Virus Genes

, Volume 54, Issue 3, pp 461–465 | Cite as

Genomic analysis of dengue virus serotype 1 (DENV-1) genotypes from Surabaya, Indonesia

  • Benediktus Yohan
  • Puspa Wardhani
  • Hidayat Trimarsanto
  • A. Aryati
  • R. Tedjo SasmonoEmail author


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.


Dengue Indonesia Surabaya DENV-1 Genome 



This study was funded by grant from the Ministry of Research, Technology, and Higher Education of the Republic of Indonesia.

Authors’ contributions

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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in studies involving human participants were approved by the Ethic Commission of the Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.

Informed consent

Informed consent was obtained from all individual participants included in the study.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher EducationJakartaIndonesia
  2. 2.Department of Clinical Pathology, School of MedicineUniversitas AirlanggaSurabayaIndonesia
  3. 3.Institute for Tropical DiseasesUniversitas AirlanggaSurabayaIndonesia
  4. 4.Agency for the Assessment and Application of TechnologyJakartaIndonesia

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