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Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements
Whole-genome sequencing (WGS) has played a significant role in understanding the epidemiology and biology of SARS-CoV-2 virus. Here, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asian countries as a genomic surveillance during the COVID-19 pandemic. Nottingham–Indonesia Collaborati...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9027902/ https://www.ncbi.nlm.nih.gov/pubmed/35458508 http://dx.doi.org/10.3390/v14040778 |
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author | Cahyani, Inswasti Putro, Eko W. Ridwanuloh, Asep M. Wibowo, Satrio Hariyatun, Hariyatun Syahputra, Gita Akbariani, Gilang Utomo, Ahmad R. Ilyas, Mohammad Loose, Matthew Kusharyoto, Wien Susanti, Susanti |
author_facet | Cahyani, Inswasti Putro, Eko W. Ridwanuloh, Asep M. Wibowo, Satrio Hariyatun, Hariyatun Syahputra, Gita Akbariani, Gilang Utomo, Ahmad R. Ilyas, Mohammad Loose, Matthew Kusharyoto, Wien Susanti, Susanti |
author_sort | Cahyani, Inswasti |
collection | PubMed |
description | Whole-genome sequencing (WGS) has played a significant role in understanding the epidemiology and biology of SARS-CoV-2 virus. Here, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asian countries as a genomic surveillance during the COVID-19 pandemic. Nottingham–Indonesia Collaboration for Clinical Research and Training (NICCRAT) initiative has facilitated collaboration between the University of Nottingham and a team in the Research Center for Biotechnology, National Research and Innovation Agency (BRIN), to carry out a small number of SARS-CoV-2 WGS in Indonesia using Oxford Nanopore Technology (ONT). Analyses of SARS- CoV-2 genomes deposited on GISAID reveal the importance of clinical and demographic metadata collection and the importance of open access and data sharing. Lineage and phylogenetic analyses of two periods defined by the Delta variant outbreak reveal that: (1) B.1.466.2 variants were the most predominant in Indonesia before the Delta variant outbreak, having a unique spike gene mutation N439K at more than 98% frequency, (2) Delta variants AY.23 sub-lineage took over after June 2021, and (3) the highest rate of virus transmissions between Indonesia and other countries was through interactions with Singapore and Japan, two neighbouring countries with a high degree of access and travels to and from Indonesia. |
format | Online Article Text |
id | pubmed-9027902 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-90279022022-04-23 Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements Cahyani, Inswasti Putro, Eko W. Ridwanuloh, Asep M. Wibowo, Satrio Hariyatun, Hariyatun Syahputra, Gita Akbariani, Gilang Utomo, Ahmad R. Ilyas, Mohammad Loose, Matthew Kusharyoto, Wien Susanti, Susanti Viruses Article Whole-genome sequencing (WGS) has played a significant role in understanding the epidemiology and biology of SARS-CoV-2 virus. Here, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asian countries as a genomic surveillance during the COVID-19 pandemic. Nottingham–Indonesia Collaboration for Clinical Research and Training (NICCRAT) initiative has facilitated collaboration between the University of Nottingham and a team in the Research Center for Biotechnology, National Research and Innovation Agency (BRIN), to carry out a small number of SARS-CoV-2 WGS in Indonesia using Oxford Nanopore Technology (ONT). Analyses of SARS- CoV-2 genomes deposited on GISAID reveal the importance of clinical and demographic metadata collection and the importance of open access and data sharing. Lineage and phylogenetic analyses of two periods defined by the Delta variant outbreak reveal that: (1) B.1.466.2 variants were the most predominant in Indonesia before the Delta variant outbreak, having a unique spike gene mutation N439K at more than 98% frequency, (2) Delta variants AY.23 sub-lineage took over after June 2021, and (3) the highest rate of virus transmissions between Indonesia and other countries was through interactions with Singapore and Japan, two neighbouring countries with a high degree of access and travels to and from Indonesia. MDPI 2022-04-08 /pmc/articles/PMC9027902/ /pubmed/35458508 http://dx.doi.org/10.3390/v14040778 Text en © 2022 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 Cahyani, Inswasti Putro, Eko W. Ridwanuloh, Asep M. Wibowo, Satrio Hariyatun, Hariyatun Syahputra, Gita Akbariani, Gilang Utomo, Ahmad R. Ilyas, Mohammad Loose, Matthew Kusharyoto, Wien Susanti, Susanti Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements |
title | Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements |
title_full | Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements |
title_fullStr | Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements |
title_full_unstemmed | Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements |
title_short | Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements |
title_sort | genome profiling of sars-cov-2 in indonesia, asean and the neighbouring east asian countries: features, challenges and achievements |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9027902/ https://www.ncbi.nlm.nih.gov/pubmed/35458508 http://dx.doi.org/10.3390/v14040778 |
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