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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
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.
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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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