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

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...

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Autores principales: Pradipta, Ariel, Kumaheri, Meutia Ayuputeri, Wahyudi, Lilik Duwi, Susanto, Anindya Pradipta, Agasi, Harryyanto Ishaq, Shankar, Anuraj H., Sudarmono, Pratiwi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8831855/
https://www.ncbi.nlm.nih.gov/pubmed/35154274
http://dx.doi.org/10.3389/fgene.2022.801332
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author Pradipta, Ariel
Kumaheri, Meutia Ayuputeri
Wahyudi, Lilik Duwi
Susanto, Anindya Pradipta
Agasi, Harryyanto Ishaq
Shankar, Anuraj H.
Sudarmono, Pratiwi
author_facet Pradipta, Ariel
Kumaheri, Meutia Ayuputeri
Wahyudi, Lilik Duwi
Susanto, Anindya Pradipta
Agasi, Harryyanto Ishaq
Shankar, Anuraj H.
Sudarmono, Pratiwi
author_sort Pradipta, Ariel
collection PubMed
description 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.
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spelling pubmed-88318552022-02-12 Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships: A Case Study From Indonesia Pradipta, Ariel Kumaheri, Meutia Ayuputeri Wahyudi, Lilik Duwi Susanto, Anindya Pradipta Agasi, Harryyanto Ishaq Shankar, Anuraj H. Sudarmono, Pratiwi Front Genet Genetics 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. Frontiers Media S.A. 2022-01-28 /pmc/articles/PMC8831855/ /pubmed/35154274 http://dx.doi.org/10.3389/fgene.2022.801332 Text en Copyright © 2022 Pradipta, Kumaheri, Wahyudi, Susanto, Agasi, Shankar and Sudarmono. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Pradipta, Ariel
Kumaheri, Meutia Ayuputeri
Wahyudi, Lilik Duwi
Susanto, Anindya Pradipta
Agasi, Harryyanto Ishaq
Shankar, Anuraj H.
Sudarmono, Pratiwi
Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships: A Case Study From Indonesia
title Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships: A Case Study From Indonesia
title_full Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships: A Case Study From Indonesia
title_fullStr Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships: A Case Study From Indonesia
title_full_unstemmed Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships: A Case Study From Indonesia
title_short Accelerating Detection of Variants During COVID-19 Surges by Diverse Technological and Public Health Partnerships: A Case Study From Indonesia
title_sort accelerating detection of variants during covid-19 surges by diverse technological and public health partnerships: a case study from indonesia
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8831855/
https://www.ncbi.nlm.nih.gov/pubmed/35154274
http://dx.doi.org/10.3389/fgene.2022.801332
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