An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia

Funder: US-CDCBackground: Chikungunya virus (CHIKV) is an important emerging and re-emerging public health problem worldwide. In Indonesia, where the virus is endemic, epidemiological information from outside of the main islands of Java and Bali is limited. Methodology/Principal Findings: Four hundred and seventy nine acutely febrile patients presenting between September 2017–2019 were recruited from three city hospitals situated in Ambon, Maluku; Banjarmasin, Kalimantan; and Batam, Batam Island as part of a multi-site observational study. CHIKV RNA was detected in a single serum sample while a separate sample was IgM positive. IgG seroprevalence was also low across all three sites, ranging from 1.4–3.2%. The single RT-PCR positive sample from this study and 24 archived samples collected during other recent outbreaks throughout Indonesia were subjected to complete coding region sequencing to assess the genetic diversity of Indonesian strains. Phylogenetic analysis revealed all to be of a single clade, which was distinct from CHIKV strains recently reported from neighbouring regions including the Philippines and the Pacific Islands. Conclusions/Significance: Chikungunya virus strains from recent outbreaks across Indonesia all belong to a single clade. However, low-level seroprevalence and molecular detection of CHIKV across the three study sites appears to contrast with the generally high seroprevalences that have been reported for non-outbreak settings in Java and Bali, and may account for the relative lack of CHIKV epidemiological data from other regions of Indonesia

Distinct Dengue Disease Epidemiology, Clinical, and Diagnosis Features in Western, Central, and Eastern Regions of Indonesia, 2017–2019

The people of Indonesia have been afflicted by dengue, a mosquito-borne viral disease, for over 5 decades. The country is the world's largest archipelago with diverse geographic, climatic, and demographic conditions that may impact the dynamics of disease transmissions. A dengue epidemiology study was launched by us to compare and understand the dynamics of dengue and other arboviral diseases in three cities representing western, central, and eastern Indonesia, namely, Batam, Banjarmasin, and Ambon, respectively. A total of 732 febrile patients were recruited with dengue-like illness during September 2017–2019 and an analysis of their demographic, clinical, and virological features was performed. The seasonal patterns of dengue-like illness were found to be different in the three regions. Among all patients, 271 (37.0%) were virologically confirmed dengue, while 152 (20.8%) patients were diagnosed with probable dengue, giving a total number of 423 (57.8%) dengue patients. Patients' age and clinical manifestations also differed between cities. Mostly, mild dengue fever was observed in Batam, while more severe cases were prominent in Ambon. While all dengue virus (DENV) serotypes were detected, distinct serotypes dominated in different locations: DENV-1 in Batam and Ambon, and DENV-3 in Banjarmasin. We also assessed the diagnostic features in the study sites, which revealed different patterns of diagnostic agreements, particularly in Ambon. To detect the possibility of infection with other arboviruses, further testing on 461 DENV RT-PCR-negative samples was performed using pan-flavivirus and -alphavirus RT-PCRs; however, only one chikungunya infection was detected in Ambon. A diverse dengue epidemiology in western, central, and eastern Indonesia was observed, which is likely to be influenced by local geographic, climatic, and demographic conditions, as well as differences in the quality of healthcare providers and facilities. Our study adds a new understanding on dengue epidemiology in Indonesia

Distinct Dengue Disease Epidemiology, Clinical, and Diagnosis Features in Western, Central, and Eastern Regions of Indonesia, 2017–2019

The people of Indonesia have been afflicted by dengue, a mosquito-borne viral disease, for over 5 decades. The country is the world's largest archipelago with diverse geographic, climatic, and demographic conditions that may impact the dynamics of disease transmissions. A dengue epidemiology study was launched by us to compare and understand the dynamics of dengue and other arboviral diseases in three cities representing western, central, and eastern Indonesia, namely, Batam, Banjarmasin, and Ambon, respectively. A total of 732 febrile patients were recruited with dengue-like illness during September 2017–2019 and an analysis of their demographic, clinical, and virological features was performed. The seasonal patterns of dengue-like illness were found to be different in the three regions. Among all patients, 271 (37.0%) were virologically confirmed dengue, while 152 (20.8%) patients were diagnosed with probable dengue, giving a total number of 423 (57.8%) dengue patients. Patients' age and clinical manifestations also differed between cities. Mostly, mild dengue fever was observed in Batam, while more severe cases were prominent in Ambon. While all dengue virus (DENV) serotypes were detected, distinct serotypes dominated in different locations: DENV-1 in Batam and Ambon, and DENV-3 in Banjarmasin. We also assessed the diagnostic features in the study sites, which revealed different patterns of diagnostic agreements, particularly in Ambon. To detect the possibility of infection with other arboviruses, further testing on 461 DENV RT-PCR-negative samples was performed using pan-flavivirus and -alphavirus RT-PCRs; however, only one chikungunya infection was detected in Ambon. A diverse dengue epidemiology in western, central, and eastern Indonesia was observed, which is likely to be influenced by local geographic, climatic, and demographic conditions, as well as differences in the quality of healthcare providers and facilities. Our study adds a new understanding on dengue epidemiology in Indonesia

Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia

Abstract: Background: Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances to suitably equipped laboratories to be sequenced. This approach is time-consuming, expensive, and frequently results in failure due to low viral load or degradation of the RNA genome. Methods: We evaluated a method designed to address this challenge, using the ‘Primal Scheme’ multiplex PCR tiling approach to rapidly generate short, overlapping amplicons covering the complete DENV coding-region, and sequencing the amplicons on the portable Nanopore MinION device. The resulting sequence data was assessed in terms of genome coverage, consensus sequence accuracy and by phylogenetic analysis. Results: The multiplex approach proved capable of producing near complete coding-region coverage from all samples tested (x¯ = 99.96%, n = 18), 61% of which could not be fully amplified using the current, long-amplicon PCR, approach. Nanopore-generated consensus sequences were found to be between 99.17–99.92% identical to those produced by high-coverage Illumina sequencing. Consensus accuracy could be improved by masking regions below 20X coverage depth (99.69–99.92%). However, coding-region coverage was reduced at this depth (x¯ = 93.48%). Nanopore and Illumina consensus sequences generated from the same samples formed monophyletic clades on phylogenetic analysis, and Indonesian consensus sequences accurately clustered by geographical origin. Conclusion: The multiplex, short-amplicon approach proved superior for amplifying DENV genomes from clinical samples, particularly when the virus was present at low concentrations. The accuracy of Nanopore-generated consensus sequences from these amplicons was sufficient for identifying the geographic origin of the samples, demonstrating that the approach can be a useful tool for identifying and monitoring DENV clades circulating in low-resource settings across Indonesia. However, the inaccuracies in Nanopore-generated consensus sequences mean that the approach may not be appropriate for higher resolution transmission studies, particularly when more accurate sequencing technologies are available

An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia

Funder: US-CDCBackground: Chikungunya virus (CHIKV) is an important emerging and re-emerging public health problem worldwide. In Indonesia, where the virus is endemic, epidemiological information from outside of the main islands of Java and Bali is limited. Methodology/Principal Findings: Four hundred and seventy nine acutely febrile patients presenting between September 2017–2019 were recruited from three city hospitals situated in Ambon, Maluku; Banjarmasin, Kalimantan; and Batam, Batam Island as part of a multi-site observational study. CHIKV RNA was detected in a single serum sample while a separate sample was IgM positive. IgG seroprevalence was also low across all three sites, ranging from 1.4–3.2%. The single RT-PCR positive sample from this study and 24 archived samples collected during other recent outbreaks throughout Indonesia were subjected to complete coding region sequencing to assess the genetic diversity of Indonesian strains. Phylogenetic analysis revealed all to be of a single clade, which was distinct from CHIKV strains recently reported from neighbouring regions including the Philippines and the Pacific Islands. Conclusions/Significance: Chikungunya virus strains from recent outbreaks across Indonesia all belong to a single clade. However, low-level seroprevalence and molecular detection of CHIKV across the three study sites appears to contrast with the generally high seroprevalences that have been reported for non-outbreak settings in Java and Bali, and may account for the relative lack of CHIKV epidemiological data from other regions of Indonesia

Community Willingness to Participate in a Dengue Study in Aceh Province, Indonesia

Background: Dengue virus infection is the most rapidly spreading vector-borne disease in the world. Essential research on dengue virus transmission and its prevention requires community participation. Therefore, it is crucial to understand the factors that are associated with the willingness of communities in high prevalence areas to participate in dengue research. The aim of this study was to explore factors associated with the willingness of healthy community members in Aceh province, Indonesia, to participate in dengue research that would require phlebotomy. Methodology/Principal Findings: A community-based cross-sectional study was carried out in nine regencies and municipalities of Aceh from November 2014 to March 2015. Interviews using a set of validated questionnaires were conducted to collect data on demography, history of dengue infection, socioeconomic status, and knowledge, attitude and practice regarding dengue fever. Two-step logistic regression and Spearman's rank correlation (rs) analysis were used to assess the influence of independent variables on dependent variables. Among 535 participants, less than 20% had a good willingness to participate in the dengue study. The factors associated with good willingness to participate were being female, working as a civil servant, private employee or entrepreneur, having a high socioeconomic status and good knowledge, attitude and practice regarding dengue. Good knowledge and attitude regarding dengue were positive independent predictors of willingness to participate (OR: 2.30 [95% CI: 1.36-3.90] and 3.73 [95% CI: 2.24-6.21], respectively). Conclusion/Significance: The willingness to participate in dengue research is very low among community members in Aceh, and the two most important associated factors are knowledge and attitude regarding dengue. To increase participation rate, efforts to improve the knowledge and attitude of community members regarding dengue fever and dengue-related research is required before such studies are launched

Implementasi Program Kios Pelayanan Publik (E-Kios) Sebagai Inovasi Pelayanan Publik Berbasis Teknologi Informasi di Kelurahan Kebraon Kota Surabaya

Penelitian ini bertujuan untuk mengetahui implementasi program E-Kios di kelurahan Kebraon dan faktor-faktor yang mempengaruhi implementasi program E-Kios tersebut. Alasan yang melatarbelakangi munculnya penelitian ini adalah permasalahan dalam pelaksanaan program E-Kios yang sebagian besar ditemui di kelurahan kota Surabaya beserta dengan beberapa kendala teknis seperti jaringan internet yang lambat, sosialisasi program E-Kios yang kurang maksimal, aparatur pemerintah yang masih kurang memahami E-Kios, dan lain sejenisnya. Hal tersebut berbanding terbalik dengan adanya data yang menunjukkan bahwa program E-Kios mendapat penghargaan Inovasi dan Teknologi pada tahun 2015 serta menjadi role model nasional dalam pelayanan publik di Surabaya. Teori pokok yang digunakan dalam penelitian ini adalah teori implementasi program, yaitu teori elaborasi dari George Edward III dengan Grindle. Teori ini terdiri atas faktor-faktor yang mempengaruhi implementasi program E-Kios yaitu komunikasi, sumber daya, disposisi, struktur birokrasi, dan sasaran program. Penelitian ini menggunakan metode penelitian kualitatif karena peneliti dihadapkan dengan permasalahan penelitian yang bersifat dinamis dan kompleks. Pemilihan informan menggunakan teknik purposive sampling dilanjutkan dengan teknik snowball sampling. Pengumpulan data diperoleh dengan wawancara terstruktur, observasi, dan perolehan data-data sekunder melalui aplikasi online program E-Kios. Teknik analisis data menggunakan analisis data kualitatif Miles dan Hubberman, yaitu reduksi data, penyajian data, dan penarikan kesimpulan pada data dan uji keabsahan data dilakukan dengan uji triangulasi data. Hasil dari penelitian ini adalah bahwa implementasi program E-Kios masih kurang maksimal karena adanya faktor disposisi, yaitu sikap yang kurang responsif dari staf kelurahan Kebraon pada saat melaksanakan program E-Kios dan komunikasi program E-Kios baik pada lingkup internal maupun eksternal yang dilaksanakan oleh staf kelurahan Kebraon dan SKPD terkait. Pada lingkup internal, terdapat staf kelurahan Kebraon yang masih belum paham terhadap pelaksanaan program E-Kios dan pada lingkup eksternal, sosialisasi program EKios masih minim dan terbatas karena hanya mengandalkan pemberitahuan lisan dari RT dan RW saja

Phylogenetic Relationships of Stress Resistant Fish in Harapan Rainforest Jambi Based on DNA Barcode

DNA barcode as an effective tool for identification and reveal phylogenetic relationships in fish. The purpose of this study was to analysis DNA sequence, genetic distance and reveal phylogenetic relationships of stress resistance fish (blackfish) in Harapan Rainforest Jambi base on DNA barcode. The research was conducted from April to August 2016 in Harapan Rainforest Jambi, Integrated Laboratory, Jambi University and Biotechnology Laboratory of the Primate Study Centre-IPB University. DNA extraction was done on five blackfish species from Harapan Rainforest Jambi, namely Nandus nebulosus, Pristolepis grootii, Trichopodus leerii, Channa striata and Channa micropeltes. As a comparison, we used stress intolerance fish (whitefish) from Harapan Rainforest Jambi, i.e., Balantiocheilos melanopterus and Hemibagrus nemurus from the gene-bank NCBI with acession number KT001040,1. DNA Extraction was performed according to Quick-Star Tissue Protocol from Qiagen. COI gene amplification with modification at denaturation and anneling temperatures. Visualization DNA band using a horizontal electrophoresis machine from Bio Rad. Sequencing DNA send to 1st Base Malaysia. DNA sequence used Biodit and MEGA X software. The alignment of the DNA bands in MEGA X produces DNA sequence along 588 bp, where 350 bp conserve and 238 bp variable sites. The composition of the base nucleotides were (T/U) =29%, C=28.6%, A=25%, and G=17.3%. The closest genetic distance was between Channa striata and Channa micropeltes (0.190)  and the farthest was found on  Nandus nebulosus and  Hemibagrus nemurus (0.303). The phylogeny tree shows that the blackfishes are separated from whitefishes. The group of blackfish is divided into Channidae group (Channa striata, Channa micropeltes) and non-Channidae group (Nandus nebulosus, Trichopodus leerii, Pristolepis grootii)

THE IMPLEMENTATION OF PACKET RADIO WIDE AREA NETWORK IN INDONESIA

ABSTRACT In this report, the implementation of TCP/IP-based packet radio technology to integrate various universities and institutions into the first Indonesia's national InterNet Wide Area Network (WAN) will be described Various efforts include 7UP/IP software development, 2FIDLC X25 card various modems (PSG AFSK GMSK and high speed MSK) will be presented In addition, various advanced networking experiment mostly via satellite will be reportedHlm. 98-10

Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia.

BACKGROUND:Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances to suitably equipped laboratories to be sequenced. This approach is time-consuming, expensive, and frequently results in failure due to low viral load or degradation of the RNA genome. METHODS:We evaluated a method designed to address this challenge, using the 'Primal Scheme' multiplex PCR tiling approach to rapidly generate short, overlapping amplicons covering the complete DENV coding-region, and sequencing the amplicons on the portable Nanopore MinION device. The resulting sequence data was assessed in terms of genome coverage, consensus sequence accuracy and by phylogenetic analysis. RESULTS:The multiplex approach proved capable of producing near complete coding-region coverage from all samples tested ([Formula: see text] = 99.96%, n = 18), 61% of which could not be fully amplified using the current, long-amplicon PCR, approach. Nanopore-generated consensus sequences were found to be between 99.17-99.92% identical to those produced by high-coverage Illumina sequencing. Consensus accuracy could be improved by masking regions below 20X coverage depth (99.69-99.92%). However, coding-region coverage was reduced at this depth ([Formula: see text] = 93.48%). Nanopore and Illumina consensus sequences generated from the same samples formed monophyletic clades on phylogenetic analysis, and Indonesian consensus sequences accurately clustered by geographical origin. CONCLUSION:The multiplex, short-amplicon approach proved superior for amplifying DENV genomes from clinical samples, particularly when the virus was present at low concentrations. The accuracy of Nanopore-generated consensus sequences from these amplicons was sufficient for identifying the geographic origin of the samples, demonstrating that the approach can be a useful tool for identifying and monitoring DENV clades circulating in low-resource settings across Indonesia. However, the inaccuracies in Nanopore-generated consensus sequences mean that the approach may not be appropriate for higher resolution transmission studies, particularly when more accurate sequencing technologies are available