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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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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. |
format | Online Article Text |
id | pubmed-8831855 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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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