Dataset Information

Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia.

ABSTRACT:

Background

Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia (n = 60) from March to September 2020 and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia.

Methods

Whole genome sequencing (WGS) was performed using next-generation sequencing (NGS) applied in the Illumina MiSeq instrument. Full-length virus genomes were annotated using the reference genome of hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2) and then visualized in UGENE v. 1.30. For phylogenetic analysis, a dataset of 88 available SARS-CoV-2 complete genomes from different countries, including Indonesia, was retrieved from GISAID.

Results

All patients were hospitalized with various severities of COVID-19. Phylogenetic analysis revealed that one and three virus samples belong to clade L and GH. These three clade GH virus samples (EPI_ISL_525492, EPI_ISL_516800 and EPI_ISL_516829) were not only located in a cluster with SARS-CoV-2 genomes from Asia but also those from Europe, whereas the clade L virus sample (EPI_ISL_516806) was located amongst SARS-CoV-2 genomes from Asia. Using full-length sequences available in the GISAID EpiCoV Database, 39 of 60 SARS-CoV-2 (65%) from Indonesia harbor the D614G mutation.

Conclusion

These findings indicate that SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia, concurrent with the COVID-19 situation worldwide.

SUBMITTER: Gunadi

PROVIDER: S-EPMC7759132 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia.

Gunadi Wibawa Hendra H Marcellus Hakim Mohamad Saifudin MS Daniwijaya Edwin Widyanto EW Daniwijaya Edwin Widyanto EW Rizki Ludhang Pradipta LP Supriyati Endah E Nugrahaningsih Dwi Aris Agung DAA Afiahayati Siswanto Iskandar Kristy K Anggorowati Nungki N Kalim Alvin Santoso AS Puspitarani Dyah Ayu DA Athollah Kemala K Arguni Eggi E Nuryastuti Titik T Wibawa Tri T

PeerJ 20201221

<h4>Background</h4>Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia (<i>n</i> = 60) from March to September 2020 and (3) to perfo ...[more]

PMID: 33391880

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Dataset Information

Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia.

Background

Methods

Results

Conclusion

Publications

Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia.

Similar Datasets

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