Kontroversi Metode Deteksi COVID-19 di Indonesia

Abstract—The governance of COVID-19 cases in Indonesia is carried out in accordance with the WHO directions. Serological tests, often mentioned as rapid antibody tests, are used for mass screening testing while the polymerase-chain-reaction (PCR)-based tests are performed for routine confirmation of COVID-19 infection cases. PCR test is one of nucleic acid amplification tests (NAAT) for detection of viral RNA. The management of the COVID-19 detection caused controversies at the beginning of pandemic period. It seems that the controversies occurred due to misperception regarding the tests, as well as misunderstanding caused by differences in individual immune responses, viral dynamics in human bodies and clinical outcomes. In response to community opinion controversies, this paper discuss the following topics, i.e. a glimpse about COVID-19, the characteristics of SARS-CoV-2, viral dynamics in human body, the dynamics of human immune response to SARS-CoV-2, basic explanation about COVID-19 and SARS-CoV-2 testing, and the last part explained the occurred controversies. Keywords: Indonesia, polymerase chain reaction, rapid test, SARS-CoV-2, serology Abstrak— Penetapan pelaksanaan deteksi kasus COVID-19 di Indonesia dilaksanakan sesuai arahan WHO. Uji serologis atau rapid test antibodi digunakan untuk test atau skrining massal sedangkan untuk uji berbasis polymerase-chain-reaction (PCR) digunakan untuk konfirmasi rutin kasus infeksi COVID-19. Uji molekuler secara PCR merupakan salah satu metode nucleic acid amplification tests (NAAT), untuk mendeteksi RNA virus. Penatalaksanaan deteksi Coronavirus disease 2019 (COVID-19) ini di awal masa pandemik menimbulkan berbagai kontroversi di masyarakat. Kontroversi terjadi terutama karena pemahaman yang berbeda dari masyarakat mengenai prinsip pengujian dan adanya salah pengertian akibat adanya perbedaan respon immun antar individu, dinamika virus COVID-19 dalam tubuh orang terinfeksi, dan luaran klinis pasien. Menanggapi kontroversi pendapat di masyarakat maka pada tulisan ini dibahas tentang sekilas COVID-19, karakteristik SARS-CoV-2, dinamika virus dan pembentukan antibodi dalam tubuh manusia, penjelasan prinsip pengujian COVID-19 dan SAR-CoV-2 serta ulasan tentang kontroversi yang terjadi. Kata kunci: Indonesia, polymerase chain reaction, rapid test, SARS-CoV-2, serolog

Uji Antimikroba Ekstrak Etanol Daun Kemuning (Murraya Paniculata (L.) Jack.) Terhadap Pertumbuhan Candida Albicans Dan Staphylococcus Aureus Serta Kesetaraannya Dibandingkan Tetrasiklin HCL

Telah dilakukan penelitian mengenai daya antimikroba ekstrak etanol daun kemuning terhadap pertumbuhan Candida albicans dan bakteri Staphylococcuss aureus. Ekstrak etanol diperoleh dengan cara perkolasi dan diuji daya antimikrobanya dengan metode difusi agar menggunakan silinder cup. Hasil penelitian menunjukkan bahwa ekstrak etanol daun kemuning hingga kadar 40% tidak menunjukkan hambatan terhadap Candida albicans tetapi dapat menghambat pertumbuhan bakteri Staphylococcus aureus dengan kesetaraan ekstrak kadar 5, 10, 20 dan 40 % terhadap antibiotika pembanding tetrasiklin HCI berturut-turut adalah 101, 137, 174, dan 216 ug/m

Kloning Dan Ekspresi Gen Pengkode Enzim Selulase Dan Xilanase Dari Bacillus Subtilis Dalam Escherichia Coli

Kloning gen pengkode endo-1 ,4-beta-glucanase (ysdC) dan endo-beta-1 ,3-1 ,4 glucanase (BSUW23_ 10175) dan xylan beta-1,4-xylosidase (xynB) dari Bacillus subtilis subsp. spizizenii str. W23 telah berhasil dilakukan pada plasmid pMMB67EH ke dalam sel inang Escherichia coli DH-5a dan Escherichia coli Origami. Amplifikasi gen target dilakukan melalui PCR (Polymerase Chain Reaction) dengan pasangan primer spesifik forward-reverse untuk masing-masing gen target. Transfonnasi sel Escherichia coli DH-5a dan Escherichia coli Origami dengan plasmid pMMB-gen target dilakukan dengan metode heat-shock sel E. coli yang dibuat kompeten dengan CaCl2. Adanya aktivitas degradasi selulosa dan xilanase pada Escherichia coli DH-Sa dan Escherichia coli Origami dideteksi secara kualitatif melalui produksi kadar total gula reduksi pada substrat carboxymethyl cellulose atau melalui pembentukan zona bening pada mediium LB-xilan-IPTG (lsopropyi-P-D-thio-galactoside) dengan pewarna Congo red untuk deteksi enzim xilanase. Dari hasil penelitian dapat disimpulkan bahwa kloning gen ysdC pengkode enzim endo-1,4-f3-glucanase, BSUW23_10175 (pengkode enzim endo-f3 -1,3-1,4 glucanase), dan xynB (pengkode -xilanase dari B. subtilis spizizenii W23 ke dalam plasmid pMMB67EH dan transformasi sel E. coli DH5a dan/atau E . coli Origami dengan plasmid rekombinan telah berhasil dilakukan. Sel E. coli transfonnan yang membawa plasmid rekombinan (pMMB-ysdC, pMMB-10175 dan pMMB-xynB) mempunyai kemampuan memecah selulosa dan xilan pada kondisi ekperimental. Set E. coli transforman yang membawa plasmid rekombinan mempunyai aktivitas selulase atau xilanase lebih tinggi dibandingkan dengan aktivitasnya pada set E. coli yang membawa empty plasmid (pMMB67EH), sedangkan set B . subtilis subsp. spizizenii str. W23 asli mempunyai enzim ekstraseluler dengan aktivitas memecah seJulosa dan xilan lebih besar dibandingkan transfonnan

Studi keanekaragaman strain isolat-isolat Pseudomonas aeruginosa dari pasien nosokomial di Surabaya dengan teknik polymerase chain reaction 16S rRNA

Telah dilakukan penelitian mengenai studi keanekaragaman strain isolat-isolat Pseudomonas aeruginosa yang berasal dari pasien nosokomial di Surabaya. Subtyping dilakukan dengan penentuan urutan nukleotida sebagian gen 16S rRNA menggunakan primer universal. Dari penelitian ini dapat disimpulkan bahwa keanekaragaman strain dari 33 isolat P. aeruginosa nosokomial yang ada belum dapat dipetakan secara jelas tetapi secara garis besar terdapat 6 kelompok strain: satu kelompok merupakan strain P. aerugirwsa yang berbeda dengan strain-strain yang ada di database Gene Bank, satu kelompok yang lain lebih dekat dengan genus Alcaligenes, sedangkan kelompok yang lain masih memerlukan konfirmasi ulang

Cloning, Characterization And Overexpression Of The Salmonella Typhi carB Gene

Salmonella typhi carAB operon is thought to be intimately involved in the pathogenesis mechanism of typhoid fever disease in human. The carAB operon consist of the carA gene and carB gene which encode two subunits of carbamoyl-phosphate synthetase, small and large subunits. The nucleotide sequence of S. typhi carA gene had been determined (Rudiretna et al, 1998) and its functional studies is still being done. But, information about the structural of the S. typhi carB gene is very little and there was not any information about functional properties of this gene. In order to obtain information related to the structure of this gene, Wahyudi, et. al (2001) had isolated the complete S. typhi carB gene and cloned this gene using the p-GemT vector into E. coli XL10. In this research attempts have been done to clone the S. typhi carB gene into the expression vector, characterize and overexpress the gene. Unfortunately, until now this work has not been succeded yet

Kajian Ekspresi Protein YsdC, BSUW23_10175 Dari XynB Dari Bacillus Subtilis Subsp.spizizenii W23 Secara Alami Dan Di Dalam Sel Inang Escherichia Coli Origami

Cellulases and xylanases are widely used in various applications such as in laundry and waste managements; and in various industries such as candy, food, drink, and pulp industries. In previous study, the genes which encoded endo-1,4-beta-glucanase (ysdC), endo-beta-1,3-1,4 glucanase (BSUW23_10175), and xylan beta-1,4- xylosidase (xynB) from Bacillus subtilis subsp. spizizenii str. W23 were cloned into broad-host-range vector pMMB67EH, in Escherichia coli Origami cells. However, these protein can be processed unproperly in Gramnegative bacteria differ than in its native Gram positive host cell. The aim of this research was to study the processing dan translocation of these native proteins in Bacillus subtilis subsp. spizizenii str. W23 and in E. coli Origami transformants cells, by in silico study dan expression study. Analyses of signal peptide, protein processing and translocation were accomplished by several softwares, i.e. PrediSi MHTMM and SignalP softwares. Expression study was performed by growing cells in Luria-Bertani (LB) broth with addition of carboxymethyl-cellulosa (CMC) or xylan as substrate and isopropyl-~-D-1-thiogalactopyranoside (IPTG) as inducer. The expressed protein was detected by sodium-dodecylsulphate-polyacrylamide gel-electrophoresis (SDS-PAGE) technique or by activity assays towards its substrates. The result showed that YsdC, BSUW23_10175 and XynB proteins were over-expressed in E. coli Origami trasformants cells. The YsdC and XynB proteins were expressed as fully active-extracellular enzyme protein, however BSUW23_10175 protein was detected as intracellular un-processed pro~in, that is differ from its native and predicted

Kontroversi Metode Deteksi COVID-19 di Indonesia

Abstract—The governance of COVID-19 cases in Indonesia is carried out in accordance with the WHO directions. Serological tests, often mentioned as rapid antibody tests, are used for mass screening testing while the polymerase-chain-reaction (PCR)-based tests are performed for routine confirmation of COVID-19 infection cases. PCR test is one of nucleic acid amplification tests (NAAT) for detection of viral RNA. The management of the COVID-19 detection caused controversies at the beginning of pandemic period. It seems that the controversies occurred due to misperception regarding the tests, as well as misunderstanding caused by differences in individual immune responses, viral dynamics in human bodies and clinical outcomes. In response to community opinion controversies, this paper discuss the following topics, i.e. a glimpse about COVID-19, the characteristics of SARS-CoV-2, viral dynamics in human body, the dynamics of human immune response to SARS-CoV-2, basic explanation about COVID-19 and SARS-CoV-2 testing, and the last part explained the occurred controversies. Penetapan pelaksanaan deteksi kasus COVID-19 di Indonesia dilaksanakan sesuai arahan WHO. Uji serologis atau rapid test antibodi digunakan untuk test atau skrining massal sedangkan untuk uji berbasis polymerase-chain-reaction (PCR) digunakan untuk konfirmasi rutin kasus infeksi COVID-19. Uji molekuler secara PCR merupakan salah satu metode nucleic acid amplification tests (NAAT), untuk mendeteksi RNA virus. Penatalaksanaan deteksi Coronavirus disease 2019 (COVID-19) ini di awal masa pandemik menimbulkan berbagai kontroversi di masyarakat. Kontroversi terjadi terutama karena pemahaman yang berbeda dari masyarakat mengenai prinsip pengujian dan adanya salah pengertian akibat adanya perbedaan respon immun antar individu, dinamika virus COVID-19 dalam tubuh orang terinfeksi, dan luaran klinis pasien. Menanggapi kontroversi pendapat di masyarakat maka pada tulisan ini dibahas tentang sekilas COVID-19, karakteristik SARS-CoV-2, dinamika virus dan pembentukan antibodi dalam tubuh manusia, penjelasan prinsip pengujian COVID-19 dan SAR-CoV-2 serta ulasan tentang kontroversi yang terjadi

Secondary Metabolites of Various Indonesian Medicinal Plants as SARS-CoV-2 Inhibitors: In Silico Study

Corona virus disease 2019 caused by SARS-CoV-2 infection emerged in late 2019 and still become a worldwide pandemic up to this point with the drug remain unavailable. Meanwhile, Indonesia has an abundance variety of medicinal plants that are potential to be developed as inhibitors. By using the key role proteins as drug targets, namely spike glycoprotein and RNA-dependent RNA polymerase (RdRp) of delta variant of SARS-CoV-2 (which is known as strongly transmitted and highly virulent), we can develop inhibitors for the target proteins from potential Indonesian medicinal plants to prevent the protein interactions for viral entry and proliferation that leading to organ disfunction and death. This study aimed to identify the secondary metabolites of various Indonesian medicinal plants as SARS-CoV-2 inhibitors. The 184 ligands from nine plants were collected from IJAH webserver and their SMILES notation were collected from PubChem. Meanwhile 3D structures of spike glycoprotein (PDB ID: 6VXX) and RdRp (PDB ID: 6M71) were obtained from protein data bank (PDB). Molecular docking was conducted between ligands and the two SARS-CoV-2 proteins using Autodock Vina in PyRx with hesperidin and remdesivir as control compounds. Several potential compounds were selected for drug-likeness analysis and toxicity analysis. Results showed that lantanolic acid has the same amino acid interaction with RdRp as the control compound. It formed a hydrogen bond with Ser784 and hydrophobic bonds with Tyr32 and Ser7709. It had lower binding affinity than the control compounds, eligible as oral drug, and had LD50 of 2589 mg/kg

Construction of a recombinant plasmid containing xynb gene from Bacillus subtilis subsp. spizizeniiW23

This study aimed to clone thexynB gene from Bacillussubtilissubsp. spizizeniiW23,encodinga xylan l,4-beta-xylosidase to pMMB67EH plasmid which then be used to transformed EscherichiacoliDH-5a and Origami host cells. The xynBgenewas amplifiedby polymerasechain reaction (PCR) technique using a pair of primers flanking the gene sequence,and chromosomal DNA of the W23 strain as a template. Analyses of the recombinant plasmid were done by restriction analyses, and PCR detection. The result showed that the xynB has been cloned on pMMB67EH vector. The recombinant plasmid contained the xynB gene which was confirmed by restriction analyses and by PCR detection using primers pair's specific for the xynB gene and for the vector. The xylanaseactivity of xynB gene in E.coliDH-5a and Origami host cells was assayedon luria-Bertani-xylan plate qualitatively with addition of isopropyl B-D-thio-galactoside (IPTG) as an inducer.Uponsprayingwith Congored, the cells bearing the pMMB-xynB recombinant plasmid showed a xylan-degrading activity by the appearance ofclear zanearound the colonies whilethe transformant bearing an empty plasmid showed no clear zone. It could be concluded that the cloning Arocess was succeeded

Konstruksi Mutan Enterobacter ludwigii Strain Lokal secara Acak Menggunakan Transposon Mutagenesis untuk Menurunkan Produksi Asam dan Meningkatkan Produksi Biogas

Penggunaan bahan bakar fosil sebagai sumber energi utama dapat menyebabkan teljadinya perubahan iklim global akibat pembakaran dan emisi gas yang berlebihan serta memicu timbulnya krisis energi. Diperlukan adanya pengembangan sumber energi alternatif yang ramah lingkungan, seperti biogas yang dihasilkan melalui proses fermentasi pada bakteri fermentatif seperti Bacillus spp., dan Enterobacter spp. Tujuan dari penelitian ini adalah untuk mengkonstruksi mulan Enterobacter ludwigii strain lokal hasil isolasi dari sedimen muara sungai Kalimas Surabaya secara transposon mutagenesis serta memperoleh mutan yang mengalami penurunan produksi asam-asam organik dan peningkatan produksi biogas dibanding dengan gaJur murninya. Transposon yang digunakan adalah mini-TnS yang terdapat pada plasmid rekombinan pUTmini-TnS-luxCDABE-Km. Proses transfer plasmid dilakukan secara konyugasi dengan menggunakan Escherichia coli S17-1 A.pir sebagai sel donor. Dari hasil konyugasi, total transkonyugan yang telah diseleksi pada media LB agar-Km 100 flglml adalah 524 koloni. Dari kuantifikasi produksi asam organik pada media PRDB secara spektrofotometri, diperoleh jwnlah mutan yang mengaJami penurunan produksi asam adalah 12 (AS), 18 (88), 30 (A24), dan 29 (B24) dari total 31 mutan tiap variasi yang diuji. Sedangkan dari uji produksi biogas pada media kompleks, mutan yang mengalami peningkatan produksi tertinggi adalah 824-37 dengan rata-rata peningkatan sebesar 15 kali dibandingkan galur murninya. Dengan dernikian, dapat disimpulkan bahwa pada penelitian telah berhasil dikonstruksi mutan E. ludwigii strain Iokal Surabaya yang mengalami penurunan produksi asam organik dan peningkatan produksi biogas