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"ABSTRACTHepatitis B virus (HBV) infects hepatocytes and causes acute and chronic hepatitis that can lead to cirrhosis and hepatocellular carcinoma (HCC) in both animals and humans. Early detection of HBV infection assists in monitoring the patient's response to anti-HBV therapy, blood donation screening, and disease management, control and eradication. This research focused on development of LAMP assay combined with lateral flow dipstick (LFD), gold nanoparticle (AuNPs) and real-time turbidimetry for screening of the hepatitis B virus. Analytical sensitivity, analytical specificity, diagnostic sensitivity, diagnostic specificity, accuracy and predictive value of each technique were determined and compared to conventional PCR and real-time PCR (gold standard method). The analytical sensitivity of LAMP-LFD and LAMP-AuNPs was 1.24x101 copies /mL, LAMP-real-time turbidimetry was 1.24x102 copies/mL, while that of conventional PCR was 1.24x104 copies/mL. Examination of the analytical specificity of all LAMP-based combinations and conventional PCR showed no cross-reactivity with HCV or human plasma. Upon exploration of one hundred unknown samples, in comparison to real-time PCR, the diagnostic sensitivity and specificity of LAMP-based assays were 100% and 90%, respectively. The accuracy, positive predictive value (PPV) and negative predictive value (NPV) of the LAMP-based assays were 98%, 97.56%, and 100%, respectively. While that of conventional PCR were 60%, 100%, 68%, 100% and 38% of diagnostic sensitivity, diagnostic specificity, accuracy, PPV and NPV, respectively. LAMP-based assays need to be simplified in terms of achieving single-step diagnosis using one master mix solution that is suitable for a point-of-care diagnostic test. "

"ABSTRAKDevelopment of the Rapid Test Kit for the Identification of Campylobacter spp. Based on Loop-mediated Isothermal Amplification (LAMP) in Combination with a Lateral Flow Dipstick (LFD) and Gold Nano-DNA Probe (AuNPs)Dueantem Thongphueak, Kosum ChansiriCenter of Excellence in Biosensors, Srinakharinwirot University, Bangkok 10110, Thailand.Thayat SriyapaiFaculty of Environmental Culture and Ecotourism, Srinakharinwirot University, Bangkok 10110, Thailand.Supatra Areekit, Somchai Santiwatanakul, Piyada WangroongsarbABSTRAKThe detection of Campylobacter spp. in meat products was developed by using loop-mediated isothermal amplification (LAMP) combined with DNA-based bioassay methods, including a lateral-flow dipstick (LFD) and gold nano-DNA probe (AuNPs) assay. The LAMP primers were designed from the conserved nucleotide regions of Campylobacter spp. The analytical sensitivity of the LAMP-LFD and LAMP-AuNPs analysis was 360 fg/μl. The analytical specificity of LAMP-based assays showed no cross-reactions to Listeria monocytogenes, Salmonella Typhimurium, Escherichia coli, Bacillus cereus, Pseudomonas aeruginosa, Staphylococcus aureus, Enterobacter aerogenes, Serratia marcescens, Vibrio parahaemolyticus, Vibrio cholerae, Klebsiella oxytoca and Citrobacter diversus.The sensitivity, specificity and accuracy of both LAMP-LFD and LAMP-AuNPs for the detection of pre-enrichment cultures from raw chicken meat samples were 100%, 95% and 96.67%, respectively. Since the processing time of LAMP-based assays is 60-90 minutes, it is applicable as a point-of-care screening test for food safety and as a process control of Campylobacter spp. contamination."

"Jumlah pengidap virus HIV di Indonesia terus meningkat dari jenis penularannya, lebih banyak melalui cairan genital daripada plasma darah. Deteksi HIV diperlukan untuk pencegahan dan pengobatan. Teknik yang lazim digunakan adalah amplifikasi DNA dengan metode PCR. Penelitian ini bertujuan menerapkan teknik amplifikasi DNA metode LAMP yang baru-baru ini dikembangkan sebagai ganti PCR karena lebih spesifik, sensitif dan efisien. LAMP menggunakan pasangan primer yang unik, sepasang primer forward dan sepasang backward yang masing-maing terdiri dari primer panjang untuk polimerisasi DNA dem sepasang primer pendek untuk melepas rantai baru DNA sehingga reaksi bisa dilakukan pada suhu tetap. Reaksi LAMP menggunakan enzim Bst DNA polymerase pada suhu 65°C dilakukanterhadap isolat genom RNA HW sudah dikonfirmasi keberadaannya dengan metode PCR."

"Penelitian ini merupakan usaha untuk mengembangkan suatu metode baru dalam mendeteksi HIV. Teknik deteksi yang biasa digunakan adalah RT-PCR dari sampel berupa RNA, Tujuan dari penelitian ini adalah untuk mengaplikasikan pengembangan metode amplifikasi DNA, LAMP (Loop-Mediated Isothermal Amplification), untuk menggantikan RT-PCR, karena metode LAMP ini dinilai lebih spesifik, sensitif, dan efisien.Reaksi LAMP telah dilakukan pada isolat RNA yang sebelumnya telah di-reverse transcription (RT) dan dikonfirmasi dengan PCR. Reaksi tersebut menggunakan enzim Bs/ DNA polimerase dan reaksinya berlangsung pada suhu 65°C. Hasil reaksi tersebut telah dikonfirmasi dengan elektroforesis dan menunjukkan ketiadaan pita hasil amplifikasi yang diharapkan. Argumentasi yang paling memungkinkan dari hasil reaksi ini antara lain, adalah kondisi kemurnian sampel, kondisi reaksi yang tidak optimal untuk reaksi LAMP, dan rancangan primer. Reaksi LAMP juga akan dilakukan pada bagian dari sekuens gen gag yang terletak pada nukleotida nomor 905-1081 dan telah diklon pada vektor pGEM-T serta telah dikonfirmasi dengan sekuensing DNA. Hasil sekuensing menunjukkan sekuens yang sama dengan data gene bank dengan ukuran yang sesuai dengan ukuran target primer komersial, yaitu sebesar 155 pb dan akan digunakan sebagai template untuk reaksi LAMP.Kesimpulan penelitian ini adalah metode LAMP helum berhasil dikembangkan untuk deteksi HIV. Rancangan primer dan kondisi reaksi adalah hal-hal yang penting dalam metode LAMP dan harus ditingkatkan untuk keberhasilan reaksi ini.

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This study was attempted to develop a new method for HIV detection. The technique that is usually used is RT-PCR for RNA detection. This research aims to apply the recently developed DNA amplification method, LAMP (Loop-Mediated Isothermal Amplification), instead of RT-PCR as this method is more specific, sensitive, and efficient.

The LAMP reaction is done on RNA isolates that have been confirmed by PCR to contain HIV RNA. This reaction has been performed at 65°C using Bst DNA polymerase after doing reverse transcription. The result showed that LAMP on RNA isolates did not result in amplification as confirmed by electrophoresis. Most probable reasons for these results are the impurity of the sample, the conditions of the reactions that are not optimal for the LAMP reaction, and the design of the primer. LAMP was also performed on a part of a gag genes sequences on nucleotides number 905-1081 that has been cloned onto a pGEM-T vector and then sequenced for confirmation. The result of DNA sequence showed the same sequence as reported in Gene Bank data, with a size similar to a commercial primary target, i.e. 155 bp and will consequently be used as a template for the LAMP reaction.

The conclusions of this study are the LAMP method has not developed yet for HIV detection. The design of the primer and the conditions of the reactions in the LAMP method are the important things for the successful of this reaction, need to be improved."

"Pandemi virus corona SARS-CoV-2 di seluruh dunia telah menyebabkan besarnya populasi manusia yang terinfeksi COVID-19. Penyebaran virus yang massive membutuhkan alat diagnostik yang cepat, sehingga keputusan terkait kebijakan kesehatan, pembatasan publik, dan keputusan karantina dapat diambil dengan tepat. Polymerase chain reaction (PCR) adalah standar emas dalam pengujian asam nukleat yang mendeteksi viral ribonucleic acid (RNA). Meskipun real-time RT- PCR sensitif dan reliabel, namun prosesnya memakan waktu yang cukup lama sehingga tidak cukup untuk menjawab kebutuhan diagnosis di masa pandemi global COVID-19. Amplifikasi isotermal merupakan salah satu metode yang dapat digunakan sebagai alternatif PCR. Metode amplifikasi isotermal yang paling banyak diterapkan adalah loop-mediated isothermal amplification (LAMP). Pada penelitian ini dilakukan perancangan prototipe berbasis pemanas poliamida yang dapat mempermudah proses reaksi LAMP. Sistem ini dapat menghasilkan suhu konstan 60˚C-65˚C dalam 30 menit dengan nilai error rata-rata pengukuran sensor suhu sebesar 1.75% dengan akurasi 98.25%. Pada pengujian perbandingan nilai suhu pada sensor dengan suhu dalam tube terdapat error rata-rata sebesar 1.75% dengan akurasi 95.45%. Kuantifikasi intensitas fluoresens juga telah berhasil dilakukan dengan tingkat zat fluorosensi yang berbeda-beda dengan membaca nilai keabuan minimal 102,76

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The SARS-CoV-2 coronavirus pandemic worldwide has caused a large number of people to be infected with COVID-19. The massive spread of the virus requires rapid diagnostic tools, so that appropriate health, public and policy decisions can be made. Polymerase chain reaction (PCR) is the gold standard in nucleic acid testing that detects viral ribonucleic acid (RNA). Although real-time RT-PCR is sensitive and reliable, the process takes a long time so it is not sufficient to answer the need for diagnosis during the global COVID-19 pandemic. Isothermal amplification is one method that can be used as an alternative PCR. The most widely applied isothermal amplification method is loop-mediated isothermal amplification (LAMP). In this study, a prototype based on a polyimide heater was designed that could facilitate the LAMP reaction process. This system can produce a constant temperature of 60˚C-65˚C in 30 minutes with an average error value of 1.75% of temperature sensor measurements with an accuracy of 98.25%. In testing the comparison of the temperature value on the sensor with the temperature in the tube, there is an average error of 1.75% with an accuracy of 95.45%. Fluorescence intensity quantification has also been successfully carried out with different levels of fluorescence intensity and can read a minimum gray value of 102,76"

"Pandemi virus SARS-CoV-2 yang terjadi telah membuat kebutuhan untuk pemeriksaan massal deteksi virus menjadi meningkat. Saat ini pemeriksaan gold standard untuk mendeteksi virus SARS-CoV-2 adalah dengan metode reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) yang berbiaya mahal. Oleh karena itu dibutuhkan metode pemeriksaan alternatif yang lebih murah, cepat, dan mudah digunakan sebagai sistem deteksi virus. Metode Loop Mediated Isothermal Amplification LAMP) dapat melakukan reaksi amplifikasi nukleotida pada suhu isothermaltanpa perlu mesin thermal cycler dan dapat diamati langsung dengan penambahan zat pewarna. Metode deteksi virus berbasis LAMP yang dikembangkan menggunakan desain primer yang menarget gen S dan ORF1ab ditambah pewarna Calcein-Mangan dan senyawa tambahan Guanidine Hydrochloride (GuHCl). Sistem deteksi dilakukan optimasi konsentrasi komponen reaksi, suhu dan template yang menggunakan plasmid DNA kontrol. Optimasi didapatkan dengan konsentrasi reaksi FIP/BIP 0,4 µM, F3/B3 0,2 µM, Loop F/P 0,4 µM, Calcein-Mangan 12 µM, dan GuHCl 40 mM. Sistem LAMP yang dikembangkan dapat mendeteksi sekuens gen target pada DNA kontrol hingga 1 copy number dalam waktu sekitar 1 jam pada inkubasi suhu 55 ºC. Meski begitu, sistem LAMP yang dikembangkan belum mapu mengamplifikasi RNA virus SARS-CoV-2 hasil ekstraksi sampel swab pasien. Hal ini disebabkan oleh enzim Bst 3.0 yang dipakai dalam sistem LAMP tidak memiliki kemampuan reverse transcriptase yang diharapkan.

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The SARS-CoV-2 virus pandemic has made the need for mass screening of virus detection increased. Currently, the gold standard  test to detect SARS-CoV-2 virus is reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) method that costly. Therefore, an alternative method that is cheaper, faster, and easier to use as a virus detection system is needed. The Loop Mediated Isothermal Amplification (LAMP) method can perform nucleotide amplification reactions at isothermal temperatures  without the need of thermal cycler  machine and can be observed directly with the addition of coloring agents. The LAMP-based virus detection method development use primers design targeting the S and ORF1ab genes with Calcein-Manganese dyes and the additive compound Guanidine Hydrochloride (GuHCl). The detection system performed optimization of the concentration of reaction components, temperature and template using plasmid DNA control. Optimization was obtained with reaction concentration of FIP/BIP 0.4 μM, F3/B3 0.2 μM, Loop F/P 0.4 μM, Calcein-Manganese 12 μM, and GuHCl 40 mM. The developed LAMP system can detect target gene sequences in control DNA up to  1 copy number in about 1 hour at 55 ºC incubation temperature. Even so, the LAMP system developed still unable to amplify the RNA of the SARS-CoV-2 virus from the extraction of patient swab samples. This issue occurred due to the Bst 3.0 enzyme that used in the reaction did not have reverse transcriptase activity as expected."

"Amplifikasi isotermal merupakan metode yang popular pada saat ini sebagai alternatif PCR (polymerase chain reaction) untuk melakukan amplifikasi asam nukleat. Tidak seperti PCR yang memerlukan perubahan suhu siklik, amplifikasi dapat dilakukan pada suhu konstan dalam metode amplifikasi isotermal. Salah satu metode amplifikasi isotermal yang sangat banyak diaplikasikan adalah loop-mediated isothermal amplification (LAMP). Sejak pertama kalinya ditemukan pada tahun 2000, LAMP dimanfaatkan secara luas untuk deteksi berbagai jenis patogen. Dalam penelitian ini, dirancang suatu prototipe yang dapat memfasilitasi reaksi LAMP. Prototipe terdiri dari dua sistem: sistem pemanas yang berfungsi untuk menyediakan suhu konstan 60oC terhadap sampel untuk aplikasi LAMP dan sistem deteksi optik berbasis fluoresens yang digunakan untuk melakukan kuantifikasi intensitas fluoresens dalam 6 tabung sampel 0,5mL dengan kadar fluorescence agent 0,5mL, 0,4mL, 0,3mL, 0,2mL, 0,1mL, dan 0mL. Agar panas dapat disalurkan sampel dengan baik, dirancang sebuah blok panas (heat block). Selain itu, sebuah housing prototipe juga dirancang untuk menyokong komponen dan mendukung proses deteksi fluoresens. Berdasarkan hasil penelitian ini, sistem pemanas sederhana menggunakan kontrol PID dan blok panas yang dirancang mampu mempertahankan suhu pada setpoint 60oC dan 65oC, sehingga dapat digunakan untuk aplikasi LAMP. Selain itu, sistem optik yang dirancang mampu memfasilitasi proses deteksi optik berbasis fluoresens. Proses kuantifikasi intensitas fluoresens menunjukkan bahwa intensitas emisi fluoresens proporsional terhadap kadar fluorescence agent dalam sampel, dimana sampel dengan total volume 0,5mL pada kadar fluorescence agent 0,5mL, 0,4mL, 0,3mL, 0,2mL, maupun 0,1mL dapat menghasilkan emisi cahaya dengan nilai keabuan minimal 121,179.

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Isothermal amplification is a popular method today as an alternative to PCR (polymerase chain reaction) for nucleic acid amplification. Unlike PCR which requires cyclic temperature changes, amplification can be carried out at a constant temperature in the isothermal amplification method. One of the most widely applied isothermal amplification methods is loop-mediated isothermal amplification (LAMP). Since it was first discovered in 2000, LAMP has been widely used to detect various types of pathogens. In this research, a prototype is designed that can facilitate the LAMP reaction. The prototype consists of two systems: a heating system which serves to provide a constant temperature of 60oC to the sample for the LAMP application and a fluorescence-based optical detection system which is used to quantify the fluorescence intensity in 6 sample tubes of 0.5mL with fluorescence agent content of 0.5mL, 0.4mL, 0.3mL, 0.2mL, 0.1mL, and 0mL. In order for heat to be transferred to the sample properly, a heat block is designed. In addition, a prototype housing is also designed to support components and support the fluorescence detection process. Based on the results of this study, the designed simple heating system with PID control and heating block are able to maintain a temperature at a setpoint of 60oC dan 65oC, so it can be used for LAMP applications. Moreover, the designed optical system is able to facilitate fluorescence-based optical detection process. The fluorescence intensity quantification process showed that fluorescent emission intensity is proportional to the content of fluorescence agent in the sample, where the sample with total volume of 0.5mL in which the fluorescence agent content is 0.5mL, 0.4mL, 0.3mL, 0.2mL, and 0.1mL can generate light emission with gray value of minimal 121.179."

"ABSTRAKBrucellosis pada sapi endemis di Pulau Jawa, Sulawesi Selatan dan Nusa Tenggara Timur. Program eradikasi brucellosis telah dilakukan namun angka prevalensi penyakit masih di atas >2%. Diagnosis brucellosis masih terbatas secara metode konvensional yaitu serologi dan biakan bakteri. Oleh karena itu pada penelitian ini dilakukan karakterisasi molekuler B. abortus isolat lokal untuk pengembangan metode diagnosik Loop-mediated Isothermal Amplification (LAMP) yang lebih efektif. Sebanyak 50 isolat B. abortus isolat lokal asal Jakarta, Bandung, Maros, Belu dan Kupang digunakan pada penelitian ini. Identifikasi biovar dan determinasi strain spesifik B. abortus isolat lokal dilakukan untuk mengetahui strain B. abortus yang menginfeksi ternak sapi di Indonesia. Sekuensing gen isolat B. abortus dikerjakan dengan target gen 16S rRNA. Sekuen nukleotida hasil sekuensing digunakan untuk desain primer set LAMP untuk diagnosis brucellosis. Hasil penelitian menunjukkan bahwa isolat B. abortus yang dominan menginfeksi ternak sapi di Indonesia adalah B. abortus biovar 1 dengan properti genom identik dengan genom B. abortus biovar 1 9-941 dan B. abortus S19 yang ada di GenBank dengan tingkat similaritas sekuen mencapai 99%. Hasil determinasi strain spesifik isolat B. abortus dengan multiplek BaSS-PCR menunjukkan semua isolat adalah B. abortus strain lapang bukan strain vaksin. Prototipe metode LAMP-Brucella menggunakan primer set LAMP hasil desain dapat digunakan untuk deteksi cepat Brucella pada sampel susu.

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ABSTRAKBovine brucellosis is reported endemic in Java, South Sulawesi and East Nusa Tenggara. Brucellosis eradication program has been carried out, however the prevalence of the disease is still high of more than 2%. The diagnosis of brucellosis is still limited in the conventional method. The aim of this study was to perform molecular characterization of B. abortus local isolates to develop Loop-mediated Isothermal Amplification (LAMP) for detection of bovine brucellosis. A total of 50 B. abortus local isolates collected from Jakarta, Bandung, Maros, Belu and Kupang were used and analyzed in this study. Identification and determination of strain B. abortus were done to observe strain specific of B. abortus that causes the bovine brucellosis in Indonesia. Gene sequencing was performed by 16S rRNA gene targets to determine the nucleotide sequence of B. abortus and to get primer sets for the development of LAMP method. The results showed that B. abortus biovar 1 is the predominant infecting cattle in Indonesia with identical genome properties of B. abortus biovar 1 9-941 and B. abortus S19 in the GenBank and has 99% sekuen similaritis. All the observed isolates were B. abortus strain field. Development of LAMP method for detection of Brucella in dairy milk has been established using prototype primer set LAMP design from the results of highly conserved sequencing of the 16S rRNA gene local isolate B. abortus."

"Latar belakang: Metode loop-mediated isothermal amplification (LAMP) merupakan metode sederhana yang dapat mengamplifikasi DNA/RNA menggunakan empat sampai dengan enam primer dalam bentuk ?pasangan? dari sekuens conserved gen. Penelitian ini bertujuan untuk mengoptimasi LAMP dalam menegakkan diagnosis kasus TB di Indonesia.Metode: Setelah uji optimasi, metode LAMP kemudian diujikan pada 122 DNA Mycobacterium tuberculosis (Mtb) sampel tersimpan, yang merupakan spesimen sputum pasien TB dengan BTA positif yang dikumpulkan dari 13 provinsi di Indonesia pada tahun 2008 untuk studi genotipe dan merupakan koleksi Pusat Biomedis dan Teknologi Dasar Kesehatan (PBTDK), Balitbangkes. Uji optimasi meliputi uji sensitifitas dan uji spesifisitas sejumlah pasangan primer LAMP terhadap larutan serial DNA Mtb H37Rv dan 12 spesies Mycobacteria. Uji LAMP dilakukan menggunakan tiga jenis instrumen yaitu LAMP turbidemeter, pelat pemanas dan penangas air. Hasil pengujian beberapa pasang primer dan instrument ini kemudian diterapkan untuk uji LAMP pada isolat spesimen klinik Indonesia, yaitu menggunakan pasangan primer dari gen gyrB, Hasil amplifikasi dideteksi dengan lampu UV.Hasil: Uji sensitivitas menunjukkan bahwa pasangan primer gen 16S rRNA dan gyrB memberikan hasil terbaik yaitu mampu mendeteksi 10.0 fg - 1.0 pg genomik DNA Mtb H37Rv. Uji spesifisitas menunjukkan bahwa pasangan primer gen gyrB merupakan pasangan primer paling spesifik. Hasil pengujian pasangan primer gyrB pada isolat klinis Indonesia didapatkan positivity rate 94,2% (114/121).Kesimpulan: Metode LAMP berpotensi untuk digunakan dalam diagnosis kasus TB di Indonesia.

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AbstractBackground: Loop-mediated isothermal amplification (LAMP) is a method already claimed as a simple technique to amplify DNA/ RNA using four to six primers as ?a set? from conserved sequence of target gene. In this study we optimize the use of LAMP for detection of Mycobacterium tuberculosis in clinical isolates from Indonesia.Methods: Procedures to perform LAMP were optimized, then the method was applied to 122 archieved samples of DNA?s Mtb from clinical TB patients with Acid Fast Bacilli (AFB) smears positive. The samples were obtained in 2008 from 13 provinces in Indonesia for genotyping study, which then become collections of Center for Biomedical and Basic Technology of Health (CBBTH), NIHRD Indonesia. The optimization tests include sensitivity and specificity tests of several sets primers, which were evaluated using 10-fold serially diluted DNA of Mtb H37Rv and 12 species of Mycobacteria. Three equipments consisted of LAMP turbidimeter, heating block and water bath were compared for its ability in DNA amplification. Detection of M. tuberculosis from clinical isolates used set primers specific for gyrB gene, amplicon was detected with UV fluorescence system.Results: The results showed that the highest sensitivity was obtained using the set primers specific for 16S rRNA and gyrB which could detect 10.0 fg to 1.0 pg genomic DNA of Mtb H37Rv. The set primers specific for gyrB gene was the most specific primers. Application of LAMP using gyrB set primers on Indonesian clinical isolates showed 94.2% (114/121) positivity rate.Conclusion: LAMP method is potentially used in TB diagnosis in Indonesia."

"Latar Belakang. Penyakit COVID-19 yang disebabkan oleh SARS-CoV-2 dengan cepat menyebar dan menjadi Pandemi serta menimbukan kerugian yang sangat besar pada masyarakat di seluruh dunia. Deteksi virus yang cepat dan akurat memegang peranan penting untuk mengendalikan penyebaran di masyarakat dan membantu pasien untuk menghindari perkembangan penyakit lebih lanjut. Saat ini real-time Reverse Transcriptase Polymerase Chain Reaction (real-time RT-PCR) merupakan reference standard diagnostic test dalam mendeteksi SARS-CoV-2 di seluruh dunia. Real-time Reverse Transcriptase Loop Mediated Isothermal Amplification (RT-LAMP) merupakan metode amplifikasi asam nukleat isotermal yang memiliki sensitivitas dan spesifisitas tinggi dan waktu pengerjaan yang jauh lebih cepat dibandingkan real-time RT-PCR. Tujuan. Penelitian bertujuan untukiDetectTM SARS-CoV-2 Detection KitSARS-CoV-2.Metode. Penelitian ini merupakan uji kesesuaian dengan studi potong lintang dan menggunakan metode pengumpulan sampel secara consecutive sampling. Subjek penelitian yaitu spesimen swab nasofaring dan orofaring dalam VTM (N=80) yang dianalisis di Laboratorium Mikrobiologi Klinik Fakultas Kedokteran Universitas Indonesia. iDetectTM SARS-CoV-2 Detection Kit menggunakan uji kesesuaian Kappa aplikasi SPSS versi 25.Hasil. Dari 72 sampel valid yang diperiksa dengan real-time RT-LAMP iDetectTM SARS- CoV-2 Detection Kit dan real-time RT-PCR, 24 sampel terdeteksi positif oleh real-time RT-PCR dan hanya tiga sampel yang terdeteksi positif oleh real-time RT-LAMP. Tiga sampel yang terdeteksi positif oleh real-time RT-LAMP termasuk ke dalam sampel - sampel yang terdeteksi positif oleh real-time RT-PCR. Secara statistik, uji reliabilitas / uji kesesuaian dari penelitian kedua alat diagnostik ini menunjukkan nilai Kappa yang sangat rendah, yaitu 0,16. Uji kesesuaian Kappa kedua alat ini menunjukkan bahwa hasil pemeriksaan alat real-time RT-LAMP iDetectTM SARS-CoV-2 Detection Kit tidak sesuai dengan alat real-time RT-PCR dalam mendeteksi SARS-CoV-2. Kesimpulan. Real-time RT-LAMP iDetectTM SARS-CoV-2 Detection Kit tidak sesuai dengan alat real-time RT-PCR dan tidak dapat digunakan sebagai alat diagnostik dalam mendeteksi SARS-CoV-2.

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Introduction. COVID-19 caused by SARS-CoV-2 quickly spread and became Global Pandemic and caused enormous losses to people around the world. Rapid and accurate virus detection plays an important role in controlling spread in the community and helping patients to avoid further disease progression. Currently, real-time Reverse Transcriptase Polymerase Chain Reaction (real-time RT-PCR) is determined as the reference standard diagnostic test for detecting SARS-CoV-2 worldwide. Real-time Reverse Transcriptase Loop Mediated Isothermal Amplification (RT-LAMP) is an isothermal nucleic acid amplification method that has high sensitivity and specificity and provide faster result than real-time RT-PCR. Aim. The research aims to compare real-time RT-LAMP iDetectTM SARS-CoV-2 Detection Kit and real-time RT-PCR in detecting SARS-CoV-2. Method. This research is a comparison test with a cross-sectional study and uses a consecutive sampling method to collect samples. The research subjects were nasopharyngeal and oropharynx swab specimens in VTM (N=80) which were analyzed at the Clinical Microbiology Laboratory, Faculty of Medicine, Universitas Indonesia. The data obtained from the real-time RT-LAMP iDetectTM SARS-CoV-2 Detection Kit and real-time RT-PCR test results were analyzed using Kappa test SPSS version 25.

Results. Of the 72 valid samples examined by the real-time RT-LAMP iDetectTM SARS- CoV-2 Detection Kit and real-time RT-PCR, 24 samples were detected positive by real- time RT-PCR and only three samples were detected positive by real-time RT-LAMP. Three samples that were detected positive by the real-time RT-LAMP were included in the samples that were detected positive by the real-time RT-PCR. Statistically, the comparison test of the research of these two diagnostic tools showed a very low Kappa value, which was 0.16. The Kappa suitability test of these two tools showed that the real- time RT-LAMP iDetectTM SARS-CoV-2 Detection Kit were not compatible with the real- time RT-PCR in detecting SARS-CoV-2. Summary. Real-time RT-LAMP iDetectTM SARS-CoV-2 Detection Kit is not compatible with real-time RT-PCR and cannot be used as a diagnostic tool in detecting SARS-CoV-2."