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"Pada bulan Desember, 2019, serangkaian kasus pneumonia dengan penyebab yang tidak diketahui muncul di China. Analisis data menunjukkan adanya coronavirus baru, yang diberi nama SARS-CoV-2. Beradasarkan WHO dan CDC pemeriksaan yang digunakan untuk mendeteksi SARS-CoV-2 adalah metode molekular RT-PCR, salah satu kit yang digunakan adalah BioCoV-19 RT-PCR. Penelitian ini bertujuan membandingkan uji RT-PCR kit BioCoV-19 RT-PCR dengan N1N2 CDC sebagai standar dalam mendeteksi SARS-CoV-2, serta melakukan uji deteksi minimal untuk mengetahui sensitivitas analitik dari kit BioCoV-19 RT-PCR, menguji reaksi silang terhadap mikroba saluran nafas lain, dan menilai secara deskriptif karakteristik subjek penelitian. Perbandingan uji kit BioCoV-19 RT-PCR dengan N1N2 CDC mendapatkan nilai sensitivitas, spesifisitas, nilai duga positif (NDP) dan nilai duga negative (NDN). Hasil pada penelitian ini menunjukkan bahwa sensitivitas dan spesifisitas BioCoV-19 RT-PCR Kit secara umum adalah 97,50% dan 100%, dengan Nilai Duga Positif (NDP) 100% dan Nilai Duga Negatif (NDN) 96,49%. Hasil uji minimal deteksi untuk primer-probe N1N2 CDC dan BioCoV-19 RT-PCR Kit setelah dilakukan dilusi bertingat sebanyak enam kali pengenceran yakni 3,5 kopi/reaksi (rerata nilai Ct 35,21). Uji reaksi silang tidak terdeteksi adanya reaksi silang dari 12 bakteri, tujuh virus dan tiga jamur. Karakteristik subjek penelitian lebih banyak pada laki-laki sebanyak (61,5%), untuk usia lebih banyak pada usia berkisar 20-40 tahun (56,29%), gejala klinis pasien saat datang lebih banyak gejala ringan.

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In December, 2019, a series of pneumonia cases of unknown cause appeared in China. Analysis of the data indicated the presence of a new coronavirus, which was named SARS-CoV-2. Based on WHO and the CDC, the tests used to detect SARS-CoV-2 are the molecular RT-PCR method, one of the kits used is BioCoV-19 RT-PCR. This study aims to compare the RT-PCR test of the BioCoV-19 RT-PCR kit with the CDC's N1N2 as a standard in detecting SARS-CoV-2, as well as to conduct a minimal detection test to determine the analytical sensitivity of the BioCoV-19 RT-PCR kit, to test cross reactions against other respiratory tract microbes, and descriptively assessed the characteristics of the research subjects. Comparison of the BioCoV-19 RT-PCR test kit with N1N2 CDC obtained sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). The results of this study showed that the sensitivity and specificity of the BioCoV-19 RT-PCR Kit in general were 97.50% and 100%, with a positive predictive value (PPV) of 100% and a negative predictive value (NPV) of 96.49%. The minimum test results for detection of the N1N2 CDC primer-probe and the BioCoV-19 RT-PCR Kit were carried out after six dilutions of 3.5 copies/reaction (mean Ct value 35.21). The cross-reaction test did not detect any positives of 12 bacteria, seven viruses and three fungi. The characteristics of the study subjects were more male (61.5%), for ages ranging from 20-40 years (56.29%), the clinical symptoms of the patients when they arrived were more mild symptoms."

"Latar Belakang: Melihat potensi tingginya jumlah virus didalam rongga mulut, dengan bukti bahwa SARS-CoV-2 ditemukan pada reseptor ACE2, perlu upaya untuk mencegah penularan dari pasien ke praktisi melalui saliva yang terkontaminasi. Virus ini menyebar lebih cepat karena SARS-CoV-2 bereplikasi disaluran pernapasan bagian atas dengan melepaskan patogen yang berpindah dari satu orang ke orang lain saat bersin dan batuk melalui penyebaran pernapasan. Diperkirakan waktu penularan bisa terjadi sebelum gejala muncul (sekitar 2,5 hari lebih awal dari munculnya gejala). Berkumur dengan hidrogen peroksida dapat menghilangkan lapisan permukaan epitel pada mukosa mulut yang diketahui terdapat reseptor ACE2 tempat terikatnya SARS- CoV-2 dan dapat menginaktivasi virus tersebut. Pedoman sementara American Dental Association (ADA) menyarankan penggunaan 1,5% Hidrogen peroksida sebagai pilihan untuk pembilasan mulut preoperatif sebagai obat kumur antiseptik. Nilai cycle threshold yang diperoleh RT – PCR bersifat semi-kuantitatif dan mampu membedakan antara viral load tinggi dan rendah. Tujuan Penelitian: Mengevaluasi perbedaan pengaruh penggunaan obat kumur diantara berkumur hidrogen peroksida 1,5% dan hidrogen peroksida 3% terhadap nilai cycle threshold RT-PCR pada pasien COVID - 19. Metode Penelitian: 42 subjek penelitian diambil dari pasien RSUP Persahabatan yang terinfeksi SARS-CoV-2 sesuai dengan kriteria inklusi dan ekslusi. Setelah dilakukan informed consent, subjek penelitian dibagi menjadi 3 kelompok, yaitu kelompok hidrogen peroksida 1,5%, kelompok hidrogen peroksida 3% dan kelompok kontrol. Subjek penelitian berkumur 30 detik di rongga mulut dan 30 detik di tenggorokan belakang dengan 15 ml sebanyak 3 kali sehari selama 5 hari. Analisis menggunakan nilai cycle threshold pada pemeriksaan RT-PCR pada hari ke-1, hari ke-3 dan hari ke-5 setelah berkumur. Hasil: Terdapat perbedaan bermakna pada hasil uji Friedman dan peningkatan nilai cycle threshold RT-PCR dari awal, hari ke-1, hari ke-3 dan hari ke-5 di keseluruhan kelompok dan masing – masing kelompok perlakuan. Peningkatan tertinggi nilai cycle threshold RT-PCR awal hingga hari ke-1 ditemukan pada kelompok hidrogen peroksida 3%, kemudian antara hari ke-1 hingga ke-3 dan hari ke-3 hingga hari ke-5 ditemukan pada kelompok hidrogen peroksida 1,5%. Kesimpulan: Berkumur hidrogen peroksida 1,5% dan hidrogen peroksida 3% berpengaruh terhadap peningkatan nilai cycle threshold RT-PCR SARS-CoV-2. Kedua konsentrasi hidrogen peroksida 1,5% dan hidrogen peroksida 3% memberikan pengaruh positif dalam menurunkan jumlah virus di rongga mulut, sehingga pilihan penggunaan konsentrasi hidrogen peroksida yang lebih kecil bisa menjadi pilihan untuk digunakan untuk berkumur.

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Background: Given the potential high number of viruses in the oral cavity, with evidence that SARS-CoV-2 is found at the ACE2 receptor, efforts are needed to prevent transmission from patient to practitioner through contaminated saliva. This virus spreads faster because SARS-CoV-2 replicates in the upper respiratory tract by releasing pathogens that are passed from one person to another when sneezing and coughing through respiratory spread. It is estimated that the time of transmission can occur before symptoms appear (about 2.5 days earlier than the onset of symptoms). Mouth rinse and gargling with hydrogen peroxide can remove the epithelial surface layer on the oral mucosa which is known to have ACE2 receptors where SARS-CoV-2 binds and can inactivate the virus. Interim guidelines of the American Dental Association (ADA) recommend the use of 1.5% hydrogen peroxide as an option for preoperative oral rinse as an antiseptic mouth rinse. The cycle threshold value obtained by RT-PCR is semi-quantitative and able to distinguish between high and low viral loads.

Objective: To evaluate the difference in the effect of using mouth rinse between 1.5% hydrogen peroxide and 3% hydrogen peroxide mouth rinse and gargling on the RT-PCR cycle threshold value in COVID-19 patients.

Methods: 42 subjects were patients recruited from Persahabatan General Hospital infected with SARS-CoV-2 according to the inclusion and exclusion criteria. Following informed consent procedure, the research subjects were divided into 3 groups, namely the 1.5% hydrogen peroxide group, the 3% hydrogen peroxide group and the control group. The subjects were instructed to rinse their mouths for 30 seconds and gargle for 30 seconds at the back of the throat with 15 ml of the mouth rinse 3 times a day for 5 days. Analysis of cycle threshold values was carried out using RT-PCR on day 1, day 3 and day 5 after mouth rinse and gargling.

Results: There were significant differences in the results of the Friedman test and an increase in the RT-PCR cycle threshold value starting from the beginning, day 1, day 3 and day 5 in the whole group and each treatment group. The highest increase RT-PCR cycle threshold value at day 1 was found in the 3% hydrogen peroxide group, while the increase between day 1 to 3 and day 3 to day 5 was found in the 1.5% hydrogen peroxide group.

Conclusion: Mouth rinse and gargling with 1.5% hydrogen peroxide and 3% hydrogen peroxide has an effect on increasing the cycle threshold value of the SARS-CoV-2 RT-PCR. Both 1.5% and 3% hydrogen peroxide concentration have a positive effect in reducing the number of viruses in the oral cavity, so the choice of using a lower hydrogen peroxide concentration can be an option to use for mouth rinse and gargling."

"Latar Belakang : COVID- 19 disebabkan SARS-COV-2. WHO menerbitkan protokol pemeriksaan laboratorium untuk deteksi virus menggunakan metode real time RT-PCR dari spesimen swab nasofaring dan orofaring. Metode ini cukup invasif. Diperlukan tehnik pemeriksaan yang relatif aman dan nyaman untuk pasien. Penelitian ini bertujuan untuk melihat efetivitas swab bukal sebagai alternatif pemeriksaan SARS-COV-2.Metode : Studi uji diagnostik ini dilaksanakan sejak tahun 2020 - 2021, mengambil spesimen swab nasofaring, swab orofaring dan swab bukal dari pasien positif COVID- 19. Dilakukan optimasi, ekstraksi RNA virus dan real time RT-PCR .Hasil Penelitian : Hasil studi mengumpulkan 68 spesimen dari pasien COVID-19. Hasil uji nasofaring, orofaring dan bukal positif adalah 24 spesimen. Hasil uji nasofaring dan orofaring positif dengan uji bukal negatif adalah 23 spesimen. Berdasarkan nilai Ct < 20 dan Ct <25, hasil kesesuaian positif dan negatif adalah 100%. Nilai Ct < 30 hasil kesesuaian positif 85,3 % dan negatif adalah 100%. Nilai Ct < 40 , hasil kesesuaian positif 51,1 % dan negatif adalah 100%. Kesimpulan : Swab bukal dapat digunakan sebagai pemeriksaan alternatif pada pemeriksaan SARS- CoV-2.

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Background: COVID-19 caused by the SARS-COV-2 virus. WHO published protocol for the detection of the virus using the real time RT-PCR from nasopharyngeal and oropharynx swab specimens. This method is invasive. Required an examination technique that is relatively safe and comfortable. This study aims to see the effectiveness of the buccal swab as an alternative to the SARS-CoV-2 examination.

Methods: This diagnostic test study from 2020 to 2021, specimens of nasopharyngeal, oropharyngeal and buccal swabs from COVID-19. Specimens underwent an optimization, viral RNA extraction and real time RT-PCR.

Result : This study collected 68 specimens from COVID- 19 patients. The results of positive nasopharyngeal, oropharynx and buccal tests were 24 specimens. The results of a positive nasopharynx and oropharynx test with a negative buccal test were 23 specimens. Based on the values ​​of Ct < 20 and Ct < 25 , the results of positive agreement and negative are 100%. The value of Ct < 30 and Ct < 40  results in a positive agreement are 85.3% and 51,1 %. The negative  results are 100%.

Conclusion : Buccal swab can be used as an alternative test for SARS-CoV-2 examination."

"Latar Belakang : Pasien yang terinfeksi COVID-19 sering menunjukkan gejala pencernaan. Dalam beberapa penelitian telah menemukan RNA SARS CoV-2 dalam spesimen faecal pasien yang terinfeksi. Tujuan : Mengetahui nilai RT-PCR faecal dan membandingkannya dengan RT-PCR naso-orofaring sebagai standar emas pada pasien COVID-19. Metode : Penelitian ini adalah studi deskriptif observasional, mendeteksi partikel virus melalui pemeriksaan RT-PCR pada faecal pasien COVID-19 yang dirawat di rumah sakit. Penelitian dilakukan di Rumah Sakit Nasional Dr. Cipto Mangunkusumo, Rumah Sakit Mitra Keluarga Depok, Rumah Sakit Mitra Keluarga Kelapa Gading, dan Rumah Sakit Ciputra, Indonesia. Swab naso-oro-orofaringeal dan spesimen feses dikumpulkan untuk deteksi RNA SARS CoV-2. Hasil : Diperoleh 98 sampel. Dalam penelitian ini memiliki nilai sensitifitas yang rendah (38,10%) juga nilai NPV (20,00%). Namun memiliki spesifisitas tinggi (92,86%) juga nilai PPV (96,97%). Kesimpulan : Penelitian ini menunjukkan bahwa hasil positif pada pemeriksaan RT-PCR faecal  sangat baik digunakan untuk membantu menegakkan diagnosis COVID-19. Namun hasil negatif tidak dapat digunakan untuk menyingkirkan COVID-19. Oleh karena itu, pemeriksaan RT-PCR faecal merupakan tes yang sangat baik sebagai tes konfirmasi COVID-19.  RT-PCR faecal kurang tepat jika digunakan sebagai tes pada awal masuk pasien COVID-19 (screening), RT-PCR swab naso-orofaring masih lebih baik digunakan sebagai standar diagnostik (screening) untuk COVID-19.

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Background: Patients infected by COVID-19 also show gastrointestinal.  In some studies have found  SARS CoV-2 RNA in faecal specimens of infected patients. Aims: This study will test the performance of faecal reserve transcription polymerase chain reaction (RT-PCR) when compared with naso-oropharyngeal swab RT-PCR as the gold standard test in COVID-19. Materials and Methods: This is an observational descriptive study by detection viral particle  by  RT-PCR on faecal from patients which suspected or probable cases of hospitalized COVID-19 infection, conducted in Dr. Cipto Mangunkusumo National Hospital, Mitra Keluarga Depok Hospital, Mitra Keluarga Kelapa Gading Hospital, and Ciputra Hospital, Indonesia. Naso-oropharyngeal swab and faecal spesimens were collected for RNA SARS CoV-2 detection. Results: We analized 98 subjects. Sensitivity and specificity of faecal were 38,10% and 92,86%, the positive and negatif predictive value were 96,97% and 20,00%. Conclusion: Faecal specimen has low sensitivity value (38.10%) and NPV (20.00%). However, it has a high specificity (92.86%) and PPV (96.97%). Positive results were very well used to help enforce the diagnosis of COVID-19, but negative results cannot be used to exlude COVID-19. This is an excellent test as a confirmation test of COVID-19, but may not be used as an additional test at beginning of diagnostik COVID-19 patients."

"Latar BelakangKasus pertama di AS memperlihatkan adanya gejala saluran cerna juga dialami oleh penderita COVID-19. Penelitian di Cina didapatkan pasien dengan keluhan pernapasan yang disertai keluhan saluran cerna adalah 47% dan ada 3% pasien yang hanya dengan keluhan saluran cerna saja tanpa gejala pernapasan.Pada penelitian RT-PCR ternyata ditemukan hasil positif tidak hanya pada saluran napas namun juga pada spesimen lain termasuk feses (29-53,42%). Pada biopsi endoskopi beberapa kasus juga ditemukan adanya virus SARS CoV-2 pada lambung, duodenum, ileum, dan juga rektum. Sedangkan penelitian menggunakan spesimen anal swab didapatkan angka 52,6% hasil positif.Terdapat laporan kasus dimana hasil pemeriksaan PCR swab nasofaring negatif, namun ternyata swab anal menunjukkan hasil positif dan persisten selama 42 hari. Metode RT-PCR dengan spesimen swab anal diharapkan dapat menjadi alternatif selain spesimen dari naso-orofaring.TujuanPada penelitian ini akan menguji performa tes PCR swab anal jika dibandingkan dengan tes PCR swab naso-orofaring sebagai alat diagnosis Covid-19.MetodePopulasi target adalah adalah pasien suspek atau probable Covid-19, usia>18 tahun. Subyek dengan diare profuse, Hematokezia atau melena masif, luka di anal, tidak disertakan dalam penelitian. Pemeriksaan RT-PCR swab anal dilakukan dengan MiRXES Fortitude Kit 2.1HasilPenelitian ini berhasil mendapatkan data dari 136 subyek. Selama penelitian tidak didapatkan komplikasi dan keluhan dari pasien selama pengambilan sampel anal. Sensitivitas RT-PCR swab anal adalah 36,67% (IK 95%: 28,04 sampai 45,28%) dan spesifisitas 93,75% (IK 95%: 81,88 sampai 100%). Nilai duga positif didapatkan 97,78% (IK 95%: 93,47 sampai100%) dan nilai duga negatif sebesar 16,48% (IK 95%:8,86 sampai 24,10%).SimpulanRT-PCR Swab anal dapat menjadi uji konfirmasi yang baik pada kasus COVID 19 dengan spesifisitas 93,8% pada kasus suspek dan probable COVID 19. Swab anal juga aman untuk dikerjakan.

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Background

The first US case of Covid 19 experiencing gastrointestinal disorders. Study in China found that patients with respiratory and gastrointestinal symptoms was 47% and there were 3% of patients with gastrointestinal symptoms only without respiratory symptoms.

It was found that positive results of RT-PCR were not only in the respiratory tract but also in other specimens including feces (29-53.42%). Endoscopic biopsy of several cases also found the SARS CoV-2 virus in the stomach, duodenum, ileum, and rectum. While the study using anal swab obtained 52.6% positive results. There was a case report that PCR examination of the nasopharyngeal swab was negative, but the anal swab was positive and persistent for 42 days. This finding certainly needs further investigation, because there may be cases of Covid-19 that were not detected by the naso-oropharygeal swab RT-PCR swab but can be detected by anal swabs. The RT-PCR method with anal swab is expected to be an alternative to the naso-oropharygeal swab.

Objective

This study test the performance of the anal PCR swab test when compared to the naso-oropharyngeal swab PCR test as a diagnostic tool for Covid-19.

Method

Subjects of this study are patients with suspected or probable Covid-19, aged> 18 years. Subjects with extensive diarrhea, massive hematoschezia or melena, and anal wounds, were not included in the study. RT-PCR anal swab examination was performed with MiRXES Fortitude Kit 2.1

Result

136 eligible subjects were analyzed. There were no complication and complaints from patients during sampling. The sensitivity of RT-PCR anal swab was 36.67% (CI: 28.04 to 45.28%) and specificity 93.75% (CI: 81.88 to 100%). The positive predictive value was 97.78% (CI: 93.47 to 100%) and the negative predictive value was 16.48% (8.86 to 24.10%).

Conclusion

RT-PCR Anal swabs can be a good confirmation tool of COVID 19 cases with a specificity of 93.8%, in suspected and probable COVID 19 cases. Anal swabs are also a safe procedure."

"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."

"Salah satu strategi untuk mengatasi pandemi Coronavirus disease-19 (COVID-19) ialah melalui diagnosis infeksi virus SARS-CoV-2 secara dini melalui Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR). Uji RT-PCR merupakan uji deteksi dan kuantifikasi asam nukleat. Salah satu metode ekstraksi asam nukleat adalah dengan bantuan material berbasis silika sebagai kolom matriks. Pada penelitian ini; dilakukan preparasi matriks Silica Coarse (SC) dalam matriks berwujud kolom suspensi, serbuk halus, dan keping cakram yang bersumber dari mineral aluminosilikat kaolin. Kemampuan pengikatan matriks SC berbasis mineral alam tersebut telah berhasil ditingkatkan dengan bantuan kation penyeimbang Na+ dan Guanidium+ yang dijenuhkan di dalam kerangka kaolin. Dilakukan pula upaya peningkatan sifat mekanik cakram SC melalui pengikatan dengan PEG 1500. Matriks Silica Coarse (SC) yang telah mengandung Na+ dan Guanidium+ kemudian dianalisa karakteristik fisikokimia-nya menggunakan instrumen FTIR, XRD, XRF, SEM, dan metode pengukuran luas area BET-distribusi pori BJH. Penelitian ini memberikan hasil bahwa matriks SC pellet basah (berwujud kolom suspensi) memberikan hasil ekstraksi yang dapat diamplifikasi lebih baik di bawah instrumen RT-PCR dibandingkan matriks SC pellet kering (berwujud serbuk halus dan cakram). Seluruh spesimen non aktif RNA virus SARS-CoV-2 yang digunakan dalam uji ekstraksi pada penelitian ini memiliki kisaran nilai ambang Ct < 20.

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One of the strategies to overcome the COVID-19 disease is through diagnostic clinical tests using the Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR) test. The RT-PCR test is a detection test and quantification test of nucleic acid. This method is initiated by pre-analytical step, known as extraction of nucleic acids. Extraction of nucleic acid requires silica-based materials as an extraction column. Herein, Silica Coarse (SC) in the form of suspension, powder and discs columns; were prepared from natural Indonesian Kaolinite as an alternative phase-extraction column to binding RNA of SARS-CoV-2. The RNA binding ability in SC was enhanced with chaotropic agents in the form of Na+ and Guanidium+ embedded on the kaolinite silicate framework. We were also improved the mechanical properties of SC discs with addition of PEG 1500. SC, embedded with Na+ and Guanidium+ respectively, then its physicochemical characteristics were studied using FTIR, XRD, XRF SEM, and BET surface area and pore measurement. This work shows that SC suspension column could extract RNA of SARS-CoV-2 that amplified better in RT-PCR test than SC dried columns, with the initial CT value of all the SARS-CoV-2 specimens in the range Ct < 20"

"Latar Belakang: Seiring berjalannya pandemi COVID-19, diperlukan tes diagnostik yang lebih baik, cepat, andal, mudah dan tersedia secara luas. Foto rontgen dada digunakan sebagai pemeriksaan awal untuk menegakkan diagnosis kerja. Kecanggihan Artificial Intelligence (AI) diketahui dapat meningkatkan presisi diagnosis Pneumonia pada foto rontgen dada. Salah satu program AI yang sedang marak digunakan adalah CAD4COVID-Xray. Tujuan: Penelitian ini bertujuan untuk mengetahui dan melihat perbedaan performa skoring AI dibanding skoring Brixia pada foto rontgen dada untuk mendiagnosis dan menentukan derajat keparahan pneumonia COVID-19. Metode: Penelitian ini menggunakan desain potong-lintang pada 300 pasien terduga dan terkonfirmasi pneumonia COVID-19. Rontgen dada dinilai secara kuantitatif menggunakan program CAD4COVID dan semi-kuantitatif menggunakan sistem skoring Brixia. Analisa performa diagnostik dinilai menggunakan estimasi AUC dan perbandingannya, serta perbandingan nilai sensitivitas, spesifisitas, nilai prediksi positif, nilai prediksi negatif dan akurasi. Hasil: AI probability score (AUC 0,542, IK95% 0,471-0,613), AI ALA score (AUC 0,442, IK95% 0,375-0,510) dan overall CXR score (AUC 0,461, IK95% 0,393-0,528) tidak memiliki kemampuan diskriminasi hasil RT-PCR SARS CoV-2 pada subjek terduga COVID-19. AI probability score (AUC = 0,888, IK95% 0,820- 0,956), AI ALA score (AUC = 0,875, IK95% 0,789-0,953) dan overall CXR score (AUC = 0,878, IK95% 0,808-0,948) memiliki kemampuan diskriminasi sangat baik untuk menentukan derajat keparahan penyakit subjek terkonfirmasi COVID-19. AI probability score (Sn 87,2%, Acc 85,6%) dan AI ALA score (Sn 82,6%, Acc 80,4%) lebih sensitif dan akurat dibandingkan overall CXR score (Sn 75,6%, Acc 78,4%) untuk mendiskriminasi derajat keparahan penyakit pneumonia COVID-19. Simpulan: AI probability score, AI ALA score dan overall CXR score tidak memiliki kemampuan membedakan hasil RT-PCR SARS CoV-2 pada subjek terduga COVID-19. AI probability score, AI ALA score dan overall CXR score memiliki kemampuan yang sangat baik untuk membedakan derajat keparahan penyakit subjek terkonfirmasi COVID-19. AI probability score dan AI ALA score lebih sensitif dan akurat dibandingkan overall CXR score untuk membedakan derajat keparahan penyakit pneumonia COVID-19.

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Background: As the COVID-19 pandemic progresses, a better, faster, reliable, easy and widely available diagnostic tests are needed. Chest X-rays are currently used as an initial examination to confirm a working diagnosis. Advancement of Artificial Intelligence (AI) is known to increase diagnosis precision of pneumonia on chest X-rays. One of the AI programs that is widely being used during the COVID-19 pandemic is CAD4COVID-Xray. Objective: This study aims to determine and compare the performance of AI scoring system using colour heat-map compared to Brixia scoring system on chest X-rays to diagnose and determine the severity of COVID-19 pneumonia. Methods: This study is a cross-sectional study, involving 300 suspected and confirmed COVID-19 pneumonia patients. Chest X-rays were assessed quantitatively using the CAD4COVID program and semi-quantitatively using the Brixia scoring system. Performance analysis is assessed using AUC estimation and its comparison, as well as comparisons of sensitivity, specificity, positive predictive value, negative predictive value and accuracy. Results: AI probability score (AUC 0.542, 95% IK 0.471-0.613), AI ALA score (AUC 0.442, 95% IK 0.375-0.510) and overall CXR score (AUC 0.461, 95% CI 0.393-0.528) did not have the ability to discriminate RT-PCR results of subjects with suspicion of COVID-19. AI probability score (AUC = 0.888, 95% CI 0.820- 0.956), AI ALA score (AUC = 0.875, 95% IK 0.789-0.953) and overall CXR score (AUC = 0.878, 95% CI 0.808-0.948) had excellent strength of agreement to determine disease severity in subjects with confirmed COVID-19. AI probability score (Sn 87.2%, Acc 85.6%) and AI ALA score (Sn 82.6%, Acc 80.4%) are more sensitive and accurate than overall CXR score (Sn 75.6%, Acc 78 ,4%) to determine the severity of COVID-19 pneumonia. Conclusions: AI probability score, AI ALA score and overall CXR score did not have the ability to discriminate RT-PCR results of subjects with suspicion of COVID-19. AI probability score, AI ALA score and overall CXR score had excellent strength of agreement to determine disease severity in subjects with confirmed COVID-19. AI probability score and AI ALA score are more sensitive and accurate than overall CXR score to determine the severity of COVID-19 pneumonia."

"Penyakit Coronavirus Disease 2019 (COVID-19) merupakan penyakit infeksi saluran pernafasan akut yang ditandai dengan batuk kering, sesak nafas, demam, dan Acute Respiratory Distress Syndrome (ARDS). Penyakit COVID-19 disebabkan oleh infeksi virus SARS-CoV-2 di saluran pernafasan manusia. Menurut Satuan Tugas COVID-19, kasus terkonfirmasi COVID-19 di Indonesia sampai tanggal 28 Juli 2021 sebanyak 3.287.727 pasien dengan penambahan kasus 47.791 pasien baru per hari. Salah satu langkah memperlambat penyebaran tersebut adalah dengan meningkatkan laju deteksi keberadaan virus SARS-CoV-2 berbasis pendeteksian asam nukleat virus SARS-CoV-2. Satuan tugas COVID-19 Indonesia telah merilis daftar kit komersial yang diizinkan beredar untuk deteksi materi genetik virus SARS-CoV-2 salah satunya adalah kit Seasun U-TOPTM COVID-19 pabrikan dari Seasun Biomaterials. Korea Selatan. Penelitian ini bertujuan untuk mengetahui baku mutu kit Seasun dalam mendeteksi virus SARS-CoV-2 di Indonesia. Pengujian baku mutu kit Seasun dilakukan dengan membandingkan nilai Cycle threshold (Ct) kit Seasun terhadap kit golden standard US CDC serta uji diagnosis kit Seasun menggunakan 20 sampel pasien positif COVID-19 dan 10 sampel pasien negatif COVID-19 berdasarkan protokol Pemantapan Mutu Eksternal (PME) Laboratorium COVID-19 Kementerian Kesehatan Republik Indonesia. Hasil analisis nilai Ct menunjukkan bahwa nilai Ct gen HRP dan gen N dari kit Seasun tidak berbeda signifikan dengan gen N1, gen N2, dan gen HRP dari golden standard US CDC berdasarkan uji ANOVA satu arah (p > 0,05; CI = 95%). Uji diagnosis menunjukkan kit Seasun terdapat hasil negatif palsu pada sampel N00212. Kit Seasun memiliki tingkat sensitivitas analitik sebesar 95% dan spesifisitas analitik sebesar 100%. Kit Seasun memiliki nilai baku mutu berada pada rentang nilai yang disetujui dan direkomendasikan oleh WHO serta dapat digunakan untuk kit deteksi SARS-CoV-2 di Indonesia

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Coronavirus Disease 2019 (COVID-19) is an acute respiratory infectious disease characterized by dry cough, shortness of breath, fever, and Acute Respiratory Distress Syndrome (ARDS). COVID-19 is caused by infection with the SARS-CoV-2 in the human respiratory tract. There were 3.287.727 confirmed cases of COVID-19 in Indonesia on July 28, 2021, with 47.791 new cases per day. The steps to slow the spread is to increase the detection rate of SARS-CoV-2 based on detection of the nucleic acid of the SARS-CoV-2. The Indonesian COVID-19 task force (Satgas COVID-19) has released a list of commercial kits allowed to detect genetic material for the SARS-CoV-2, one of them is the Seasun U-TOPTM COVID-19 kit. This study aims to determine the quality standard of the Seasun kit in detecting SARS-CoV-2 in Indonesia. The Seasun kit quality standard test was carried out by comparing the Cycle threshold (Ct) value of Seasun kit against the United States CDC golden standard kit and the Seasun kit diagnostic test using 20 samples of positive and 10 samples of negative COVID-19 patients based on the External Quality Assurance COVID-19 Laboratory protocol of the Ministry of Health of Republic of Indonesia. The results showed that the Ct values ​​of the HRP gene and the N gene from the Seasun kit were not significantly different from the N1 gene, N2 gene, and the HRP gene from the CDC golden standard based on ANOVA one-way (p > 0,05; CI = 95%). The diagnostic test showed that the Seasun kit had false-negative results in sample N00212 so that the Seasun kit had analytical sensitivity of 95% and analytical specificity of 100%. Seasun kit ​​approved and recommended by WHO to become a SARS-CoV-2 detection kit in Indonesia."

"Latar Belakang. Coronavirus Disease-19 (COVID-19) sampai sekarang masih menjadi ancaman kesehatan global. Baku emas diagnosis COVID-19 adalah pemeriksaan RT-PCR dari sampel usap nasofaring. Pengambilan sampel dengan cara ini memiliki kekurangan seperti rasa tidak nyaman pada pasien, risiko perdarahan, dan risiko paparan pada tenaga medis. Saliva merupakan salah satu alternatif sampel yang bisa digunakan untuk tujuan ini. Tujuan. Mengetahui sensitivitas, spesifisitas, nilai duga positif, nilai duga negatif, dan akurasi RTPCR saliva. Metode. Penelitian potong lintang pasien dewasa suspek COVID-19 pada April-Juni 2021 di instalasi gawat darurat rumah sakit Siloam Lippo Village. Pasien yang memenuhi syarat dan menyatakan setuju dilakukan pemeriksaan RT-PCR dari sampel usap nasofaring dan saliva. RTPCR dikerjakan dengan menilai gen N dan gen ORF1AB menggunakan alat Rotorgen QPlex-5Plus dengan batas positif CT Value < 40. Hasil. Sebanyak 126 pasien suspek COVID-19 yang eligible ikut penelitian selama periode studi. Enam pasien menolak mengikuti penelitian. Analisis akhir dikerjakan pada 120 pasien dengan proporsi laki-laki 42,5% dan median usia 50 tahun. Hasil RT-PCR positif ditemukan pada 69 (57,5%) sampel saliva dan 75 (62,5%) sampel usap nasofaring. Sensitivitas uji RT-PCR COVID19 dari sampel saliva adalah 86,67% (95% CI 76,84- 93,42), spesifisitasnya 91,11% (95% CI 78,78- 97,52). Nilai NDP yang didapat adalah 94,20% (95% CI 86,39-97,65) dan nilai NDN yang didapat 80,39% (95% CI 69,57-88,03). Akurasi yang didapat adalah 88,33% (95% CI 81,2093,47). Rerata CT value RT-PCR dari sampel saliva lebih tinggi dibandingkan sampel nasofaring, baik pada gen N (mean saliva 26,22 vs nasofaring 22,18; p= 0,01) maupun ORF1AB (mean saliva 26,39 vs nasofaring 23,24; p= 0,01). Simpulan. Saliva yang diambil dengan metode drooling merupakan sampel yang akurat untuk pemeriksaan RT-PCR COVID-19.

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Background. Coronavirus Disease-19 (COVID-19) is still a global health problem. Diagnostic gold standard for COVID-19 is RT-PCR of the nasopharyngeal swab specimen. However, this method has several issues such as patient’s discomfort, risk of bleeding, and risk of exposure to examiner. Saliva is a viable alternative sample for this examination. Aim. To find out the sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of saliva RT-PCR. Method. Crossectional study in adult patient with suspect ofCOVID-19 during April-June 2021 in emergency unit Lippo Village Hospital. Eligible and agreed patient are examined with RT-PCR from nasopharyngeal swab and saliva. RT-PCR was done by targeting gene N and ORF1AB using Rotorgen QPlex-5-Plus with CT value cut off 40. Result. A total of 126 suspected COVID-19 cases were admitted to ER during study period. Six patients were disagree to join. Final analysis was carried out on 120 patients (42.5% male, media age 60). Positive RT-PCR was found in 69 (57.5%) saliva specimens and 75 (62.5%) nasopharyngeal specimens. Sensitivity of saliva specimens was 86.67% (95% CI 76.84- 93.42), with specificity of 91.11% (95% CI 78.78-97.52). NDP of saliva was 94.20% (95% CI 86.39-97.65) with NDN of 80.39% (95% CI 69.57-88.03). Saliva’s accuracy was 88.33% (95% CI 81.20-93.47). Mean CT value of saliva specimens was higher than nasopharyngeal specimens in both gene N (mean saliva 26.22 vs nasopharyngeal 22.18; p= 0.01) and ORF1AB (mean saliva 26.39 vs nasopharyngeal 23.24; p= 0.01). Conclusion. Saliva collected with drooling method is an accurate sample for COVID-19 RT-PCR."