Genomic characterization of Zika virus isolated from Indonesia

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.

Pathogenic viruses: Molecular detection and characterization

“…Albeit, data reliability and accuracy is still being improved, third generation sequencing offers powerful genomic analysis at lower cost in the future (Chiu and Miller, 2016;Kulski, 2016). It has also been applied to sequence genomes of pathogenic viruses (Marston et al, 2013;McGinnis et al, 2016;Yudhaputri et al, 2017).…”

“…The virus can cause fatal diseases especially when it infects children and newborn infants (Wiyatno et al, 2016). Genomic characterization of Zika virus by whole genome sequencing, followed by phylogenetic analysis showed that the Zika virus isolated from Indonesia is distantly related to the Brazilian Zika virus which has been linked to microcephaly (Yudhaputri et al, 2017). In addition, phylogenetic analysis has also been employed to study the evolution and phylodynamic pattern of human influenza A/H3N2 virus circulating in Indonesian archipelago from 2008 to 2010.…”

“…In addition, advances in viral genomics offer the opportunity to develop more effective antiviral drugs. Genome sequences provide a route to investigate mechanisms of virus pathogenesis and a repertoire of antiviral drug targets from which novel antiviral drugs can be developed (Yudhaputri et al, 2017). Beside their roles in virus detection and characterization, molecular methods are applicable to develop vaccines and therapeutics to combat pathogenic viruses (Artika et al, 2013;Garcia-Sastre and Mena, 2013).…”

“…This may happen due to aerosolization of PCR products especially during the post-PCR analysis. PCR contamination has been an issue in laboratories Yudhaputri et al, 2017;Dhenni et al, 2018 I.M. Artika, et al Infection, Genetics andEvolution 81 (2020) 104215 conducting the detection of emerging pathogenic viruses.…”

Knowledge towards Zika among medical students, interns and general practitioners in Indonesia: A cross-sectional study in Aceh

“…[4][5][6] On February 1, 2016, the World Health Organization (WHO) declared Zika as a public health emergency of international concern, and as of March 10, 2017, 31 countries and territories have reported microcephaly and/or central nervous system malformation cases potentially associated with Zika. 6 No Zika cases have been reported in Indonesia so far, but serology studies, 7,8 case reports from travellers 9,10 and molecular virology studies 11,12 provide evidence that Zika virus is present in the country. After Zika was declared a public health emergency, studies assessing knowledge of Zika were conducted among medical [13][14][15][16][17][18] and non-medical university students.…”