Yohan Benediktus, Wardhani Puspa, Trimarsanto Hidayat, Aryati A, Sasmono R Tedjo
Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jl. Diponegoro 69, Jakarta, 10430, Indonesia.
Department of Clinical Pathology, School of Medicine, Universitas Airlangga, Surabaya, Indonesia.
Virus Genes. 2018 Jun;54(3):461-465. doi: 10.1007/s11262-018-1558-z. Epub 2018 Apr 3.
Dengue has caused a significant public health impact globally. With the diverse genetic of the causative viruses, analysis of dengue virus (DENV) genomes is important to supplement epidemiological data with information that can be used to reconstruct the history of epidemics in time and space. We have reported the clinical and virological characteristics of dengue in Surabaya, Indonesia and revealed the presence of all four DENV serotypes and the predominance of DENV-1. The further classification of Surabaya DENV-1 into two different genotypes warrants in-depth genomic analysis to study the dynamics of both genotypes and their contribution to virus evolution, virus transmission, and disease. We performed full-length genome sequencing to nine isolates' representatives from DENV-1 Genotype I and Genotype IV. Phylogenetic and evolutionary analyses suggested the more recent introduction of Genotype I viruses compared to the more endemic Genotype IV. Comparative analysis of Surabaya DENV-1 genomes and other sequences available publicly revealed that the majority of the DENV-1 codons were under strong purifying selection, while seven codon sites identified to be under positive selection. We highlight a unique codon site under the positive pressure in the NS1 gene of DENV-1. Our results provide additional genomic data of DENV from Indonesia that may contribute to the better understanding of dengue disease dynamics.
登革热已在全球范围内对公共卫生造成重大影响。由于致病病毒的基因多样，分析登革热病毒（DENV）基因组对于用可用于及时重建时空流行病史的信息补充流行病学数据很重要。我们报告了印度尼西亚泗水登革热的临床和病毒学特征，揭示了所有四种DENV血清型的存在以及DENV-1的优势地位。泗水DENV-1进一步分为两种不同基因型，这需要进行深入的基因组分析，以研究这两种基因型的动态及其对病毒进化、病毒传播和疾病的影响。我们对来自DENV-1基因型I和基因型IV的九个分离株代表进行了全长基因组测序。系统发育和进化分析表明，与更具地方性的基因型IV相比，基因型I病毒是最近才传入的。对泗水DENV-1基因组与其他公开可用序列的比较分析表明，大多数DENV-1密码子处于强烈的纯化选择之下，而有七个密码子位点被确定处于正选择之下。我们强调了DENV-1 NS1基因中一个处于正选择压力下的独特密码子位点。我们的结果提供了来自印度尼西亚的DENV额外基因组数据，这可能有助于更好地理解登革热疾病动态。
