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Analysis of SARS-CoV-2 Genomes from West Java, Indonesia.
Viruses. 2021 10 18; 13(10)V

Abstract

West Java Health Laboratory (WJHL) is one of the many institutions in Indonesia that have sequenced SARS-CoV-2 genome. Although having submitted a large number of sequences since September 2020, however, these submitted data lack advanced analyses. Therefore, in this study, we analyze the variant distribution, hotspot mutation, and its impact on protein structure and function of SARS-CoV-2 from the collected samples from WJHL. As many as one hundred sixty-three SARS-CoV-2 genome sequences submitted by West Java Health Laboratory (WJHL), with collection dates between September 2020 and June 2021, were retrieved from GISAID. Subsequently, the frequency and distribution of non-synonymous mutations across different cities and regencies from these samples were analyzed. The effect of the most prevalent mutations from dominant variants on the stability of their corresponding proteins was examined. The samples mostly consisted of people of working-age, and were distributed between female and male equally. All of the sample sequences showed varying levels of diversity, especially samples from West Bandung which carried the highest diversity. Dominant variants are the VOC B.1.617.2 (Delta) variant, B.1.466.2 variant, and B.1.470 variant. The genomic regions with the highest number of mutations are the spike, NSP3, nucleocapsid, NSP12, and ORF3a protein. Mutation analysis showed that mutations in structural protein might increase the stability of the protein. Oppositely, mutations in non-structural protein might lead to a decrease in protein stability. However, further research to study the impact of mutations on the function of SARS-CoV-2 proteins are required.

Authors+Show Affiliations

Bandung Institute of Technology, Bandung, West Java 40132, Indonesia.Bandung Institute of Technology, Bandung, West Java 40132, Indonesia.Bandung Institute of Technology, Bandung, West Java 40132, Indonesia.Bandung Institute of Technology, Bandung, West Java 40132, Indonesia.Bandung Institute of Technology, Bandung, West Java 40132, Indonesia.Bandung Institute of Technology, Bandung, West Java 40132, Indonesia.Bandung Institute of Technology, Bandung, West Java 40132, Indonesia.West Java Health Laboratory, Bandung, West Java 40161, Indonesia.West Java Health Laboratory, Bandung, West Java 40161, Indonesia.West Java Health Laboratory, Bandung, West Java 40161, Indonesia.West Java Health Laboratory, Bandung, West Java 40161, Indonesia.West Java Health Laboratory, Bandung, West Java 40161, Indonesia.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

34696527

Citation

Fibriani, Azzania, et al. "Analysis of SARS-CoV-2 Genomes From West Java, Indonesia." Viruses, vol. 13, no. 10, 2021.
Fibriani A, Stephanie R, Alfiantie AA, et al. Analysis of SARS-CoV-2 Genomes from West Java, Indonesia. Viruses. 2021;13(10).
Fibriani, A., Stephanie, R., Alfiantie, A. A., Siregar, A. L. F., Pradani, G. A. P., Yamahoki, N., Purba, W. S., Alamanda, C. N. C., Rahmawati, E., Rachman, R. W., Robiani, R., & Ristandi, R. B. (2021). Analysis of SARS-CoV-2 Genomes from West Java, Indonesia. Viruses, 13(10). https://doi.org/10.3390/v13102097
Fibriani A, et al. Analysis of SARS-CoV-2 Genomes From West Java, Indonesia. Viruses. 2021 10 18;13(10) PubMed PMID: 34696527.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Analysis of SARS-CoV-2 Genomes from West Java, Indonesia. AU - Fibriani,Azzania, AU - Stephanie,Rebecca, AU - Alfiantie,Afifah Alifia, AU - Siregar,Agust Leo Fany, AU - Pradani,Gusti Ayu Prani, AU - Yamahoki,Nicholas, AU - Purba,William Steflandel, AU - Alamanda,Cut Nur Cinthia, AU - Rahmawati,Ema, AU - Rachman,Rifky Waluyajati, AU - Robiani,Rini, AU - Ristandi,Ryan Bayusantika, Y1 - 2021/10/18/ PY - 2021/09/18/received PY - 2021/10/12/revised PY - 2021/10/14/accepted PY - 2021/10/26/entrez PY - 2021/10/27/pubmed PY - 2021/11/11/medline KW - Indonesia KW - SARS-CoV-2 KW - West Java KW - mutation KW - protein stability KW - variant JF - Viruses JO - Viruses VL - 13 IS - 10 N2 - West Java Health Laboratory (WJHL) is one of the many institutions in Indonesia that have sequenced SARS-CoV-2 genome. Although having submitted a large number of sequences since September 2020, however, these submitted data lack advanced analyses. Therefore, in this study, we analyze the variant distribution, hotspot mutation, and its impact on protein structure and function of SARS-CoV-2 from the collected samples from WJHL. As many as one hundred sixty-three SARS-CoV-2 genome sequences submitted by West Java Health Laboratory (WJHL), with collection dates between September 2020 and June 2021, were retrieved from GISAID. Subsequently, the frequency and distribution of non-synonymous mutations across different cities and regencies from these samples were analyzed. The effect of the most prevalent mutations from dominant variants on the stability of their corresponding proteins was examined. The samples mostly consisted of people of working-age, and were distributed between female and male equally. All of the sample sequences showed varying levels of diversity, especially samples from West Bandung which carried the highest diversity. Dominant variants are the VOC B.1.617.2 (Delta) variant, B.1.466.2 variant, and B.1.470 variant. The genomic regions with the highest number of mutations are the spike, NSP3, nucleocapsid, NSP12, and ORF3a protein. Mutation analysis showed that mutations in structural protein might increase the stability of the protein. Oppositely, mutations in non-structural protein might lead to a decrease in protein stability. However, further research to study the impact of mutations on the function of SARS-CoV-2 proteins are required. SN - 1999-4915 UR - https://www.unboundmedicine.com/medline/citation/34696527/Analysis_of_SARS_CoV_2_Genomes_from_West_Java_Indonesia_ L2 - https://www.mdpi.com/resolver?pii=v13102097 DB - PRIME DP - Unbound Medicine ER -