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印尼、东盟及东亚周边国家的 SARS-CoV-2 基因组特征、挑战与成就

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

机构信息

COMGen Division, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.

Research Center for Biotechnology, National Research and Innovation Agency (Badan Riset dan Inovasi Nasional/BRIN), Bogor 16911, Indonesia.

出版信息

Viruses. 2022 Apr 8;14(4):778. doi: 10.3390/v14040778.

DOI:10.3390/v14040778
PMID:35458508
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9027902/
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.

摘要

全基因组测序（WGS）在了解 SARS-CoV-2 病毒的流行病学和生物学方面发挥了重要作用。在这里，我们调查了在 COVID-19 大流行期间，将 SARS-CoV-2 WGS 用于东南亚和东亚国家的基因组监测。诺丁汉-印度尼西亚临床研究与培训合作（NICCRAT）倡议促进了诺丁汉大学与印度尼西亚生物技术研究与创新机构（BRIN）的一个团队之间的合作，使用牛津纳米孔技术（ONT）在印度尼西亚进行了少量的 SARS-CoV-2 WGS。对 GISAID 上提交的 SARS-CoV-2 基因组的分析表明，收集临床和人口统计学元数据的重要性，以及开放获取和数据共享的重要性。由 Delta 变异株爆发定义的两个时期的谱系和系统发育分析表明：（1）在 Delta 变异株爆发之前，B.1.466.2 变异株在印度尼西亚最为流行，其 Spike 基因的独特突变 N439K 的频率超过 98%；（2）Delta 变异株 AY.23 亚系于 2021 年 6 月后占据主导地位；（3）印度尼西亚与其他国家之间病毒传播率最高的是与新加坡和日本的互动，这两个邻国与印度尼西亚的往来程度很高。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/8d61eda94684/viruses-14-00778-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/dba612909a91/viruses-14-00778-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/2ea8e499eec5/viruses-14-00778-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/306aa93a6240/viruses-14-00778-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/c6527f7b856f/viruses-14-00778-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/0c0245823234/viruses-14-00778-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/8d61eda94684/viruses-14-00778-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/dba612909a91/viruses-14-00778-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/2ea8e499eec5/viruses-14-00778-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/306aa93a6240/viruses-14-00778-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/c6527f7b856f/viruses-14-00778-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/0c0245823234/viruses-14-00778-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9298/9027902/8d61eda94684/viruses-14-00778-g006.jpg

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