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Volume 14
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10.3390/v14040778
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Article

Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements

by
Inswasti Cahyani
1,
Eko W. Putro
2,
Asep M. Ridwanuloh
2,
Satrio Wibowo
3,
Hariyatun Hariyatun
2,
Gita Syahputra
2,
Gilang Akbariani
3,
Ahmad R. Utomo
4,
Mohammad Ilyas
5,
Matthew Loose
1,
Wien Kusharyoto
2 and
Susanti Susanti
3,5,6,*
1
COMGen Division, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
2
Research Center for Biotechnology, National Research and Innovation Agency (Badan Riset dan Inovasi Nasional/BRIN), Bogor 16911, Indonesia
3
PathGen Diagnostik Teknologi, Center for Innovation and Utilization of Science and Technology, National Research and Innovation Agency (Badan Riset dan Inovasi Nasional/BRIN), Bogor 16911, Indonesia
4
Graduate School of Biomedical Science, Universitas YARSI, Jakarta 10510, Indonesia
5
Molecular Pathology Research Group, Academic Unit of Translational Medical Science, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
6
Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Muhammadiyah, Purwokerto 53182, Indonesia
*
Author to whom correspondence should be addressed.
Viruses 2022, 14(4), 778; https://doi.org/10.3390/v14040778
Submission received: 1 March 2022 / Revised: 1 April 2022 / Accepted: 5 April 2022 / Published: 8 April 2022
(This article belongs to the Collection SARS-CoV-2 and COVID-19)
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Abstract

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.
Keywords: ASEAN; COVID-19; genomic surveillance; GISAID; nanopore; NICCRAT; SARS-CoV-2; variants of concern; whole-genome sequencing ASEAN; COVID-19; genomic surveillance; GISAID; nanopore; NICCRAT; SARS-CoV-2; variants of concern; whole-genome sequencing

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MDPI and ACS Style

Cahyani, I.; Putro, E.W.; Ridwanuloh, A.M.; Wibowo, S.; Hariyatun, H.; Syahputra, G.; Akbariani, G.; Utomo, A.R.; Ilyas, M.; Loose, M.; et al. Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements. Viruses 2022, 14, 778. https://doi.org/10.3390/v14040778

AMA Style

Cahyani I, Putro EW, Ridwanuloh AM, Wibowo S, Hariyatun H, Syahputra G, Akbariani G, Utomo AR, Ilyas M, Loose M, et al. Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements. Viruses. 2022; 14(4):778. https://doi.org/10.3390/v14040778

Chicago/Turabian Style

Cahyani, Inswasti, Eko W. Putro, Asep M. Ridwanuloh, Satrio Wibowo, Hariyatun Hariyatun, Gita Syahputra, Gilang Akbariani, Ahmad R. Utomo, Mohammad Ilyas, Matthew Loose, and et al. 2022. "Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements" Viruses 14, no. 4: 778. https://doi.org/10.3390/v14040778

APA Style

Cahyani, I., Putro, E. W., Ridwanuloh, A. M., Wibowo, S., Hariyatun, H., Syahputra, G., Akbariani, G., Utomo, A. R., Ilyas, M., Loose, M., Kusharyoto, W., & Susanti, S. (2022). Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements. Viruses, 14(4), 778. https://doi.org/10.3390/v14040778

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