cord-000049-rl7sdzd7	2009	Here we have applied the loop-mediated isothermal amplification (LAMP) method to amplify GMO-related DNA sequences, ''internal'' commonly-used motifs for controlling transgene expression and event-specific (plant-transgene) junctions. Moreover, the sensitivity and ability to amplify targets, even with a high background of DNA, here demonstrated, highlights the advantages of this isothermal amplification when applied for GMO detection. Here we assess the LAMP protocol for the detection of GMOs using primers that target event-specific sequences for transgenic MS8 and RF3 oilseed rape (Brassica napus L.) and generic GMO sequences such as the cauliflower mosaic virus 35S promoter (P-35S) and the promoter and terminator for the nopaline synthase gene (P-nos and T-nos, respectively) from Agrobacterium spp. LAMP sensitivity was assessed by the detection of ten RoundUp Ready™ GMO targets in a background of 100 ng of genomic oilseed rape DNA (Figure 3 ).
cord-000625-cpjlzutk	2012	In order to develop a field applicable technique that offers high detection sensitivity and specificity for the diagnosis of BU, we explored the use of the pocket warmer LAMP (pwLAMP) technique, a DNA amplification method using isothermal conditions (60uC) provided by a disposable pocket warmer [34] . In order to develop a simple and rapid test that can be used to diagnose Buruli ulcer under field conditions, we modified the conventional LAMP assay by using a disposable pocket warmer as a heating device for generating a constant temperature for the test reaction and employed the use of crude sample preparations consisting of boiled and unboiled extracts of the clinical specimen instead of using purified DNA as the diagnostic specimen. Thirty clinical specimens from suspected Buruli ulcer patients were investigated by the modified LAMP (or pocket warmer LAMP) and the conventional LAMP, as well as IS2404 PCR, a reference method for the detection of Mycobacterium ulcerans.
cord-001762-dtvzwin8	2015	title: Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been used to detect viral RNA molecules because of its simplicity and high sensitivity for a number of viruses. RT-LAMP for the detection of Potato virus X (PVX) was developed and compared with conventional reverse transcription polymerase chain reaction (RT-PCR) to demonstrate its advantages over RT-PCR. This study showed similar results in that the RT-LAMP assay included two loop primers and took only 15 min for detection of PVX. Simple and rapid detection of Potato leafroll virus (PLRV) by reverse transcription loop-mediated isothermal amplification (RT-LAMP) Reverse transcription loop-mediated isothermal amplification of DNA for detection of Potato virus Y Rapid detection and differentiation of Dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay Development of loop-mediated isothermal amplification assay for specific and rapid detection of camelpox virus in clinical samples
cord-002081-vi6rth9o	2016	In this work, a rapid one-step SNP detection method, real-time loop-mediated isothermal amplification (RT-LAMP), was first applied for CYP2C19 polymorphisms testing. The optimized method was established with specifically designed primers for target amplification by real-time detection in approximately 30 min under isothermal conditions. The successful establishment of an inexpensive, rapid and real-time LAMP protocol for CYP2C19*2 and CYP2C19*3 detection is significant for the extension of this technique for genotyping other SNPs. Our results suggest applications for this RT-LAMP assay system for both basic research and clinical diagnosis in pharmacogenomics. In this study, the successful establishment of an inexpensive, rapid and real-time LAMP protocol for CYP2C19 SNP genotyping expanded the scope of application of this technique to human gene mutation detection. In summary, as a rapid, feasible and cost-efficient point-of-care (POC) SNP detection method, we demonstrated that RT-LAMP could quantitatively detect human genomic DNA with high specificity and sensitivity in a single step.
cord-002720-lrkscs71	2017	title: Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification The assay detected viral RNA at 14.5 TCID(50)/mL in virus-spiked serum or urine samples within 15 min, although it was slightly less sensitive than reference real time RT-PCR assay. We then evaluated the utility of this assay as a molecular diagnostic test using 90 plasma or serum samples and 99 urine samples collected from 120 suspected cases of arbovirus infection in the states of Paraíba and Pernambuco, Brazil in 2016. Therefore, it is difficult to detect ZIKV in blood samples from patients after the acute phase of infection, even with sensitive molecular diagnostic methods, such as reverse transcription-polymerase chain reaction (RT-PCR) 14, 18, 19 . These results suggested that the RT-LAMP assay could be used as a rapid, sensitive diagnostic test for ZIKV, the Tp value (i.e., less than 15 min) can be used as an indicator of the number of RNA copies in each reaction.
cord-002982-zwvesrct	2018	More recently, a loop-mediated isothermal amplification (LAMP) assay was successfully designed for field use in the grape powdery mildew pathosystem; however, false negatives or false positives were prevalent in grower-conducted assays due to the difficulty in perceiving the magnesium pyrophosphate precipitate at low DNA concentrations. The detection of airborne pathogen inoculum has been improved through the development of quantitative PCR (qPCR) assays that allow for near real-time monitoring of inoculum concentration (Carisse et al., 2009b; Rogers, Atkins & West, 2009; Temple & Johnson, 2011; Thiessen et al., 2016) . The use of a fluorescence resonance energy transfer (FRET)-based probe, allows for specific detection of LAMP products and target quantification from field samples without inhibiting amplification , and several portable fluorescence-reading LAMP devices have been made commercially available, such as the Genie (Optigene Ltd., West Sussex, UK) and Bioranger (Diagenetix, Inc., Honolulu, HI, USA).
cord-003342-wmmbkmrg	2015	In this study, a set of LAMP primers were designed targeting the prfA gene sequence of Listeria monocytogenes, and dimethyl sulfoxide (DMSO) as well as Touchdown LAMP were employed to increase the sensitivity and specificity of the LAMP reactions. The results indicate that the detection limit of this novel LAMP assay with the newly designed primers and additives was 10 fg per reaction, which is ten-fold more sensitive than a commercial Isothermal Amplification Kit and hundred-fold more sensitive than previously reported LAMP assays. This highly sensitive LAMP assay has been shown to detect 11 strains of Listeria monocytogenes, and does not detect other Listeria species (including Listeria innocua and Listeria invanovii), providing some advantages in specificity over commercial Isothermal Amplification Kits and previously reported LAMP assay. Loop-mediated isothermal amplification, developed and reported by Notomi et al., in 2000 [1] , can specifically, sensitively and rapidly amplify nucleic acids with two pairs of primers recognizing 6 independent sequences of a target gene under isothermal conditions.
cord-004133-32w6g7qk	2019	Studies were included if they involved direct amplification and detection of genetic material from one of six representative sample types: blood, dried blood spot, serum and plasma, saliva and sputum, swabs, urine, and stool. However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.''s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.''s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] .
cord-004307-4sltubqk	2020	The activation of somatic mutations conferring sensitivity to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors has been widely used in the development of advanced or metastatic primary lung cancer therapy. In the present study, a loop-mediated isothermal amplification (LAMP) method was used to identify EGFR mutations, and its efficiency was compared with the Therascreen quantitative PCR assay. Following removal of normal lung tissues, DNA samples were extracted as aforementioned, and investigated using Therascreen EGFR PCR and a LAMP assay. The additional Case X experiments also identified a novel EGFR mutation using direct sequencing which was not identified using Therascreen or LAMP; however, this mutation may have been detected as an exon 19 deletion by the primers of the similarly targeted mutation. A rapid, sensitive assay to detect EGFR mutation in small biopsy specimens from lung cancer Epidermal growth factor receptor gene mutation in non-small cell lung cancer using highly sensitive and fast TaqMan PCR assay
cord-005377-36io7zsm	2012	The main isothermal methods reviewed here include loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), and helicase-dependent amplification (HDA). Development and evaluation of a novel loop mediated isothermal amplification (LAMP) method for rapid detection of SARS Corona virus Rapid detection of norovirus from fecal specimens by real-time reverse transcription-loop-mediated isothermal amplification assay Rapid detection and quantification of Japanese encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification. Rapid and real-time detection of chikungunya virus by reverse transcription loop mediated isothermal amplification assay Development and evaluation of reverse transcription Loop mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus Development of a quantitative real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective and sensitive detection of human rhinovirus serotypes Development and evaluation of a real-time nucleic acid sequence based amplification assay for rapid detection of influenza A
cord-104321-fpoztmcl	2017	The aim of this study was to identify the SRY gene for embryo sex determination in human during pregnancy using loop mediated isothermal amplification (LAMP) method. LAMP positive amplicons have been confirmed by adding a number of fluorescent dsDNA intercalating dye including ethidium bromide and SYBR ® Premix Ex Taq TM II after the reaction is completed or metal indicators such as magnesium sulphate (MgSO 4 ), calcium chloride (CaCl 2 ), SYBR Green I, propidium iodide, GeneFinder TM , calcein, hydroxynaphthol blue (HNB), phenol red and Gel-Red TM prior to the reaction, allowing observation with the naked eye (37) (38) (39) (40) . Development of Loop mediated isothermal amplification (LAMP) of SRY gene in Almasi MA and Almasi G JRI human blood samples for sex determination. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products Visual detection of potato leafroll virus by one-step reverse transcription loop-mediated isothermal amplification of DNA with hydroxynaphthol blue dye
cord-252686-viz05uam	2019	Abstract Recent study proves that the combination of loop mediated isothermal nucleic acid amplification (LAMP) with one-step strand displacement (OSD) is of great help to improve the sequence specificity during genetic detection. With the purpose of improving the detection specificity and achieving more simple and reliable readout, we recently developed an innovation in which one-step nucleic strand displacement reaction (usually shortened as OSD) was adapted, instead of traditional fluorescent intercalating dyes, to probe the products of isothermal amplifications (e.g., LAMP). These results exhibited the MBs based LAMP-HCR strategy realized robust NoV detection and was more resistant to interference than the real-time fluorescence assay, where the fluorescence signal could be decreased with the increased concentrations of fecal samples ( Fig. 1D and Fig. S6 , in SI).
cord-256845-5pjam7em	2017	In the case the sensitivity of the test might be ameliorated through further studies, the RT-LAMP could be extremely useful, due to its low costs and rapidity, in those situations where the Table 2 Results obtained on the samples tested with RT-nPCR (PCR) and LAMP and evaluated with agarose gel electrophoresis (LAMP GEL) and hydroxynaphtol blue dye (LAMP HNB detection of FCoV must be repeated over time and on a high number of cats (e.g. breeding catteries). Visual detection of turkey coronavirus RNA in tissues and feces by reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynaphthol blue dye Comparison of real-time reverse transcriptase polymerase chain reaction of peripheral blood mononuclear cells, serum and cell-free body cavity effusion for the diagnosis of feline infectious peritonitis Feline coronavirus quantitative reverse transcriptase polymerase chain reaction on effusion samples in cats with and without feline infectious peritonitis
cord-258057-ti0rpt0q	2020	A loop-mediated isothermal amplification (LAMP) assay was established to detect PPV infection. The optimized LAMP program was as follows: 50 min at 59 °C followed by 3 min at 80 °C.The amplified products were analyzed both by visual inspection after staining with SYBR Green I dye and by conventional agarose gel electrophoresis. To verify the specificity of PPV detection by LAMP, the DNA (PPV, PCV2, PRV) and cDNA samples (PRRSV, CSFV) were amplified as sample templates by the LAMP reaction at 59.0℃ for 50 min and terminated at 80℃ for 3 min, respectively. The LAMP detection limit for PPV based on visual observation by addition of J o u r n a l P r e -p r o o f SYBR Green I and by gel electrophoresis analysis was 10 1 copies. Rapid detection of porcine parvovirus DNA by sensitive loop-mediated isothermal amplification Rapid and sensitive diagnosis of porcine parvovirus by loop-mediated isothermal amplification (LAMP) method
cord-264676-k531q3ir	2009	title: In situ reverse-transcription loop-mediated isothermal amplification (in situ RT-LAMP) for detection of Japanese encephalitis viral RNA in host cells In this study, we aimed to establish a new approach, named as in situ reverse-transcription loop-mediated isothermal amplification (in situ RT-LAMP), in order to detect JE virus infection in cultured cells and in PBMCs isolated from infected mice. When the in situ RT-LAMP was run with the DIG-labeled primer, no positive reaction was shown in either JE virus-infected (Fig. 5A ) or uninfected (Fig. 5B ) BHK-21 cells. Detection of Japanese encephalitis virus in mouse peripheral blood mononuclear cells using an in situ reverse transcriptase polymerase chain reaction Rapid detection and quantification of Japanese encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification Rapid detection and differentiation of Dengue virus serotypes by real-time reverse transcription loop-mediated isothermal amplification assay Development and evaluation of reverse transcription-loop-mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus
cord-265172-rn9pkk52	2020	title: Emergent carotid artery stenting following intravenous alteplase infusion after rapid negative diagnosis for COVID-19 by loop-mediated isothermal amplification assay: A case report Conclusions This case report suggests that eCAS for hAIS due to ICS following intravenous alteplase can be an effective treatment, along with appropriate antiplatelet medication and management in select patients. This case report suggests that eCAS for hAIS due to ICS following intravenous alteplase can be an effective treatment, along with appropriate antiplatelet medication and management in select patients. Carotid artery stenting (CAS) is a standard treatment procedure for internal carotid artery stenosis (ICS) 8 ; however, the efficacy and safety of emergent CAS (eCAS) for hyperacute ischemic stroke (hAIS) due to ICS have not been sufficiently established. This case report demonstrates that eCAS for AIS due to ICS following intravenous alteplase infusion can be an effective treatment option along with appropriate antiplatelet medication and management in select patients.
cord-268627-nnx46nwf	2011	In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed for detection of porcine epidemic diarrhea virus (PEDV). The results showed that the optimal reaction condition for RT-LAMP amplifying PEDV N gene was achieved at 63°C for 50 min. The total RNAs were extracted from the culture supernatants of PEDV, TGEV, PRV, PRRSV, and IBV using the RNA extraction kit (KeyGen Biotech, China) and the genomic DNA of PrV was extracted from virus-infected Vero cell culture using the DNA extraction kit (Omega, Norcross, USA) according to the manufacturer''s instructions. As shown in Fig. 2a , the DNA products of the RT-LAMP at different temperatures showed multiple of characteristic ladder bands; however, the intensity of DNAs determined by Gel Analyzer software from the reactions at 63°C was stronger than that at other reaction temperatures, which was judged as the optimal temperature for RT-LAMP amplifying PEDV N gene. The sensitivity of the RT-LAMP assay was first compared with the conventional RT-PCR amplifying the tenfold serial dilutions of RNA templates of PEDV.
cord-268993-2sjh17mw	2020	BACKGROUND: Molecular assays based on reverse transcription-loop-mediated isothermal amplification (RT-LAMP) may be useful for rapid diagnosis of the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) because of the easy performance and the option to bypass RNA extraction. OBJECTIVES: This study was designed to evaluate the clinical performance of the CE-labeled variplexTM real time SARS-CoV-2 RT-LAMP assay in comparison to commercial RT-PCRs. STUDY DESIGN: RNA extracted from pharyngeal swabs was tested by variplex™ RT-LAMP and Corman''s LightMix™ E gene RT-PCR as reference. Samples of respiratory secretions from Coronavirus infection disease (COVID-19) and negative control patients were analyzed by variplex™ without RNA extraction and tested in parallel with the Allplex™ and VIASURE BD MAX RT-PCRs. RESULTS: Using isolated RNA variplex™ RT-LAMP showed a sensitivity of 75% compared to LightMix E gene RT-PCR but contrary to the latter it produced no false-positive results.
cord-271434-30nh2gc7	2020	In this work, we develop an automated centrifugal microfluidic system (Figure 1 ) consisting of a microfluidic disc and a customized instrument for rapid sample-to-answer detection of SARS-CoV-2 armored RNA particles with high sensitivity and specificity. Virus lysis buffer, RT-LAMP reagents, and mineral oil were sequentially injected into the microfluidic disc for on-chip release of viral nucleic acids, amplification of target RNA, and sealing of reaction unit. To demonstrate the automated detection of viral nucleic acids by the centrifugal microfluidic system, we loaded different concentrations of SARS-CoV-2 armored RNA particles with N gene (0.5, 1, 10, 10 2 , 10 3 copies/μL) into five reaction units of the microfluidic disc, and used the instrument to carry out on-chip release of viral nuclei acids, RT-LAMP, and realtime fluorescence signal detection.
cord-271504-t3y1w9ef	2020	A confirmed case should have at least one of the following criteria: (i) a positive result for 2019-nCoV nucleic acid, using real-time PCR tests from respiratory or blood samples; (ii) a high homogeneity between viral gene sequencing from respiratory or blood samples and known 2019-nCoV; and (iii) serum samples positive for IgM or IgG to 2019-nCoV, or seroconversion in IgG, or a fourfold or more significant increase in IgG antibody titer to 2019-nCoV in the recovery phase than in the acute phase [25] . Using blood samples taken from alleged COVID-19 patients, the researchers detected antibodies targeting the spike protein that prevented the virus from killing cells in laboratory tests. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] . Given that antiviral drugs have previously demonstrated reasonable inhibition of coronaviruses and therapeutic efficacy against coronavirus outbreaks, umifenovir, chloroquine, hydroxychloroquine, lopinavir-ritonavir, and ribavirin have been recommended in the latest guidelines for diagnosis and treatment of COVID-19, updated on 17 February 2020 [189] .
cord-271735-gprd79di	2019	Development of fluorescent reverse transcription loop-mediated isothermal amplification (RT-LAMP) using quenching probes for the detection of the Middle East respiratory syndrome coronavirus Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of West Nile virus Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay Detection of respiratory syncytial virus genome by subgroups-A, B specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) Development of a reverse transcription-loop-mediated isothermal amplification assay for detection of pandemic (H1N1) 2009 virus as a novel molecular method for diagnosis of pandemic influenza in resource-limited settings Real-time sequence-validated loop-mediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV) Development of real-time fluorescent reverse transcription loop-mediated isothermal amplification assay with quenching primer for influenza virus and respiratory syncytial virus Development of real-time fluorescent reverse transcription loop-mediated isothermal amplification assays for rhinovirus detection
cord-276718-3lujp0oy	2014	title: Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India In the present study, the standardization and validation of a one step, four tube reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) for rapid detection and serotyping of the DENV targeting NS1 gene using the Genie® II flourometer was carried out. In the present study, the RT-LAMP assay was developed for the detection and serotyping of DENV infection targeting the serotype specific regions of the NS1 gene using a real-time flourometer (Genie ® II from Optigene, U.K.). The performance of the RT-LAMP assay was validated by testing the samples simultaneously by the CDC real time PCR that is most sensitive and specific method for detection and differentiation of the DENV (CDC Dengue). Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay
cord-276957-pk33dl8q	2020	To accelerate clinical diagnostic testing for COVID-19, we conducted a prospective cohort study to develop and validate a novel RT-LAMP assay capable of detecting SARS-CoV-2 RNA for potential use in centralized facilities and point-of-care settings. The detection results obtained using the RT-LAMP assay showed good concordance with those obtained using the RT-qPCR In Cohort I, 35 of 37 nasopharyngeal swabs from 24 COVID-19 patients were confirmed to be SARS-CoV-2 positive according to the criteria of RT-qPCR (28 samples) and NGS confirmation (7 samples) (see Table S3 in the supplemental material). Subsequently, we evaluated the RT-LAMP and standard RT-qPCR assays on 329 nasopharyngeal swabs from a cohort of 129 suspected COVID-19 patients and on serial upper respiratory samples from an asymptomatic carrier, and the inconsistent samples between RT-LAMP and RT-qPCR were further subjected to next-generation sequencing (NGS) for SARS-CoV-2 confirmation.
cord-279229-2226jnfl	2005	In this paper, we review a novel method of DNA amplification known as loop-mediated isothermal amplification (LAMP) of a target nucleic acid. Screening for KHV has become very important as trade of fancy carp is an easy route for geographical spread of the virus and a rapid and efficient system like LAMP is very Figure 2 Loop-mediated isothermal amplification reaction amplifying the haemolysin gene from Edwardsiella tarda isolates. Rapid detection of a fish iridovirus using loop-mediated isothermal amplification (LAMP) Rapid diagnosis of Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD) in salmonid fish by a novel DNA amplification method, loop-mediated isothermal amplification (LAMP) Rapid diagnosis of herpes simplex virus infection by a loop-mediated isothermal amplification method A loop mediated isothermal amplification (LAMP) method for detection of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss) Rapid diagnosis of human herpesvirus 6 infection by a novel DNA amplification method, loop-mediated isothermal amplification
cord-280442-jtvez46y	2019	To evaluate this novel detection method, PCR assays (including conventional RT-PCR, qRT-PCR and nRT-PCR) and reverse-transcription LAMP (RT-LAMP) monitored by electrophoresis were also conducted and the specificity and sensitivity of the assays were compared with those of the mRT-LAMP-LFD assay. A total of 13 IBV strains, 7 NDV strains, and the PCR and LAMP target sequences of 6 NDV and 1 turkey coronavirus strains (TCoV) synthesized by Sangon Biotech (Shanghai, China) Co, as well as 6 other avian virus strains, were used for the determination of the specificities of RT-PCR and RT-LAMP assays. Statistical significance difference studies showed that the mean detection rates of mRT-LAMP-LFD were significantly higher than that of conventional RT-PCR assays when detecting IBV or NDV alone (P < 0.05). The mean IBV and NDV detection rates of different samples, detected by mRT-LAMP-LFD, were both 95%, and were significantly higher than those detected by conventional RT-PCR and qRT-PCR (P < 0.05, Figure 6B) .
cord-282126-gmjnbnx5	2012	We developed and evaluated a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detecting Duck hepatitis A virus type 1 (DHAV-1). The RT-LAMP assay was highly specific; no cross-reactivity was observed from the samples of other related viruses, bacteria, allantoic fluid of normal chicken embryos, or the livers of uninfected ducks. To detect the limit of the RT-LAMP and RT-PCR assay, DHAV-1 total RNAs were extracted from the serially 10-fold diluted allantoic fluid, ranging from 10 4 to 10 -3 50 % egg lethal dose (ELD 50 ) per 100 ll. To compare the sensitivity of the RT-LAMP assay with the conventional RT-PCR, the two assays were used to detect the same RNAs which were extracted from 10-fold serial dilutions (from 10 4 to 10 -3 ELD50 per 100 ll) of allantoic fluid. A one-step RT-LAMP assay with high specificity and sensitivity was developed for rapid diagnosis of DHAV-1, which has no cross-reaction with DEV, MPV, AIV, R.
cord-283415-1nu399lz	2012	title: Development of A Loop-Mediated Isothermal Amplification (LAMP) for the Detection of F5 Fimbriae Gene in Enterotoxigenic Escherichia coli (ETEC) The objective of this study was to establish a loop-mediated isothermal amplification (LAMP) method for the detection of F5 fimbriae gene in Enterotoxigenic Escherichia coli. However, the invention of Loop-mediated isothermal amplification (LAMP) provides new ideas and technologies for establishing a rapid detection method of F5 fimbriae gene. The result of detecting by established LAMP were positive only for F5 fimbriae gene, and no positive DNA products of the LAMP assay were observed when these control strains (F4ab, F6, F41, and F18ab) were used as templates (Fig. 3) . Development of loop-mediated isothermal amplification (LAMP) for detection of Escherichia coli producing Shiga toxin II variant Rapid and sensitive detection of heat-labile and heat-stable I enterotoxin genes of enterotoxigenic Escherichia coli by loop-mediated isothermal amplification
cord-284644-9k2oox64	2017	Optimized RT-LAMP assays were applied on clinical samples from patients having influenza like illness and results were compared with conventional one-step RT-PCR and real-time RT-PCR. CONCLUSIONS: RT-LAMP assay is rapid, sensitive, specific and cost effective method for detection of influenza A viruses than conventional one-step RT-PCR and it can serve as a good alternate for diagnosis and surveillance studies during influenza outbreaks in resource-limited setups of developing countries. The objectives of the current study were to (1) optimize RT-LAMP assay for detection of influenza A viruses and their subtypes (H1N1, H3N2 and pdm09/H1N1); (2) determine sensitivity and specificity of RT-LAMP assay; (3) clinical evaluation of RT-LAMP assay and conventional one-step RT-PCR in comparison to WHO recommended rRT-PCR taken as standard. Development and evaluation of reverse transcription loop-mediated isothermal amplification assay for rapid and real-time detection of the swine-origin influenza A H1N1 virus
cord-285088-krim73zt	2020	title: One-pot Detection of COVID-19 with Real-time Reverse-transcription Loop-mediated Isothermal Amplification (RT-LAMP) Assay and Visual RT-LAMP Assay Objective This study was to establish one-pot real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and one-pot visual RT-LAMP assay for the detection of COVID-19. The analytic sensitivities of the newly developed real-time RT-LAMP assay and visual RT-LAMP assay were determined with pUC57-N DNA ranging from 2-0.02 fg, and the reaction mixtures were heated at the optimal temperature for 60 min in a StepOneTM System (Applied Biosystems, Foster City, CA, USA) or in a water bath, when water bath was used, the reaction tube was sunk into water. The detection limits of the one-pot real-time RT-LAMP assay and the one-pot visual RT-LAMP assay were determined using pUC57-N DNA ranging from 2-0.02 fg at 59 °C for 60 min in a StepOneTM System (Applied Biosystems, Foster City, CA, USA) or in a water bath.
cord-287104-4k8pqbc0	2019	title: Development of Rapid and Specific Detection for the Human Aichivirus A Using the Loop-Mediated Isothermal Amplification from Water Samples In this study, developed a LAMP method to achieve a rapid, specific and highly sensitive detection of AiV-A. A newly developed method was more rapid (approximately 2–8 h), specific and equivalent detection of AiV-A than with the conventional PCRs. In addition, confirm system of positive LAMP reaction was developed by using the restriction enzyme Aci I and Hae III. A method for detecting AiV-A specific genes by using reverse transcription nested polymerase chain reaction (RT-PCR) assay, have been reported [15] [16] [17] . In this study, developed a rapid, specific and highly sensitive detection of AiV-A by using a LAMP assay. In this study, developed a LAMP assay that could rapid, specific, and sensitive detection of AiV-A from water samples.
cord-288887-lshsgex3	2007	The loop-mediated isothermal amplification (LAMP) assay originally described [Notomi et al., 2000] is based on the principle of autocycling strand displacement DNA synthesis for the detection of a specific DNA sequence with specific characteristics: (1) all reactions can be conducted under isothermal conditions ranging from 60 to 658C; (2) the specificity of the reaction is extremely high because it uses six primers [Nagamine et al., 2002] recognizing eight distinct regions on the target nucleotides; and (3) a simple detection method such as visual judgment using Fluorescent Detection Reagent (Eiken Chemical Co., Ltd.) is possible. This study describes (a) the evaluation of a newly developed RT-LAMP assay for the detection of NVs and compares the results with that of the routine RT-PCR assay, (b) comparisons between the RT-LAMP assay and conventional RT-LAMP detection kits for NVs (Eiken Chemical Co., Ltd.), and (c) application of the RT-LAMP assay for outbreaks of acute gastroenteritis.
cord-295491-zlah6u5s	2018	The aim of this study was to test two commercially available reaction mixtures in a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to detect feline Coronavirus (FCoV) in body cavity effusions of cats with and without FIP, in order to minimize the time from sampling to obtaining results. The aim of this study was to test specificity and sensitivity of two commercially available reaction mixtures in a reverse transcription LAMP (RT-LAMP) to detect FCoV in body cavity effusions of cats with and without FIP, and to minimize the time from sampling to obtaining results. The FIP group (n = 34) included cats with a definitive diagnosis of FIP by one or more methods: All effusions of cats with FIP tested positive for FCoV by RT-PCR by a commercial laboratory, and in 26/34 samples putative disease-causing mutations could be detected.
cord-296977-yzhsdz9c	2020	; https://doi.org/10.1101/2020.11.04.20225888 doi: medRxiv preprint imaging camera and SYBR Green I derived fluorescence transduction by naked eye or smartphone camera 27 ; (3) Microfluidic cartridge combining immune-capture, lysis and LAMP to detect viable bacteria using a reader platform comprising two light sources for fluorometric and/or turbidimetric analysis resorting to a smartphone camera 30 ; (4) a hermetic container providing power-free chemical-based heating for LAMP amplification followed by detection using a smartphone flashlight and camera for fluorometric detection 32 ; (5) Centrifugal platform combining silica-based DNA extraction and integrated LFA strips to multiplex the detection of multiple LAMP products using anti-DIG antibodies and colorimetric detection 32 ; (6) Centrifugal platform with automated bead-beating lysis followed by direct RT-LAMP by continuous measurement of fluorescence with UVC illumination and a standard camera 22 ; and (7) Centrifugal platform incorporating non-contact heating of the disc and colorimetric detection of LAMP products using a white LED for illumination and filtered photodiodes for signal acquisition 24 .
cord-297974-sduz0j35	2020	Here we describe a method to detect SARS-CoV-2 RNA of a single infected individual within a bulk sample comprised of up to 26 individual patient samples by combining a hybridizationcapture-based RNA extraction approach with smartphone app-assisted colorimetric detection of RT-LAMP products, a procedure that can be performed in less than one hour ( Figure 1A) . To investigate whether it is possible to detect single infected individuals in pools of gargle lavage samples, we created eleven pools of 25 patient samples each, all of which had been tested negative in RT-qPCR assay and in the Cap-iLAMP assays for the Orf1a and the N gene ( Figure 2D ). All tested gargle lavages from single healthy individuals (n=6) and 11 pools of 25 healthy individuals (n=275) correctly tested negative for both the Orf1a gene and N gene in the Cap-iLAMP assay ( Figure 2C and E), indicating that false positive results which were sometimes observed when samples are added directly into the iLAMP reaction (Supp.
cord-302663-gb2vgs97	2006	Reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting the structural glycoprotein gene of yellow head virus (YHV). The RT-LAMP assay is a novel method of gene amplification that amplifies nucleic acid with high specificity, sensitivity and rapidity under isothermal conditions with a set of four specially designed primers that recognize six distinct sequences of the target. The development of a loop-mediated isothermal amplification (LAMP) assay for detection of white spot disease virus (WSDV) DNA was described by Kono et al. Ten-fold serial dilutions (10 −1 to 10 −8 diluted) of RNA extracted from YHV-infected shrimp was used as a template for RT-LAMP according to determined conditions. In order to determine the sensitivity of detection limit, RT-LAMP and nested RT-PCR were carried out using various concentrations (10 −1 to 10 −8 dilution) of RNA extracted from YHV-infected shrimp as template.
cord-302829-1o1jo8uk	2008	A method of loop-mediated isothermal amplification (LAMP) was employed to develop a rapid and simple detection system for porcine circovirus type 2 (PCV2). DNA was extracted from blood, lymph nodes, lung, liver, kidney, heart and spleen samples taken from PCV2-infected and healthy pigs, using a DNeasy Tissue Kit (Qiagen) according to the manufacturer''s instructions. In order to evaluate the optimal tissues for viral detection and to compare the sensitivity of PCV2 detection by LAMP and PCR, DNAs from tissue samples of blood, heart, lung, liver, kidney, lymph nodes and spleen from PCV2-infected pigs were extracted and subjected to LAMP and PCR. Quantitation of porcine circovirus type 2 isolated from serum/plasma and tissue samples of healthy pigs and pigs with postweaning multisystemic wasting syndrome using a TaqMan-based real-time PCR Porcine postweaning multisystemic wasting syndrome in Korean pig: detection of porcine circovirus 2 infection by immunohistochemistry and polymerase chain reaction
cord-304343-m7tbdfri	2019	Similarly, inhibiting the mTOR signaling pathway can prevent apoptosis and even enhance necroptosis, whereas starvation, which induces autophagy, protects cells from zVAD-mediated necroptotic death [194] . For instance, autophagy has been demonstrated to be actively involved in the replication of influenza A virus (IAV), which induces autophagosome formation during the early phase of infection and later inhibits autophagosomal maturation by preventing autophagosomal-lysosomal fusion and promoting autophagosomes to accumulate in virus-infected cells [253] . (5) A novel anti-cancer molecule, HA15, which targets HSPA5/BIP was shown to induce endoplasmic reticulum stress and increase the unfolded protein response, resulting in cancer cell death through autophagy and apoptosis. (5) A novel anti-cancer molecule, HA15, which targets HSPA5/BIP was shown to induce endoplasmic reticulum stress and increase the unfolded protein response, resulting in cancer cell death through autophagy and apoptosis. In addition, the novel anti-cancer molecule HA15, which targets HSPA5/BIP, was shown to induce ER stress and increase the unfolded protein response, resulting in cancer cell death via autophagy and apoptosis [304] .
cord-305399-98sqovwb	2019	A simple and accurate reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was developed and evaluated for the detection of porcine pegivirus (PPgV). The results indicated that RT-LAMP assay developed in this study could be a highly specific, sensitive, and cost-effective alternative for a rapid detection of PPgV in field settings. The final volume of 25 μl reaction mixtures for RT-LAMP was prepared, which contained 1 μl of Bst DNA polymerase (NEB, USA) (8000 U/ml), 2.5 μl of 10 × Isothermal Amplification Buffer, 5 μl of Betaine (5 M), 1 μl of MgSO 4 (100 mM), 5 μl of dNTP (2.5 mM), 2 μl of each inner primers FIP and BIP (10 μmol), 0.25 μl of each outer primers F3 and B3 (10 μmol), 0.25 μl of each loop primers LF and LB (10 μmol), 1.25 μl of AMV reverse transcriptase (TaKaRa, China) (40 U/μl), 2 μl of RNA template, and the sterile distilled water was set as a negative control template.
cord-307068-360qs3ov	2007	A new method was developed for detection of human papillomavirus (HPV) by loop‐mediated isothermal amplification (LAMP), which was compared with the polymerase chain reaction (PCR), and real‐time PCR for specificity and sensitivity. In order to evaluate the reliability of HPV type‐specific LAMP detecting HPV DNA from clinical samples, tissue specimens were obtained from 27 patients with external genital polypoid lesions. In this study, a LAMP-based HPV typespecific DNA amplification method was developed and were compared its specificity and sensitivity with PCR and real-time PCR. Type-specific real-time PCR was used to measure the quantity of the DNAs of HPV-6, -11, -16, and -18 in each sample. The sensitivity of HPV-6, -11, -16, and -18 type-specific LAMP determined by turbidity assay were 1,000 copies/tube (Fig. 3) . The sensitivity of amplification of LAMP for detection of viral DNA was nearly the same as that of real-time PCR.
cord-310657-04pp0o74	2020	Using a mismatch-tolerant amplification technique, we developed a simple, rapid, sensitive and visual reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection based on its N gene. In this study, we applied the mismatch-tolerant technique to develop novel real-time fluorescent and visual RT-LAMP assays for the rapid and sensitive detection of SARS-CoV-2 RNA, and evaluated the novel assays using clinical samples. The novel RT-LAMP assay has a high sensitivity, with a LOD of 118.6 copies per reaction, and shows no cross-reactivity with 17 common human respiratory viruses, including four other human coronaviruses (OC43, 229E, HKU-1 and NL63). In view of a mean viral load of 1.4 × 10 6 copies/mL in nasal swabs of COVID-19 patients, the novel assay is sufficiently sensitive for the detection of SARS-CoV-2 at an early stage of infection using nasal swab specimens. The RT-LAMP assay has a high sensitivity, with a LOD of 118.6 copies of SARS-CoV-2 RNA per 25 µL reaction, and good specificity regarding common respiratory viruses.
cord-312222-aw5849rc	2020	METHODS: This prospective service improvement project piloted an RT-LAMP method on nasal and pharyngeal swabs on 21 residents of a high dependency care home, with two index COVID-19 cases, and compared it to multiplex tandem reverse transcription polymerase chain reaction (RT-PCR). We recorded vital signs of patients to correlate clinical and laboratory information and calculated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of a single swab using RT-LAMP compared with the current standard, RT-PCR, as per Standards for Reporting Diagnostic Accuracy Studies (STARD) guidelines. Since then, a number [13] of other groups have published high-quality studies demonstrating that RT-LAMP has the potential to replace RT-PCR as a means for detecting SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) within RNA extracted from nose -throat swabs and endotracheal secretions/bronchoalveolar lavage fluid [5, 14, 15] .
cord-316816-yjbcvf3o	2010	title: Visual detection of turkey coronavirus RNA in tissues and feces by reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynaphthol blue dye A sensitive reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the rapid visual detection of turkey coronavirus (TCoV) infection. In conclusion, RT-LAMP with HNB dye was shown to be a sensitive, simple assay for the rapid diagnosis of TCoV infection, either directly from feces or in association with virus isolation methods. The objective of this study was to develop and validate a reversetranscription loop-mediated isothermal amplification (LAMP) method for the direct detection of viral RNA from tissues and feces collected from experimentally and naturally infected birds. Embryo tissues (ileum and ileumecaecal junction portions) were prepared by infecting 25-day-old embryonated turkey eggs with 0.3 ml 10 2.4 EID 50 TCoV via the amniotic sac, as described previously [9, 10] . Reverse transcription loop-mediated isothermal amplification for rapid detection of infectious bronchitis virus in infected chicken tissues
cord-318120-vfznyyz6	2015	title: Development of a pan-serotype reverse transcription loop-mediated isothermal amplification assay for the detection of dengue virus To facilitate needed diagnosis, we developed and optimized a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay that detects all 4 serotypes of dengue virus (DENV). Development of simple and rapid assay to detect viral RNA of tick-borne encephalitis virus by reverse transcription-loop-mediated isothermal amplification A real-time reverse transcription loop-mediated isothermal amplification assay for the rapid detection of yellow fever virus Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loopmediated isothermal amplification assay Development and evaluation of reverse transcription-loop-mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus
cord-321886-0b3ocoh9	2010	title: Loop-mediated isothermal amplification for rapid detection and differentiation of wild-type pseudorabies and gene-deleted virus vaccines A loop-mediated isothermal amplification (LAMP) assay was developed specifically for detection and differentiation of pseudorabies virus (PRV). Because of its sensitivity, specificity, and simplicity, the LAMP assay could be a useful method for early and rapid differentiation of swine vaccinated with PRV gE-deleted vaccine from swine infected with wild virus. Based on PRV-gG-LAMP, 26 of the 70 piglets were infected with wild-type PRV and may or may not have been vaccinated. Many different PCR assays can differentiate between the wild-type PRV and gene-deleted virus vaccines (Liu et al., 2007) , but LAMP is easier to perform and provides more rapid results. (2008) described a LAMP system for PRV detection but that LAMP system could not differentiate between swine infected with wild-type PRV and swine vaccinated with PRV gE-deleted.
cord-322238-8iwljdoi	2010	Loop-mediated isothermal amplification (LAMP) was developed to detect the TGEV by incubation at 60°C for 1 h and the product specificity was confirmed by HphI digestion. By using serial sample dilutions as templates, the detection limit of LAMP was about 10 pg RNA, 10 times more sensitive than that of PCR and could be comparable to the nest-PCR. Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method, which amplifies DNA/RNA with high specificity, sensitivity and rapidity under isothermal condition [5] . As a kind of nucleic acid amplification method, LAMP could not only qualitatively detect the TGEV, but also quantitatively analyze the virus. In conclusion, this study demonstrates that the LAMP method established could detect only the TGEV and no cross-reaction with other viruses, the detection limit was about 10 pg RNA, which was 10 times more sensitive than that of PCR and could be comparable to the nest-PCR.
cord-323845-s78t5qxj	2006	title: Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) A one step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of viral hemorrhagic septicaemia virus (VHS). Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) The aim of the present study was to develop a onestep, single-tube, accelerated RT-LAMP reaction for rapid detection of different serotypes of VHS virus. The specificity of the VHS-LAMP primers and conditions to VHS virus was confirmed by its aptitude to amplify only RNA from VHS virus serotypes, with no amplification of IHNVor non-infected fish (Fig. 5) . Detection of viral hemorrhagic septicaemia virus (VHS) in rainbow trout (Oncorhynchus mykiss) by reverse transcription followed by polymerase chain reaction. A loop mediated isothermal amplification (LAMP) method for detection of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss)
cord-324094-23kzr8rq	2008	We have developed two real-time assays ie., SYBR green I based real time reverse transcription polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplification (LAMP) assay for rapid detection as well as typing of some of the emerging viruses of biomedical importance viz. We have developed two real-time assays ie., SYBR green I based real time reverse transcription polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplifi cation (LAMP) assay for rapid detection as well as typing of some of the emerging viruses of biomedical importance viz. A one-step single tube real-time accelerated reverse transcription loop mediated isothermal amplifi cation (RT-LAMP) assays for rapid detection of some of the recently emerged human viral pathogens viz. Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplifi cation assay Development and evaluation of reverse transcription Loop mediated isothermal amplifi cation assay for rapid and Real-time detection of Japanese encephalitis virus
cord-328042-e1is656g	2020	The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits, followed by reverse transcription and quantitative PCR detection. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) using a primer set targeting the N gene, as well as RT-qPCR using a primer set targeting the E gene, showing that the RNA extraction protocol presented here can be combined with a variety of detection methods at high throughput. Here, we show that the magnetic bead-based protocol yields RNA extracts comparable to the commercially available QIAcube viral RNA extraction kit, as determined by the commonly applied detection methods RT-qPCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP) [16] .
cord-331641-u27ohm5p	2018	In this study, we devised a Direct-LAMP procedure, amplifying nucleic acids with various samples (including whole blood, dried blood spot, buccal swab and saliva) without DNA purification, which is essential for conventional nucleic acid detection methods. To evaluate the performance of the Direct-LAMP, a serial dilution of the target concentrations of whole blood sample and saliva sample with two different genotypes (wild type and homozygous mutation which confirmed by sequencing) of MTHFR C677T and ALDH2 Glu504Lys, respectively, were used to determine the detection limit. Here, we have established a rapid, easy-to-use and accurate SNP detection platform using Direct-LAMP, which enables us to use whole blood, dried blood spot, buccal swab or saliva as samples for genotyping without DNA purification. In this study, we presented a Direct-LAMP for SNP detection by using whole blood, dried blood spot, buccal swab or saliva as samples without DNA purification.
cord-332820-6qx6svs5	2020	The pipeline utilises a series of in-house buffers to first inactivate patient samples received from care homes and hospitals, and to then extract RNA before using a CE marked commercial kit to detect SARS-CoV-2 by RT-qPCR. Herein, we describe the use of loop mediated isothermal amplification PCR coupled with reverse transcription (RT-LAMP) as a robust method for SARS-CoV-2 detection in clinical specimens 6 . Our results demonstrate that within the CCC pipeline, RT-LAMP can readily replace RT-qPCR as a means for detecting SARS-CoV-2 transcripts within RNA extracted from nosethroat swabs and endotracheal secretions/bronchoalveolar lavage fluid. The RT-LAMP assay reproducibility and precision were determined by extracting RNA 5 times from a confirmed COVID-19 positive patient sample through the CCC pipeline and assessing by N gene and 18S RT-LAMP in 5 independent experiments, performed by two different operators ( Figure 4D ).
cord-332961-ebr623rm	2017	In this study, we report a sensitive and specific real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid and quantitative detection of CMNV. In this study, we developed a rapid and sensitive reverse transcription loopmediated isothermal amplification (RT-LAMP) method for the detection of CMNV in infected shrimp. For CMNV quantitative detection of samples, a standard curve was generated for CMNV qRT-LAMP by plotting a graph between different concentrations of pMD19-T-CMNV plasmids, ranging from 10 8 to 10 0 copy numbers, to cycle threshold (Ct) values, obtained through real-time monitoring of the amplification. The lowest detection limit of the newly developed CMNV RT-LAMP method was 6.2 pg of total RNA when the reactions were tested using 1 lL of 10-fold serially diluted RNA from shrimp artificially infected with CMNV (Fig. 3A) . Sensitive and specific detection of Cryptosporidium species in PCR-negative samples by loop-mediated isothermal DNA amplification and confirmation of generated LAMP products by sequencing
cord-333220-tcvs4beg	2008	It has two major components, a disposable polymethyl methacrylate (PMMA) micro-reactor and a temperature-regulated optical detection unit (base apparatus) for real-time monitoring of the turbidity changes due to the precipitation of DNA amplification by-product, magnesium pyrophosphate. It has two major components, a disposable PMMA micro-reactor and a temperature-regulated optical detection unit (base apparatus) for real-time monitoring of the turbidity changes due to precipitation of DNA amplification by-product, magnesium pyrophosphate. Our integrated isothermal device has two major components, a disposable polymethyl methacrylate (PMMA) micro-reactor and a temperature-regulated optical detection unit (base apparatus) for real-time monitoring of the turbidity changes due to the precipitation of DNA amplification by-product, magnesium pyrophosphate. To confirm the results of the LAMP reaction for HBV DNA template amplification and detection in the integrated isothermal device, seven clinical serum specimens were obtained from patients with chronic hepatitis B at National Taiwan University Hospital.
cord-333331-ddcz7zck	2011	An improved, sensitive, specific, and rapid one-step reverse transcription loop-mediated isothermal amplification (LAMP) assay targeting the 5′ untranslated region (UTR) was developed to detect hepatitis C virus (HCV) infection. A variety of molecular diagnostic assays, such as reverse transcriptase PCR [12] , nucleic-acid-sequence-based amplification [13] , transcription-mediated amplification [29] , branched-chain DNA assay [26] , and in-house realtime PCR [8] , have been developed for the detection of HCV RNA. Confirmed cases of HCV infection were verified by a positive result in an enzyme-linked immunosorbent assay (Kehua Bio-engineering, Shanghai, China) for antibodies against HCV or a quantitative real-time PCR for HCV RNA. Given that the sensitivity of the AP-LAMP assay for detecting HCV is higher than that of the pre-LAMP method, the pathway of AP-based amplification was investigated. Reverse transcription-loop-mediated isothermal amplification assay for rapid detection of hepatitis E virus
cord-333524-a6p6ma8r	2020	19 The current most common diagnostic method used to identify SARS-CoV-2 infection is a molecular technique for detecting viral RNA through nucleic acid amplification, RT-PCR. Nucleic acid amplification tests (NAATs) are the most common diagnostic tests used to detect pathogens, and many of the current SARS-CoV-2 detection techniques are primarily based on NAATs. 21 NAATs involve nucleic acid amplification, a process that initiates with a small quantity of starting nucleic acids and uses primers that target specific, short nucleic acid sequences in conjunction with enzymes to amplify or increase the quantity of starting nucleic acids. 34 This test incorporates a nested nucleic acid amplification technique showing higher sensitivity of detection than LAMP alone and conventional RT-PCR for minimally processed SARS-CoV-2 samples. 55 The technique first uses RT-LAMP for reverse transcription and isothermal amplification of viral RNA, and then employs the Cas12a enzyme to identify sequences of SARS-CoV-2, allowing cleavage of a reporter molecule ( Figure 5 ).
cord-334518-mjr6u7ak	2020	To accelerate clinical diagnostic testing for COVID-19, we conducted a prospective cohort study to develop and validate a novel RT-LAMP assay capable of detecting SARS-CoV-2 RNA for potential use in centralized facilities and point-of-care settings. Subsequently, we evaluated the RT-LAMP and standard RT-qPCR assays on 329 nasopharyngeal swabs from a cohort of 129 suspected COVID-19 patients and on the serial upper respiratory samples from an asymptomatic carrier, and the insistent samples between RT-LAMP and RT-qPCR were further subjected to next-generation sequencing (NGS) for SARS-CoV-2 confirmation. . https://doi.org/10.1101/2020.05.20.20108530 doi: medRxiv preprint As described in the Materials and Methods, we developed a rapid and simple RT-LAMP assay to detect SARS-CoV-2 RNA, and positive reactions resulted in a color change from purple to blue due to decreased magnesium concentration in the presence of extensive Bst DNA polymerase activity, while negative reactions retained the purple color.
cord-338899-qt17jhg0	2008	Emergence or reemergence of severe arboviral hemorrhagic fevers caused by mosquitoborne viruses, such as dengue virus and Chikungunya (CHIK) virus, have been frequently reported in the Indian subcontinent in the past few years. We report clinical observations and laboratory investigations involving virus isolation methods and molecular assays performed for 296 clinically suspected cases of CHIK fever. Of particular interest was the applicability of a novel method of gene amplificatio called real-time loop-mediated isothermal amplifica tion (RT-LAMP) as a rapid, sensitive, and specifi real-time method to detect and quantify CHIK virus in the acute phase of the infection. All 132 patients who had clinically suspected CHIK virus but whose RT-PCR and RT-LAMP results were negative presented 17 days after the onset of fever; this may be the reason for the negative test results. The RT-LAMP allows rapid, realtime detection of CHIK virus in acute-phase serum samples, without requiring sophisticated equipment, and has potential usefulness for clinical diagnosis and surveillance of CHIK virus in developing countries.
cord-338942-q4neat3x	2019	Isothermal deoxyribonucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), exhibit characteristics ideal for point-of-care (POC) applications, since their instrumentation is simpler in comparison with the standard method of polymerase chain reaction. Nucleic acids amplification methods are primarily required to be performed, as the original number of either DNA or ribonucleic acid (RNA) copies in the clinical sample is insufficient for their direct detection. A microfluidic disk-based LAMP chip, integrating sample preparation and detection, was developed [44] (Fig. 2B ). Loop-mediated isothermal amplification integrated on microfluidic chips for point-of-care quantitative detection of pathogens An integrated rotary microfluidic system with DNA extraction, loop-mediated isothermal amplification, and lateral flow strip based detection for point-ofcare pathogen diagnostics An integrated microfluidic loop-mediated-isothermal-amplification system for rapid sample pre-treatment and detection of viruses Development and application of a loop-mediated isothermal amplification method on rapid detection Escherichia coli O157 strains from food samples
cord-342145-cq6xe5r7	2020	The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital''s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. For samples with a CT ≤ 30 as measured by RT-qPCR with E-Sarbeco primers, we found overall satisfactory sensitivity and specificity values for SARS-CoV-2 RNA detection by the RT-LAMP assay using RNA samples isolated from pharyngeal swab specimens ( Fig. 3 and Table 1 ).
cord-343136-kftffes0	2020	A novel reverse-transcriptase loop mediated amplification (RT-LAMP) method targeting genes encoding the Spike (S) protein and RNA-dependent RNA polymerase (RdRP) of SARS-CoV-2 has been developed. Limit of detection of the LAMP assay was evaluated by using a nasopharyngeal (NP) swab sample infected with SARS-CoV-2 for which the viral load was quantified using digital droplet PCR (see Supplementary Methods). Twenty four replicates from a serial dilution containing 25-50 copies of SARS-CoV-2 which equates to 1X LOD (patient sample NP swab in VTM viral load confirmed by digital droplet PCR) per reaction were tested using dual-target RT-LAMP (Table 3) . The dual-target RT-LAMP test for SARS-CoV-2 developed in this study has comparable analytical sensitivity and specificity, limit of detection, precision, and achieved excellent agreement compared to the reference RT-PCR methods used internationally.
cord-343632-cv3qgno3	2020	Here we report a method to identify SARS-CoV-2 (COVID-19) virus RNA from purified RNA or cell lysis using loop-mediated isothermal amplification (LAMP) using a visual, colorimetric detection. Here we describe a molecular diagnostic approach for SARS-CoV-2 RNA detection using loop-mediated isothermal amplification (LAMP) and simple visual detection of amplification for potential use in rapid, field applications. This study describes testing and validation of 5 sets LAMP primers targeting two fragments of the SARS-CoV-2 genome using short (~300bp) RNA fragments made with in vitro transcription and RNA samples from patients. https://doi.org/10.1101/2020.02.26.20028373 doi: medRxiv preprint With current diagnostic methods, e.g. RT-qPCR, purified RNA is used in the input. Although a small number of samples were tested here, the colorimetric LAMP assay enables reliable SARS-CoV-2 detection without sophisticated instrumentation, matching the RT-qPCR performance in field and point-of-care settings. /2020 In conclusion, colorimetric LAMP provides a simple, rapid method for SARS-CoV-2 RNA detection.
cord-344636-go5cw92q	2020	In this work, we developed a COVID-19 diagnosis kit for the rapid detection of SARS-CoV-2, using one-step reverse transcription and loop-mediated isothermal amplification (RT-LAMP). Positive amplification products were obtained even for 2 copies of the synthetic viral DNA fragment template in 30 min when using the S17 primers (lane 4 in Fig. 1D ), demonstrating that the LAMP reaction was rapid and sensitive. To assess the potential of RT-LAMP in detecting RNA virus of SARS-CoV-2, we then tested the performance of these primers with synthesized RNA fragments of the N gene, S gene and Orf1ab gene obtained from in vitro transcription (Appendix S1). The ultimate aim is to develop an enclosed device that integrates RNA extraction, purification, reverse transcription (RT) and loop-mediated isothermal amplification (LAMP) to detect the SARS-CoV-2 virus directly from a throat swab sample.
cord-346846-yle3z5z2	2020	The face-to-face proximity of clinicians and patients during slitlamp examination potentially places eyecare providers at a high risk of aerosolised particles from respiratory droplets. The use of slitlamp barriers has become increasingly common during the current COVID-19 global pandemic. 2 We decided to evaluate the ability of the Slit Lamp Shield to reduce potential droplet exposure. In our simulation (Video S1), a clinician attired in personal protective equipment including surgical mask and face shield was positioned in the examination position. Without the shield, dye was found on the clinician''s face shield, mask, gown, gloves, desk and the machine itself. When the experiment was repeated with the shield in position, most of the dye was located on the outside of the shield, with smaller amounts on the clinician gloves, desk and machine ( Figure 1) . Importantly, there was no dye on the clinician''s face shield or mask.
cord-348243-e5tdb08v	2020	METHODS: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). To allow for the comparison of different nucleic acid detection methods for SARS-CoV-2 we collected redundant material from nasopharyngeal swabs obtained for qPCR testing in clinical routine due to suspected COVID-19. We first tested two recently described assays for SARS-CoV-2 detection on isolated RNA from patient samples. In summary, our multiplex RT-LAMP protocol is a simple and sensitive way to detect SARS-CoV-2 RNA from clinical samples. Currently, a test based on our multiplexed RT-LAMP assay would-in contrast to a good specificity-most likely miss to identify those infected patients with very low amounts of viral RNA in the nose or throat and would not yet reach the sensitivity of the gold-standard qPCR assays.