Whole genome sequencing of Indonesian dengue virus isolates using next-generation sequencing

Benediktus Yohan; Rama Dhenni; Rahma F Hayati; Frilasita Aisyah Yudhaputri; Dionisius Denis; Yanuarni WB Pamai; Anna Matiana Afida; Ingrid A Hutagalung; Sotianingsih Haryanto; Hidayat Trimarsanto; Khin Saw Aye Myint; R. Tedjo Sasmono

doi:10.22146/ijbiotech.38788

Whole genome sequencing of Indonesian dengue virus isolates using next-generation sequencing

https://doi.org/10.22146/ijbiotech.38788

Benediktus Yohan⁽¹⁾, Rama Dhenni⁽²⁾, Rahma F Hayati⁽³⁾, Frilasita Aisyah Yudhaputri⁽⁴⁾, Dionisius Denis⁽⁵⁾, Yanuarni WB Pamai⁽⁶⁾, Anna Matiana Afida⁽⁷⁾, Ingrid A Hutagalung⁽⁸⁾, Sotianingsih Haryanto⁽⁹⁾, Hidayat Trimarsanto⁽¹⁰⁾, Khin Saw Aye Myint⁽¹¹⁾, R. Tedjo Sasmono^(12*)

(1) Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jalan Diponegoro No. 69, Jakarta 10430, Indonesia
(2) Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jalan Diponegoro No. 69, Jakarta 10430, Indonesia
(3) Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jalan Diponegoro No. 69, Jakarta 10430, Indonesia
(4) Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jalan Diponegoro No. 69, Jakarta 10430, Indonesia
(5) Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jalan Diponegoro No. 69, Jakarta 10430, Indonesia
(6) Santa Elisabeth Hospital,Jalan Anggrek Blok II, Lubuk Baja Kota, Kota Batam, Kepulauan Riau 29444, Indonesia
(7) Dr. H.M. Anshari Saleh Hospital, Jalan Brig. Jend. H. Hasan Basri No. 1, Alalak Utara, Banjarmasin Utara, Banjarmasin, South Kalimantan 70125, Indonesia
(8) Dr. M. Haulussy Hospital, Jalan Dr. Kayadoe, Benteng, Nusaniwe, Ambon, Maluku 97116, Indonesia
(9) Faculty of Medicine and Health Science, Jambi University, Jalan Letjen Suprapto No. 33, Telanaipura, Jambi 36361, Indonesia
(10) Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jalan Diponegoro No. 69, Jakarta 10430, Indonesia; Agency for the Assessment and Application of Technology, Jalan MH Thamrin 8, Jakarta 10340, Indonesia
(11) Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jalan Diponegoro No. 69, Jakarta 10430, Indonesia
(12) Eijkman Institute for Molecular Biology, Ministry of Research, Technology, and Higher Education, Jalan Diponegoro No. 69, Jakarta 10430, Indonesia
(*) Corresponding Author

Abstract

Indonesia is a tropical country and hyperendemic for dengue. The disease prevalently affected Indonesian and it caused high morbidity and substantial economic burden. This vector-borne viral disease is caused by infection of dengue viruses (DENVs), which are the member of Flaviviridae family. While most of dengue studies in Indonesia focused on the epidemiology, the clinical aspects, the vectors, and to certain extent the virology, there were still gaps in the DENVs genomic aspects. Considering their high mutation rate, the DENVs were known for their high genetic diversity and it might affect the characteristics of the viruses. Comprehensive DENV genomic data were thus important for many aspects of disease management, including virus surveillance, pathogenesis, diagnostics, antiviral drug design, and vaccine development. We established in this study a method for DENV whole genome sequencing using the advanced Next-Generation Sequencing (NGS) and Nextera XT DNA library preparation kit, coupled with simplified bioinformatic analysis methods. The Indonesian DENVs from four serotypes were isolated from patients’ sera, while library was prepared from enriched templates and sequenced using Illumina NGS. Our study highlighted the potential of a robust NGS method in producing whole genome sequence of DENVs, which would be important for future dengue studies.

Keywords

dengue, genome; next-generation sequencing and Indonesia.

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DOI: https://doi.org/10.22146/ijbiotech.38788