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.
【저자키워드】 COVID-19, SARS-CoV-2, Phylogenetic analysis, Whole genome sequencing, D614G mutation, Indonesia, 【초록키워드】 Europe, Hospitalized, severity, NGS, Genome, variant, SARS-CoV-2 virus, virus, Asia, Region, SARS-CoV-2 genome, Next-generation sequencing, Patient, Cluster, clade, dataset, WGS, dissemination, distribution, GISAID, Analysis, COVID-19 patient, Illumina Miseq, sequence, circulating, COVID-19 situation, reference genome, full-length, virus genome, Complete, NC_045512.2, Result, collected, applied, was performed, appear, full-length genome sequence, retrieved, virus sample, 【제목키워드】 Genome, SARS-CoV-2 virus strain,