Genetic characterization of dengue virus 4 complete genomes from East Java, Indonesia

Abstract

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.

Epidemiologi, Biologi, Patogenesis, Manifestasi Klinis, dan Diagnosis Infeksi Virus Dengue di Indonesia: Kajian Literatur Komprehensif

“…Rata-rata cakupan urutan referensi DENV-4 untuk urutan Jember, yang mengukur cakupan genom, adalah 98,58% (95% CI 96,98-100,18). Semua 13 urutan dikuratori dan disimpan ke GenBank dengan nomor aksesi mulai dari OL314735 hingga OL314747 setelah jaminan kualitas dan prosedur pengisian celah (Wardhani et al, 2023).…”

“…Nyamuk menghabiskan antara tiga dan empat belas hari inkubasi (Sigle et al, 2022). Di seluruh dunia, ada empat serotipe virus dengue (DENV) yang berbeda secara genetik (DENV-1, -2, -3, dan -4) (Wardhani et al, 2023). Satu serotipe menghasilkan kekebalan seumur hidup terhadap infeksi, tetapi hanya sejumlah kecil kekebalan silang yang diberikan kepada nyamuk lain pada bulan-bulan awal setelah infeksi (De Santis et al, 2023).…”