Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements
Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements
Abstract A year after the World Health Organisation (WHO) declared COVID-19 as a pandemic, much has been learned with respect to SARS-CoV-2 epidemiology, vaccine production and disease treatment. Whole-genome sequencing (WGS) has played a significant role in contributing to our understanding of the epidemiology and biology of this virus. In this paper, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asia and the impact of technological development, access to resources, and demography of individual countries on its uptake. Facilitated by the Nottingham-Indonesia Collaboration for Clinical Research and Training (NICCRAT) initiative, we showcased a bilateral collaboration between the University of Nottingham and the Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia) to establish WGS of SARS-CoV-2 using Oxford Nanopore Technology? (ONT) in Indonesia. Analyses of SARS-CoV-2 genomes deposited on GISAID from Southeast and East Asian countries reveals the importance of collecting clinical and demographic metadata and the importance of open access and data sharing. Lineage and phylogenetic analyses per 1 June 2021 found that: 1) B.1.466.2 variants were the most predominant in Indonesia, with mutations in the spike protein including D614G at 100%, N439K at 99.1%, and P681R at 69.7% frequency, 2) The variants of concern (VoCs), B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta) were first detected in Indonesia in January 2021, 2) B.1.470 was first detected in Indonesia and spread to the neighbouring regions, and 3) The highest rate of virus transmissions between Indonesia and the rest of the world appears to be through interactions with Singapore and Japan, two neighbouring countries with high degree of access and travels to and from Indonesia. Overall, we conclude that WGS of SARS-CoV-2 using ONT platforms fits well with the Indonesian context and can catalyse the increase of sequencing rates in the country.
Ilyas Mohammad、Kusharyoto Wien、Akbariani Gilang、Utomo Ahmad R、Ridwanuloh Asep M、Wibowo Satrio、Cahyani Inswasti、Hariyatun Hariyatun、Syahputra Gita、Loose Matthew W.、Putro Eko W、Susanti Susanti
Molecular Pathology Research Group, School of Medicine, University of NottinghamResearch Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia)Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia)||PT. PathGen Diagnostik TeknologiBiomedical Postgraduate Program, Universitas YarsiResearch Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia)Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia)||PT. PathGen Diagnostik TeknologiSchool of Life Sciences, University of NottinghamResearch Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia)Research Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia)School of Life Sciences, University of NottinghamResearch Centre for Biotechnology, Indonesian Institute of Sciences (LIPI/Lembaga Ilmu Pengetahuan Indonesia)PT. PathGen Diagnostik Teknologi||Molecular Pathology Research Group, School of Medicine, University of Nottingham||Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Muhammadiyah
医学研究方法基础医学生物科学研究方法、生物科学研究技术
ASEANCOVID-19genomic surveillanceGISAIDnanoporeNICCRATSARS-CoV-2variant of concernswhole-genome sequencing
Ilyas Mohammad,Kusharyoto Wien,Akbariani Gilang,Utomo Ahmad R,Ridwanuloh Asep M,Wibowo Satrio,Cahyani Inswasti,Hariyatun Hariyatun,Syahputra Gita,Loose Matthew W.,Putro Eko W,Susanti Susanti.Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements[EB/OL].(2025-03-28)[2025-05-06].https://www.biorxiv.org/content/10.1101/2021.07.06.451270.点此复制
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