Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements
Inswasti Cahyani,
Eko W. Putro,
Asep M. Ridwanuloh,
Satrio Wibowo,
Hariyatun Hariyatun,
Gita Syahputra,
Gilang Akbariani,
Ahmad R. Utomo,
Mohammad Ilyas,
Matthew Loose,
Wien Kusharyoto,
Susanti Susanti
Affiliations
Inswasti Cahyani
COMGen Division, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
Eko W. Putro
Research Center for Biotechnology, National Research and Innovation Agency (Badan Riset dan Inovasi Nasional/BRIN), Bogor 16911, Indonesia
Asep M. Ridwanuloh
Research Center for Biotechnology, National Research and Innovation Agency (Badan Riset dan Inovasi Nasional/BRIN), Bogor 16911, Indonesia
Satrio Wibowo
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
Hariyatun Hariyatun
Research Center for Biotechnology, National Research and Innovation Agency (Badan Riset dan Inovasi Nasional/BRIN), Bogor 16911, Indonesia
Gita Syahputra
Research Center for Biotechnology, National Research and Innovation Agency (Badan Riset dan Inovasi Nasional/BRIN), Bogor 16911, Indonesia
Gilang Akbariani
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
Ahmad R. Utomo
Graduate School of Biomedical Science, Universitas YARSI, Jakarta 10510, Indonesia
Mohammad Ilyas
Molecular Pathology Research Group, Academic Unit of Translational Medical Science, Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
Matthew Loose
COMGen Division, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
Wien Kusharyoto
Research Center for Biotechnology, National Research and Innovation Agency (Badan Riset dan Inovasi Nasional/BRIN), Bogor 16911, Indonesia
Susanti Susanti
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
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.