ACADSTAFF UGM

CREATION
Title : Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia
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) dr. Eggi Arguni, M.Sc., Ph.D., Sp.A(K). (16) Prof. dr. Titik Nuryastuti, M.Si., Ph.D, SpMK(K) (17) Prof. dr. Tri Wibawa, Ph.D., Sp.MK(K) (18)
Date : 21 2020
Keyword : COVID-19, D614G mutation,Indonesia,Phylogenetic analysis,SARS-CoV-2,whole genome sequencing COVID-19, D614G mutation,Indonesia,Phylogenetic analysis,SARS-CoV-2,whole genome sequencing
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.
Group of Knowledge : Bedah (Umum, Plastik, Orthopaedi, Urologi, Dll)
Original Language : English
Level : Internasional
Status :
Published
Document
No Title Document Type Action
1 [fulldoc] Dec20_Full-length genome characterization.pdf
Document Type : [PAK] Full Dokumen
[PAK] Full Dokumen View
2 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia.pdf
Document Type : [PAK] Cek Similarity
[PAK] Cek Similarity View
3 31_BuktiKorespondensi_SARSCOV2_D614G.pdf
Document Type : [PAK] Bukti Korespondensi Penulis
[PAK] Bukti Korespondensi Penulis View
4 peerj-10575.pdf
Document Type : [PAK] Full Dokumen
[PAK] Full Dokumen View