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

PeerJ

article

Gunadi¹  Hendra Wibawa²  Marcellus¹  Mohamad Saifudin Hakim³  Edwin Widyanto Daniwijaya⁴  Ludhang Pradipta Rizki³  Endah Supriyati⁵  Dwi Aris Agung Nugrahaningsih⁶  Afiahayati⁷  Siswanto⁸  Kristy Iskandar⁹  Nungki Anggorowati^1,10  Alvin Santoso Kalim¹  Dyah Ayu Puspitarani¹  Kemala Athollah¹  Eggi Arguni^1,11  Titik Nuryastuti³  Tri Wibawa³ 

[1] Pediatric Surgery Division, Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada;Disease Investigation Center Wates, Yogyakarta, Ministry of Agriculture;Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada;Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital;Centre of Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada;Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada;Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada;Department of Physiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital;Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital;Department of Anatomical Pathology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada;Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada

关键词: COVID-19;    D614G mutation;    Indonesia;    Phylogenetic analysis;    SARS-CoV-2;    Whole genome sequencing;   

DOI  :  10.7717/peerj.10575

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY