| Penulis/Author |
Prof. dr. Gunadi, Ph.D, Sp.BA., Subsp.DA(K) (1) ; drh. Hendra Wibawa, M.Si., Ph.D. (2); MARCELLUS (3); dr. Mohamad Saifudin Hakim, M.Sc, Ph.D. (4); dr. Marselinus Edwin Widyanto Daniwijaya, Ph.D., Sp. MK (5); dr. Raden Ludhang Pradipta Rizki, M.Biotech., Sp.MK (6); Endah Supriyati (7); dr. Dwi Aris Agung Nugrahaningsih, M.Sc., Ph.D (8); Afiahayati, S.Kom., M.Cs., Ph.D (9); dr. Siswanto, Sp.P(K) (10); dr. Kristy Iskandar, M.Sc, Ph.D, Sp.A. Subsp.Neuro.(K) (11); dr. Nungki Anggorowati, Sp.PA(K)., Ph.D. (12); ALVIN SANTOSO KALIM (13); Dyah Ayu Puspitarani (14); KEMALA ATHOLLAH (15); Prof. dr. Eggi Arguni, M.Sc., Ph.D., Sp.A(K). (16); Prof. dr. Titik Nuryastuti, M.Si., Ph.D., Sp.MK(K). (17); Prof. dr. Tri Wibawa, Ph.D., Sp.MK(K) (18) |
| Abstrak/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. |
