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

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.

Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia

“…The National Genomic Surveillance Consortium, a joint initiative of the Indonesian Ministry of Health and the Ministry of Research and Technology/National Agency for Research and Innovation, was established in January 2021. This partnership has encouraged extensive technological and public health partnerships, contributing to an increase in the number of SARS-CoV-2 whole-genome sequence uploads to the public database Global Initiative on Sharing All Influenza Data (GISAID) from 1210 in April 2021 to 5791 in August 2021 [ 13 ].…”

Full-genome sequencing and mutation analysis of SARS-CoV-2 isolated from Makassar, South Sulawesi, Indonesia

“…Genomic surveillance plays an important role in the containment of the virus, and in mitigating the emergence of new variants. From March 2020 to April 2021, 1,210 SARS-CoV-2 sequences were identified, accounting for 0.073% of the 1,668,360 infections recorded in Indonesia, with a monthly average of 140 days between specimen collection and sequence upload to Global Initiative on Sharing All Influenza Data (GISAID) ( Pradipta et al, 2022 ). By 10th December 2021, a total of 10,094 SARS-CoV-2 genome sequences had been submitted to GISAID from Indonesia ( GISAID, 2021 ).…”