Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Oct:510:248-251.
doi: 10.1016/j.virol.2017.07.026. Epub 2017 Jul 26.

Genomic characterization of Zika virus isolated from Indonesia

Frilasita A Yudhaputri  1 , Hidayat Trimarsanto  2 , Aditya Perkasa  1 , Benediktus Yohan  1 , Sotianingsih Haryanto  3 , Ageng Wiyatno  1 , Amin Soebandrio  1 , Khin Saw Myint  1 , Jeremy P Ledermann  4 , Ronald Rosenberg  4 , Ann M Powers  4 , R Tedjo Sasmono  5
Affiliations

Genomic characterization of Zika virus isolated from Indonesia

Frilasita A Yudhaputri et al. Virology. 2017 Oct.

Abstract

Zika virus (ZIKV) JMB-185 strain was isolated from a febrile patient in Jambi, Indonesia in 2014. To understand its genetic characteristics, we performed whole genome sequencing using the Ion Torrent PGM platform on the supernatant of the first passage. The phylogenetic analysis showed that the isolate was not closely related to the Brazilian ZIKV associated with microcephaly or isolates from the recent Singapore Zika outbreak. Molecular evolution analysis indicated that JMB-185 strain may have been circulating in the Southeast Asia region, including Indonesia since 2000. We observed high nucleotide sequence identity between Indonesia, Thailand, Singapore, and American strains although unique amino acid substitutions were also observed. This report provides information on the genomic characteristics of Indonesian ZIKV which may be used for further studies.

Keywords: Amino acid substitution; Genome; Indonesia; Zika virus.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
MCC (Maximum Clade Credibility) phylogenetic tree of whole open reading frame (ORF) of ZIKV JMB-185 (red label) and other ZIKV Asian-American strains. For clarity, the tree only showed the Asia-America lineage (black clade, inset), truncated at HQ234499 Malaysian 1966 strain from the overall tree. Highly similar strains were condensed with numbers in brackets denoting number of strains in the condensed clades. Strains associated with microcephaly resided with other American strains in the green condensed Americas 2014–2016 clade. Strains associated with recent Zika outbreak in Singapore depicted as blue condensed clade. The condensed French Polynesia clades were labeled orange. Visible black circles at each node represented posterior support about or greater than 0.85 for the particular node.
Fig. 2
Fig. 2
Comparative analysis of amino acid substitutions in the 9 positions unique for Indonesian isolate among Zika viruses. Dataset include strains from Asian-American lineage only. The first row represented almost all of the Asian-American strains, including the Brazilian strains that caused microcephaly are represented. The Indonesian isolate is represented in second row. The gene location and amino acid positions depicted above the sequences.
See this image and copyright information in PMC

References

    1. Baronti C, Piorkowski G, Charrel RN, Boubis L, Leparc-Goffart I, de Lamballerie X. Complete coding sequence of zika virus from a French polynesia outbreak in 2013. Genome Announc. 2014;2 http://dx.doi.org/10.1128/genomeA.00500-14. - DOI - PMC - PubMed
    1. Bollati M, Alvarez K, Assenberg R, Baronti C, Canard B, Cook S, Coutard B, Decroly E, de Lamballerie X, Gould EA, Grard G, Grimes JM, Hilgenfeld R, Jansson AM, Malet H, Mancini EJ, Mastrangelo E, Mattevi A, Milani M, Moureau G, Neyts J, Owens RJ, Ren J, Selisko B, Speroni S, Steuber H, Stuart DI, Unge T, Bolognesi M. Structure and functionality in flavivirus NS-proteins: perspectives for drug design. Antivir. Res. 2010;87:125–148. http://dx.doi.org/10.1016/j.antiviral.2009.11.009. - DOI - PMC - PubMed
    1. Brinton MA, Basu M. Functions of the 3′ and 5′ genome RNA regions of members of the genus Flavivirus. Virus Res. 2015;206:108–119. http://dx.doi.org/10.1016/j.virusres.2015.02.006. - DOI - PMC - PubMed
    1. Buathong R, Hermann L, Thaisomboonsuk B, Rutvisuttinunt W, Klungthong C, Chinnawirotpisan P, Manasatienkij W, Nisalak A, Fernandez S, Yoon I-K, Akrasewi P, Plipat T. Detection of Zika Virus Infection in Thailand, 2012–2014. Am. J. Trop. Med. Hyg. 2015;93:380–383. http://dx.doi.org/10.4269/ajtmh.15-0022. - DOI - PMC - PubMed
    1. Calvet G, Aguiar RS, Melo ASO, Sampaio SA, de Filippis I, Fabri A, Araujo ESM, de Sequeira PC, de Mendonça MCL, de Oliveira L, Tschoeke DA, Schrago CG, Thompson FL, Brasil P, Dos Santos FB, Nogueira RMR, Tanuri A, de Filippis AMB. Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. Lancet Infect. Dis. 2016 http://dx.doi.org/10.1016/S1473-3099(16)00095-5. - DOI - PubMed

Publication types