Dengue infections are still a worldwide burden, especially in Indonesia. There is no specific medication against the dengue virus. Recently, many types of research have been conducted to discover a new drug for dengue virus using natural resource extracts. Indonesia, as a tropical country, has a wide biodiversity. There are several medicinal plants in Indonesia that are believed to possess anti-dengue activity, such as Myristica fatua, Cymbopogon citratus, and Acorus calamus plants. We conducted an in vitro laboratory experiment of several extracts from Indonesian herbs combined with in silico analysis. The extracts were evaluated for safety and antiviral activity in Huh7it-1 cell lines, using a single dose of 20 µg/mL and dose-dependent (5, 10, 20, 40, 80 and 160 µg/mL) of plant extracts against dengue virus serotype 2 (DENV-2) NGC strain. The DMSO 0.1% was used as a negative control. The cytotoxic aspect was assessed by counting the cell viability, while the antiviral activity was calculated by counting the average inhibition. The selectivity index (SI) of plant extracts were performed from a ratio of CC50/EC50 value. In silico analysis was conducted to determine the free energy of binding between NS5 of dengue virus with bioactive compounds contained in Myristica fatua, Cymbopogon citratus and Acorus calamus extract plants. We determined that all extracts were not toxic against Huh7it-1 cell lines. The methanolic extracts of A. calamus, C. citratus, and M. fatua showed inhibition of DENV-2 at a dose of 20 µg/mL to 96.5%, 98.9%, and 122.7%, respectively. The dose-dependent effects showed that M. fatua has the best inhibition activity towards DENV-2. Molecular docking result showed that artesunic acid within M. fatua has the best free energy of binding (−7.2 kcal/mol), followed by homoegonol (−7.1 kcal/mol) which was slightly different from artesunic acid among others. The methanolic extracts of A. calamus, C. citratus, and M. fatua showed prospective anti-dengue activities both in vitro and in silico. Future research should be conducted to find the pure extracts of all useful herbs as a new candidate of antiviral drug.

Early diagnosis of dengue virus (DENV) infection is affirmative for patient management and control of the disease. Detection of nonstructural-1 (NS1) antigen has been proven to provide early detection of DENV infection. Commercial NS1 antigen assays are available in Indonesia with variable sensitivity. In an attempt to develop an NS1-based diagnostic test, we successfully cloned NS1 gene of DENV2 to a glutathione Stransferase-based vector pGEX6P-1 in Escherichia coli system. The recombinant protein (pG2NS12) was o expressed in E. coli BL21. After induction with isopropyl-β-D-thiogalactoside 0.1 mM for 4 h at 25 C a recombinant protein GST-NS1 with molecular size of approximately 75 kDa was obtained. The fusion protein-1 was insoluble and found in the pellet fraction of the cell lysate. Addition of lysozyme (10 mg mL) and DNase-I-1 (7.2 mg mL) in the lysis buffer was necessary to collect proteins from the pellet fraction. The proteins in the cell pellet were fractionated through Sephadex-G100 column, and GST-NS1 was further purified with Glutathione-Sepharose 4B beads. To obtain pure recombinant NS1 protein to be used in the immunization of mice, the fusion protein was cut with PreScission Protease® by addition of 0.075% Triton-X 100 was necessary to cut the fusion protein. We found that antibodies that recognized the recombinant NS1 protein and DENV2 virus were produced in mice immunized with purified NS1 protein. Therefore, our recombinant NS1 could be used to produce antibody that is potentially useful for developing diagnostic assay to determine the presence of dengue virus NS1 antigen in patient sera.

COVID-19 is a disease caused by SARS-CoV-2, a new virus from genus β-coronaviruses. This disease has been declared a pandemic by WHO on 11 March 2020 until now. The nucleic acid tests are the most frequently used assays because of their high sensitivity and specificity. One of the tests is the GeneXpert, a real-time reverse transcription polymerase chain reaction (rRT-PCR)-based assay platform. The use of the GeneXpert shows great public health interest because of the rapid (50 min), the minimum number of trained staff, and less infrastructure and equipment. However, there are limited data on the application of the GeneXpert for the detection of SARS-CoV-2. Therefore, we conducted a comparative study between the GeneXpert and in-house N1N2 CDC rRT-PCR assay. Of 86 samples, 17 were rRT-PCR positive while 13 were GeneXpert positive. Of rRT-PCR positive 17 samples, 7 were GeneXpert negative [58.82% (10/17] sensitivity]. We also found that 3 GeneXpert positive samples showed rRT-PCR negative (95.65% [66/69] specificity). It is concluded that negative results by the GeneXpert can not rule out the possibility of SARS-CoV-2 infection, particularly in close-contact individuals and the interpretation of the positive result should be analyzed carefully, particularly amplification with Ct>40.

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Background: SARS-CoV-2 rapid mutation generates many concerning new strains. Although lockdown had been applied to contain the disease, the household remains a critical place for its transmission. This study aimed to assess the variation of SARS-CoV-2 strains and their clinical manifestations within family clusters in Jakarta, Indonesia. Method: Naso-oropharyngeal swab specimens from family clusters positive for SARS-CoV-2 were collected for whole-genome sequencing. Their baseline data, symptoms, and source of infection were recorded. The whole-genome data was then analyzed with the bioinformatics program to evaluate the SARS-CoV-2 genome characteristic and submitted to GISAID for strain identification. The phylogenetic tree was built to observe the relationship between virus strain within the family cluster and its clinical manifestation. Result: This study obtained eight family clusters from twenty-two patients. Half of the cluster's source of infection was a family member who had to work at the office. The infection rate ranged from 37.5% to 100%. The phylogenetic tree showed that the same virus within a cluster could generate various clinical outcomes. Five clusters had one family member with pneumonia, while others had mild to no symptoms. Four breakthrough cases were detected in this study, which were infected by the virus from GH and GK clade.  Conclusion: Our study observed the SARS-CoV-2 transmission to the household setting through the workplace, which might become a common pathway if the pandemic status is removed. Although vaccination is expected to reduce the burden of COVID-19, adequate control measures remain essential, given that breakthrough infections are evident.