Abstract
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.
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Acknowledgements
This study was funded by grant from the Ministry of Research, Technology, and Higher Education of the Republic of Indonesia.
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BY, PW, AA, and RTS conceived and designed the study. PW and AA collected the samples. BY and PW performed the experiments. BY and HT performed the data analysis. BY wrote the first draft. HT and RTS reviewed and edited the manuscript. All authors read and approved the final manuscript.
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All procedures performed in studies involving human participants were approved by the Ethic Commission of the Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.
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Yohan, B., Wardhani, P., Trimarsanto, H. et al. Genomic analysis of dengue virus serotype 1 (DENV-1) genotypes from Surabaya, Indonesia. Virus Genes 54, 461–465 (2018). https://doi.org/10.1007/s11262-018-1558-z
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DOI: https://doi.org/10.1007/s11262-018-1558-z