Gunadi, Gunadi and Wibawa, Hendra and Hakim, Mohamad Saifudin and Marcellus, Marcellus and Trisnawati, Ika and Khair, Riat El and Triasih, Rina and Irene, Irene and Afiahayati, Afiahayati and Iskandar, Kristy and Siswanto, Siswanto and Anggorowati, Nungki and Daniwijaya, Edwin Widyanto and Supriyati, Endah and Nugrahaningsih, Dwi Aris Agung and Budiono, Eko and Retnowulan, Heni and Puspadewi, Yunika and Puspitawati, Ira and Sianipar, Osman and Afandy, Dwiki and Simanjaya, Susan and Widitjiarso, William and Puspitarani, Dyah Ayu and Fahri, Fadil and Riawan, Untung and Fauzi, Aditya Rifqi and Kalim, Alvin Santoso and Ananda, Nur Rahmi and Setyati, Amalia and Setyowireni, Dwikisworo and Laksanawati, Ida Safitri and Arguni, Eggi and Nuryastuti, Titik and Wibawa, Tri and Herini, Elisabeth S. and Widowati, Titis and Satria, Cahya Dewi and Sumardi, Sumardi and Riyanto, Bambang Sigit and Gani, Munawar and Maulana, Satria and Rizki, Ludhang Pradipta and Intansari, Umi Solekhah and Herningtiyas, Elizabeth Henny and Harahap, Nur Imma Fatimah and Poermadjaja, Bagoes and Hutasoit, Sintong H. M. T. and Indaryati, Indaryati and Setyawan, Havid and Athollah, Kemala and Inggriani, Maria Patricia (2021) Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. BMC Medical Genomics, 14 (1). ISSN 17558794
Full text not available from this repository. (Request a copy)Abstract
Background: Transmission within families and multiple spike protein mutations have been associated with the rapid transmission of SARS-CoV-2. We aimed to: (1) describe full genome characterization of SARS-CoV-2 and correlate the sequences with epidemiological data within family clusters, and (2) conduct phylogenetic analysis of all samples from Yogyakarta and Central Java, Indonesia and other countries. Methods: The study involved 17 patients with COVID-19, including two family clusters. We determined the full-genome sequences of SARS-CoV-2 using the Illumina MiSeq next-generation sequencer. Phylogenetic analysis was performed using a dataset of 142 full-genomes of SARS-CoV-2 from different regions. Results: Ninety-four SNPs were detected throughout the open reading frame (ORF) of SARS-CoV-2 samples with 58 (54/94) of the nucleic acid changes resulting in amino acid mutations. About 94 (16/17) of the virus samples showed D614G on spike protein and 56 of these (9/16) showed other various amino acid mutations on this protein, including L5F, V83L, V213A, W258R, Q677H, and N811I. The virus samples from family cluster-1 (n = 3) belong to the same clade GH, in which two were collected from deceased patients, and the other from the survived patient. All samples from this family cluster revealed a combination of spike protein mutations of D614G and V213A. Virus samples from family cluster-2 (n = 3) also belonged to the clade GH and showed other spike protein mutations of L5F alongside the D614G mutation. Conclusions: Our study is the first comprehensive report associating the full-genome sequences of SARS-CoV-2 with the epidemiological data within family clusters. Phylogenetic analysis revealed that the three viruses from family cluster-1 formed a monophyletic group, whereas viruses from family cluster-2 formed a polyphyletic group indicating there is the possibility of different sources of infection. This study highlights how the same spike protein mutations among members of the same family might show different disease outcomes. © 2021, The Author(s).
| Item Type: | Article |
|---|---|
| Additional Information: | Cited by: 11; All Open Access, Gold Open Access, Green Open Access |
| Uncontrolled Keywords: | Adult; Aged; Aged, 80 and over; Child; COVID-19; Family; Female; High-Throughput Nucleotide Sequencing; Humans; Indonesia; Male; Middle Aged; Mutation; Phylogeny; RNA, Viral; SARS-CoV-2; Severity of Illness Index; Spike Glycoprotein, Coronavirus; Whole Genome Sequencing; amino acid; nucleic acid; virus spike protein; coronavirus spike glycoprotein; spike protein, SARS-CoV-2; virus RNA; adult; aged; Article; child; cladistics; clinical article; coronavirus disease 2019; female; high throughput sequencing; human; Indonesia; male; middle aged; molecular epidemiology; molecular phylogeny; monophyly; nonhuman; open reading frame; polyphyly; school child; Severe acute respiratory syndrome coronavirus 2; single nucleotide polymorphism; very elderly; virus genome; virus isolation; virus mutation; whole genome sequencing; chemistry; classification; epidemiology; family; genetics; isolation and purification; metabolism; mutation; pathology; phylogeny; severity of illness index; virology |
| Subjects: | R Medicine > RP Public Health and Nutrition |
| Divisions: | Faculty of Medicine, Public Health and Nursing > Biomedical Sciences |
| Depositing User: | Sri JUNANDI |
| Date Deposited: | 28 Sep 2024 02:43 |
| Last Modified: | 28 Sep 2024 02:43 |
| URI: | https://ir.lib.ugm.ac.id/id/eprint/4511 |
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