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"Latar Belakang. Saat ini sedang terjadi pandemi COVID-19 di seluruh dunia, pandemi ini dimulai dari Wuhan, Cina. Virus SARS-CoV-2 penyebab COVID-19 sangat menular dan penyebarannya sangat cepat, sehingga memerlukan penanganan khusus seperti isolasi atau karantina. Gejala penyakit COVID-19 menyerupai gejala infeksi saluran pernapasan akut yang disebabkan oleh patogen lain seperti SARS, influenza, rhinovirus, dll. Diagnosis penyakit COVID-19 perlu ditentukan untuk membedakan dari ISPA yang diakibatkan oleh patogen lain. Beberapa uji diagnostik telah di kembangkan untuk deteksi cepat penyebab COVID-19.Tujuan. Tujuan penelitian ini adalah membandingkan alat diagnostik kit antigen ”Genbody COVID-19 Test Ag®” dengan rRT-PCR yang menjadi refensi test, untuk mendapatkan alat diagnostik yang murah, cepat dan akurat serta memiliki kemampuan yang setara dengan rRT-PCR.Metode. Penelitian ini merupakan uji banding dengan desain penelitian potong lintang dan metode pengumpulan spesimen secara consecutive sampling pada pasien contact tracing COVID-19. Penelitian dilakukan di Fasilitas Pelayanan Kesehatan (FASYANKES) Puskesmas Kecamatan Tanah Abang, Sawah Besar, Senen dan Laboratorium Mikrobiologi Klinik (LMK) FKUI pada bulan Oktober 2020-Desember 2020. Sampel penelitian merupakan swab Nasofaring dan oropharing dari pasien contact tracing COVID-19 yang dilakukan pemeriksaan rRT-PCR menggunakan reagen LiliF COVID-19 Real Time PCR kit dan pemeriksaan antigen menggunakan “Genbody COVID-19 Test Ag®”. Analisis penelitian ini menggunakan tabel 2x2.Hasil. Dari 233 sampel sebanyak 80 (34,33%) sampel positif rRT-PCR dan 53 (22,74%) sampel yang positif pada kit antigen. Kit antigen yang digunakan pada penelitian ini mempunyai sensitivitas 66,25% (55,89-76,61), spesifisitas 100% (100-100), Nilai Duga Positif (NDP) 100% (100-100), Nilai Duga Negatif (NDN) 85% (79,78-90,22) dan akurasi 88,41%. Pada hasil rRT-PCR dengan CT < 20, kit test antigen mempunyai sensitivitas 97,14% (91,62-102,66), spesifisitas 100% (100-100) dan pada CT ≥ 21-≥ 30 sensitivitas kit antigen terus menurun.Kesimpulan. Pemeriksaan COVID-19 menggunakan kit test antigen “Genbody COVID-19 Test Ag®” mempunyai sensitivitas rendah yang tidak sesuai dengan rekomendasi WHO. Kit antigen ini mempunya sensitivitas yang tinggi pada sampel dengan hasil rRT-PCR pada CT rendah (CT <20).

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Introduction. Currently, the COVID-19 pandemic is happening over the world, this pandemic started in Wuhan, China. The SARS-CoV-2 virus that causes COVID-19 is highly contagious, spreads very quickly and requiring special handling such as isolation or quarantine. The symptoms of COVID-19 resemble an acute respiratory infection caused by other pathogens such as SARS, influenza, rhinovirus, etc. The diagnosis of COVID-19 disease needs to be determined to distinguish it from acute respiratory infection caused by other pathogens. Several diagnostic tests have been developed for rapid detection of the cause of COVID-19.

Aim. The research aims to compare the antigen kit "Genbody COVID-19 Test Ag®" with rRT-PCR as a reference test to obtain an affordable, fast and accurate diagnostic tool and have equivalent capabilities as rRT-PCR.

Method. The research is a comparative testing with a cross-sectional design and consecutive sampling method for collecting specimens in COVID-19 contact tracing patients. The research was conducted at the Health Service Facility (FASYANKES) Puskesmas Kecamatan Tanah Abang, Sawah Besar, Senen and Laboratorium Mikrobiologi Klinik (LMK) FKUI in October 2020-December 2020. The research samples were nasopharyngeal and oropharyngeal swabs from COVID-19 contact tracing patients who were carried out rRT-PCR test using LiliF COVID-19 Real Time PCR kit and antigen test using “Genbody COVID-19 Test Ag®”. The research analysis used a 2x2 table.

Results. Of the 233 samples, 80 (34.33%) were positive for rRT-PCR and only 53 (22.74%) were positive for the antigen kit. The antigen kit used in this research had a sensitivity of 66.25% (55.89-76.61), specificity 100% (100-100), Positive Prediction Value (NDP) 100% (100-100), Negative Suggestion Value ( NDN) 85% (79.78-90.22) and accuracy 88.41%. On the results of rRT-PCR with CT < 20, the antigen test kit had a sensitivity of 97.14% (91.62-102.66), specificity 100% (100-100) and at CT 21-30 the sensitivity of the antigen kit continued to decrease.

Summary. The COVID-19 examination using the “Genbody COVID-19 Test Ag®” antigen test kit has a low sensitivity which is not in accordance with WHO recommendations. This antigen kit has high sensitivity in rRT-PCR results at CT (CT < 20)."

"Latar Belakang. SARS-CoV-2 sebagai penyebab COVID-19 pertama kali terdeteksi pada sampel klaster pasien di Provinsi Hubei, China pada Desember 2019. Pada mulanya klaster pasien tersebut memiliki gejala seperti demam, batuk, sesak nafas, dan gejala lainnya yang tidak spesifik. Alat uji Rapid Antigen Test (RAT) dapat dijadikan alternatif untuk diagnosis klinis COVID-19. Tujuan. Penelitian ini bertujuan untuk mendapatkan rekomendasi mengenai alternatif spesimen dan metode deteksi SARS-CoV-2. Metode. Desain penelitian ini merupakan uji diagnostik studi potong lintang dengan pengumpulan spesimen secara consecutive sampling. Subjek penelitian yaitu pasien yang memiliki kontak dengan kasus infeksi SARS-CoV-2 yang terkonfirmasi dengan atau tanpa gejala klinis COVID-19 di Fasilitas Pelayanan Kesehatan (Fasyankes) dan Laboratorium Mikrobiologi Klinik (LMK) FKUI dengan jumlah sampel 221. Analisis data dengan tabulasi silang dan perhitungan sensitivitas, spesifisitas, PPV, dan NPV. Hasil. Deteksi antigen menggunakan spesimen nasal memiliki nilai sensitivitas 32,35%, spesifisitas 99,35%, PPV 95,65%, NPV 76,77%, akurasi 78,73%. Tingkat positifitas pada spesimen nasofaring 34,84%, spesimen orofaring 30,32%, dan nasal 30,77%. Kesimpulan. Hasil uji rRT-PCR pada beberapa jenis spesimen menunjukkan bahwa spesimen nasal dan orofaring dapat dijadikan pilihan selain spesimen nasofaring. Penggunaan kit deteksi antigen dapat dilakukan untuk pelacakan kontak COVID-19 atau untuk diagnosis, terutama untuk daerah yang memiliki keterbatasan akses diagnosis menggunakan rRT-PCR.

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Introduction. The SARS-CoV-2 as the cause of COVID-19 was first detected in a cluster sample of patients in Hubei Province, China in December 2019. The first patient had symptoms such as fever, cough, shortness of breath, and other non-specific symptoms. Rapid Antigen Test can be used as an alternative for diagnosis of COVID-19. Aim. This study aims to obtain recommendations alternative specimens and detection methods for SARS-CoV-2. Method. The design of this study is a cross-sectional diagnostic test with consecutive sampling. The research subjects were patients who had contact with confirmed cases of SARS-CoV-2 infection with or without clinical symptoms of COVID-19 at Health Service Facilities (Fasyankes) and Laboratorium Mikrobiologi Klinik (LMK) FKUI with a total sample of 221. Data analysis using cross tabulation to calculate the sensitivity, specificity, PPV, and NPV. Results. The positivity rate for nasopharyngeal specimens was 34.84%, oropharyngeal specimens 30.32%, and nasal specimens 30.77%. Antigen detection using nasal specimens has sensitivity 32.35%, specificity 99.35%, PPV 95.65%, NPV 76.77%, accuracy 78.73%. Conclusion. The results of the rRT-PCR test on several types of specimens indicate that nasal and oropharynx specimens can be used as an alternative to nasopharyngeal specimens. The use of antigen detection kits can be carried out for COVID-19 contact tracing or for diagnosis, especially for areas that have limited access to diagnosis using rRT-PCR."

"Rapid swab antigen SARS-CoV-2 merupakan pemeriksaan alternatif dalam mendeteksi SARS-CoV-2. Salah satu faktor yang mempengaruhi pemeriksaan rapid swab antigen SARS-CoV-ialah viral load yang direpresentasikan dengan cycle threshold (CT) pada pemeriksaan rRT-PCR. Hasil CT yang tinggi membuat sensitivitas pemeriksaan rapid swab antigen SARS-CoV-2 rendah. Tujuan utama pada penelitian ialah untuk menentukan nilai CT tertinggi pada pemeriksaan rRT-PCR yang mampu memberikan hasil reaktif pada pemeriksaan COVID-19 Ag (Standard Q SD Biosensor). Penelitian merupakan penelitian observasional dengan metode potong lintang dilakukan pada poliklinik demam RS dr. Cipto Mangunkusumo pada tanggal Juli 2020- Desember 2021. Total subjek dalam penelitian berjumlah 235 terdiri dari 24,7% subjek dengan rRT-PCR SARS-CoV-2 positif dan 75,3% subjek dengan rRT-PCR SARS-CoV-2 negatif. Median CT tertinggi pada pemeriksaan rRT-PCR SARS-CoV-2 yang mampu memberikan hasil reaktif pada pemeriksaan COVID-19 Ag (Standard Q SD Biosensor) ialah 28,22 (13,33- 39,16), sedangkan median CT tertinggi pada COVID-19 Ag (Standard Q SD Biosensor) non-reaktif ialah 34,45 (26,08-39,65). Sensitivitas, spesifisitas, NPV, PPV, dan LR positif dan LR negatif hasil COVID-19 Ag (Standard Q SD Biosensor) pada CT ≤ 40 adalah 63.8%, 99.4%, 89.3%, 97.4%, 112.9, dan 0.4. Pada CT ≤ 33 sensitivitas, spesifisitas, NPV, PPV, dan LR positif dan LR negatif ialah 77.1%, 99.4%, 95.7%, 96.4%, 136.5, dan 0.2 sedangkan pada CT ≤ 25 sensitivitas, spesifisitas, NPV, PPV, dan LR positif dan LR negatif adalah 92.3%, 99.4%, 99.4%, 92.3%, 163.4, dan 0.1. Titik potong CT rRT-PCR SARS-CoV-2 tertinggi ialah 26,06 dengan hasil sensitivitas 100% dan spesifisitas 99,4%. Pemeriksaan COVID-19 Ag (Standard Q SD Biosensor) dapat dipakai untuk keperluan diagnosis, contact tracing atau community surveilance.

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SARS-CoV-2 rapid antigen swab is an alternative test for detecting SARS-CoV-2 infection. One of the factors that influence the examination is viral load, which is represented by the cycle threshold (CT) in the rRT-PCR examination. The higher CT value will result in lower sensitivity of SARS-CoV-2 rapid antigen swab examination. The main objective of the study was to determine the highest CT value in rRT-PCR examination which still able to give reactive results on the COVID-19 Ag test (Standard Q SD Biosensor). The study was a cross-sectional study carried out at the fever polyclinic in dr. Cipto Mangunkusumo Hospital between July 2020 - December 2021. The study consisted of 235 subjects, 24.7% of subjects were SARS-CoV-2 positives and 75.3% of subjects were negative for SARS-CoV-2 infections. Median highest CT value in the SARS-CoV-2 rRT-PCR examination which able to give reactive results on the COVID-19 Ag (Standard Q SD Biosensor) test was 28.22 (13.33-39.16) while the median CT value on the non-reactive COVID-19 Ag (Standard Q SD Biosensor) was 34.45 (26.08-39.65). The sensitivity, specificity, NPV, PPV, and LR positive and LR negative results of COVID-19 Ag (Standard Q SD Biosensor) were 63.8%, 99.4%, 89.3%, 97.4%, 112.9, and 0.4 at CT value ≤ 40. The sensitivity, specificity, NPV, PPV, and LR positive and LR negative at CT value ≤ 33 were 77.1%, 99.4%, 95.7%, 96.4%, 136.5, and 0.2, while at CT ≤ 25 sensitivity, specificity, NPV, PPV, and LR positive and LR negative were 92.3%, 99.4%, 99.4%, 92.3%, 163.4, and 0.1. The cut-off point for the highest CT value was 26.06 with a sensitivity of 100% and a specificity of 99.4%. In conclusion, COVID-19 Ag (Standard Q SD Biosensor) was acceptable for diagnosis, contact tracing or community surveillance."

"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."

"COVID-19 merupakan penyakit yang dapat mudah menular, baik melalui kontak langsung maupun tidak langsung. Di Indonesia, tepatnya di Jakarta terdapat 424.009 kasus konfirmasi COVID-19 memiliki sekitar 1.346.243 kontak erat. COVID-19 menjadi salah satu penyakit yang mudah menular melalui kontak erat. Oleh karena itu, dalam mencegah penyebaran COVID-19, dibutuhkan adanya contact tracing, karantina, dan isolasi untuk memutus rantai penularan COVID-19. Tujuan dari penelitian ini adalah untuk mengetahui efektivitas contact tracing, karantina, dan isolasi dalam mengendalikan COVID-19. Desain penelitian menggunakan kajian sistematis (systematic review). Literatur diperoleh melalui pencarian pada 4 database, yaitu PubMed, ProQuest, ScienceDirect, dan Scopus. Literatur yang didapatkan sebanyak 18 artikel (8 artikel menggunakan observational study dan 10 artikel menggunakan modeling study) yang dipublikasikan pada tahun 2020 dan 2021. Literatur yang digunakan melaporkan manfaat dari contact tracing, karantina, dan isolasi terhadap pengendalian COVID-19. Menurut penelitian yang dilakukan, contact tracing efektif dalam mencari kontak erat, sehingga dapat mencegah adanya onward transmission (penularan lebih lanjut) COVID-19. Sedangkan studi permodelan menyatakan bahwa dengan dilakukannya karantina sebesar 50% hingga 100%, dapat menurunkan kasus terkonfirmasi COVID-19 sebesar 61,39% hingga 87,12%. Isolasi kasus dapat mengontrol epidemi jika dikombinasikan dengan pelacakan/karantina kontak, sehingga dapat membuat nilai R dibawah 1 dan karenanya secara efektif dapat mengendalikan pandemi COVID-19.

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COVID-19 is a disease that can be easily transmitted, either through direct or indirect contact. In Indonesia, to be precise in Jakarta, there are 424.009 confirmed cases of COVID-19 and around 1.346.243 close contacts. COVID is a disease that is easily transmitted through close contact. Therefore, preventing the spread of COVID-19 requires contact tracing, quarantine, and isolation to break the chain of transmission of COVID-19. This study aimed to determine the effectiveness of contact tracing, quarantine, and isolation in controlling COVID-19. The method used is a systematic review. Literatures was obtained by searching 4 databases, namely PubMed, ProQuest, ScienceDirect, and Scopus. The literature obtained was 18 articles (8 articles observational studies and 10 articles modeling studies) published in 2020 and 2021. The literature reported the benefits of contact tracing, quarantine, isolation for controlling COVID-19. According to research conducted, contact tracing is effective in finding close contacts to prevent onward transmission of COVID-19. Meanwhile, a modeling study states that quarantine by 50% to 100% can reduce confirmed cases of COVID-19 by 61,39% to 87,12%. Case isolation can control the epidemic when combined with contact tracing/quarantine, so it can bring the R-value below 1 and therefore can effectively control the COVID-19 pandemic.

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"Latar Belakang: Reseptor ACE2 tidak hanya terdapat pada paru-paru, tetapi juga pada saluran pencernaan yang memungkinkan terjadinya infeksi SARS-COV-2 pada enterosit, menimbulkan manifestasi klinis gastrointestinal, dan terdeteksinya RNA virus pada pemeriksaan swab anal. Studi lain di seluruh dunia menunjukkan hasil yang berbeda-beda serta belum didapatkan penelitian serupa di Indonesia. Tujuan: Penelitian ini bertujuan untuk mengetahui luaran klinis infeksi COVID- 19 pada pasien yang dilakukan swab anal, mendapatkan hubungan hasil pemeriksaan PCR SARS-CoV-2 swab anal dengan manifestasi klinis gastrointestinal dan derajat keparahan pada pasien COVID-19 di Indonesia. Metode: Merupakan cabang penelitian dari penelitian utama yang berjudul “Nilai RT-PCR Swab Anal untuk Diagnosis COVID-19 pada Orang Dewasa di Indonesia”. Penelitian ini merupakan studi analitik dengan desain potong lintang. Sampel penelitian merupakan pasien COVID-19 yang menjalani rawat inap di RSUPN dr. Cipto Mangunkusumo (RSCM), RS Mitra Keluarga Depok, RS Mitra Keluarga Kelapa Gading, dan RS Ciputra selama periode April 2020 sampai dengan Januari 2021. Dikumpulkan data demografi, manifestasi klinis, derajat keparahan, dan hasil swab anal PCR SARS-CoV-2.Hasil: 136 subjek penelitian dengan swab nasofaring positif dianalisis. 52 pasien (38,2%) dengan swab anal PCR SARS-CoV-2 positif dan 84 pasien (61,8%) dengan swab anal negatif. Manifestasi klinis saluran cerna tersering, yaitu: mual-muntah 69 pasien (50,7%), nafsu makan menurun sebanyak 62 pasien (45,6%), dan nyeri perut sebanyak 31 pasien (22,8). Terdapat 114 pasien (83,8%) tergolong dalam derajat ringan-sedang dan 22 pasien (16,2%) tergolong dalam berat-kritis. Terdapat hubungan yang bermakna secara proporsi statistik antara variabel hasil pemeriksaan PCR SARS-CoV-2 swab anal dengan manifestasi klinis gastrointestinal berupa keluhan diare atau mual-muntah (nilai p 0,031). Tidak terdapat hubungan yang bermakna secara proporsi statistik antara variabel hasil pemeriksaan PCR SARS-CoV-2 swab anal dengan derajat keparahan (nilai p 0,844).Simpulan: Terdapat hubungan antara hasil pemeriksaan PCR SARS-CoV-2 swab anal dengan manifestasi klinis gastrointestinal berupa keluhan diare atau mual- muntah dan tidak terdapat hubungan antara variabel hasil pemeriksaan PCR SARS- CoV-2 swab anal dengan derajat keparahan infeksi COVID-19.

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Background: ACE2 receptor is not only found in the lungs, but also in the digestive tract, which allows the occurrence of enterocyte infection, gastrointestinal clinical manifestations, and detection of viral RNA on anal swab PCR. Studies around the world show various results, yet there has been no similar study to be found in Indonesia.

Objective: This study aims to determine the clinical outcome of COVID-19 patients with gastrointestinal manifestations who were tested by anal swab, the relationship between anal swab PCR for SARS-CoV-2 test result with gastrointestinal clinical manifestations as well as the severity of COVID-19 patients in Indonesia.

Methods: This research is a branch of study titled. The Value of Anal Swab RT- PCR for COVID-19 Diagnosis in Adult Indonesian Patients. This is an analytical study with cross-sectional design. Samples were obtained from hospitalized COVID-19 patients at RSUPN dr. Cipto Mangunkusumo (RSCM), Mitra Keluarga Hospital Depok, Mitra Keluarga Kelapa Gading Hospital, and Ciputra Hospital from April 2020 to January 2021. Demographic data, clinical manifestations, severity, and SARS-CoV-2 PCR anal swab were collected.

Results: 136 subjects with positive nasopharyngeal swab were analyzed. Result showed that 52 patients (38.2%) had positive anal swabs PCR SARS-CoV-2 and 84 patients (61.8%) had negative anal swabs. Common gastrointestinal clinical manifestations were: nausea and vomiting in 69 patients (50.7%), anorexia in 62 patients (45.6%), and abdominal pain in 31 patients (22.8). There were 114 patients (83,8%) classified as mild-moderate and 22 patients (16,2%) as severe-critical. There was a statistically significant relationship between anal swab PCR for SARS- CoV-2 test result with gastrointestinal clinical manifestations (diarrhea or nausea- vomiting) (p value 0.031). There was no statistically significant relationship found between anal swab PCR for SARS-CoV-2 test result with the severity of COVID- 19 infection (p value 0.844).

Conclusions: There is a relationship between anal swab PCR SARS-CoV-2 test result with gastrointestinal clinical manifestations (diarrhea or nausea-vomiting) and there is no relationship between anal swab PCR SARS-CoV-2 test result with severity of COVID-19 infection."

"Swab stick adalah alat pengambilan sampel virus melalui penyapuan jaringan lunak pada bagian hidung. Alat ini yang masih import, menjadi kristis saat kekurangan ketersediaan dalam negri Indonesia saat pandemik Covid-19 lalu. Oleh karena itu, Universitas Indonesia melalui Research Center for Biomedical Engineering, FTUI melakukan kolaborasi dengan empat industri lokal, dalam pengembangan dan produksi swab stick dalam negri, dengan mengacu ISO 13485:2016, peralatan kesehatan sistim manajemen kualitas – persyaratan untuk tujuan regulasi. Industri yang dilibatkan, telah memiliki pengalaman panjang dalam produksi bahan baku polimer, pemrosesan plastik, teknologi flocking dan pengemasan medis, untuk keyakinan pencapaian jaminan kualitas swab stick yang sesuai dengan produk yang ada. Laporan ini mendeskripsikan jaminan kualitas desain, purwarupa dan produksi swab stick. Rangkaian pengujian berupa uji geometri, tarik, kelekatan penyapu, permukaan, penyerapan sapuan dan residu paska produksi. Kerja pengembangan menghasilkan produk swab stick dengan kekakuan 400 MPa, lengkungan pada 15 N, kerapatan 1,5-2,5 Dtex, sudut kontak air 78 derajat dan penyerapan air 25-35 mikro Liter. Lebih lanjut, tidak ditemukan residu bahan beracun pada produk. Produk swab stick yang berkualitas tersebut diharapkan sebagai produk nasional yang mendekati 100% TKDN dalam rangka meningkatkan ketersediaan peralatan kesehatan, terutama menghadapi COVID-19 di Indonesia. Produk ini secara formal didaftarkan dengan nama dagang Sterilized Nasopharynx Swab Stick HS 19

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Swab sticks are a means of sampling a person by swabbing the nasopharyngeal pathway. This tool is at a critical point, where domestic availability in Indonesia is lacking because it is purely dependent on foreign supplies during the coronavirus disease 2019 pandemic. Therefore, a collaboration of national companies and the Research Center for Biomedical Engineering, Universitas Indonesia, addressed this scarcity by producing a national swab stick. Since there was no swab stick manufacturer in Indonesia, the production referred to ISO 13485:2016. The companies contributing have strong experience in resin production, plastic processing, flocking technology, and medical packaging to ensure the product quality. We propose a series of measurements, and have conclude that the product has stiffness around 400 MPa, deflected at 15N, a density of 1.5–2.5 Dtex, water contact angle at 78 degrees, and adsorbsivity around 25–35L of liquid water. Moreover, there was no any residual toxic substance around the flocked swab. These qualities shall be developed further into a national product with nearly 100% local content in order to increase availability of the national medical device and fight COVID-19 in Indonesia. The product was formally registered under the trade name Sterilized Nasopharynx Swab Stick HS 19."

"Latar Belakang: COVID-19 merupakan penyakit yang disebabkan oleh infeksi SARS-CoV-2 yang dapat mengalami mutasi sehingga membentuk beberapa varian baru. Perubahan varian tersebut dapat menyebabkan proses transmisi virus yang cepat hingga meningkatnya mortalitas dan morbiditas pada pasien COVID-19. Adanya mikrobiota pada saluran pernafasan yang merupakan bagian dari sistem kekebalan tubuh dapat memberikan perlindungan dari infeksi dan pathogenesis SARS-CoV-2 pada tubuh manusia. Akan tetapi, patogenesis virus dari beberapa varian SARS-CoV-2 yang berbeda dapat menghambat homeostasis dari komunitas mikroba pada saluran pernafasan. Oleh sebab itu perlu dilakukan identifikasi varian SARS-CoV-2 dan profil komunitas bakteri pada sampel swab naso/orofaring pasien COVID-19, untuk mendapatkan data awal profil komunitas mikroba dan korelasinya dengan varian SARS-CoV-2.Metode: Penelitian menggunakan sampel swab naso/orofaring pasien COVID-19. Sekuensing sampel dilakukan sebanyak dua kali. Sekuensing pertama bertujuan untuk mengidentifikasi varian SARS-CoV-2 menggunakan Whole Genome Sequencing (WGS) dari Oxford Nanopore Technologies (ONT). Sekuensing kedua bertujuan untuk mengidentifikasi keragaman bakteri pada naso/orofaring pasien COVID-19 menggunakan amplifikasi gen 16S rRNA. Kemudian analisis bioinformatika dilakukan untuk memperoleh profil komunitas mikroba pada beberapa varian SARS-CoV-2.Hasil: Ditemukan enam varian SARS-CoV-2 yang dideteksi pada sampel terpilih yang dikoleksi selama bulan Maret-Juni 2021, dengan hasil varian yang mendominasi adalah varian Delta, Alpha, dan Lokal. Pada varian Alpha dan Delta didominasi oleh genus bakteri Streptococcus, Prevotella, dan Veillonella. Pada varian lokal, genus yang mendominasi yaitu Corynebacterium, Staphylococcus, dan Salmonella.Kesimpulan: Komunitas bakteri yang ditemukan pada sampel swab naso/orofaring pasien COVID-19 memiliki tingkat keragaman yang signifikan antar varian SARS-CoV-2. Komunitas bakteri yang ditemukan didominasi oleh genus Prevotella, Streptococcus, Corynebacterium, dan Veillonella. Persentase jumlah bakteri paling banyak yaitu genus Prevotella sebesar 27%. Genus bakteri Prevotella dan Veillonella banyak ditemukan pada varian SARS-COV-2 Alpha dan Delta, yang memiliki potensi meningkatkan inflamasi dan tingkat keparahan pada pasien COVID-19.

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Background: COVID-19 is a disease caused by infection of a SARS-CoV-2 virus that can undergo mutations to form several new variants. These variants could lead to a more rapid transmission, which increases mortality and morbidity in COVID-19 patients. The presence of microbiota in the respiratory tract as part of the immune system provides protection from viral infections and pathogenesis in the human body. However, pathogenesis of different SARS-CoV-2 variants plays a role in inhibiting the homeostasis of the microbial community in the respiratory tract. Therefore, it is necessary to identify the SARS-CoV-2 variants and profile the bacterial community profile in naso/oropharynx using swab samples of COVID-19 patients, to obtain initial data regarding the microbial community profile of COVID-19 patients and potential correlation with the SARS-CoV-2 variants.

Methods: This study used naso/oropharyngeal swab samples from COVID-19 patients. Sample sequencing was performed twice. The first sequencing aims to identify variants of SARS-CoV-2 using Whole Genome Sequencing (WGS) with Oxford Nanopore Technologies (ONT) platform. The second sequencing aims to identify bacterial diversity in the naso/oropharynx of COVID-19 patients using 16S rRNA gene amplification followed by profiling of the microbial community using bioinformatic analysis.

Results: Six variants of SARS-CoV-2 were identified in the selected samples collected during March-June 2021, with the dominant variants being Delta, Alpha, and Local variants. The microbial community of samples belonging to the Alpha and Delta variants was dominated by the bacterial genera Streptococcus, Prevotella, and Veillonella. Meanwhile, in the samples identified as having local variant, the dominant genera were Corynebacterium, Staphylococcus, and Salmonella.

Conclusion: The bacterial diversity in the swab samples naso/oropharyngeal of COVID-19 patients varied significantly among SARS-CoV-2 variants. The bacterial community was dominated by the genera Prevotella, Streptococcus, Corynebacterium, and Veillonella. The highest percentage of genus was Prevotella by 27%. The genera Prevotella and Veillonella were found in the SARS-CoV-2 Alpha and Delta variants, which have the potential to increase inflammation and severity in COVID-19 patients."

"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."

"Pendahuluan: Pemeriksaan baku emas swab nasoorofaring dengan metode Reverse transcriptase polymerase chain reaction (RT-PCR) merupakan prosedur diagnostik yang dilakukan pada pasien dengan suspek COVID-19. Metode lain yang digunakan yaitu dengan pemeriksaan serologi yang mulai terbentuk dalam beberapa hari hingga minggu.Tujuan: Untuk mengetahui hubungan antara hasil swab nasoorofaring dan uji serologi terhadap luaran pasien COVID-19 dalam evaluasi masa rawat 14 hariMetode: Analisis observasional kohort retrospektif terhadap pasien COVID-19 yang dirawat di RS Rujukan Respirasi Nasional Persahabatan, Jakarta, Indonesia secara total sampling diperoleh dari bulan Maret 2020 sampai Mei 2020. Kami meninjau rekam medis 132 pasien dengan diagnosis probable case dan confirmed case COVID-19 yang memenuhi kriteria inklusi.Hasil: Sebanyak 132 pasien yang termasuk dalam penelitian ini, didominasi oleh laki-laki sebanyak 51,5% dengan usia rerata 50,23 tahun. Derajat pneumonia berturut-turut yaitu derajat ringan, sedang, dan berat (17,4%, 57,6%, dan 25,0%). Proporsi pasien dengan komorbid sebanyak 71,2%. Proporsi penggunaan alat bantu napas terbanyak yaitu penggunaan kanula hidung (69,7%) diikuti berturut-turut oleh Ventilator, non rebreathing mask dan high flow nasal cannule (13,6%, 9,1% dan 7,6%).. Proporsi kematian sebesar 18,3%, dengan proporsi kematian pada confirmed case sebanyak 21,3% dan probable case sebanyak 19,3%. Tingkat kematian pada confirmed case berkorelasi terhadap jenis kelamin laki-laki (p =0,009), derajat pneumonia berat (p=0,000), penggunaan alat bantu napas bukan kanula hidung (p=0,000) dan komorbid (p=0,021). Tingkat kematian pada probable case berkorelasi dengan derajat pneumonia berat (p=0,000), penggunaan alat bantu napas bukan kanula hidung (p=0,000).Kesimpulan: Kombinasi penggunaan swab nasoorofaring dan hasil uji serologi dapat memprediksi luaran pasien COVID-19 dalam evaluasi masa rawat 14 hari. Derajat pneumonia berat dan penggunaan alat bantu napas bukan kanula hidung merupakan prediktor buruk terhadap luaran pasien COVID-19.

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Introduction: Reverse transcriptase polymerase chain reaction (RT-PCR) to detect SARS- CoV-2 is a gold standard method in a patient with suspected COVID-19 and achievable by means of nasopharyngeal and oropharyngeal swab. Serological test is another method to detect the antibody which is produced in a several days or week.

Aims: To determine the association between nasooropharyngeal swab and serological test to predict the mortality of COVID-19 patient after 14-days admission.

Methods: We performed an observational retrospective cohort analysis of COVID-19 patients treated at National Respiratory Referral Hospital Persahabatan Jakarta, Indonesia. Subjects by means of total sampling were COVID-19 patients between March to May 2020. We reviewed the medical records of 132 patients categorized as probable and confirmed cases whom met the inclusion criteria. Their 14-days course of the treatment were observed.

Results: We included 132 patients, which dominated by males (51.5%) with mean age of

50.23 years old. Cases were mild pneumonia, moderate pneumonia, and severe pneumonia (17.4%, 57.6%, and 25.0%, respectively). Most patients presented with comorbidities (71,2%). Most patients required oxygen supplementation by nasal cannula (69.7%), followed by mechanical ventilator, non-rebreathing mask, and high flow nasal cannula (13.6%, 9.1%, and 7.6%, respectively). Patient deaths were 18.3%, including 21.3% among confirmed cases and 19.3% among probable cases. Mortality among confirmed case were correlated with male sex (p=0.009), severe pneumonia (p=0.000), supplemental oxygen delivery requiring device other than nasal cannula (p=0.000), and comorbidities (p=0.021). Mortality among probable cases were correlated with severe pneumonia (p=0.000), and supplemental oxygen delivery requiring device other than nasal cannula (p=0.000).

Conclusions: Combination of nasooropharyngeal swab and serological test results predicted the 14-days outcomes of COVID-19 patients. Severe pneumonia and supplemental oxygen delivery requiring device other than nasal cannula were predictors of poor COVID-19 outcomes as observed from our study."