Global disparities in SARS-CoV-2 genomic surveillance
File(s)s41467-022-33713-y.pdf (4.16 MB)
Published version
Author(s)
Type
Journal Article
Abstract
Genomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times (TAT) on variant detection in 189 countries. In two years of pandemic, 78% of high income countries (HICs) sequenced >0.5% of their COVID-19 cases, while 42% of low (LICs) and middle income countries (MICs) reached that mark. Around 25% of the genomes from HICs were submitted within 21 days, a pattern observed in 5% of the genomes from LICs and MICs. We found that sequencing around 0.5% of the cases, with a TAT <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness, and efforts must be made to support LICs and MICs improve their local sequencing capacity.
Date Issued
2022-11-16
Date Acceptance
2022-09-29
Citation
Nature Communications, 2022, 13 (7003), pp.1-13
ISSN
2041-1723
Publisher
Nature Research
Start Page
1
End Page
13
Journal / Book Title
Nature Communications
Volume
13
Issue
7003
Copyright Statement
© The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
License URL
Sponsor
Medical Research Council-São Paulo Research Foundation (FAPESP)
Wellcome Trust
Bill & Melinda Gates Foundation
Wellcome Trust
Identifier
https://www.nature.com/articles/s41467-022-33713-y
Grant Number
MR/S0195/1
204311/Z/16/Z
INV-034540
224190/Z/21/Z
Subjects
Bulgarian SARS-CoV-2 sequencing group
Communicable Diseases Genomics Network (Australia and New Zealand)
COVID-19 Impact Project
Danish Covid-19 Genome Consortium
Fiocruz COVID-19 Genomic Surveillance Network
GISAID core curation team
Network for Genomic Surveillance in South Africa (NGS-SA)
Swiss SARS-CoV-2 Sequencing Consortium
Publication Status
Published
Date Publish Online
2022-11-16