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Analysis of SARS-CoV-2 Genomes from West Java, Indonesia.

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  • Additional Information
    • Source:
      Publisher: MDPI Country of Publication: Switzerland NLM ID: 101509722 Publication Model: Electronic Cited Medium: Internet ISSN: 1999-4915 (Electronic) Linking ISSN: 19994915 NLM ISO Abbreviation: Viruses Subsets: MEDLINE
    • Publication Information:
      Original Publication: Basel, Switzerland : MDPI
    • Subject Terms:
      Genome, Viral/*genetics ; SARS-CoV-2/*genetics ; Viral Proteins/*genetics ; Viral Proteins/*metabolism; COVID-19/pathology ; Coronavirus Nucleocapsid Proteins/genetics ; Coronavirus Papain-Like Proteases/genetics ; Coronavirus RNA-Dependent RNA Polymerase/genetics ; Mutation/genetics ; Phosphoproteins/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Viroporin Proteins/genetics ; Disease Hotspot ; Female ; Humans ; Indonesia ; Male ; Molecular Docking Simulation ; Protein Stability ; Whole Genome Sequencing
    • 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.
    • References:
      Commun Biol. 2021 Feb 15;4(1):228. (PMID: 33589648)
      Viruses. 2022 Apr 08;14(4):. (PMID: 35458508)
      Bioinformatics. 2014 Oct 15;30(20):2981-2. (PMID: 24996895)
      Bioinformatics. 2011 Jun 15;27(12):1711-2. (PMID: 21505037)
      PLoS One. 2020 Dec 22;15(12):e0243703. (PMID: 33351801)
      Glob Chall. 2017 Jan 10;1(1):33-46. (PMID: 31565258)
      Bioinformatics. 2016 Dec 1;32(23):3676-3678. (PMID: 27503228)
      Nat Commun. 2019 May 28;10(1):2342. (PMID: 31138817)
      Sci Rep. 2020 Jul 2;10(1):10895. (PMID: 32616763)
      Pathogens. 2020 Oct 10;9(10):. (PMID: 33050463)
      Curr Protoc Bioinformatics. 2015 Dec 17;52:5.8.1-5.8.15. (PMID: 26678386)
      J Mol Biol. 2016 Feb 22;428(4):720-725. (PMID: 26410586)
      Mol Syst Biol. 2022 Feb;18(2):e10673. (PMID: 35156767)
      Nature. 2021 Aug;596(7871):276-280. (PMID: 34237773)
      J Med Virol. 2021 Apr;93(4):2132-2140. (PMID: 33090512)
      Sci Rep. 2021 Mar 23;11(1):6625. (PMID: 33758205)
      Cell Mol Immunol. 2021 Mar;18(3):746-748. (PMID: 33473190)
      Nat Med. 2021 Sep;27(9):1495-1496. (PMID: 34400842)
      Infect Dis Rep. 2021 Jun 21;13(2):582-596. (PMID: 34205538)
      Nature. 2021 May;593(7857):130-135. (PMID: 33684923)
      Antiviral Res. 2018 Jan;149:58-74. (PMID: 29128390)
    • Contributed Indexing:
      Keywords: Indonesia; SARS-CoV-2; West Java; mutation; protein stability; variant
    • Accession Number:
      0 (Coronavirus Nucleocapsid Proteins)
      0 (ORF3a protein, SARS-CoV-2)
      0 (Phosphoproteins)
      0 (Spike Glycoprotein, Coronavirus)
      0 (Viral Proteins)
      0 (Viroporin Proteins)
      0 (nucleocapsid phosphoprotein, SARS-CoV-2)
      0 (spike protein, SARS-CoV-2)
      EC 2.7.7.48 (Coronavirus RNA-Dependent RNA Polymerase)
      EC 2.7.7.48 (NSP12 protein, SARS-CoV-2)
      EC 3.4.22.2 (Coronavirus Papain-Like Proteases)
      EC 3.4.22.2 (papain-like protease, SARS-CoV-2)
    • Publication Date:
      Date Created: 20211026 Date Completed: 20211110 Latest Revision: 20240403
    • Publication Date:
      20260130
    • Accession Number:
      PMC8538575
    • Accession Number:
      10.3390/v13102097
    • Accession Number:
      34696527