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

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 di...

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Autores principales: Fibriani, Azzania, Stephanie, Rebecca, Alfiantie, Afifah Alifia, Siregar, Agust Leo Fany, Pradani, Gusti Ayu Prani, Yamahoki, Nicholas, Purba, William Steflandel, Alamanda, Cut Nur Cinthia, Rahmawati, Ema, Rachman, Rifky Waluyajati, Robiani, Rini, Ristandi, Ryan Bayusantika
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8538575/
https://www.ncbi.nlm.nih.gov/pubmed/34696527
http://dx.doi.org/10.3390/v13102097
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author Fibriani, Azzania
Stephanie, Rebecca
Alfiantie, Afifah Alifia
Siregar, Agust Leo Fany
Pradani, Gusti Ayu Prani
Yamahoki, Nicholas
Purba, William Steflandel
Alamanda, Cut Nur Cinthia
Rahmawati, Ema
Rachman, Rifky Waluyajati
Robiani, Rini
Ristandi, Ryan Bayusantika
author_facet Fibriani, Azzania
Stephanie, Rebecca
Alfiantie, Afifah Alifia
Siregar, Agust Leo Fany
Pradani, Gusti Ayu Prani
Yamahoki, Nicholas
Purba, William Steflandel
Alamanda, Cut Nur Cinthia
Rahmawati, Ema
Rachman, Rifky Waluyajati
Robiani, Rini
Ristandi, Ryan Bayusantika
author_sort Fibriani, Azzania
collection PubMed
description 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.
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spelling pubmed-85385752021-10-24 Analysis of SARS-CoV-2 Genomes from West Java, Indonesia Fibriani, Azzania Stephanie, Rebecca Alfiantie, Afifah Alifia Siregar, Agust Leo Fany Pradani, Gusti Ayu Prani Yamahoki, Nicholas Purba, William Steflandel Alamanda, Cut Nur Cinthia Rahmawati, Ema Rachman, Rifky Waluyajati Robiani, Rini Ristandi, Ryan Bayusantika Viruses Article 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. MDPI 2021-10-18 /pmc/articles/PMC8538575/ /pubmed/34696527 http://dx.doi.org/10.3390/v13102097 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Fibriani, Azzania
Stephanie, Rebecca
Alfiantie, Afifah Alifia
Siregar, Agust Leo Fany
Pradani, Gusti Ayu Prani
Yamahoki, Nicholas
Purba, William Steflandel
Alamanda, Cut Nur Cinthia
Rahmawati, Ema
Rachman, Rifky Waluyajati
Robiani, Rini
Ristandi, Ryan Bayusantika
Analysis of SARS-CoV-2 Genomes from West Java, Indonesia
title Analysis of SARS-CoV-2 Genomes from West Java, Indonesia
title_full Analysis of SARS-CoV-2 Genomes from West Java, Indonesia
title_fullStr Analysis of SARS-CoV-2 Genomes from West Java, Indonesia
title_full_unstemmed Analysis of SARS-CoV-2 Genomes from West Java, Indonesia
title_short Analysis of SARS-CoV-2 Genomes from West Java, Indonesia
title_sort analysis of sars-cov-2 genomes from west java, indonesia
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8538575/
https://www.ncbi.nlm.nih.gov/pubmed/34696527
http://dx.doi.org/10.3390/v13102097
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