Pradipta Ariel, Kumaheri Meutia Ayuputeri, Wahyudi Lilik Duwi, Susanto Anindya Pradipta, Agasi Harryyanto Ishaq, Shankar Anuraj H, Sudarmono Pratiwi
Genomik Solidaritas Indonesia (GSI) Lab, Jakarta, Indonesia.
Indonesia Medical Education and Research Institute, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia.
Front Genet. 2022 Jan 28;13:801332. doi: 10.3389/fgene.2022.801332. eCollection 2022.
Early detection of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) variants and use of data for public health action requires a coordinated, rapid, and high throughput approach to whole genome sequencing (WGS). Currently, WGS output from many low- and middle-income countries (LMIC) has lagged. By fostering diverse partnerships and multiple sequencing technologies, Indonesia accelerated SARS-CoV-2 WGS uploads to GISAID from 1,210 in April 2021 to 5,791 in August 2021, an increase from 11 submissions per day between January to May, to 43 per day between June to August. Turn-around-time from specimen collection to submission decreased from 77 to 5 days, allowing for timely public health decisions. These changes were enabled by establishment of the National Genomic Surveillance Consortium, coordination between public and private sector laboratories with WGS capability, and diversification of sequencing platform technologies. Here we present how diversification on multiple levels enabled a rapid and significant increase of national WGS performance, with potentially valuable lessons for other LMICs.
早期发现严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变体并将数据用于公共卫生行动，需要一种协调、快速且高通量的全基因组测序（WGS）方法。目前，许多低收入和中等收入国家（LMIC）的WGS产出滞后。通过建立多样化的合作伙伴关系和采用多种测序技术，印度尼西亚将SARS-CoV-2的WGS数据上传至全球共享流感数据倡议组织（GISAID）的数量从2021年4月的1210份加速提升至2021年8月的5791份，从1月至5月期间每天提交11份增至6月至8月期间每天提交43份。从样本采集到提交的周转时间从77天缩短至5天，从而能够及时做出公共卫生决策.这些变化得益于国家基因组监测联盟（National Genomic Surveillance Consortium） 的成立、具备WGS能力 的公共部门和私营部门实验室之间 的协调以及测序平台技术 的多样化。在此，我们介绍多层次 的多样化如何实现国家WGS性能 的快速显著提升，这可能为其他低收入和中等收入国家提供宝贵经验。
