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


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
Issue number1
StatePublished - Dec 2022
Externally publishedYes


FundersFunder number
Branco Weiss Fellowship
Commonwealth & Development Office
Community Jameel
Corona-ômica-RJE-26/210.179/2020, 440931/2020-7, 307145/2021-2, E-26/211.107/2021
Fonds voor Wetenschappelijk Onderzoek—VlaanderenG0E1420N, G098321N
Medical Research Council-São Paulo Research Foundation
Royal Society Sir Henry Dale Fellowship204311/Z/16/Z
US Public Health Service Ruth L. Kirschstein National Research Service Award5T35HL007649-35
National Institutes of HealthF31 AI154824, R01 AI153044, U19 AI135995
Centers for Disease Control and Prevention75D30120C09570
U.S. Food and Drug Administration
U.S. Department of Veterans Affairs
Bill and Melinda Gates FoundationINV-034540, INV-034652
Rockefeller Foundation
Janssen Research and Development
National Center for Advancing Translational SciencesUL1TR001863
George Mason University
Wellcome Trust
Memphis Research ConsortiumMR/R015600/1
Medical Research Council
Engineering and Physical Sciences Research CouncilEP/V002910/1
European Commission
Fundação de Amparo à Pesquisa do Estado de São Paulo18/14389-0, MR/S0195/1
Fonds Wetenschappelijk Onderzoek
Ministry of Education, Youth and ScienceKП‐06‐H43/1-27.11.2020, 220414/Z/20/Z
Ministério da Ciência, Tecnologia e Inovação
Conselho Nacional de Desenvolvimento Científico e Tecnológico0494/20 01.20.0026.00, UFMG-NB3 1139/20, 312688/2017-2, 439119/2018-9, 14/2020—23072.211119/2020-10
KU LeuvenC14/18/094
Oxford Martin School, University of Oxford
Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro202.922/2018
Foreign, Commonwealth and Development Office


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