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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."

"Pendahuluan: COVID-19 telah dilaporkan menyebabkan berbagai gejala, termasuk gejala pernapasan dan gejala gastrointestinal seperti mual, muntah, dan diare. Standar emas untuk pengujian COVID-19 adalah RT-PCR menggunakan koleksi swab nasofaring. Namun, beberapa penelitian menunjukkan bahwa pengambilan swab nasofaring memiliki beberapa keterbatasan, terutama untuk mendeteksi gejala gastrointestinal. Salah satu variabel dalam pengujian RT-PCR adalah Nilai CT yang diketahui dapat meningkatkan spesifisitas pengujian. Namun, belum ada penelitian yang menghubungkan Nilai CT pasien dengan pengambilan sampel swab anal dengan gejala gastrointestinal terkait COVID-19. Metode: Penelitian ini menggunakan desain penelitian analitik, khususnya penelitian potong lintang. Data sekunder diperoleh dan diolah yang berisi data pribadi, pekerjaan, dan hasil CT Value. Analisis lebih lanjut dilakukan pada hubungan antara gejala gastrointestinal dan tingkat Nilai CT pada swab anal. Hasil: Distribusi tingkat Nilai CT responden berdasarkan cut off >25 untuk tinggi, dan <25 untuk rendah dan sedang. Dari 37 subjek, 1 orang (2,7%) memiliki Nilai CT rendah dan 36 pasien memiliki Nilai CT tinggi. Distribusi gejala subjek didapatkan 15 pasien (40,5%) tidak mengalami gejala gastrointestinal dan sebanyak 22 pasien (59,5%) mengalami gejala gastrointestinal. Gejala gastrointestinal umum yang dilaporkan pada pasien meliputi: mual (54,1%), muntah (18,9%), sakit perut (16,2%) dan diare (13,5%). Namun, tidak ada hubungan yang signifikan (p>0,05) antara Nilai CT pada pengambilan anal swab dengan gejala gastrointestinal pada pasien COVID-19. Kesimpulan: Hubungan antara Nilai CT pada pengambilan anal swab dengan gejala gastrointestinal pada pasien COVID-19 tidak menunjukkan hubungan yang signifikan. Penelitian lebih lanjut tentang faktor risiko yang mempengaruhi hasil nilai CT direkomendasikan.

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Introduction: COVID-19 has been reported to cause a range of symptoms, including respiratory symptoms and gastrointestinal symptoms such as nausea, vomiting, and diarrhea. The gold standard for COVID-19 testing is RT-PCR using nasopharyngeal swab collection. However, several studies have shown that taking nasopharyngeal swabs have some limitation, particularly to detect gastrointestinal symptoms. One of the variables in RT-PCR testing is CT Value, which known can increase specifity of the test. However, there has been no study linking the CT Value of patients with anal swab sampling with COVID-19 related gastrointestinal symptoms. Methods: This study used an analytical research design, particularly a cross-sectional study. Secondary data were obtained and processed which contained personal data, work, and CT Value results. Further analysis was conducted on the relationship between gastrointestinal symptoms and the level of CT Value on anal swabs. Result: The distribution of respondents' CT Value levels were based on a cut off of >25 for high, and <25 for low and moderate. From 37 subjects, 1 person (2.7%) had a low CT Value and 36 patients had a high CT Value. The distribution of the subject's symptoms found 15 patients (40.5%) had no gastrointestinal symptoms and as many as 22 patients (59.5%) had gastrointestinal symptoms. Common gastrointestinal symptoms reported in patients include: nausea (54.1%), vomiting (18.9%), abdominal pain (16.2%) and diarrhea (13.5%). However, there was no significant relationship (p>0.05) between CT Value in anal swab taking and gastrointestinal symptoms in COVID-19 patients. Conclusion: The association between CT Value in anal swab taking and gastrointestinal symptoms in COVID-19 patients did not show a significant relationship. Further research on risk factors affecting the CT value results are recommended"

"Coronavirus disease atau COVID-19 merupakan pandemi global yang mudah menular melalui droplet dan populasi yang paling berisiko adalah lansia dengan tingkat kematian akibat COVID-19 di Indonesia per 27 Juni 2020 adalah sebanyak 42,9%. Hal tersebut dapat menimbulkan kecemasan tersendiri bagi lansia, terlebih lagi secara psikologis lansia lebih mudah cemas daripada populasi lain. Kecemasan diketahui merupakan salah satu faktor penting penyebab kerentanan terinfeksi Coronavirus. Maka dari itu penulisan ini dibuat untuk menemukan gambaran ansietas pada 10 lansia sebelum tindakan swab PCR SARS CoV-2 di RSUI. Data yang dipakai adalah data umum, data skrining COVID-19, riwayat penyakit dalam, riwayat merokok, dan kuesioner kecemasan menggunakan Geriatric Anxiety Inventory Short Form (GAI-SF). Berdasarkan data yang didapatkan, terdapat banyak faktor yang mungkin mempengaruhi munculnya ansietas pada lansia seperti kecemasan terhadap hasil swab PCR. Hasil pengkajian GAI-SF juga menyatakan bahwa semua lansia mengalami ansietas dengan dua diantaranya memiliki gejala GAD. Antar pasien juga memiliki beberapa kesamaan terkait COVID-19 dan hubungannya dengan kecemasan. Sebagai kesimpulan, masalah ansietas pada lansia terkait COVID-19 sebelum tindakan swab PCR memiliki nilai yang tinggi disebabkan karena beberapa faktor sehingga perlu diberikan rekomendasi khusus. Penulis merekomendasikan penyediaan kursi prioritas untuk lansia, bilik swab khusus lansia dengan aromaterapi dan musik relaksasi jika memungkinkan, dan edukasi terkait COVID-19 oleh perawat melalui selebaran maupun follow up secara daring.

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Coronavirus disease or called COVID-19 is a global pandemic that is easily transmitted through droplets and the population with higher risk of it are the elderly within death rate in Indonesia per June 27, 2020 is 42.9%. This problem can cause anxiety in the elderly even more as psychologically the elderly are more vulnerable to feel anxious than other populations. Whereas anxiety is one of the important factors causing decreased immunity which makes the elderly more susceptible to Coronavirus. Therefore, this paper was made to find an overview of anxiety in 10 elderly people before the swab polymerase chain reaction severe acute respiratory syndrome coronavirus-2 or swab PCR SARS CoV-2 procedure at RSUI. The data used are general data, COVID-19 screening data, history disease, smoking history, and anxiety questionnaires using Geriatric Anxiety Inventory Short Form (GAI-SF). Based on the data obtained, there are many factors that might influence the emergence of anxiety in the elderly such as anxiety about the swab PCR results. The results of the GAI-SF also stated that all respondents were experiencing anxiety with two of them were having general anxiety disorder symptoms. Furthermore, inter-patients also have some similarities related to COVID-19 and anxiety. In conclusion, the anxiety problem among elderly related to COVID-19 before the swab PCR procedure has a high value due to several factors so that special recommendations for the elderly should be given. The recommendation are using priority seats for the elderly, special swab PCR’s room with aromatheraphy and music of relaxation if possible, and nurses could give COVID-19 educations through flyer or follow up them within online educations"

"Pada akhir tahun 2019 dilaporkan beberapa kasus pneumonia di Wuhan, Cina yang disebabkan oleh Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Penyakit yang ditimbulkan oleh virus ini disebut sebagai coronavirus disease 2019 (COVID-19). Jumlah kasus COVID-19 terus mengalami peningkatan dan penyebarannya terjadi pada seluruh kelompok usia termasuk anak-anak. Pemeriksaan real-time reverse transcription-polymerase chain reaction (rRT-PCR) telah diotorisasi oleh Food and Drug Administration (FDA) dan pada pemeriksaan ini dikenal istilah cycle threshold (Ct). Nilai Ct sering dijadikan acuan dalam menentukan tingkat keparahan penyakit pada anak, akan tetapi masih terdapat kontroversi apakah nilai Ct berhubungan dengan tingkat keparahan penyakit. Penelitian ini bermaksud mencari hubungan bermakna antara nilai Ct khususnya gen ORF1ab dan gen N dengan tingkat keparahan COVID-19 pada anak yang dibagi menjadi tingkat keparahan ringan dan sedang sampai kritis. Didapat 52 responden anak dalam penelitian ini, dengan 24 responden terdeteksi gen ORF1ab dan 49 responden terdeteksi gen N. Rerata nilai Ct gen ORF1ab kelompok ringan (33,5 ± 4,4) lebih tinggi dibandingkan dengan kelompok sedang sampai kritis (31,0 ± 6,0). Median nilai Ct gen N kelompok ringan (34,8 [21,3 – 39,4]) lebih tinggi dibandingkan dengan kelompok sedang sampai kritis (31,7 [19,4 – 38,9]). Tidak didapatkan hubungan bermakna baik antara nilai Ct gen ORF1ab (nilai p = 0,25) maupun gen N (nilai p = 0,159) dengan tingkat keparahan COVID-19 pada anak. Berdasarkan hasil penelitian ini, diperlukan berbagai pertimbangan dalam menginterpretasi nilai Ct.

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At the end of 2019, several cases of pneumonia were reported in Wuhan, China caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The disease caused by this virus is known as Coronavirus Disease 2019 (COVID-19). The number of cases of COVID-19 continues to increase and its spread occurs in all age groups including children. Real-time reverse transcription-polymerase chain reaction (rRT-PCR) has been authorized by the Food and Drug Administration (FDA) and in this method a cycle threshold (Ct) value were obtained. The Ct value is often used as a reference in determining the clinical severity in children, but there is still controversy whether the Ct value is related to the clinical severity. This study intends to find a significant relationship between the Ct values, especially the ORF1ab gene and the N gene, with the COVID-19 clinical severity in children which is divided into mild and moderate to critical severity. There were 52 children in this study, with 24 children have ORF1ab gene detected and 49 children have N gene detected. The mean of ORF1ab gene Ct value in mild group (33.5 ± 4.4) was higher than moderate to critical group (31.0 ± 6.0). The median of N gene Ct value ​​in mild group (34.8 [21.3 – 39.4]) was higher than moderate to critical group (31.7 [19.4 – 38.9]). There was no significant relationship between the Ct value of the ORF1ab gene (p value = 0.25) and the N gene (p value = 0.159) with COVID-19 clinical severity in children. Based on the results of this study, various considerations are needed in interpreting the Ct value."

"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."

"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: 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 2019 (COVID-19), yang disebabkan oleh sindrom pernafasan akut parah coronavirus 2 (SARS-CoV-2), telah mengakibatkan pandemik global. Penelitian ini bertujuan untuk menganalisis hubungan faktor risiko Kejadian Ikutan Paska Imunisasi (KIPI) dan efektivitas vaksinasi SARS-CoV-2. Studi observasional ini, menggunakan desain studi cross-sectional dengan total sampel penelitian 261 orang dan pengumpulan data dilakukan menggunakan Google Form. Hasil dari penelitian ini menunjukkan gejala KIPI paling banyak ditemukan pada onset <24 jam. Gejala umum yang ditemukan adalah sakit di tempat suntikan, fatigue, nyeri otot dan nyeri sendi. Sebagian besar keparahan KIPI adalah tingkat mild dan hanya beberapa peserta yang mengkonsumsi pengobatan. Hasil dari penelitian ini menyatakan bahwa peserta dengan jenis kelamin perempuan, peserta dengan penyakit penyerta, usia remaja – dewasa, jenis vaksin mRNA (BNT162b2) memiliki risiko KIPI yang lebih tinggi dan berpengaruh secara signifikan secara statistik (p<0.005). Efektivitas vaksin COVID-19 dalam mencegah infeksi cukup tinggi dengan persentase ≥79% pada setiap jenis dan dosis vaksin. Kesimpulan penelitian ini menunjukkan bahwa vaksin COVID-19 aman untuk diberikan karena KIPI sebagian besar ringan dan otomatis hilang dan menurun setelah 1 hingga 3 hari dan persentase efektivitas vaksin dalam mencegah infeksi COVID-19 cukup baik.

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The coronavirus that causes severe acute respiratory syndrome (COVID-19) is coronavirus 2 (SARS-CoV- 2). This virus has caused a global pandemic. This study aims to analyze relationship between risk factors for Adverse Events Following Immunization (AEFI) and the effectiveness of the SARS-CoV-2 vaccination. This observational study used a cross-sectional study design with a total sample of 261 people, data were collected using Google Forms. Results of this study showed the most AEFI symptoms are found at the onset of <24 hours. Common symptoms found are pain at injection site, fatigue, muscle aches and joint pain. Most of the AEFI severity was mild and only a few participants took medication. Results of this study stated that participants with female gender, comorbidities, adolescents - adults, type of mRNA (BNT162b2) vaccine had a higher risk of AEFI and statistically significant (p<0.005). Effectiveness of the COVID-19 vaccine is quite high with a percentage of ≥79% for each type and dose of vaccine. Conclusion of this study shows that the COVID-19 vaccines are safe to give because most of AEFIs are mild and automatically disappear and decrease after 1 to 3 days and percentage of effectiveness of the vaccine in preventing COVID-19 infection is good."

"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."

"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."