ArticleNature communications2022
Global disparities in SARS-CoV-2 genomic surveillance.
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Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 204 papers, 4 of them syntheses that pooled it.
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204citing papers in PubMed, 4 pooled it
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Who cites it
204 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Local genomic epidemiology investigations of SARS-CoV-2 during the early pandemic response: A global systematic review.Epidemiology and infection · 2026Pooled it
- Impact of temperature and humidity on SARS-CoV-2 transmissibility: a systematic review and meta-analysis.Frontiers in public health · 2025Pooled it
- Technological Barriers to Routine Genomic Surveillance for Vaccine Development Against SARS-CoV-2 in Africa: A Systematic Review.Influenza and other respiratory viruses · 2024Pooled it
- Targeted next-generation sequencing to diagnose drug-resistant tuberculosis: a systematic review and meta-analysis.The Lancet. Infectious diseases · 2024Pooled it
- Global Genomic Surveillance.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Lassa virus live tracking and lineage assignment: how nextstrain can enhance surveillance and public health in Africa and beyond.Emerging microbes & infections · 2026Article
- Respiratory pandemic risk in the Anthropocene: A One Health framework and GISRS+ agenda.One health (Amsterdam, Netherlands) · 2026Review
- A generalized lineage nomenclature for viral genomic epidemiology.Nature microbiology · 2026Article
- Genomic surveillance of SARS-CoV-2 in Tunisia during the omicron era: insights from the national influenza & other respiratory viruses laboratory.Virology journal · 2026Article
- Review
- Mapping the frontiers of genomic disease surveillance research in the ASEAN region: scientometric insights for precision public health and next-generation epidemic intelligence.Briefings in bioinformatics · 2026Article
- Leveraging synthetic and genetic data to improve epidemic forecasting.PLoS computational biology · 2026Article
- From concept to capability: CBRNE-grade, equity-first benchmarks for preventing HKU5-CoV-2 spillover.Infectious diseases & immunity · 2026Article
- Performance of mechanically sheared DNA in multiplexed Oxford Nanopore sequencing forMicrobial genomics · 2026Article
- Home is where the host is: evolutionary history of geographic spread, host switching and adaptive genomic signatures in two generalist group BMicrobial genomics · 2026Article
- Differential Binding and Neutralising Antibody Responses Across COVID-19 Severity in a Saudi Multicentre Cohort.Viruses · 2026Article
- SARS-CoV-2 saltational events are recurrent and trace to persistent human infections.bioRxiv : the preprint server for biology · 2026Article
- Genomic surveillance inequities in emerging infectious diseases: Why fragile settings like Somalia are critical to global health security.New microbes and new infections · 2026Article
- Genomic Surveillance of SARS-CoV-2 in Senegal (2020-2024): Variant Turnover, Omicron Introductions, and Interregional Spread.Influenza and other respiratory viruses · 2026Article
- AI-driven big data analysis and predictive modeling of infectious disease immunity: from correlates to causal, multiscale understanding.Archives of microbiology · 2026Review
144 more citing papers are in PubMed but not listed here.
Corrections and comments
- Update of
Authors and funding
54 authors.
Anderson F Brito *Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA. andersonfbrito@gmail.com.ORCID 0000-0001-5785-7222
Elizaveta Semenova *Department of Computer Science, University of Oxford, Oxford, UK.ORCID 0000-0002-8271-2575
Gytis Dudas *Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.ORCID 0000-0002-0227-4158
Gabriel W HasslerDepartment of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
Chaney C KalinichDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
Moritz U G KraemerDepartment of Biology, University of Oxford, Oxford, UK.ORCID 0000-0001-8838-7147
Joses HoGISAID Global Data Science Initiative, Munich, Germany.ORCID 0000-0002-9186-6322
Houriiyah TegallyKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
George GithinjiKEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.ORCID 0000-0001-9640-7371
Charles N AgotiKEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.ORCID 0000-0002-2160-567X
Lucy E MatkinDepartment of Biology, University of Oxford, Oxford, UK.ORCID 0000-0003-0952-5818
Charles WhittakerMRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.ORCID 0000-0002-5003-2575
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
Benjamin P HowdenMicrobiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.ORCID 0000-0003-0237-1473
Vitali SintchenkoSydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.ORCID 0000-0002-9261-3650
Neta S ZuckermanCentral Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel.
Orna MorCentral Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel.ORCID 0000-0003-3207-4226
Heather M BlankenshipMichigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, USA.
Tulio de OliveiraKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.ORCID 0000-0002-3027-5254
Raymond T P LinNational Centre for Infectious Diseases, Singapore, Singapore.ORCID 0000-0001-6654-026X
Marilda Mendonça SiqueiraLaboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
Paola Cristina ResendeLaboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.ORCID 0000-0002-2884-3662
Ana Tereza R VasconcelosLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil.ORCID 0000-0002-4632-2086
Fernando R SpilkiFeevale University, Institute of Health Sciences, Novo Hamburgo, RS, Brazil.ORCID 0000-0001-5804-7045
Renato Santana AguiarLaboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.ORCID 0000-0001-5180-3717
Ivailo AlexievNational Center of Infectious and Parasitic Diseases, Sofia, Bulgaria.
Ivan N IvanovNational Center of Infectious and Parasitic Diseases, Sofia, Bulgaria.
Ivva PhilipovaNational Center of Infectious and Parasitic Diseases, Sofia, Bulgaria.
Christine V F CarringtonDepartment of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago.
Nikita S D SahadeoDepartment of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago.
Ben BrandaGISAID Global Data Science Initiative, Munich, Germany.
Céline GurryGISAID Global Data Science Initiative, Munich, Germany.
Sebastian Maurer-StrohGISAID Global Data Science Initiative, Munich, Germany.
Dhamari NaidooHealth Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India.
Karin J von EijeDepartment of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.ORCID 0000-0003-0627-5673
Mark D PerkinsEmerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.
Maria van KerkhoveEmerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.ORCID 0000-0002-6135-0018
Sarah C HillRoyal Veterinary College, Hawkshead, UK.
Ester C SabinoInstituto Todos pela Saúde, São Paulo, SP, Brazil.
Oliver G PybusDepartment of Biology, University of Oxford, Oxford, UK.ORCID 0000-0002-8797-2667
Christopher DyeDepartment of Biology, University of Oxford, Oxford, UK.
Samir BhattMRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
Seth FlaxmanDepartment of Computer Science, University of Oxford, Oxford, UK.ORCID 0000-0002-2477-4217
Marc A SuchardDepartment of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.ORCID 0000-0001-9818-479X
Nathan D GrubaughDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
Guy BaeleDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.ORCID 0000-0002-1915-7732
Nuno R FariaDepartment of Biology, University of Oxford, Oxford, UK. nfaria@ic.ac.uk.ORCID 0000-0002-9747-8822
Funding
Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9MTechnology CoreU19AI135995 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Kristian Graugaard Andersen · 2018 to 2026
$32.0MShort-Term Reserch Training: Students in Health SchoolsT35HL007649 · NHLBI · YALE UNIVERSITY · PI Sarwat I Chaudhry, Erica L Herzog · 1987 to 2026
$5.7MStatistical Innovation to Integrate Sequences and Phenotypes for Scalable Phylodynamic InferenceR01AI153044 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Marc A. Suchard · 2021 to 2026
$2.4MScalable Inference in Statistical Models of Viral Evolution and Human HealthF31AI154824 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI HASSLER, GABRIEL WILLIAM · 2021 to 2022
$64kMedical Research Council MR/R015600/1Medical Research Council MR/S019510/1NCATS NIH HHS UL1 TR001863NHLBI NIH HHS T35 HL007649NIAID NIH HHS F31 AI154824NIAID NIH HHS R01 AI153044NIAID NIH HHS U19 AI135995Wellcome TrustWorld Health Organization 001
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.
Indexed as
COVID-19SARS-CoV-2Genome, ViralGenomicsHumansPandemics
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