Whole genome sequencing of Indonesian dengue virus isolates using next-generation sequencing

Indonesia is a tropical country and hyperendemic for dengue. The disease prevalently affected Indonesian and it caused high morbidity and substantial economic burden. This vector-borne viral disease is caused by infection of dengue viruses (DENVs), which are the member of Flaviviridae family. While most of dengue studies in Indonesia focused on the epidemiology, the clinical aspects, the vectors, and to certain extent the virology, there were still gaps in the DENVs genomic aspects. Considering their high mutation rate, the DENVs were known for their high genetic diversity and it might affect the characteristics of the viruses. Comprehensive DENV genomic data were thus important for many aspects of disease management, including virus surveillance, pathogenesis, diagnostics, antiviral drug design, and vaccine development. We established in this study a method for DENV whole genome sequencing using the advanced Next-Generation Sequencing (NGS) and Nextera XT DNA library preparation kit, coupled with simplified bioinformatic analysis methods. The Indonesian DENVs from four serotypes were isolated from patients’ sera, while library was prepared from enriched templates and sequenced using Illumina NGS. Our study highlighted the potential of a robust NGS method in producing whole genome sequence of DENVs, which would be important for future dengue studies

Glucose-6-phosphate dehydrogenase (G6PD) deficiency phenotype and genotype profile in Kodi Sub-district, West Sumba, Indonesia

Primaquine is the only drug licensed for prevention of relapse in vivax and ovale malarias. It causes mild to severe hemolysis when administered to patients with G6PD deficiency. Because current methods for identifying these patients are not well-suited to care in malaria endemic areas like those in Indonesia, most patients do not receive anti-relapse therapy. This study examined a new rapid diagnostic test for G6PD deficiency (Carestart™ G6PD diagnostic kit, AccessBio, New Jersey) that requires no cold chain, and no specialized training or equipment. A validated ROT for G6PD would permit far broader application of primaquine in the prevention, control and treatment of malaria. The general objective of the work described in this thesis is to evaluate the sensitivity and specificity of a Carestart™ G6PD diagnostic kit and provide G6PD phenotype and genotype profile in Wainyapu Village, Kodi Sub-district, West Sumba District, East Nusa Tenggara Province, Indonesia, an area of hypo- to meso-endemic falciparum and vivax malaria. In summary, the following aspects have been studied: 1. Performance of a G6PD Rapid Diagnostic Test. In November 2010 we surveyed 1090 randomly selected residents of Wainyapu. In the field we conducted the experimental G6PD RDT test alongside (in blinded fashion) a standard qualitative test dye reduction kit, and a surrogate G6PD quantitative gold standard. The results indicate that the RDT has superior specificity and inferior sensitivity compared to the qualitative dye reduction test. 2. G6PD Molecular variant profile of Wainyapu Village, West Sumba, Indonesia. G6PD Molecular profile of the study population was carried out on 30 randomly selected samples consisting of 20 G6PD deficient individuals and 10 G6PD normal individuals. Full exon sequencing revealed the finding of 5 different G6PD variants and evidence on historical antecedents of human migration from these regions to Indonesia in considerable numbers during several thousand years

Glucose-6-phosphate dehydrogenase (G6PD) deficiency phenotype and genotype profile in Kodi Sub-district, West Sumba, Indonesia

Primaquine is the only drug licensed for prevention of relapse in vivax and ovale malarias. It causes mild to severe hemolysis when administered to patients with G6PD deficiency. Because current methods for identifying these patients are not well-suited to care in malaria endemic areas like those in Indonesia, most patients do not receive anti-relapse therapy. This study examined a new rapid diagnostic test for G6PD deficiency (Carestart™ G6PD diagnostic kit, AccessBio, New Jersey) that requires no cold chain, and no specialized training or equipment. A validated ROT for G6PD would permit far broader application of primaquine in the prevention, control and treatment of malaria. The general objective of the work described in this thesis is to evaluate the sensitivity and specificity of a Carestart™ G6PD diagnostic kit and provide G6PD phenotype and genotype profile in Wainyapu Village, Kodi Sub-district, West Sumba District, East Nusa Tenggara Province, Indonesia, an area of hypo- to meso-endemic falciparum and vivax malaria. In summary, the following aspects have been studied: 1. Performance of a G6PD Rapid Diagnostic Test. In November 2010 we surveyed 1090 randomly selected residents of Wainyapu. In the field we conducted the experimental G6PD RDT test alongside (in blinded fashion) a standard qualitative test dye reduction kit, and a surrogate G6PD quantitative gold standard. The results indicate that the RDT has superior specificity and inferior sensitivity compared to the qualitative dye reduction test. 2. G6PD Molecular variant profile of Wainyapu Village, West Sumba, Indonesia. G6PD Molecular profile of the study population was carried out on 30 randomly selected samples consisting of 20 G6PD deficient individuals and 10 G6PD normal individuals. Full exon sequencing revealed the finding of 5 different G6PD variants and evidence on historical antecedents of human migration from these regions to Indonesia in considerable numbers during several thousand years

Immunogenicity and Reactogenicity of CoronaVac: A Cohort Study

The ongoing COVID-19 pandemic remained a major public health concern despite a large-scale deployment of vaccines. One of the vaccines is CoronaVac, an inactivated vaccine. The efficacy of the vaccine was estimated at 50.7–83.5% in clinical trials. However, the real-world efficacy often differed. This study described CoronaVac post-vaccination reactogenicity and immunogenicity. Serum was collected on days 0, 28, 56 and 84 from participants who received CoronaVac in March–May 2021. Anti-SARS-CoV-2 Spike receptor binding domain was measured using an Elecsys® quantitative assay. Participants were interviewed for adverse events (AEs) one week after vaccination. Reported AEs were fatigue, fever, runny nose, headache, muscle pain, pain at injection site, and paresthesia. Females reported more incidents than males. However, the frequency was similar between immunologically naïve and pre-immune participants. In the naïve group, the antibody titer was 61.7 ± 84.2 U/mL (mean ± SD) on day 28 and increased to 99.3 ± 91.9 U/mL on day 56. The titer peaked on day 56 across all age groups, but a reduction of 18.0–26.3% was observed on day 84. A titer-boosting effect was observed in pre-immune participants with a baseline titer of 139.0 ± 101.0 U/mL, which increased to 206.7 ± 77.4 U/mL on day 28, and remained steady until day 84. Hence, CoronaVac elicited an antibody response in naïve and pre-immune participants, with mild AEs

Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center study.

We determined the prevalence and epidemiological characteristics of COVID-19 in Jakarta and neighboring areas, Indonesia from March 2020 to February 2021, based on nasopharyngeal/oropharyngeal (NP/OP) swab specimens that were tested at the Eijkman Institute for Molecular Biology, Jakarta. NP/OP swab specimens were collected from COVID-19 suspects or individuals in contact tracing programs from primary healthcare centers (PHC) and hospitals. The specimens were screened for the SARS-CoV-2 by qRT-PCR. Demography data and clinical symptoms were collected using national standardized laboratory form. Of 64,364 specimens, 10,130 (15.7%) were confirmed positive for SARS-CoV-2, with the peak prevalence of infection in March 2020 (26.3%) follow by in January 2021 (23.9%) and February 2021 (21.8%). We found that the positivity rate of the specimens from Jakarta, West Java, and Banten was 16.3%, 13.3%, and 16.8%, respectively. Positivity rate was higher in specimens from hospitals (16.9%) than PHC (9.4%). Of the positive specimens, 29.6% were from individuals aged >60 years old, followed by individuals aged 41-60 years old (24.2%). Among symptomatic cases of SARS-CoV-2, the most common symptoms were cough, fever, and a combination of both cough & fever. In conclusion, this study illustrates the prevalence and epidemiological characteristics from one COVID-19 diagnostic center in Jakarta and neighbouring areas in Indonesia