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"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 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."

"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."

"Background: real-time RT-PCR was recommended by WHO for COVID-19 diagnosis. The cycle threshold (Ct) values were expected to have an association with clinical manifestation. However, the diagnostic modalities such as quantitative molecular detection and virus isolation were not yet available for the routine test. This study has been conducted to analyze the relationship between the Ct values of qualitative rRT-PCR and the clinical manifestation and to describe the factors determining the result. Methods: from March to April 2020, specimens were sent to our laboratory from different healthcare centers in Jakarta. The patient's characteristic and clinical manifestation were extracted from the specimen's epidemiology forms. The specimens extracted and tested using rRT-PCR, and the Ct value were collected. The data were analyzed using the appropriate statistic test.Results: from 339 positive results, the mild to moderate case was 176 (52%) and the severe cases was 163 (48%). Female was dominant in the mild to moderate cases (58%), while the male was prevalent in the severe cases (60%). The median age for mild to moderate case was 35 years old and severe cases was 49 years old. Statistical analysis found relationship between both group with gender (p = 0.001) and age (p < 0.001), but not with the Ct value. Conclusion: many variables in specimen sampling and processing could affect the Ct value result. In addition, the disease's severity was depended with the host immune response, regardless the number of virus. There was suggested no significant difference between the Ct values of mild-moderate and severe COVID-19, and thus should not be loosely interpreted."

"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."

"Latar Belakang. SARS-CoV-2 menimbulkan beban yang sangat besar pada masyarakat, sistem ekonomi dan kesehatan di seluruh dunia. Berbagai langkah diambil untuk mengendalikan penyebarannya. Langkah – langkah tergantung pada diagnosis yang tepat waktu dan akurat dari orang yang terinfeksi virus. Penyebaran COVID-19 yang cepat, deteksi virus yang cepat dan tepat memegang peranan penting untuk mengendalikan infeksi dan membantu pasien untuk mencegah perkembangan penyakit lebih lanjut. Metode real-time reverse transcriptase-PCR (rRT-PCR) sangat dianjurkan untuk deteksi SARS-CoV-2 sebagai uji kualitatif spesifik dan sederhana. Selain metode menggunakan rRT-PCR, telah terdapat metode dengan pendekatan yang berbeda untuk mendeteksi SARS-CoV-2. Salah satu metode tersebut adalah VereCoVTM yang memiliki cara kerja berdasarkan teknik PCR dan hibridisasi, namun performa dari VereCoVTM masih belum diketahui.Tujuan. Penelitian bertujuan untuk mengetahui kesesuaian dan kaitannya dengan gejala klinis menggunakan uji VereCoVTM dengan rRT-PCR dalam mendeteksi SARS-CoV-2.Metode. Penelitian ini menggunakan consecutive sampling. Sampel penelitian yaitu sampel swab nasofaring dan orofaring yang diambil kemudian dianalisis di Laboratorium Mikrobiologi Klinik Fakultas Kedokteran Universitas Indonesia. Analisis data menggunakan Kappa Cohen. Selanjutnya, dilakukan analisis data kesesuaian hasil pemeriksaan kedua uji pada pasien dengan gejala dan pasien tanpa gejala.Hasil. Perbedaan positivity rate antara VereCoVTM dan rRT-PCR sebesar 68% menunjukkan bahwa VereCoV™ memberikan hasil negatif palsu. Jika disandingkan terhadap data hasil rRT-PCR, maka ambang batas deteksi VereCoVTM setara dengan nilai Ct<32 atau setara dengan 118 salinan RNA. Tidak dijumpai reaksi silang dengan beberapa mikroorganise. Konsistensi antara kedua uji ditunjukan oleh koefisien Kappa (=0,609). Hal ini menggambarkan kesesuian yang moderate atau sedang. Analisis lebih lanjut menunjukkan bahwa kesesuaian kedua pemeriksaan meningkat pada pasien yang bergejala (90%), sebaliknya menurun pada pasien tanpa gejala (76,5%). VereCoVTM lebih sesuai digunakan untuk mendeteksi SARS-CoV-2 pada pasien yang bergejala. Hasil negatif pada VereCoVTM tidak dapat mengesampingkan kemungkinan infeksi COVID-19, sehingga perlu pemeriksaan lebih lanjut untuk mendukung diagnosis yang tepat.Kesimpulan. VereCoV™ lebih cocok untuk mendeteksi SARS-Cov-2 pada pasien yang bergejala. VereCoVTM tidak menunjukan adanya reaksi silang dengan beberapa mikroorganisme, yang terdapat pada saluran pernapasan.

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Background. SARS-CoV-2 places an enormous burden on society, economic systems and health around the world. Various steps were taken to control its spread. These steps depend on timely and accurate diagnosis of the person infected with the virus. The rapid spread of COVID-19, rapid and precise detection of the virus play an important role in controlling infection and helping patients to prevent further disease progression. The real-time reverse transcriptase-PCR (rRT-PCR) method is highly recommended for the detection of SARS-CoV-2 as a simple and specific qualitative test. In addition to the method using rRT-PCR, there have been methods with different approaches to detect SARS-CoV-2. One of these methods is VereCoVTM which has a working method based on PCR and hybridization techniques, but the performance of VereCoVTM is still unknown.

Aim. The aim of the study was to determine the suitability and relation to clinical symptoms using the VereCoVTM test with rRT-PCR in detecting SARS-CoV-2.

Method. This study used consecutive sampling. The samples of the study was swab samples of the nasopharynx and oropharynx which were taken and analyzed at the Clinical Microbiology Laboratory, Faculty of Medicine, Universitas Indonesia. Data was then analyze using Kappa Cohen. Furthermore, the data analysis of the suitability of the results of the two tests was carried out in patients with symptoms and patients without symptoms.

Results. The difference in positivity rate between VereCoVTM and rRT-PCR of 68% indicates that VereCoV™ gives a false negative result. When compared to the rRT-PCR data, the VereCoVTM detection threshold is equivalent to a Ct value <32 or equivalent to 118 copies of RNA. No cross reactions were found with some microorganisms. Consistency between the two tests is indicated by the Kappa coefficient (= 0.609). This describes a moderate or moderate fit. Further analysis showed that the concordance of the two examinations increased in symptomatic patients (90%), on the contrary decreased in asymptomatic patients (76.5%). VereCoVTM is more suitable for detecting SARS-CoV-2 in symptomatic patients. A negative result on VereCoVTM cannot rule out the possibility of COVID-19 infection, so further tests are needed to support a correct diagnosis.

Summary. VereCoV™ is more suitable for detecting SARS-Cov-2 in symptomatic patients. VereCoVTM did not show any cross-reactivity with some microorganisms, which are present in the respiratory tract."

"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."

"Demam akut yang disertai gejala mirip demam Dengue nyeri kepala, nyeri sendi, ruam, perdarahan perifer seperti mimisan, ptekie adalah gejala yang paling sering dikeluhkan oleh pasien. Gejala-gejala tersebut seringkali diakibatkan infeksi arbovirus yang sangat endemik di Indonesia sebagai negara tropis. Deteksi agen penyebab infeksi tersebut sangat diperlukan untuk penatalaksanaan yang tepat. Studi ini melakukan uji optimasi untuk deteksi molekuler virus penyebab demam mirip demam Dengue, meliputi DENV, ZIKV, WNV, JEV, YFV, CHIKV, dan Hantavirus menggunakan RT PCR. Primer pada studi ini dirancang menggunakan perangkat lunak online Primer-BLAST dari NCBI dan primer-primer tersebut memenuhi kriteria untuk reaksi RT PCR. Kontrol positif pada real time RT-PCR menggunakan DNA sintetik yang dirancang sesuai dengan amplicon target virus. DNA sintetik sepanjang 1.047 pasang basa dirancang untuk digunakan pada virus ZIKV, JEV, YFV, WNV, CHIKV, dan Hantavirus. Suhu penempelan optimum pada primer-primer adalah 600C kecuali primer flavivirus universal yaitu 560C. Limit deteksi primer JEV mencapai 4.355 salinan DNA setiap reaksi real time RT PCR. Tidak terdapat reaksi silang maupun positif palsu pada sampel RNA DENV serotipe 2 maupun pada sampel orang sehat yang digunakan pada studi ini. Sebagai kesimpulan, studi ini menghasilkan primer dan protokol real time RT-PCR yang berpotensi untuk dikembangkan lebih lanjut untuk digunakan dalam uji diagnostik pada sampel pasien demam akut menyerupai gejala demam Dengue.

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Acute fever with Dengue like fever symptoms headache, rash, joint pain, perifer bleeding like ptechie, rinhorrhea is general symptoms that often being complained by patient. Usually the etiology agent of the symptoms are arbovirals which are endemic in Indonesia as a tropical country. In this case, molecular detection is very important to confirm the etiology of disease for prompt and adequate management. This study optimized viral molecular detection as an etiology agent for Dengue like fever symptoms using real time RT PCR. The viruses that were investigated were DENV, ZIKV, WNV, JEV, YFV, CHIKV, and Hantavirus. Primer were designed used Primer BLAST software from NCBI. Those primers fulfilled the good primer requirements and could be used in real time RT PCR reaction. Synthetic DNA with 1.047 base pairs was designed based on amplicon target to be used as control positive for ZIKV, JEV, YFV, WNV, CHIKV, and Hantavirus. The optimal annealing temperature for all primers were at 600C except for flavivirus universal primer was at 560C. The limit of detection of JEV primer was 4355 copies DNA per reaction. Cross reactivity between all primers with DENV serotype 2 RNA and healthy person sample were not found. This study still need RNA viruses as negative or positive control and clinical sample to determine the sensitivity and specificity. As a conclusion, this study provided primers and real time RT PCR protocol that potentially be further developed as diagnostic tools for patient with Dengue like fever symptoms. "

"Penelitian ini mengembangkan metode deteksi spesies babi (Sus scrofa) pada sampel daging campuran menggunakan automasi ekstraksi DNA magLEAD gC. DNA dianalisis menggunakan PCR dan TaqMan probe RT-PCR dengan primer spesifik untuk gen Cytochrome c oxidase I (COI), Cytochrome b (Cytb), dan NADH5 dehydrogenase 5 (ND5). Hasil menunjukkan bahwa ekstraksi DNA otomatis menghasilkan konsentrasi DNA 129,4–388,5 ng/μL pada daging mentah dan 66,4–89,5 ng/μL pada bakso dengan rasio kemurnian A260/A280 dan 260/A230 > 1,8. Primer COI, Cytb dan ND5 dapat mendeteksi DNA babi. PCR dan RT-PCR in vitro menunjukkan ketiga primer hanya mendeteksi DNA babi. Efisiensi amplifikasi RT-PCR primer COI, Cytb, dan ND5 adalah 144,14% (R2=0,982), 88,05% (R2=0,998), dan 81,25% (R2=0,997) dengan batas deteksi 0,0001 ng/μL, 0,001 ng/μL, dan 0,001 ng/μL. Primer/probe Cytb dan ND5 mendeteksi bakso dengan campuran daging babi hingga 0,1% (w/w).

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This study developed a method to detect pig species (Sus scrofa) in mixed meat samples using automated DNA extraction with the magLEAD gC. DNA was analyzed using PCR and TaqMan probe RT-PCR with specific primers for the genes Cytochrome c oxidase I (COI), Cytochrome b (Cytb), and NADH5 dehydrogenase 5 (ND5). Results showed that automated DNA extraction produced DNA concentrations of 129.4–388.5 ng/μL in raw meat and 66.4–89.5 ng/μL in processed meatballs with purity ratios A260/A280 dan 260/A230 > 1.8. The COI, Cytb and ND5 primers could be used to detect pig DNA. In vitro PCR and RT-PCR showed that all three primers only detected pig DNA. The RT-PCR amplification efficiency for COI, Cytb, and ND5 primers were 144,14% (R2=0,982), 88,05% (R2=0,998), dan 81,25% (R2=0,997) with detection limits of 0.0001 ng/μL, 0.001 ng/μL, and 0.001 ng/μL. The Cytb and ND5 primers/probes detected meatballs with pig meat content as low as 0.1% (w/w)."