Deteksi Virus Penyebab Infeksi Saluran Pernafasan Akut di Rumah Sakit (Studi Pendahuluan dengan Uji Fast-Track® Diagnostik)

Abstract Acute respiratory infections (ARI) is the leading cause of morbidity and mortality in the world and Indonesia. Information on the virus that causes ARI is still limited. The aim of this study was to detect the virus that causes ARI hospitalized cases in three sentinel surveillance hospitals of severe ARI. Laboratory testing of 30 nasal and throat swab specimens from ARI hospitalized cases at Deli Serdang Hospital, Wonosari Hospital and Kanudjoso Djati Hospital during August - September 2016. Laboratory testing were carried out at the Virology Laboratory of the Center for Biomedical Research and Development and Basic Health Technology. This research is a preliminary study using Fast-Track Diagnostics multiplex Real-time RT-PCR to detect 21 viruses. The viruses that have been detected are Human Metapneumovirus (21.2%), Human Parainfluenza Virus 1 (12.1%), Influenza B (6.1%), Human Coronavirus-OC43 (6.1%), Human CoronavirusNL63 (6.1%), Human Parainfluenza Virus 2 (3.0%), Human Rhinovirus (3.0%), and Human Adenovirus (3.0%). Of the 17 samples that tested positive for viruses, 14 of them were single cases of infection while the other three were cases of co-infection between Human Coronavirus-NL63 and Human Parainfluenza Virus 1, Human Metapneumovirus with Human Coronavirus-OC43, and Human Adenovirus with Human Rhinovirus. The most detected virus from ARI hospitalized cases are the Human Metapneumovirus. Abstrak Infeksi saluran pernafasan akut (ISPA) merupakan penyakit menular yang menjadi penyebab utama 1 morbiditas dan mortalitas di dunia dan Indonesia. Informasi virus penyebab ISPA masih terbatas. Tujuan dari penelitian ini adalah mendeteksi virus penyebab kasus ISPA rawat inap di tiga rumah sakit sentinel surveilans ISPA berat. Pemeriksaan pada 30 spesimen swab hidung dan tenggorok dari kasus ISPA rawat inap di RSUD Deli Serdang, RSUD Wonosari, dan RS Kanudjoso Djati selama bulan Agustus–September 2016. Pemeriksaan dilakukan di Laboratorium Virologi Pusat Penelitian dan Pengembangan Biomedis dan Teknologi Dasar Kesehatan. Penelitian ini merupakan penelitian pendahuluan menggunakan FastTrack Diagnostics multiplex Real-time RT-PCR untuk mendeteksi 21 virus. Virus-virus yang berhasil dideteksi adalah Human Metapneumovirus (21,2%). Human Parainfluenza Virus 1 (12,1%), Influenza B (6,1%), Human Coronavirus-OC43 (6,1%), Human Coronavirus-NL63 (6,1%), Human Parainfluenza Virus 2 (3,0%), Human Rhinovirus (3,0%), dan Human Adenovirus (3,0%). Dari 17 sampel yang dinyatakan positif mengandung virus, 14 diantaranya merupakan kasus infeksi tunggal sedangkan tiga lainnya merupakan kas us koinfeksi antara Human Coronavirus-NL63 dengan Human Parainfluenza Virus 1, Human Metapneumovirus dengan Human Coronavirus-OC43, dan Human Adenovirus dengan Human Rhinovirus. Virus yang paling banyak terdeteksi dari spesimen kasus ISPA rawat inap adalah Human Metapneumovirus

Deteksi Virus Rabies pada Kasus Ante-Mortem dengan RT-PCR

Rabies virus detection using Reverse Transcriptase Polymerase Chain Reaction (RT – PCR) was considered to have high sensitivity and specificity. This method is relatively faster and easy to perform in comparison with other methods such as Fluorescent Antibody Test (FAT) and Mouse Inoculation Test (MIT). Therefore, the RT PCR method is used as ante mortem diagnosis of rabies. A total of 74 specimens such as saliva, conjuctival swabs and under tongue swabs were collected from the bites of animal transmitting rabies cases. The 74 specimens were collected from 28 human cases of suspected rabies outbreaks in 2009-2013 that has been tested in the Virology Laboratory, Center for Biomedical and Basic Technology of Health. All specimens examined by RT - PCR method using two primer pairs that amplify the partial gene regions of the N and G genes of the rabies virus. Two of the 74 specimens gave positive results of rabies by RT - PCR, i.e saliva and under-tongue swab from human cases of animal bites in 2009. RT-PCR assay can be used for ante mortem diagnosis of the rabies virus. The laboratory results are influenced by the type of specimen and collection time.Key words : Rabies, Outbreak, RT-PCR AbstrakDeteksi virus rabies menggunakan metode Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) dinilai memiliki sensitivitas dan spesifisitas yang tinggi. Kemudahan pengerjaan dan hasil pemeriksaan yang relatif cepat dibandingkan dengan metode Fluorescent Antibody Test (FAT) dan Mouse Inoculation Test (MIT) yang merupakan metode standar WHO yang menjadikan RT-PCR lebih banyak digunakan untuk deteksi ante mortem virus rabies. Sebanyak 74 spesimen kasus gigitan hewan penular rabies (GHPR) yaitu saliva, apus selaput mata dan apus bawah lidah yang berasal dari 28 kasus tersangka rabies pada kejadian luar biasa pada tahun 2009-2013 yang telah diperiksa oleh laboratorium Virologi Pusat Biomedis dan Teknologi Dasar Kesehatan. Seluruh spesimen diperiksa dengan metode RT-PCR menggunakan 2 pasang primer yaitu primer yang mengamplifikasi sebagian region pada gen N dan gen G dari virus rabies tersebut. Dua dari 74 spesimen memberikan hasil positif rabies berdasarkan hasil pemeriksaan dengan RT-PCR, yaitu spesimen saliva dan swab bawah lidah dari kasus gigitan anjing pada tahun 2009. Pemeriksaan ante mortem terhadap virus rabies dapat menggunakan metode RT-PCR dengan memperhatikan waktu pengambilan dan jenis spesimen.Kata Kunci : Rabies, KLB, RT-PC

Detection of neuraminidase inhibitor-resistant influenza A (H1N1)pdm09 viruses obtained from influenza surveillance in Indonesia

Background: Influenza antiviral resistance has been shown to occur in many countries and is commonly found in influenza A(H1N1)pdm09 and A(H3N2). In this study, we monitored and investigated the neuraminidase inhibitor resistance of influenza A(H1N1)pdm09 viruses through the influenza surveillance system in Indonesia. Methods: A total of 4752 clinical specimens were collected from patients with influenza-like illness and severe acute respiratory infection during the year 2016. An allelic discrimination assay was conducted by a single base substitution or a single-nucleotide polymorphism that is specific to the H275 wild-type and Y275 mutant. Sequencing was performed to confirm the H275Y mutations, and we analysed the phylogenetic relationship. Results: The first occurrence of oseltamivir-resistant influenza A(H1N1)pdm09 was observed in the samples from the influenza-like illness surveillance. Two H275Y oseltamivir-resistant viruses (0.74%) out of 272 influenza A(H1N1)pdm09 positives were found. Both of them were collected from untreated patients. Conclusion: The number of oseltamivir-resistant influenza A(H1N1)pdm09 viruses in Indonesia is very low. However, it is necessary to continue with active surveillance for oseltamivir resistance in severe and mild cases

The first case of laboratory-confirmed dengue virus infection in Mimika, Papua province, Indonesia

Abstrak Latar belakang: Dengue merupakan penyakit bersumber vektor yang berkontribusi cukup besar dalam menyebabkan masalah kesehatan baik di negara tropis maupun subtropis. Hingga saat ini virus dengue telah menyebar ke seluruh provinsi di Indonesia sejak pertama kali ditemukan di Surabaya pada tahun 1968. Kabupaten Mimika di propinsi Papua, Indonesia, merupakan daerah non-endemis dengue dan tidak pernah melaporkan munculnya kasus dengue. Walau begitu, pada tahun 2012 ditemukan 13 kasus tersangka dengue yang dirawat di Rumah Sakit Umum di Mimika. Studi ini bertujuan memberi gambaran karakteristik genetik virus dengue dari kasus terkonfirmasi (laboratory-confirmed) pertama di kabupaten Mimika, propinsi Papua, Indonesia. Metode: Isolasi virus pada sel nyamuk C6/36, RT-PCR dan penentuan serotipe dilakukan untuk mengkonfirmasi adanya virus dengue (DENV) di dalam serum pasien tersangka dengue dari kabupaten Mimika, propinsi Papua, Indonesia. Sekuensing dan analisis pohon filogenetik terhadap complete-coding sequence (CDS) gen E dilakukan terhadap sampel yang telah positif DENV untuk penentuan genotipe virus. Hasil: Sebanyak 4 kasus tersangka dengue terkonfirmasi positif DENV berdasarkan pemeriksaan RT-PCR, sedangkan 2 sampel berhasil dilakukan kultur pada sel C6/36. Hasil penentuan serotipe menunjukkan bahwa virus DENV dari kabupaten Mimika, propinsi Papua, Indonesia, termasuk ke dalam serotipe DENV 3.  Analisis CDS gen E menunjukkan DENV 3 termasuk ke dalam genotipe I. Kesimpulan: Studi ini melaporkan kasus pertama dengue yang terkonfirmasi secara laboratorium dari kabupaten Mimika, propinsi Papua, Indonesia, yang merupakan daerah non-endemis dengue. Kata Kunci: dengue, penentuan serotipe, penentuan genotipe, kabupaten Mimika Abstract Background: Dengue is the most important vector-borne disease that poses serious health problem both in tropical and subtropical countries. Since the first outbreak in Surabaya in 1968, dengue infection has spread in all provinces in Indonesia. Mimika district in Papua province, Indonesia, is a non-endemic dengue area with no laboratory-confirmed case reported. However, until 2012 there were 13 suspected dengue infection admitted to local General Hospital in Mimika district, Papua province, Indonesia. This study described the genetic characteristics of first laboratory-confirmed dengue virus (DENV) infection in Mimika district, Papua province, Indonesia. Methods: Viral isolation in C6/36 cell line, RT-PCR and serotyping were carried out to confirm the presence of DENV within serum patient of suspected DENV cases from Mimika district, Papua Province, Indonesia. Direct sequencing and phylogenetic analysis of complete coding sequence (CDS) of E gene was performed to the samples that have already confirmed positive DENV for viral genotyping. Results: Four cases were confirmed to be DENV by RT-PCR while only 2 samples were able to be culture in C6/36 mosquito cell line. Serotyping confirmed that the DENV from Mimika district, Papua province were DENV3 serotype. The genotyping showed that the DENV3 from Mimika district were belonged to genotype I. Conclusion: This study reported the first laboratory-confirmed of DENV cases in non-endemic dengue area, Mimika district, Papua Province, Indonesia. Keywords: dengue, serotyping, genotyping, Mimika district </p

Genotypes of dengue virus circulate in dengue sentinel surveillance in Indonesia

Latar Belakang: Demam berdarah dengue disebabkan oleh infeksi virus dengue (DENV) yang terdiri atas serotipe 1 sampai dengan serotipe 4. Masing-masing serotipe dibedakan lagi menjadi beberapa genotipe. Studi ini dilakukan untuk mendeteksi genotipe DENV yang bersirkulasi di lokasi surveilans sentinel dengue. Metode: Untuk menentukan genotipe dilakukan analisis genetik menggunakan perangkat bioinformatik. Urutan nukleotida yang lengkap dari gen selubung DENV diperoleh melalui amplifikasi genetik menggunakan primer overlapping untuk masing-masing serotipe. Pohon filogenetik dibuat menggunakan perangkat lunak MEGA 6.0, metode Neighbor Joining dengan 1000 replikasi dan parameter Kimura-2. Sekuen nukleotida dari GenBank yang telah diketahui genotype DENV digunakan sebagai referen. Hasil: Jumlah sampel dengan gen selubung DENV yang dapat diamplifikasi adalah 64 dari 204 kasus yang terkonfirmasi. Empat belas sekuen dari DENV-1, 22 sekuen DENV-2, dan 28 sekuens DENV-3. Dari studi ini belum didapatkan sekuen untuk DENV-4. DENV-1 dan DENV-2 masing-masing masuk dalam kelompok genotipe I dan Cosmopolitan, sementara DENV-3 masuk dalam kelompok genotipe I. Kesimpulan: Genotipe  DENV di lokasi surveilans sentinel dengue  sama dengan genotype yang sebelumnya dilaporkan bersirkulasi di Indonesia. (Health Science Journal of Indonesia 2016;7(2):69-74) Kata kunci: surveilans sentinel dengue, virus dengue, genotype  Abstract Background: Dengue hemorrhagic fever was caused by dengue virus (DENV). This virus has four serotypes, DENV-1 to DENV-4, in which each serotype consists of various genotypes. This study present the distribution of DENV genotype circulate in dengue sentinel surveillance sites. Methods: We performed molecular analyses using bioinformatics tools to identify genotype of DENV. Sequencing targeting envelope gene was carried out on DENV-positive samples. Full-length sequence of envelope gene was obtained using overlapping primers for DENV 1, 2, 3 and 4. Phylogenetic tree was generated by Neighbor Joining using MEGA 6.0 with 1000 bootstrap replications and Kimura 2-parameter model.  Known genotype of DENV sequences from Indonesia and other countries obtained from GenBank were included in the analyses as references. Results: A total of 64 complete coding sequences of envelope gene from DENV-1, DENV-2 and DENV-3 were successfully sequenced from 204 confirmed DENV cases. There are fourteen sequences of DENV-1, 22 sequences of DENV-2 and 28 sequences of DENV-3. Unfortunately, there was no complete coding sequence of envelope gene obtained for DENV-4. DENV-1 and DENV-2 were grouped into genotype I and cosmopolitan genotype, respectively. The DENV-3 was grouped into genotype I. These viruses were belongs to various genotypes that have been circulating previously in Indonesia. Conclusion: This finding suggests that the distribution of DENV genotype in sentinel sites remained stable. (Health Science Journal of Indonesia 2016;7(2):69-74) Key words: dengue sentinel surveillance, dengue virus, genotype

Linkage disequilibrium suggests genomic stability in Omicron clades of SARS-CoV-2 from the ASEAN countries

After more than 2 years of pandemic caused by SARS-CoV2, COVID-19 is still a national concern in many countries worldwide. One of the key investigations is to understand the factors contributing to the evolutionary dynamics of SARS-CoV2 as a pathogen. Currently, almost all countries have lifted border control orders and have allowed inter-country travel with minimal restrictions. This provides better resolutions on genomic patterns and the evolution of circulating SARS-CoV-2 in each community with the influence of imported strains. In this report, we surveyed genomes of SARS-CoV-2 strains circulating in the Association of Southeast Asian Nations (ASEAN) countries. This project serves as a collaborative effort from the ASEAN Member States that had participated in the programme ‘Strengthening Laboratory Capacity on COVID-19 Bio Genomic for ASEAN Countries