Global disparities in SARS-CoV-2 genomic surveillance

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, Bulgarian SARS-CoV-2 sequencing group

Research output: Contribution to journalArticlepeer-review

115 Scopus citations

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 on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <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 low- and middle-income countries improve their local sequencing capacity.

Original languageEnglish
Article number7003
JournalNature Communications
Volume13
Issue number1
DOIs
StatePublished - Dec 2022
Externally publishedYes

Funding

FundersFunder number
Oxford Martin School, University of Oxford
Medical Research Council
Rockefeller Foundation
Branco Weiss Fellowship
Commonwealth & Development Office
George Mason University
Fonds Wetenschappelijk Onderzoek
Medical Research Council-São Paulo Research Foundation
European Commission
Wellcome Trust
Janssen Research and Development
Community Jameel
Sir Henry Wellcome Fellowship
Ministério da Ciência, Tecnologia e Inovação
U.S. Food and Drug Administration
U.S. Department of Veterans Affairs
Foreign, Commonwealth and Development Office
Engineering and Physical Sciences Research CouncilEP/V002910/1
Memphis Research ConsortiumMR/R015600/1
Ministry of Education, Youth and ScienceKП‐06‐H43/1-27.11.2020, 220414/Z/20/Z
Bill and Melinda Gates FoundationINV-034540, INV-034652
Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro202.922/2018
Royal Society Sir Henry Dale Fellowship204311/Z/16/Z
KU LeuvenC14/18/094
Centers for Disease Control and Prevention75D30120C09570
Fonds voor Wetenschappelijk Onderzoek—VlaanderenG0E1420N, G098321N
National Institutes of HealthF31 AI154824, R01 AI153044, U19 AI135995
Conselho Nacional de Desenvolvimento Científico e Tecnológico0494/20 01.20.0026.00, UFMG-NB3 1139/20, 312688/2017-2, 439119/2018-9, = 404096/2020-4, 14/2020—23072.211119/2020-10
Corona-ômica-RJE-26/210.179/2020, 440931/2020-7, 307145/2021-2, E-26/211.107/2021
Fundação de Amparo à Pesquisa do Estado de São Paulo18/14389-0, MR/S0195/1
US Public Health Service Ruth L. Kirschstein National Research Service Award5T35HL007649-35

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