展,因此在提取方法比較研究中,多數(shù)學(xué)者仍使用含病毒的臨床腹瀉樣本和鼠諾如病毒等作為質(zhì)控品添加到陰性樣品中,但存在難以獲得、量值不均一、生物安全隱患等不足。
本實(shí)驗(yàn)室前期基于Qβ噬菌體制備平臺(tái),成功制備了內(nèi)含GⅡ型NoVs檢測(cè)靶標(biāo)的裝甲R(shí)NA,證實(shí)其均勻性和穩(wěn)定性良好,拷貝數(shù)高,可實(shí)現(xiàn)對(duì)NoVs核酸檢測(cè)中的RNA提取、反轉(zhuǎn)錄、擴(kuò)增等過程的定性、定量質(zhì)量控制和評(píng)估(Villanova, 2007; 張奇, 2017)。由于牡蠣中的NoVs主要集中在消化腺,因此,本研究將牡蠣消化腺勻漿物與NoVs裝甲R(shí)NA混勻后室溫孵育,該人工污染的方法與用活牡蠣自然富集諾如病毒相比,簡(jiǎn)單有效,并且具有量值明確便于定量評(píng)估、可批量制備重復(fù)實(shí)驗(yàn)等多種優(yōu)點(diǎn)。將人工污染后的樣品分別以TRIzol法、High Pure Viral Nucleic Acid Kit、柱式病毒RNAOUT、Viral RNA Kit 4種提取方法提取病毒RNA,依據(jù)本實(shí)驗(yàn)室建立的GⅡ型諾如病毒標(biāo)準(zhǔn)曲線分析了不同提取方法對(duì)不同狀態(tài)樣品中裝甲R(shí)NA的回收率,研究結(jié)果表明,無(wú)論是勻漿樣品還是凍干樣品,本研究涉及的4種RNA提取方法的回收效率相差較大。
有研究分別用磁珠法和TRIzol法提取血清樣品中丙型肝炎病毒RNA,發(fā)現(xiàn)磁珠法提取的RNA更適合于血清樣品中丙型肝炎病毒的檢測(cè)(范公忍等, 2015)。Zhang等(2015)比較了TRIzol、異硫氰酸胍和二氧化硅納米顆粒對(duì)丙型肝炎病毒RNA的提取效率,發(fā)現(xiàn)二氧化硅納米顆粒的提取效率最高。上述研究結(jié)果中,TRIzol法并沒有顯示出明顯的優(yōu)勢(shì),可能是這些研究中的血清樣品與本研究中的消化腺樣品基質(zhì)的差異,導(dǎo)致了本研究與上述研究結(jié)果的不同。
以二氧化硅或其衍生材料為基礎(chǔ)的固相吸附技術(shù)是目前大多柱式提取試劑盒的核心技術(shù),可以特異性地吸附RNA,樣本中的蛋白質(zhì)、脂質(zhì)等其他組分可通過高鹽緩沖液去除,然后用低鹽緩沖液從二氧化硅材料中洗脫RNA,能較為有效地去除抑制物(Zhang, 2015; Xu, 2017),但在提取RNA的總量上與傳統(tǒng)的TRIzol法、異硫氰酸胍方法相比,相差較大。不同試劑盒離心柱的二氧化硅材料及尺寸(小體積或大體積)等因素的差異或許是導(dǎo)致試劑盒提取效率不同的原因之一。此外,High Pure Viral Nucleic Acid Kit與柱式病毒RNAOUT試劑盒可以破壞較為分散的細(xì)胞并高效地暴露RNA,可能更適合血液、血漿、細(xì)胞培養(yǎng)物等樣品;另外,High Pure Viral Nucleic Acid Kit使用過程中需要添加Poly(A),可特異性結(jié)合病毒基因組RNA,以增強(qiáng)后期純化柱對(duì)病毒基因組的吸附作用,然而牡蠣樣品鹽分高,多糖等抑制物較多,很可能弱化了這一步驟的實(shí)際效果,從而最終導(dǎo)致該試劑盒對(duì)牡蠣消化腺樣本中添加的裝甲R(shí)NA回收率較低。與這2種試劑盒相比,Viral RNA Kit的裂解液等避免使用抑制RT-PCR的試劑,在操作上要求不高,處理步驟少,減少過度操作,RNA降解程度低,RT-PCR抑制物殘留量少,該試劑盒較適用于牡蠣組織樣品。
此外,考慮到保存期等因素,目前生物基質(zhì)標(biāo)準(zhǔn)樣品大多數(shù)為凍干樣品,為了探討樣品冷凍干燥后,是否會(huì)影響RNA的提取,本研究還分析了4種方法對(duì)凍干樣品的提取效果,TRIzol法與Viral RNA Kit的回收率與勻漿樣品相比無(wú)明顯差異,一方面表明這2種方法對(duì)樣本狀態(tài)適用性的多樣化,另一方面,與新鮮樣品相比,凍干樣品脫水徹底,可在常溫條件下長(zhǎng)時(shí)間保存,已有研究表明,凍干可延長(zhǎng)單純裝甲R(shí)NA穩(wěn)定性(Stevenson, 2008),本研究進(jìn)一步表明,在牡蠣內(nèi)臟這樣高鹽、富含多糖的復(fù)雜基質(zhì)樣本中,凍干對(duì)裝甲R(shí)NA的回收、檢測(cè)等沒有影響,從而為今后研制諾如病毒裝甲R(shí)NA牡蠣內(nèi)臟基質(zhì)凍干標(biāo)準(zhǔn)樣品提供了研究基礎(chǔ)。
Chen LL, Chen J, Liao NB. Epidemiological characteristics of Norovirus infectious diarrhea in Zhejiang Province from 2014 to 2016. Chinese Journal of Health Laboratory Technology. 2018, 28(7): 863–866 [陳莉莉, 陳江, 廖寧波. 2014年-2016年浙江省諾如病毒感染性腹瀉流行病學(xué)特征分析. 中國(guó)衛(wèi)生檢驗(yàn)雜志, 2018, 28(7): 863–866]
Das A, Beckham TR, McIntosh MT. Comparison of methods for improved RNA extraction from blood for early detection of Classical swine fever virus by real-time reverse transcription polymerase chain reaction. Journal of Veterinary Diagnostic Investigation, 2011, 23(4): 727–735
Ettayebi K, Crawford SE, Murakami K,. Replication of human noroviruses in stem cell-derived human enteroids. Science, 2016, 353(6306): 1387–1393
Francoise SG, Parnaudeau S, Schaeffer J,. Detection and quantitation of noroviruses in shellfish. Applied and Environmental Microbiology, 2009, 75(3): 618–624
Fan GR, Chen TB, Li B,. Comparison of effects between two kinds of nucleic acid extraction method for detecting HCV RNA and their application. Laboratory Medicine and Clinic, 2015, 12(1): 48–50 [范公忍, 陳天寶,李冰, 等. 兩種核酸提取方法對(duì)丙型肝炎病毒RNA檢測(cè)效果的比較及應(yīng)用評(píng)價(jià). 檢驗(yàn)醫(yī)學(xué)與臨床, 2015, 12(1): 48–50]
Jiang W, Yao L, Jiang YH,. Molecular cloning and expressionof FUT2-like gene in the Oyster (). Progress in Fishery Sciences, 2014, 35(5): 70–75 [姜薇, 姚琳, 江艷華, 等. 太平洋牡蠣()類FUT2基因的克隆與組織表達(dá). 漁業(yè)科學(xué)進(jìn)展, 2014, 35(5): 70–75]
Jiang T, Han CH, Zhang HY,The detection of Noroviruses in oysters sold in Beijing by using Taqman-based one-step reverse transcription-polymerase chain reaction assays and quantitative analysis. Chinese Journal of Food Hygiene, 2017, 29(2): 126–130 [江濤, 韓春卉, 張宏元, 等. 北京市市售牡蠣中諾如病毒核酸檢測(cè)及定量分析. 中國(guó)食品衛(wèi)生雜志, 2017, 29(2): 126–130]
Ma Y, Duan Y, Wei Y,. Heat shock protein 70 enhances mucosal immunity against human norovirus when coexpressed from a vesicular stomatitis virus vector. Journal of Virology, 2014, 88(9): 5122–5137
Kanwar N, Hassan F, Barclay L,. Evaluation of RIDA?; GENE norovirus GI/GII real time RT-PCR using stool specimens collected from children and adults with acute gastroenteritis. Journal of Clinical Virology, 2018, 104:1–4
Le Guyader F, Loisy F, Atmar RL,. Norwalk virus-specific binding to oyster digestive tissues. Emerging Infectious Diseases, 2006, 12(6): 931–936
Pan Y, Zhang Y, Jia T,. Development of a microRNA delivery system based on bacteriophage MS2 virus-like particles. FEBS Journal, 2012, 279(7): 1198–1208
Persson S, Eriksson R, Lowther J,. Comparison between RT droplet digital PCR and RT real-time PCR for quantification of noroviruses in oysters. International Journal of Food Microbiology, 2018, 284: 73–83
Ren LH, Zhang JH, Fang JG,. A study on the daily rhythm of respiration, excretion and calcification in oysters. Progress in Fishery Sciences, 2013, 34 (1): 75–81 [任黎華, 張繼紅, 方建光, 等. 長(zhǎng)牡蠣呼吸、排泄及鈣化的日節(jié)律研究. 漁業(yè)科學(xué)進(jìn)展, 2013, 34(1): 75–81]
Stevenson J, Hymas W, Hillyard D. The use of Armored RNA as a multi-purpose internal control for RT-PCR. Journal of Virological Methods, 2008, 150(1–2): 73–76
Tan SC, Chin YB. DNA, RNA, and protein extraction: The past and the present. Journal of Biomedicine and Biotechnology, 2009, 2009(3): 1–10
Uhrbrand K, Koponen IK, Schultz AC,. Evaluation of air samplers and filter materials for collection and recovery of airborne norovirus. Journal of Applied Microbiology, 2017, 124(4): 990–1000
Villanova GV, Gardiol D, Taborda MA,. Strategic approach to produce low-cost, efficient, and stable competitive internal controls for detection of RNA viruses by use of reverse transcription-PCR. Journal of Clinical Microbiology, 2007, 45(11): 3555
Westrell T, Dusch V, Ethelberg S,. Norovirus out breaks linked to oyster consumption in the United Kingdom, Norway, France, Sweden and Denmark, 2010. Euro Surveillance, 2010, 15(12): 1–4
Xu R, Shieh YC, Stewart DS. Comparison of RNA extraction kits for the purification and detection of an enteric virus surrogate on green onions via RT-PCR methods,?Journal of Virological 2017, 239: 61–68
Yan Y, Wu Y, Guo J,. Sentinel surveillance and gene analysis of acute gastroenteritis norovirus in Guizhou province in 2011. Chinese Journal of Virology, 2013 (1): 51–55 [閻巖, 吳悅, 郭軍,等. 貴州省2011年急性胃腸炎諾如病毒的哨點(diǎn)監(jiān)測(cè)及其基因特征分析. 病毒學(xué)報(bào), 2013(1): 51–55]
Yao L, Jiang YH, Li FL,. Codon Optimization and prokaryotic expression of α-1 and 2-fucosyltransferase in Oyster (). Progress in Fishery Sciences, 2016, 37(1): 74–79 [姚琳, 江艷華, 李風(fēng)鈴,等. 太平洋牡蠣()類α-1,2-巖藻糖基轉(zhuǎn)移酶的密碼子優(yōu)化與原核表達(dá). 漁業(yè)科學(xué)進(jìn)展, 2016, 37(1): 74–79]
Yu JX, Lai SJ, Wang X,. Analysis of epidemic characteristics of Norovirus from 2009 to 2013 in 27 provinces (municipalities and autonomous regions) of China. Chinese Journal of Epidemiology, 2015, 36(3): 199–204 [余建興, 賴圣杰, 王鑫, 等. 中國(guó)27省(市、自治區(qū)) 2009–2013年門診腹瀉病例諾如病毒流行特征分析. 中華流行病學(xué)雜志, 2015, 36(3): 199–204]
Zhang Q, Yao L, Jiang YH,. Development of Armored RNA reference material of Norovirus based on Qbeta bacteriophage. China Biotechnology, 2018, 38(1): 42–50 [張奇, 姚琳, 江艷華, 等. 基于Qbeta噬菌體裝甲R(shí)NA技術(shù)的諾如病毒RNA標(biāo)準(zhǔn)參考樣品的研制. 中國(guó)生物工程雜志, 2018, 38(1): 42–50]
Zhang B, Chen K, Ni E. Comparison of three methods for extraction of HCV RNA in sera collected from individuals with hyperlipidemia, hyperbilirubinemia and hyperglobulinemia. Journal of Virological Methods, 2015, 212: 44–46
Application of Armored RNA to Compare Four Norovirus RNA Extraction Methods in Oysters
QU Meng, JIANG Yanhua, LI Fengling, YAO Lin①, PANG Fengjiao, WANG Lianzhu, ZHAI Yuxiu
(Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Qingdao 266071)
Norovirus (NoVs) is the most prevalent worldwide foodborne pathogen and causes acute viral gastroenteritis. NoVs are transmitted mainly via the fecal–oral route and by person-to-person contact. It is thought that the majority of NoVs infections are caused by the consumption of contaminated food; the ingestion of contaminated oysters is the primary cause of foodborne NoVs infection since oyster digestive diverticula accumulate viral particles from seawater via filter feeding. Real time RT-PCR is commonly used to detect NoVs RNA in oysters; however, these assays are often hampered by the low viral titer in oysters and PCR inhibition due to matrix carryover during RNA extraction. Extraction is a critical step for obtaining sufficient high-quality viral RNA for amplification; however, studies comparing and evaluating NoVs RNA extraction and detection methods in shellfish are often limited by the lack of standard samples with clear quantitative values and a lack of biosafety hazards. In this study, four RNA extraction methods (TRIzol reagent, Viral RNA Kit, High Pure Viral Nucleic Acid Kit, and Column Virus RNAOUTKit) were used on oyster digestive gland homogenate samples and artificial freeze-dried samples contaminated with NoVs armored RNA (3.0′1010copies/sample) as a reference material. RNA extracted by the four methods was analyzed by real time RT-PCR and quantified using previously established standard curves. For the homogenized samples, the TRIzol method had the highest recovery rate (6.8± 0.89)% and was significantly higher than that by the Viral RNA Kit (4.51±2.28)%. The recovery rates of these two methods were both significantly higher than those by the High Pure Viral Nucleic Acid Kit (0.24±0.05)% and Column Virus RNAOUTkit [(0.11±0.02)%,?0.05]. For the freeze-dried samples, the Viral RNA Kit had the highest recovery rate (8.71±0.17)% and was significantly higher than that by the TRIzol method (7.12±0.64)%. The recovery rates of these two methods were both significantly higher than those of the High Pure Viral Nucleic Acid Kit (0.33±0.12)% and Column Virus RNAOUTkit [(0.06± 0.01)%,?0.05]. This study indicated that the TRIzol method and Viral RNA Kit could extract target RNA from oyster digestive gland homogenate samples with an ideal recovery rate; moreover, armored RNA could serve as a good reference material for comparing RNA extraction methods.
Norovirus; Armored RNA; Oyster; RNA extraction method; Comparison
Q33
A
2095-9869(2019)06-0180-06
10.19663/j.issn2095-9869.20180907002
http://www.yykxjz.cn/
曲夢(mèng), 江艷華, 李風(fēng)鈴, 姚琳, 逄鳳嬌, 王聯(lián)珠, 翟毓秀. 裝甲R(shí)NA在牡蠣中諾如病毒4種RNA提取方法比較研究中的應(yīng)用. 漁業(yè)科學(xué)進(jìn)展, 2019, 40(6): 180–185
Qu M, Jiang YH, Li FL, Yao L, Pang FJ, Wang LZ, Zhai YX. Application of armored RNA to compare four norovirus RNA extraction methods in oysters. Progress in Fishery Sciences, 2019, 40(6): 180–185
* 國(guó)家重點(diǎn)研發(fā)計(jì)劃(2017YFC1600703)、科技部科技基礎(chǔ)性工作專項(xiàng)(2013FY113300)和現(xiàn)代農(nóng)業(yè)產(chǎn)業(yè)技術(shù)體系 (CARS-47)共同資助[This work was supported by National Key Research and Development Program of China (2017YFC1600703); Special Program for Science and Technology Basic Research of the Ministry of Science and Technology China (2013FY113300); Central Public-interest Scientific Institution Basal Research Found, CAFS (2016HY-ZD11);China Aquaculture Research System (CARS-47)]. 曲 夢(mèng), E-mail: 1874213448@qq.com
姚 琳,副研究員,E-mail: yaolin@ysfri.ac.cn
2018-09-07,
2018-10-31
YAO Lin, E-mail: yaolin@ysfri.ac.cn
(編輯 江潤(rùn)林)