Evaluation of Reverse Transcription Loop-Mediated Isothermal Amplification assays for Rapid Detection of Human Enterovirus 71 and Coxsackievirus A16 in Clinical Samples

A sensitive reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for human enterovirus 71 (EV71) and Coxsackievirus A16 (CVA16) infection was further evaluated. The one step reaction was performed in a single tube at 65?C for 45 min for EV71 and 35 min for CVA16. The detection limits of RT-LAMP assays for both EV71 and CVA16 were 0.1 of a 50% tissue culture infective dose (TCID50) per reaction, based on 10—Fold dilutions of a titrated EV71 or CVA16 strain. The specific assay showed there were no cross-reactions with Coxsackievirus A (CVA) viruses (CVA 2, 4, 5, 7, 9, 10, 14, and 25), Coxsackievirus B (CVB) viruses (CVB 1, 2, 3, 4, and 5) or ECHO viruses (ECHO 3, 6, 11, and 19). In parallel with commercial quantitative real-time polymerase chain reaction (qRT-PCR) diagnostic kits for EV71 and CVA16, the RT-LAMP assay was evaluated with 515 clinical specimens, the results showed the RT-LAMP assay and the qRT-PCR assay were in complete agreement for 513/515 (99.6%) of the specimens. Two samples with discrepant results from two methods were further verified by nested reverse transcription polymerase chain reaction (nRT-PCR) assay and sequencing to be true positives for CVA16. In conclusion, RT-LAMP assay is demonstrated to be a sensitive and specific assay and have a great potential for the rapid and visual screening of EV71 and CVA16 in China, especially in those resource-limited hospitals and rural clinics of provincial and municipal regions.

Development of loop-mediated isothermal amplification for rapid detection of Entamoeba histolytica

Objective:To develop a loop-mediated isothermal amplification(LAMP) assay for the detection of Entamoeba histolytica(E.histolytica),the causative agent of amebiasis.Methods:The LAMP primer set was designed from E.histolytica hemolysin gene HLY6.Genomic DNA of E.histolytica trophozoites strain HK9 was used to optimize the LAMP mixture and conditions.Amplification of DNA in the LAMP mixture was monitored through visual inspection for turbidity of the LAMP mix as well as addition of fluorescent dye.Results:Positive LAMP reactions turned turbid while negative ones remained clear.Upon addition of a fluorescent dye,all positive reactions turned green while the negative control remained orange under ambient light After elecrophoresis in 1.5% agarose gels,a ladder of multiple bands of different sizes can be oliserved in positive samples while no bands were detected in the negative control.The sensitivity of the assay was found to be S parasites per reaction which corresponds to approximately 1S.8 ng/μL DNA.The specificity of the assay was verified by the absence of amplified products when DNA from other gastrointestinal parasites such as the morphologically similar but non-pathogenic species,Entamoeba dispar. and other diarrhea-causing organisms such as Blastocystis hominis and Escherichia coli were used.Conclusions:The I.AMP assay we have developed enables the detection of E.histolytica with rapidity and ease,therefore rendering it is suitable for laboratory and field diagnosis of amebiasis.

Detection of Staphylococcus aureus in Dairy Food by Loop-mediated Isothermal Amplification

[ Objective ] This study was to investigate the creditability of applying loop-mediated isothermal amplification method （LAMP） to detect Staphylococcus aureus in dairy products. [ Methods] The primers for heat resistant nuclease gene （nuc） of Staphylococcus aureus were designed for establishing the LAMP method for rapidly detecting Staphylococcus aureus. [ Results ] The results of LAMP detection on Staphylococcus aureus in various dairy products were completely identical with that by bacterial isolation test; meanwhile it has a high specificity and a 10-fold sensitivity over the hemi-nested PCR. [ Conclusion] LAMP can be used for the detection of Staphylococcus aureus in dairy products.

Rapid,specific and sensitive detection of Vibrio vulnificus by loop-mediated isothermal amplification targeted to vvhA gene

Vibrio vulnificus is an estuarine bacterial pathogen for human.The rapid,specific and sensitive detection of V.vulnificus is urgently needed for early disease diagnosis and timely treatment of V.vulnificus infection.In the study,a loop-mediated isothermal amplification（LAMP） technique was developed for V.vulnificus detection with a set of primers,composed of two out primers and two inner primers targeted to vvh A gene.The optimal amplification temperature was 63°C and the reaction only took 35 min.The amplification products could not only be detected by agarose gel electrophoresis with ladder-like pattern bands,but also could be visualized using calcein with naked eye directly.Forty-five strains were tested for the specificity of LAMP assay,and all the V.vulnificus strains were identified correctly while other strains were negative results.The sensitive of the new LAMP assay was 100-fold more sensitive than the conventional PCR.Meanwhile,all the V.vulnificus strains were detected correctly in spiked,clinical and environmental samples by the new LAMP assay.Compared with other well-known techniques,the new LAMP assay targeted to vvh A gene was extremely rapid,simple,sensitive and specific for V.vulnificus identification.

Rapid detection of Shigella and Salmonella in rhesus monkeys by loop-mediated isothermal amplification assay

Objective To establish a loop-mediated isothermal amplification( LAMP) method for detecting diarrhea pathogens( Shigella and Salmonella) in rhesus monkeys and evaluate the application of the LAMP method for detecting bacterial diseases in nonhuman primate laboratory animals. Materials and Methods A total of 205 fecal samples of rhesus monkeys were detected in this LAMP assay. The specificity and sensitivity of LAMP for Shigella and Salmonella were analyzed,and real-time polymerase chain reaction( REAL-TIME PCR) assay was employed as control. Results The LAMP method established here needed only 45 min to complete the reaction at 63℃. Its detection limit was 10 pg / μL and with a high specificity. The positive rate of Shigella and Salmonella was 1. 5% and 6. 3%,respectively. Conclusions Here we have established a fast and simple Shigella and Salmonella LAMP detection method that has strong specificity and high sensitivity and is suitable for rapid detection of bacterial disease in macaques. The development of this rapid detection kit is underway,and it will be helpful to the diarrhea detection.

Sensitive and rapid detection of two toxic microalgae Alexandrium by loop-mediated isothermal amplification

A loop-mediated isothermal amplification （LAMP） assay was designed and evaluated for rapid de- tection of the toxic microalgae Alexandrium catenella and A. minutum, which can produce paralytic shellfish poisoning （PSP）. Two sets of four specific primers targeting these two species were derived from the sequence of internal transcribed spacer （ITS） of ribosomal DNA. The method worked well in less than an hour under isothermal conditions of 65℃. LAMP specificity was validated in closely related algae as a comparison, suggesting the strict specificity of the LAMP primers. Two visual inspection approaches were feasible to interpret the positive or negative results. The detection lim- its of A. catenella and A. minutum samples using the LAMP assay were found to be 5.6 and 4.5 pg DNA, respectively. The sensitivity of this LAMP assay was 10 or 100-fold higher than Polymerase Chain Reaction （PCR） method in detecting the two microalgae. These characteristics of species specificity, sensitivity, and rapidity suggest that this method has the potentiality in the monitoring of red tide caused by A. catenella and A. minutum.

The Development of a Loop-Mediated Isothermal Amplification (LAMP) Procedure for Plague Diagnostic

Plague caused by Yersinia pestis is one of the infectious diseases subject to the International Health Regulations (IHR). Permanent monitoring of the focal plague areas is mandatory in order to enable prompt control measures to prevent the spread of the disease. Therefore, the availability of efficient diagnosis tests is of paramount importance. Here, we describe a loop-mediated isothermal amplification (LAMP)-based procedure for rapid Y. pestis detection. We constructed a set of LAMP primers, which were used in assays to establish the reaction conditions that would lead to the quick visualization of the results by evaluating the test tube with the naked eye. The primers were specifically designed to target the caf1 gene located on pFra/Tox (pMT), a prototypical plasmid of Y. pestis. The LAMP procedure was performed at 65°C for 45 min in a water bath and allowed for the detection of at least 10 pg of bacterial DNA. Due to its simplicity, specificity, sensitivity and rapidity, the LAMP technique is an additional tool that may be implemented in routine plague diagnoses, especially in emergencies.

Efficient detection of pathogen virus in sand dabs,Paralichthys olivaceus using loop-mediated isothermal amplification(LAMP)

Viral hemorrhagic septicemia virus（VHSV） and marine birnavirus（MABV） are the causative pathogens for some of the most explosive epidemics of emerging viral diseases in many Asian countries, leading to huge economic losses in aquaculture. Rapid molecular detection for surveillance or diagnosis has been a critical component in reducing the prevalence of pathogen infection. The loop-mediated isothermal amplification（LAMP） of DNA is currently one of the most commonly used molecular diagnostic tools, as it is simple, quick, and easy to amplify target DNA under isothermal conditions. In the present study, a novel and highly specific LAMP assay for the sensitive and rapid detection of VHSV and MABV infection in fish was developed. Using a set of synthesized primers matching a specific region of the genome, the efficiency and specificity of the LAMP assay were optimized in terms of the reaction temperature and DNA polymerase concentration, as they are the main determinants of the sensitivity and specificity of the LAMP assay. In particular, we demonstrated that our assay could be applied to efficient detection of VHSV and MABV infection in the wild fish, Paralichthys olivaceus. Our results demonstrate the simplicity and convenience of this method for the detection of viral infection in aquatic organisms.

Rapid and Visualized Detection Method of Canine Parvovirus Using Loop-Mediated Isothermal Amplification

[Objective] To develop a rapid and visualized detection method using loop-mediated isothermal amplification （LAMP）, improve the detection rate of canine parvovirus （CPV） and reduce the testing cost. [ Method] According to the conserved regions of the VP2 gene of CPV, six primers were designed to amplify the special DNA sequences by LAMP. In addition, the reaction conditions of LAMP were optimized, and the sensitivity, specificity, repeatability and stability were verified. [ Result] The optimal reaction time of the LAMP method for CPVwas 60 min. The products obtained by LAMP had high specificity without cross-reaction with other generic viruses. The sensitivity of the LAMP was 100 times higher than that of PCR. [ Conclusion] The LAMP method for detecting CPV has high practical value. It has many advantages such as high specificity, high sensitivity, simple operation, low cost and rapid analysis, and it does not require special equipment. Therefore, this method is more suitable for the detection of CPV.

Development of Reverse Transcriptase Loop-Mediated Isothermal Amplification for Rapid and Visualized Detection of Classical Swine Fever Virus

[ Objective] To develop a rapid and visualized detection method of classical swine fever virus （CSFV） using reverse transcriptase loopmediated isothermal amplification （RT-LAMP）. [ Method ] A total of six special primers were designed based on the conserved sequences of CSFV gene. After optimizing, the reaction of RT-LAMP was carded out at 63℃ for 45 rain. The RT-LAMP products were analyzed by agarose gel electro- phoresis. The sensitivity, specificity and repeatability were verified, respectively. [ Result] The RT-LAMP method could be used for detecting CSFV rather than six generic viruses. The sensitivity of RT-LAMP was 100 times higher than that of RT-PCR. The detection of 27 clinical samples by RT- LAMP and RT-PCR showed that RT-LAMP is more reliable and convenient. [ Conclusion] The RT-LAMP method is sensitive and reliable for the detection of CSFV.

Detection of coat protein gene of nervous necrosis virus using loopmediated isothermal amplification

Objective:To establish a novel and highly specific loop-mediated isothermal amplification(LAMP) assay for the identification of nervous necrosis virus(NNV) infection.Methods:A set of synthesized primers was used to match the sequences of a specific region of the nnr gene from the National Center for Biotechnology Information database,not originating from NNV-infected fish,the efficiency and specificity of LAMP were measured dependent on the concentration of DNA polymerase and the reaction temperature and time.In addition,to determine species-specific LAMP primers,cross reactivity testing was applied to the reaction between NVV and other virus families including viral hemorrhagic septicemia virus and marine birnavirus.Results:The optimized LAMP reaction carried out at 64 ℃ for 60 min,and above 4 U Bst DNA polymerase.The sensitivity of LAMP for the detection of nnv was thus about 10 times greater than the sensitivity of polymerase chain reaction.The LAMP assay primers were specific for the detection NNV infection in Epinephelus septemfasciatus.Conclusions:The development of LAMP primers based on genetic information from a public database,not virus-infected samples,may provide a very simple and convenient method to identify viral infection in aquatic organisms.

Rapid identification of Dendrobium officinale using Loop-Mediated Isothermal Amplification (LAMP) method

Dendrobium officinale is not only an ornamental plant, but also a valuable medicinal herb that is widely used in traditional Chinese medicine. However, distinguishing D. officinale from other Dendrobium species is usually a difficult task. In this study,we developed a rapid identification protocol for D. officinale using the loop-mediated isothermal amplification(LAMP) method. A set of primers were specifically designed to detect a modified internal transcribed spacer region of D. officinale at 65 ℃ within 40 min after adding SYBR~? Green I, which was used for the detection of D. officinale. Unlike commonly used adulterants, reaction mixtures containing D. officinale DNA changed from orange to green, and this color change was easily observed with the naked eye. Thus, this methodology can be used to accurately differentiate D. officinale from other Dendrobium species, is quick as all D. officinale samples were amplified within 40 min, and specific as samples of the adulterants were not amplified. The specificity of this LAMP-based method was confirmed by testing 17 samples of D. officinale and 32 adulterant samples from other Dendrobium species. This LAMP-based rapid identification method does not require expensive equipment or specialized techniques and can be used in field surveys for accurate and fast on-site identification.

A Pilot Study of Quantitative Loop-mediated Isothermal Amplification-guided Target Therapies for Hospital-acquired Pneumonia

Background： It is important to achieve the definitive pathogen identification in hospital-acquired pneumonia （HAP）, but the traditional culture results always delay the target antibiotic therapy. We assessed the method called quantitative loop-mediated isothermal amplification （qLAMP） as a new implement for steering of the antibiotic decision-making in HAP. Methods： Totally, 76 respiratory tract aspiration samples were prospectively collected from 60 HAP patients. DNA was isolated from these samples. Specific DNA fragments for identifying 11 pneumonia-related bacteria were amplified by qLAMP assay. Culture results of these patients were compared with the qLAMP results. Clinical data and treatment strategies were analyzed to evaluate the effects of qLAMP results on clinical data. McNemar test and Fisher＇s exact test were used for statistical analysis. Results： The detection of Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumonia, Stenotrophomonas maltophilia, Streptococcus pneumonia, and Acinetobacter baumannii by qLAMP was consistent with sputum culture （P 〉 0.05）. The qLAMP results of 4 samples for Haemophilus influenzae, Legionella pneumophila, or Mvcoplasma pneumonia （MP） were inconsistent with culture results; however, clinical data revealed that the qLAMP results were all reliable except 1 MP positive sample due to the lack of specific species identified in the final diagnosis. The improvement of clinical condition was more significant （P 〈 0.001） in patients with pathogen target-driven therapy based on qLAMP results than those with empirical therapy. Conclusion： qLAMP is a more promising method for detection of pathogens in an early, rapid, sensitive, and specific manner than culture.

Gold Nanoparticles Based Colorimetric Detection of Target DNA After Loop-mediated Isothermal Amplification

We have developed a rapid, simple and label-free colorimetric method for the identification of target DNA It is based on loop-mediated isothermal amplification（LAMP）. Plain gold nanoparticles（AuNPs） are used to indicate the occurrence of LAME The amplified product is mixed with AuNPs in an optimized ratio, at which the deoxyribonucleotides（dNTPs） bind to the AuNPs via ligand-metal interactions and thus enhance AuNPs stability. If a target DNA is amplified, the dramatic reduction of the dNTPs leads to the aggregation of AuNPs and a color change from red to blue. The success of the method strongly depends on the ionic strength of the solution and the initial concentration of dNTPs. Unlike other methods for the identification of isothermal products, this method is simple and can be readily applied on site where instrumentation is inadequate or even lacking.

等温扩增技术在水产品寄生虫检测中的应用研究进展

水产品中寄生虫可引起食源性疾病,已成为影响食品安全的重要因素之一。近年来,基于传统分子生物学发展而来的等温扩增技术以其恒温、高效、耗时短、不过度依赖设备和仪器等优点,逐渐应用于分子诊断和疾病检测。该文在介绍等温扩增技术原理与特点的基础上,综述了其在水产品中寄生虫检测方面的应用研究进展,提出存在问题与解决办法,并展望了等温扩增技术的应用前景,以期为快检技术在水产品质量安全控制技术中的研究开发提供理论参考。

LAMP技术特点及其用于肝炎病毒检测的相关研究进展

环介导等温扩增(LAMP)为一种用于检测靶标DNA、RNA的恒温扩增核酸检测技术,为分子即时检验(POCT)领域中应用最广泛技术,近年来广泛应用于动植物病毒感染、传染性疾病诊断,具有诊断效能高、操作简单等优势。肝炎病毒检测,为该病临床诊断、预后评估重要环节。近年来有学者将LAMP技术应用于肝炎病毒检测中,获得良好效果。且随LAMP技术不断优化,其诊断效能进一步提升。

猴痘病毒实时荧光LAMP检测方法的建立

为建立一种特异性强、灵敏度高、操作简单的猴痘病毒(Monkeypox virus, MPXV)检测方法,试验针对MPXV保守区OPG002基因片段设计特异性引物,通过优化环介导等温扩增技术(loop-mediated isothermal amplification, LAMP)反应体系中内引物、环引物体积及反应温度建立了一种MPXV实时荧光LAMP检测方法,对该方法的特异性和灵敏度进行了分析,并应用该方法检测了临床样品和模拟样品。结果表明:建立的MPXV实时荧光LAMP检测方法于64℃恒温反应60 min即可完成DNA检测;该方法能特异性地检出MPXV,最低检出限为25 copies/μL,灵敏度是普通PCR方法的20倍;该方法对12份临床样品的检测结果均为阴性,可检测出质粒浓度为0.5×10~2~0.5×10~6 copies/μL的模拟阳性样品。说明建立的MPXV荧光LAMP检测方法具有特异性强、灵敏度高、操作简单的优点,可用于MPXV的快速鉴别诊断。

基于重组酶介导等温扩增-CRISPR/Cas12a的青鱼物种快速鉴定研究

目的 建立一种快速、特异、灵敏地鉴定青鱼物种的方法。方法 以青鱼线粒体16SrRNA基因的保守序列设计特异性crRNA,并根据crRNA设计重组酶介导等温扩增(recombinase-mediatedisothermal amplification,RAA)引物;建立青鱼的RAA-CRISPR/Cas12a快速鉴定方法,并对该方法的检测时间进行优化;同时,评估该方法的特异性和灵敏度,并对青鱼及其近缘物种的市售样品进行检测。结果 该方法仅需25 min完成检测;对青鱼物种的鉴定表现出显著的特异性,并对其近缘物种如草鱼、赤眼鳟、鳡鱼、倒刺鲃的检测结果均呈阴性;方法灵敏度为1.0×10-3ng/μL(以基因组DNA计);与DNA条形码技术相比,该方法在市售样品的检测结果上表现一致。结论 建立了青鱼物种的RAA-CRISPR/Cas12a现场快速检测方法,该方法具备快速、特异、灵敏的特点,为水产市场或野外环境中快速检测青鱼物种提供了技术手段。

捻转血矛线虫LAMP-LFD检测方法的建立

为了建立一种用于检测捻转血矛线虫的特异、灵敏、快速的检测方法,用环介导等温扩增技术(LAMP)结合横向流动试纸条(LFD),针对捻转血矛线虫mt-COⅠ基因的保守序列设计特异性引物和探针,对反应温度、反应时间、Mg^(2+)浓度、dNTP浓度进行优化,建立了捻转血矛线虫环介导等温扩增技术与横向流动试纸条检测技术(LAMP-LFD)相结合的核酸检测方法。结果显示,建立的LAMP-LFD检测方法最低检测限为100 fg,对奥斯特线虫、夏伯特线虫、毛首线虫DNA检测均为阴性;50份临床样品检测结果与粪便虫卵检测法结果的符合率为96%。该方法操作方便、结果判定快速简单,有望成为流行区域和基层检测捻转血矛线虫的新方法。

塞内卡病毒LAMP可视化快速检测方法的建立及初步应用

为建立塞内卡病毒(SVA)的快速检测方法,本研究在SVA高度保守区域,分别设计了5对特异性LAMP引物,并通过反应条件优化、敏感性试验、特异性试验以及临床样本检测,建立了一种经济、特异、敏感的SVA检测方法。在62℃水浴55 min扩增出大于220 bp的特异性阶梯状条带,以质粒为模板进行敏感性试验结果表明该方法在5.1 copies/μL时仍可以检测出SVA,比普通PCR敏感1000倍。特异性试验结果显示该方法与猪肺炎支原体(MPH)、猪伪狂犬病病毒(PRV)、猪圆环病毒2型(PCV2)、猪圆环病毒3型(PCV3)、猪瘟病毒(CSFV)、猪繁殖与呼吸综合增病毒(PRRSV)均无交叉反应,应用该方法检测72例临床疑似病料,阳性率为33%(24例)。与普通PCR相比较,该方法操作简便、快速、特异、经济,本研究提供了一种更适于临床检测的SVA检测方法。