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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References

Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, et al. 2016. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44(W1):W3–W10. doi:10.1093/nar/gkw343.

Aryati A, Trimarsanto H, Yohan B, Wardhani P, Fahri S, Sasmono RT. 2013. Performance of commercial dengue NS1 ELISA and molecular analysis of NS1 gene of dengue viruses obtained during surveillance in Indonesia. BMC Infect Dis. 13(1):611. doi:10.1186/ 1471-2334-13-611. 00000.

Aw PPK, de Sessions PF, Wilm A, Hoang LT, Nagarajan N, Sessions OM, Hibberd ML. 2014. Nextgeneration whole genome sequencing of dengue virus. Methods Mol Biol. 1138:175–195. doi:10.1007/ 978-1-4939-0348-1_12. 00008.

Capobianchi MR, Giombini E, Rozera G. 2013. Nextgeneration sequencing technology in clinical virology. Clin Microbiol Infect. 19(1):15–22. doi:10.1111/ 1469-0691.12056.

Christenbury JG, Aw PPK, Ong SH, Schreiber MJ, Chow A, Gubler DJ, Vasudevan SG, Ooi EE, Hibberd ML. 2010. A method for full genome sequencing of all four serotypes of the dengue virus. J Virol Methods. 169(1):202–206. doi:10.1016/j.jviromet.2010.06.013. 00012 PMID: 20600330.

Costa RL, Voloch CM, Schrago CG. 2012. Comparative evolutionary epidemiology of dengue virus serotypes. Infect Genet Evol. 12(2):309–314. doi:10.1016/j. meegid.2011.12.011. 00035.

Ewels P, Magnusson M, Lundin S, Käller M. 2016. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 32(19):3047–3048. doi:10.1093/bioinformatics/ btw354.

Fahri S, Yohan B, Trimarsanto H, Sayono S, Hadisaputro S, Dharmana E, Syafruddin D, Sasmono RT. 2013. Molecular surveillance of dengue in Semarang, Indonesia revealed the circulation of an old genotype of dengue virus serotype-1. PLoS Negl Trop Dis. 7(8):e2354. doi:10.1371/journal.pntd.0002354.

Goncalvez A, Escalante A, Pujol F, Ludert J, Tovar D, Salas R, Liprandi F. 2002. Diversity and evolution of the envelope gene of dengue virus type 1. Virology. 303(1):110–119. doi:10.1006/viro.2002.1686.

Guzman MG, Halstead SB, Artsob H, Buchy P, Farrar J, Gubler DJ, Hunsperger E, Kroeger A, Margolis HS, Martínez E, et al. 2010. Dengue: a continuing global threat. Nat Rev Microbiol. 8(12 Suppl):S7–16. doi: 10.1038/nrmicro2460.

Haryanto S, Hayati RF, Yohan B, Sijabat L, Sihite IF, Fahri S, Meutiawati F, Halim JAN, Halim SN, Soebandrio A, Sasmono RT. 2016. The molecular and clinical features of dengue during outbreak in Jambi, Indonesia in 2015. Pathog Glob Health. 110(3):119– 129. doi:10.1080/20477724.2016.1184864.

Holmes E, Burch S. 2000. The causes and consequences of genetic variation in dengue virus. Trends Microbiol. 8(2):74–77. doi:10.1016/s0966-842x(99)01669-8.

Holmes E, Twiddy S. 2003. The origin, emergence and evolutionary genetics of dengue virus. Infect Genet Evol. 3(1):19–28. doi:10.1016/s1567-1348(03) 00004-2.

Holmes EC. 2009. RNA virus genomics: a world of possibilities. J Clin Invest. 119(9):2488–2495. doi:10. 1172/JCI38050.

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649. doi:10.1093/bioinformatics/ bts199.

Koo C, Ping T Wei, Helen X, Janet O, Rajarethinam J, Lai, Yee Ling, Ng, Lee-Ching, Chanditha H Hapuarachchige. 2018. Highly selective transmission success of dengue virus type 1 lineages in a dynamic virus population: An evolutionary and fitness perspective. iScience. 6:38–51. doi:10.1016/j.isci.2018.07. 008.

Lambrechts L, Scott TW, Gubler DJ. 2010. Consequences of the expanding global distribution of Aedes albopictus for dengue virus transmission. PLoS Negl Trop Dis. 4(5):e646. doi:10.1371/journal.pntd.0000646. 00193.

Lanciotti RS, Gubler DJ, Trent DW. 1997. Molecular evolution and phylogeny of dengue-4 viruses. J Gen Virol. 78(9):2279–2284. doi:10.1099/ 0022-1317-78-9-2279.

Lanciotti RS, Lewis JG, Gubler DJ, Trent DW. 1994. Molecular evolution and epidemiology of dengue-3 viruses. J Gen Virol. 75 ( Pt 1)(1):65–75. doi:10.1099/ 0022-1317-75-1-65.

Leitmeyer K, Vaughn D, Watts D, Salas R, Villalobos I, de C, Ramos C, Rico-Hesse R. 1999. Dengue virus structural differences that correlate with pathogenesis. J Virol. 73(6):4738–47.

Lestari CSW, Yohan B, Yunita A, Meutiawati F, Hayati RF, Trimarsanto H, Sasmono RT. 2017. Phylogenetic and evolutionary analyses of dengue viruses isolated in Jakarta, Indonesia. Virus Genes. 53(6):778–788. doi:10.1007/s11262-017-1474-7.

Martina BEE, Koraka P, Osterhaus ADME. 2009. Dengue virus pathogenesis: an integrated view. Clin Microbiol Rev. 22(4):564–581. doi:10.1128/CMR. 00035-09.

Masyeni S, Yohan B, Somia IKA, Myint KSA, Sasmono RT. 2018. Dengue infection in international travellers visiting Bali, Indonesia. J Travel Med. 25(1):1–7. doi: 10.1093/jtm/tay061.

Megawati D, Masyeni S, Yohan B, Lestarini A, Hayati RF, Meutiawati F, Suryana K, Widarsa T, Budiyasa DG, et al. 2017. Dengue in Bali: clinical characteristics and genetic diversity of circulating dengue viruses. PLoS Negl Trop Dis. 11(5):e0005483. doi: 10.1371/journal.pntd.0005483.

Ong S, Yip J, Chen Y, Liu W, Harun S, Lystiyaningsih E, Heriyanto B, Beckett C, Mitchell W, Hibberd M, et al. 2008. Periodic re-emergence of endemic strains with strong epidemic potential-a proposed explanation for the 2004 Indonesian dengue epidemic. Infect Genet Evol. 8(2):191–204. doi:10.1016/j.meegid.2007.12. 005.

Organization WH. 2012. Global strategy for dengue prevention and control, 2012-2020. Geneva: WHO Press. Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. 2014. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol. 61(1):9–19. doi: 10.1016/j.jcv.2014.06.013.

Sasmono RT, Aryati A, Wardhani P, Yohan B, Trimarsanto H, Fahri S, Setianingsih TY, Meutiawati F. 2014. Performance of Simplexa dengue molecular assay compared to conventional and SYBR green RTPCR for detection of dengue infection in Indonesia. PLoS ONE. 9(8):e103815. doi:10.1371/journal.pone. 0103815.

Sasmono RT, Wahid I, Trimarsanto H, Yohan B, Wahyuni S, Hertanto M, Yusuf I, Mubin H, Ganda IJ, Latief R, Bifani PJ, Shi PY, Schreiber MJ. 2015. Genomic analysis and growth characteristic of dengue viruses from Makassar, Indonesia. Infect Genet Evol. 32:165– 177. doi:10.1016/j.meegid.2015.03.006.

Twiddy SS, Farrar JJ, Vinh Chau N, Wills B, Gould EA, Gritsun T, Lloyd G, Holmes EC. 2002. Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus. Virology. 298(1):63–72. doi:10.1006/viro.2002.1447.

Usme-Ciro JA, Méndez JA, Laiton KD, Páez A. 2014. The relevance of dengue virus genotypes surveillance at country level before vaccine approval. Hum Vaccin Immunother. 10(9):2674–2678. doi:10.4161/hv. 29563.

van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. 2014. Ten years of next-generation sequencing technology. Trends Genet. 30(9):418–426. doi:10.1016/j.tig.2014. 07.001.

Yohan B, Wardhani P, Trimarsanto H, Aryati A, Sasmono RT. 2018. Genomic analysis of dengue virus serotype 1 (DENV-1) genotypes from Surabaya, Indonesia. Virus Genes. 54(3):461–465. doi:10.1007/ s11262-018-1558-z.

Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol. 7(1-2):203–214. doi:10.1089/ 10665270050081478.



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

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