TY - JOUR
T1 - Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships
T2 - A Case Study From Indonesia
AU - Pradipta, Ariel
AU - Kumaheri, Meutia Ayuputeri
AU - Wahyudi, Lilik Duwi
AU - Susanto, Anindya Pradipta
AU - Agasi, Harryyanto Ishaq
AU - Shankar, Anuraj H.
AU - Sudarmono, Pratiwi
N1 - Funding Information:
The work was supported by Wellcome Trust Grant 222574/Z/ 21/Z supplement for SARS-CoV-2 genomic surveillance. The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript.
Publisher Copyright:
Copyright © 2022 Pradipta, Kumaheri, Wahyudi, Susanto, Agasi, Shankar and Sudarmono.
PY - 2022/1/28
Y1 - 2022/1/28
N2 - 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.
AB - 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.
KW - genome sequencing platform
KW - GISAID
KW - Indonesia
KW - SARS-CoV-2
KW - turn-around-time
KW - variant
KW - whole-genome-sequencing
UR - http://www.scopus.com/inward/record.url?scp=85124531909&partnerID=8YFLogxK
U2 - 10.3389/fgene.2022.801332
DO - 10.3389/fgene.2022.801332
M3 - Article
AN - SCOPUS:85124531909
VL - 13
JO - Frontiers in Genetics
JF - Frontiers in Genetics
SN - 1664-8021
M1 - 801332
ER -
