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"Leptospirosis merupakan penyakit akibat infeksi bakteri Leptospira spp. patogen yang umumnya terjadi di negara tropis dan subtropis serta memiliki karakteristik berupa gejala klinis yang kurang spesifik. Vektor dari penyakit tersebut adalah tikus maupun hewan peliharaan, seperti anjing dan sapi. Microscopic agglutination test (MAT) merupakan uji baku emas leptospirosis yang telah ditetapkan WHO. Akan tetapi, uji tersebut kurang sensitif di fase awal terjadinya infeksi dan memiliki prosedur yang rumit. Konfirmasi melalui metode real-time polymerase chain reaction (RT-PCR) dengan gen secY menggunakan darah utuh dan serum dapat dilakukan untuk pengembangan diagnosis leptospirosis. Tujuan dari penelitian ini adalah mendeteksi gen secY pada sampel darah utuh dan serum pada pasien terduga leptospirosis yang meliputi pasien suspek dan probable di Klaten, Jawa Tengah dengan metode RT-PCR. Selain itu, penelitian ini juga bertujuan untuk membandingkan positivity rate hasil RT-PCR sampel darah utuh dan serum dari 111 pasien terduga leptospirosis di Klaten, Jawa Tengah. Metode penelitian ini meliputi isolasi DNA, kuantifikasi DNA, amplifikasi DNA dengan RT-PCR menggunakan probe dan pewarna ROX, serta analisis hasil RT-PCR. Hasil RT-PCR menunjukkan terdeteksinya gen secY pada sampel darah utuh dan serum, dengan positivity rate darah utuh sebesar 5,41% (6/111) dan serum sebesar 18,92% (21/111), sedangkan positivity rate pada pasien suspek adalah sebesar 19,51% (16/82) dan pada pasien probable sebesar 27,59% (8/29). Dengan demikian, darah utuh dan serum dapat digunakan untuk mendeteksi leptospirosis dengan RT-PCR menggunakan gen secY dengan serum sebagai sampel yang lebih sensitif dibandingkan darah utuh. Akan tetapi, perlu dilakukan upaya untuk meningkatkan kualitas metode deteksi, berupa proses ekstraksi, optimasi primer, maupun penggunaan gen pendamping. Selain itu, hasil RT-PCR tersebut juga dapat dikonfirmasi melalui analisis sekuens sebagai analisis lanjutan.

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Leptospirosis is a disease caused by infection with pathogenic Leptospira spp. bacteria that commonly occurs in tropical and subtropical countries and has characteristics in the form of less specific clinical symptoms. The vectors of the disease are rats and domestic animals, such as dogs and cattle. Microscopic agglutination test (MAT) is the WHO gold standard test for leptospirosis. However, the test is less sensitive in the early phase of infection and has a complicated procedure. Confirmation through real-time polymerase chain reaction (RT-PCR) method with secY gene using whole blood and serum can be done for the development of leptospirosis diagnosis. The aim of this study is to detect secY gene in whole blood and serum samples of presumed leptospirosis patients including suspected and probable patients in Klaten, Central Java using RT-PCR method. In addition, this study also aimed to compare the positivity rate of RT-PCR results of whole blood and serum samples from 111 presumed leptospirosis patients in Klaten, Central Java. The method of this research includes DNA isolation, DNA quantification, DNA amplification by RT-PCR using ROX probes and dyes, and analysis of RT-PCR results. RT-PCR results showed the detection of secY gene in whole blood and serum samples, with a positivity rate in whole blood is 5.41% (6/111) and in serum is 18.92 (21/111), meanwhile the positivity rate in suspected patients is 19.51% (16/82) and in probable patients is 27.59% (8/29). Thus, whole blood and serum can be used to detect leptospirosis by RT-PCR using the secY gene with serum as the more sensitive sample than whole blood. However, efforts need to be made to improve the quality of the detection method, in the form of the extraction process, primer optimization, and the use of companion genes. In addition, the RT-PCR results can also be confirmed through sequence analysis as a follow-up analysis."

"COVID-19 merupakan penyakit yang disebabkan oleh virus SARS-CoV-2 yang mengakibatkan pandemi global. Jakarta adalah salah satu kota di Indonesia dengan angka kasus dan kematian tertinggi akibat COVID-19. Salah satu cara paling efektif untuk mengurangi keparahan dan resiko penularan COVID-19 adalah dengan vaksinasi. Vaksin dapat merangsang respons imunitas humoral tubuh yang menghasilkan antibodi netralisasi. Selain vaksin, antibodi netralisasi dapat diinduksi secara natural oleh imunitas tubuh. Hybrid immunity merupakan gabungan antara antibodi netralisasi yang diinduksi secara natural dan yang diinduksi oleh vaksin. SARS-CoV-2 terus bermutasi memunculkan berbagai varian yang menyebabkan peningkatan jumlah kasus dan munculnya gelombang COVID-19 baru di Indonesia, yaitu gelombang Delta pada Juni 2021 dan gelombang Omicron pada Januari 2022. Penelitian ini bertujuan untuk mengevaluasi perubahan antibodi netralisasi 3 bulan setelah vaksinasi dosis lengkap dari beberapa jenis vaksin, yaitu vaksin virus inaktivasi (CoronaVac), vaksin viral vektor (ChAdOx1 nCoV-19), dan vaksin mRNA (BNT162b2) serta pengaruh riwayat infeksi SARS-CoV-2 pada penerima vaksin terhadap berbagai varian SARS-CoV-2 (Wuhan, Delta, Omicron B.1.1.529 dan BA.2). Penelitian dilakukan dengan menggunakan uji Surrogate Virus Neutralization Test (sVNT) yang memiliki prinsip kerja seperti enzyme-linked immunosorbent assay (ELISA) dan meniru interaksi antara receptor binding domain (RBD) dan angiotensin-converting enzyme 2 (ACE2) dalam pelat ELISA dengan RBD dan ACE2 yang telah mengalami pemurnian dengan sampel serum partisipan populasi umum (n = 76). Hasil penelitian menunjukkan adanya perbedaan signifikan antara antibodi netralisasi sebelum dan 3 bulan setelah vaksinasi dosis lengkap, tetapi tidak terdapat perbedaan signifikan pada antibodi netralisasi yang dihasilkan dari masing-masing jenis vaksin. Hal tersebut kemungkinan disebabkan oleh waktu pengambilan sampel setelah terjadi gelombang Omicron COVID-19 sehingga terjadi hybrid immunity yang menyebabkan tingginya kadar antibodi netralisasi yang merata pada setiap jenis vaksin. Partisipan dengan riwayat infeksi SARS-CoV-2 memiliki kadar antibodi netralisasi yang lebih tinggi. Terdapat perbedaan antibodi netralisasi yang signifikan terhadap berbagai varian SARS-CoV-2 dengan penurunan kadar antibodi netralisasi yang signifikan terhadap varian Omicron B.1.1.529 dan BA.2. Kesimpulan dari penelitian ini adalah vaksinasi dosis lengkap berhasil meningkatkan kadar antibodi netralisasi hingga 3 bulan pascavaksinasi yang dipengaruhi oleh riwayat infeksi SARS-CoV-2.

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COVID-19 is a disease caused by the SARS-CoV-2 virus which has resulted in a global pandemic. Jakarta is one of the cities in Indonesia with the highest number of COVID-19 cases and deaths. One of the most effective ways to reduce the severity and transmission risk of COVID-19 is by getting vaccinated. Vaccines can stimulate the body's humoral immune response to produce neutralizing antibodies. Apart from vaccines, neutralizing antibodies can be induced naturally by the body's immunity. Hybrid immunity is a combination of naturally induced neutralizing antibodies and those induced by vaccines. The continuously mutating SARS-CoV-2 has led to the emergence of various variants which have resulted in an increase in the number of cases and the emergence of new COVID-19 waves in Indonesia, namely the Delta variant which appeared in June 2021 and the Omicron variant in January 2022. This study aims to evaluate changes in neutralizing antibodies 3 months after complete doses of several types of vaccines, namely inactivated virus vaccine (CoronaVac), viral vector vaccine (ChAdOx1 nCoV-19), and mRNA vaccine (BNT162b2) and the effect of a history of SARS-CoV-2 infection in vaccine recipients against various variants SARS-CoV-2 (Wuhan, Delta, Omicron B.1.1.529 and BA.2). The study was conducted using the Surrogate Virus Neutralization Test (sVNT) test which has a working principle like the enzyme-linked immunosorbent assay (ELISA) and mimics the interaction between the receptor binding domain (RBD) and angiotensin-converting enzyme 2 (ACE2) in ELISA plates using RBD and ACE2 that had undergone purification with sera samples of general population participants (n = 76). The results showed that there were significant differences between the neutralizing antibodies before and 3 months after the full dose of vaccination, but there were no significant differences in the neutralizing antibodies produced from each type of vaccine. This was probably caused by the sampling time after the Omicron COVID-19 wave occurred, resulting in hybrid immunity which resulted in high levels of neutralizing antibodies that were evenly distributed in each type of vaccine. Participants with a history of SARS-CoV-2 infection had higher levels of neutralizing antibodies. There were significant differences in neutralizing antibodies against various variants of SARS-CoV-2 with a significant decrease in levels of neutralizing antibodies against Omicron B.1.1.529 and BA.2 variants. The conclusion of this study is that full dose vaccination has succeeded in increasing neutralizing antibody levels for up to 3 months after vaccination which are affected by a history of SARS-CoV-2 infection."

"Tuberkulosis (TB) merupakan penyakit infeksi yang disebabkan bakteri Mycobacterium tuberculosis dan dapat menyerang paru-paru serta organ lainnya. Sesuai dengan ketentuan target product profiles (TPP) TB gagasan World Health Organization (WHO), diperlukan pengembangan alat tes cepat penunjang yang dapat mendeteksi berbagai jenis kasus TB menggunakan sampel alternatif, salah satunya berupa urine. Tujuan penelitian ini adalah memperoleh informasi dasar terkait profil protein urine kelompok TB dan kelompok sehat melalui metode separasi protein sodium dodecyl sulphate- polyacrylamide gel electrophoresis (SDS-PAGE), sebagai langkah penelitian awal penentuan marka protein TB. Metode penelitian diawali dengan pooling sampel urine subjek terkonfirmasi TB Paru (5), TB Ekstra-paru (5), TB-HIV (5), dan TB Klinis (5), serta lima subjek sehat sesuai kelompok. Isolasi protein dan SDS-PAGE dilakukan terhadap pooling sampel tersebut, dilanjutkan dengan pewarnaan coomassie brilliant blue, serta analisis profil protein hasil SDS-PAGE menggunakan ImageJ. Profil protein kelompok sehat dan empat kelompok TB menunjukkan perbedaan jumlah dan intensitas pita protein yang terekspresi. Kelompok TB-HIV memiliki 12 pita protein terekspresi dengan intensitas pita protein yang tinggi dibandingkan dengan kelompok TB lain maupun kelompok sehat. Kelompok sehat hanya memiliki satu pita protein terekspresi pada kisaran berat molekul 66,01 kDa. Sementara, hampir seluruh kelompok TB menunjukkan keseragaman protein yang tampak pada kategori pita protein berberat molekul menengah dan rendah. Terdapat tiga pita protein yang memiliki keseragaman pada keempat profil kelompok TB dengan intensitas dan konsentrasi terestimasi yang cukup tinggi, yaitu pita dengan berat molekul 52,83±56,31kDa, 48kDa, dan 23,8±24,57kDa. Melalui metode SDS-PAGE, profil protein urine kelompok sehat dan kelompok TB dapat diamati dengan keseragaman pita terekspresi pada kelompok TB yang juga berpotensi dalam penemuan marka protein TB yang inklusif. Untuk penelitian selanjutnya perlu dilakukan langkah identifikasi protein pada pita protein yang memiliki keseragaman.

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Tuberculosis is an infectious disease caused by Mycobacterium tuberculosis which can cause infection in lungs and various other organs. In accordance with the provisions from WHO TB target product profiles (TPP), it is necessary to develop a rapid test that could detect various types of TB cases using an alternative sample, urine. The aim of this study was to obtain basic information regarding urine protein profile of TB groups and the healthy group through SDS-PAGE protein separation method, as an initial research step to determine TB protein markers. This research begins with pooling urine samples of confirmed subjects with pulmonary TB (5), extra-pulmonary TB (5), TB-HIV (5), and clinical TB (5), as well as 5 healthy subjects according to groups, after isolation and protein separation using SDS-PAGE, gel was stained using Commassie Brilliant Blue dye, and the end results were analyzed using ImageJ. The urine protein profiles of the healthy group and the four TB groups showed differences in the number, intensity, and estimated concentration of the expressed protein bands. The TB-HIV group had high-intensity protein expression and was dominantly expressed in the low molecular weight category. The protein profile of TB groups showed uniformity in the intermediate and low molecular weight categories. There are three protein bands that have uniformity in the four profiles of the TB group with fairly high estimated intensity and concentration, namely bands with molecular weights of 52.83±56.31kDa, 48kDa, and 23.8±24.57kDa. Through the SDS-PAGE method, the urine protein profiles of the healthy and TB groups were successfully observed, and the uniformity of protein bands expressed in the TB group also has the potential for the discovery of inclusive TB protein markers. For further research, it is necessary to identify the protein band that has uniformity."

"Leptospirosis adalah penyakit menular yang disebabkan oleh bakteri Leptospira spp. yang terjadi di seluruh dunia, termasuk Indonesia. Gejala penyakit ini mirip dengan penyakit menular lainnya, membuat diagnosis klinis sulit. Hasil diagnosis klinis didukung oleh serodiagnostik IgM MAT dan LFA, tetapi terbatas hanya pada beberapa layanan kesehatan sekunder. Serodiagnostik ini memiliki kelemahan karena kurang sensitif dan spesifik serta membutuhkan waktu analisis yang lama sehingga metode tersebut kurang tepat untuk deteksi dini leptospirosis. Salah satu metode molekuler seperti PCR dapat menjadi alternatif deteksi dini leptospirosis karena lebih akurat, sensitif dan spesifik. LipL32 dapat digunakan sebagai biomarker karena mampu mendeteksi bakteri patogen penyebab kematian. Deteksi leptospirosis melalui PCR konvensional menggunakan gen LipL32 menggunakan sampel serum darah telah banyak dilakukan di beberapa negara Asia, namun belum ada penelitian serupa di Indonesia. Penelitian ini bertujuan untuk mendeteksi leptospirosis melalui metode PCR konvensional menggunakan gen LipL32 menggunakan 30 sampel serum darah pasien RSCM yang secara klinis diduga leptospirosis. Metode yang digunakan terdiri dari isolasi DNA, kuantifikasi konsentrasi dan kemurnian DNA, PCR dan elektroforesis. Hasil penelitian menunjukkan terdapat 25 sampel positif leptospirosis dan setelah dibandingkan dengan MAT dan LFA IgM menunjukkan bahwa PCR konvensional memiliki sensitivitas yang lebih tinggi (83%) dibandingkan dengan MAT dan LFA IgM.Leptospirosis is an infectious disease caused by the bacteria Leptospira spp. happening all over the world, including Indonesia. Symptoms of this disease are similar to those of other infectious diseases, making clinical diagnosis difficult. Clinical diagnosis results are supported by IgM MAT and LFA serodiagnostics, but are limited to a few secondary health services. This serodiagnostic has weaknesses because it is less sensitive and specific and requires a long analysis time so that the method is not appropriate for early detection of leptospirosis. One of the molecular methods such as PCR can be an alternative for early detection of leptospirosis because it is more accurate, sensitive and specific. LipL32 can be used as a biomarker because it is able to detect pathogenic bacteria that cause death. Detection of leptospirosis through conventional PCR using the LipL32 gene using blood serum samples has been widely carried out in several Asian countries, but there has been no similar study in Indonesia. This study aims to detect leptospirosis through conventional PCR methods using the LipL32 gene using 30 samples of blood serum from RSCM patients clinically suspected of leptospirosis. The method used consisted of DNA isolation, quantification of DNA concentration and purity, PCR and electrophoresis. The results showed that there were 25 positive samples of leptospirosis and after being compared with MAT and LFA IgM showed that conventional PCR had a higher sensitivity (83%) compared to MAT and LFA IgM."

"COVID-19 merupakan penyakit menular yang disebabkan oleh SARS-CoV-2 dan ditetapkan sebagai pandemi global pada 11 Maret 2020 oleh WHO. Pemerintah Republik Indonesia mulai melaksanakan program vaksinasi booster untuk meningkatkan durabilitas sistem imun, khususnya pada tenaga kesehatan untuk memicu reaksi imunogenitas pada tubuh melalui produksi antibodi netralisasi (NAb). Namun, NAb memiliki durabilitas tertentu dan mungkin akan mengalami penurunan yang turut dipengaruhi oleh adanya SARS-CoV-2 varian baru yang muncul seperti varian Delta dan Omicron. Tujuan dari penelitian ini adalah mengevaluasi antibodi netralisasi yang dihasilkan oleh tenaga kesehatan di Jakarta sebelum dan setelah 12 bulan vaksinasi booster COVID-19, mengevaluasi antibodi netralisasi setelah 12 bulan vaksinasi booster COVID-19 terhadap 4 varian SARS-CoV-2 berupa varian wild type, Delta, Omicron (B.1.1.529), dan Omicron (BA.2), dan mengevaluasi antibodi netralisasi pada partisipan yang mengalami breakthrough infection dengan partisipan yang tidak mengalami breakthrough setelah 12 bulan vaksinasi booster COVID-19. Metode yang digunakan dalam penelitian ini adalah uji Surrogate Virus Neutralization Test (sVNT) yang sesuai untuk digunakan dalam mendeteksi antibodi netralisasi karena memiliki hasil yang baik dengan waktu deteksi singkat. Hasil penelitian yang diperoleh adalah terdapat kenaikan antibodi netralisasi yang signifikan pada saat 12 bulan pascavaksinasi booster dibandingkan dengan saat pravaksinasi booster. Selain itu, terdapat perbedaan kadar antibodi netralisasi antara keempat varian dengan penurunan antibodi netralisasi yang cukup signifikan sekitar 10—20% pada varian Omicron (B.1.1.529 dan BA.2). Tidak terdapat perbedaan antibodi netralisasi yang signifikan pada partisipan yang mengalami breakthrough infection dengan partisipan yang tidak mengalami breakthrough infection, namun, seluruh partisipan breakthrough infection memiliki tingkat keparahan COVID-19 kategori ringan. Kesimpulan penelitian ini adalah vaksinasi booster pertama pada partisipan menunjukkan durabilitas imun pada bulan ke-12 pascavaksinasi booster pertama yang masih tergolong baik dan kemungkinan berpengaruh terhadap rendahnya tingkat keparahan gejala COVID-19 pada partisipan yang mengalami breakthrough infection. Varian baru SARS-CoV-2 seperti Omicron (B.1.1.529 dan BA.2) menyebabkan penurunan respons kekebalan tubuh sehingga perlu dilaksanakan vaksinasi booster lanjutan.

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COVID-19 is an infectious disease caused by SARS-CoV-2 and was declared as global pandemic on 11 March 2020 by WHO. The Government of the Republic of Indonesia has started implementing a booster vaccination program to increase the durability of the immune system, especially for healthcare workers to trigger an immunogenic reaction in the body through the production of neutralizing antibodies (NAb). However, NAb has a certain durability and may experience a decrease which is also influenced by the emergence of new SARS-CoV-2 variants such as the Delta and Omicron variants. The purpose of this study was to evaluate the neutralization antibodies produced by healthcare workers in Jakarta before and after 12 months of the COVID-19 booster vaccination, to evaluate the neutralization antibodies after 12 months of the COVID-19 booster vaccination against 4 variants of SARS-CoV-2 in the form of wild type variants, Delta, Omicron (B.1.1.529), and Omicron (BA.2), and evaluated neutralizing antibodies in participants who experienced a breakthrough infection with participants who did not experience a breakthrough after 12 months of the COVID-19 booster vaccination. The method used in this study is the Surrogate Virus Neutralization Test (sVNT) which is suitable for detecting neutralizing antibodies because it has good results with a short detection time. The results of the study were that there was a significant increase in neutralizing antibodies 12 months after the booster vaccination compared to the prevaccination booster. In addition, there were differences in neutralizing antibody levels between the four variants with a significant decrease in neutralizing antibodies of around 10—20% in the Omicron variants (B.1.1.529 and BA.2). There was no significant difference in neutralizing antibodies in participants who experienced a breakthrough infection and participants who did not experience a breakthrough infection. However, all breakthrough infection participants had a mild level of COVID-19 severity. The conclusion of this study is that the first booster vaccination in participants shows immune durability at the 12th month after the first booster vaccination which is still relatively good and may have an effect on the lower severity of COVID-19 symptoms in participants who experience a breakthrough infection. New variants of SARS-CoV-2 such as Omicron (B.1.1.529 and BA.2) cause a decrease in the body's immune response so that further booster vaccinations are necessary."

"Pandemi Coronavirus Disease 2019 (COVID-19) terjadi akibat cepatnya penyebaran Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) sehingga membutuhkan uji yang cepat dan tepat. Real-time polymerase chain reaction(real-time PCR) menggunakan sampel swab nasofaring merupakan standar baku emas, namun sifatnya yang invasif dan tingginya risiko aerosolisasi menjadi kekurangan sampel swab nasofaring. Saliva dinilai dapat menjadi sampel alternatif dalam uji deteksi COVID-19 karena proses koleksi yang tidak invasif, risiko aerosolisasi rendah, serta dapat dilakukan tanpa kontak langsung dengan tenaga kesehatan. Oleh karena itu, tujuan penelitian ini adalah 1) mengevaluasi potensi saliva dalam uji deteksi COVID-19 menggunakan metode real-time PCR dan gen deteksi Envelope (E) serta RNA-dependent RNA polymerase (RdRp), 2) membandingkan hasil real-time PCR sampel swab nasofaring dengan sampel saliva untuk mendapatkan nilai diagnostik, serta 3) mengetahui pengaruh penyimpanan saliva pada suhu -80°C selama tiga dan enam bulan terhadap nilai cycle threshold (Ct) dari real-time PCR yang dilakukan. Metode yang dilakukan meliputi isolasi RNA dengan QIAamp Viral RNA mini kit, kuantifikasi RNA dengan spektrofotometer, amplifikasi dengan real-time PCR, serta analisis data. Hasil real-time PCR menunjukkan bahwa gen E dan RdRp terdeteksi pada 45 dari 128 sampel dengan rentang nilai Ct 14,953—34,8509 dan rata-rata 24,98. Nilai diagnostik yang dihasilkan berupa nilai sensitivitas sebesar 87,2%, spesifisitas 95,1%, positive predictive value (PPV) 91,1%, dan negative predictive value(NPV) 92,8%. Saliva yang disimpan dalam suhu -80°C menunjukkan nilai Ct yang tidak berbeda secara signifikan setelah 3 dan 6 bulan penyimpanan. Kesimpulan penelitian adalah saliva dapat digunakan sebagai sampel alternatif dalam deteksi COVID-19 dengan metode real-time PCR dan gen deteksi E serta RdRp menggunakan sampel yang disimpan selama 3 dan 6 bulan tanpa buffer di suhu -80°C meskipun belum memenuhi kriteria standar WHO.

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The Coronavirus Disease 2019 (COVID-19) pandemic occurred as a result of the rapid spread of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) thus requiring rapid and appropriate testing. Real-time polymerase chain reaction (real-time PCR) using nasopharyngeal swab samples is the gold standard, but its invasive nature and high risk of aerosolization is a shortage of nasopharyngeal swab samples. Saliva is considered to be an alternative sample in the COVID-19 detection test because the collection process is non-invasive, has a low risk of aerosolization, and can be done without direct contact with health workers. Therefore, the aims of this study were 1) to evaluate the potential of saliva in the COVID-19 detection test using the real-time PCR method and the Envelope (E) detection gene and RNA-dependent RNA polymerase (RdRp), 2) to compare the results of real-time PCR nasopharyngeal swab samples with saliva samples to obtain diagnostic value, and 3) to determine the effect of storing saliva at -80°C for three and six months on the cycle threshold (Ct) value of the real-time PCR performed. The methods used included RNA isolation with the QIAamp Viral RNA mini kit, RNA quantification with a spectrophotometer, amplification with real-time PCR, and data analysis. Real-time PCR results showed that the E and RdRp genes were detected in 45 of 128 samples with a Ct value range of 14.953-34.8509 and an average of 24.98. The resulting diagnostic value was a sensitivity value of 87.2%, a specificity of 95.1%, a positive predictive value (PPV) of 91.1%, and a negative predictive value (NPV) of 92.8%. Saliva stored at -80°C showed Ct values that were not significantly different after 3 and 6 months of storage. The conclusion of the study is that saliva can be used as an alternative sample in detecting COVID-19 with the real-time PCR method and detecting E and RdRp genes using samples stored for 3 and 6 months without buffer at -80°C even though they do not meet WHO standard criteria."

"Kendala utama dalam diagnosis penyakit tuberkulosis (TB) paru di Indonesia adalah sulitnya pengeluaran sputum sebagai spesimen diagnostik dari pengidap TB paru, terutama pada kelompok anak dan lansia. Pengembangan spesimen alternatif, seperti urine, sangat dibutuhkan untuk meningkatkan notifikasi kasus TB paru pada subjek yang belum terdiagnosis secara optimal. Penelitian ini mengevaluasi potensi urine pada 60 sampel terkonfirmasi TB paru positif, sebagai studi kasus-kontrol dengan subjek yang memiliki kondisi target. Tujuan penelitian ini meliputi evaluasi multiplex polymerase chain reaction (PCR), untuk mendeteksi gen ESAT6, IS6110, dan MPT64, serta real-time PCR untuk deteksi gen ESAT6 dalam menunjang diagnosis TB paru. Selain itu, penelitian ini diharapkan dapat menggambarkan nilai sensitivitas masing-masing metode dan gen diagnostik yang digunakan. Metode penelitian meliputi preparasi sampel urine, isolasi DNA, kuantifikasi DNA, amplifikasi DNA (multiplex PCR dan real-time PCR), elektroforesis DNA, dan analisis data. Hasil evaluasi menunjukkan kemurnian total DNA yang diisolasi dari urine berdasarkan A260/A280   (Mean 3,08  SD 1,08). Evaluasi multiplex PCR dengan gen deteksi ESAT6, IS6110, dan MPT64 memberikan nilai sensitivitas sebesar 68,3% (41/60), dan real-time PCR dengan gen deteksi ESAT6 sebesar 71,67% (43/60). Nilai sensitivitas real-time PCR diperoleh dengan ketentuan limit of detection (LOD) sebesar 13,04 kopi/μl. Nilai sensitivitas kedua metode tersebut menunjukkan bahwa urine dapat menjadi spesimen alternatif untuk pendeteksian Mycobacterium tuberculosis (Mtb) secara molekuler.

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The main obstacle in the diagnosis of pulmonary tuberculosis (TB) in Indonesia is the difficulty of extracting sputum, as a diagnostic specimen for people with pulmonary TB, especially in the group of children and the elderly. The development of alternative specimens, such as urine, is urgently needed to increase the notification of pulmonary TB cases in subjects who have not been diagnosed optimally. This study evaluated the urine potency of 60 samples of confirmed positive pulmonary TB, as a case-control study with subjects with the target condition. The objectives of this study include the evaluation of multiplex polymerase chain reaction (PCR), to detect the ESAT6, IS6110, and MPT64 genes, as well as real-time PCR to detect the ESAT6 gene in supporting the diagnosis of pulmonary TB. In addition, this study is expected to describe the sensitivity value of each diagnostic method and gene used. Research methods include urine sample preparation, DNA isolation, DNA quantification, DNA amplification (multiplex PCR and real-time PCR), DNA electrophoresis, and data analysis. The evaluation results showed the total purity of DNA isolated from urine based on A260/A280   (Mean 3,08  SD 1.08). Evaluation of multiplex PCR with ESAT6, IS6110, and MPT64 detection genes gave a sensitivity value of 68,3% (41/60), and real-time PCR with ESAT6 detection genes of 71,67% (43/60). Real-time PCR sensitivity value was obtained with the limit of detection (LOD) of 13,04 copies/μl. The sensitivity values of both methods indicate that urine can be an alternative specimen for molecular detection of Mycobacterium tuberculosis."