Outbreaks of dengue virus (DENV) in Indonesia have been mainly caused by the DENV serotype-1; -2; or -3. The DENV-4 was the least-reported serotype in Indonesia during the last five decades. We recently conducted a molecular epidemiology study of dengue in the Jember regency, East Java province, Indonesia. Dengue is endemic in the region and outbreaks occur annually. We investigated the clinical characteristics and etiology of dengue-like febrile illness in this regency to understand the disease dynamics. A total of 191 patients with clinical symptoms similar to dengue were recruited during an 11-month study in 2019–2020. Children accounted for the majority of cases and dengue burden was estimated in 41.4% of the cases based on NS1 antigen, viral RNA, and IgG/IgM antibody detection with the majority (73.4%) being primary infections. Secondary infection was significantly associated with a higher risk of severe dengue manifestation. All four DENV serotypes were detected in Jember. Strikingly, we observed the predominance of DENV-4, followed by DENV-3, DENV-1, and DENV-2. Genotype determination using Envelope gene sequence revealed the classification into Genotype I, Cosmopolitan Genotype, Genotype I, and Genotype II for DENV-1, -2, -3, and -4, respectively. The predominance of DENV-4 in Jember may be associated with a new wave of DENV infections and spread in a non-immune population lacking a herd-immunity to this particular serotype.

Background : NS1 is currently widely used for diagnosis of dengue virus (DENV) infection. Various methods are used to diagnose DENV infection (DVI), either ELISA, immunochromatography (ICT) or most recently the fluorescence immunoassay (FIA) method which are commercially available. Objective: This study aimed to compare the detection capabilities of dengue NS1 antigens using (1) Dengue NS1 ICT Ag (Standard Q - SD Biosensor, Inc.), (2) Dengue NS1 ICT Ag (SD Bioline - Standard Diagnostic, Inc), and (3) Dengue NS1 Ag FIA (Standard F - SD Biosensor, Inc.) Methods: This study consisted of serum samples (n=80) with the number of DVI patients (n=50), non-DVI (n=30). All samples were examined using all three commercial kits for NS1 antigen testing. All DVI samples showed results of reverse-transcriptase polymerase chain reaction (RT-PCR - SIMPLEXAᵀᴹ Dengue - Focus Diagnostics) and/or positive dengue NS1 (Panbio® Dengue Early ELISA) antigen. Results: Standard F showed the highest sensitivity (82%) compared to Standard Q (74%) and SD Bio line (74%). These three commercial kits had the same specificity 100%. The positive predictive value all of these kits was 100% each. The negative prediction value of Standard F, Standard Q, and SD Bio line were 76.9%, 63.8%, 63.8%, respectively. These three NS1 antigen tests had a good agreement (κ 0.681-0.774). Conclusions: FIA test performance (Standard F SD - Biosensor, Inc.) were a quick and easy examination, showing a higher sensitivity and specificity than ICT for detecting DENV infection. Further research is needed to confirm the diagnosis of primary or secondary infection.

Dengue is an endemic arboviral disease with continuous transmission in Indonesia for more than five decades. A recent outbreak in Jember, East Java province, demonstrated the predominance of DENV-4, a serotype known for its low global spread and limited transmission. While epidemiological factors such as new serotype introduction and lacking herd immunity may explain its predominance, viral factors may also contribute. Using next-generation sequencing, we generated 13 representative complete genomes of DENV-4 responsible for the outbreak. Phylogenetic and evolutionary analyses on complete genomes were performed to understand the spatial and temporal dynamics of the viruses. Further analyses were done to study amino acid variations in DENV genes, as well as the potential events of recombination and selection pressure within the genomes. We revealed the DENV-4 genetic factors that may lead to its predominance in the 2019 Jember dengue outbreak. A combination of selection pressure and mutational genetic changes may contribute to the DENV-4 predominance in East Java, Indonesia. The possible intra-serotype recombination events involving the non-structural protein 5 (NS5) gene were also observed. Altogether, these genetic factors may act as additional factors behind the complex dengue outbreak mechanism.