Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships: A Case Study From Indonesia

Ariel Pradipta, Meutia Ayuputeri Kumaheri, Lilik Duwi Wahyudi, Anindya Pradipta Susanto, Harryyanto Ishaq Agasi, Anuraj H. Shankar, Pratiwi Sudarmono

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Article number801332
JournalFrontiers in Genetics
Volume13
DOIs
Publication statusPublished - 28 Jan 2022

Keywords

  • genome sequencing platform
  • GISAID
  • Indonesia
  • SARS-CoV-2
  • turn-around-time
  • variant
  • whole-genome-sequencing

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