Please use this identifier to cite or link to this item:
https://www.arca.fiocruz.br/handle/icict/51701
GLOBAL DISPARITIES IN SARS-COV-2 GENOMIC SURVEILLANCE
SARS-CoV-2
Disparidades globais
Desigualdades socioeconômicas
Author
Brito, Anderson F.
Semenova, Elizaveta
Dudas, Gytis
Hassler, Gabriel W.
Kalinich, Chaney C.
Kraemer, Moritz U.G.
Ho, Joses
Tegally, Houriiyah
Githinji, George
Agoti, Charles N.
Matkin, Lucy E.
Whittaker, Charles
Howden, Benjamin P.
Sintchenko, Vitali
Zuckerman, Neta S.
Mor, Orna
Blankenship, Heather M.
Oliveira, Tulio de
Lyn, Raymond T. P
Siqueira, Marilda Agudo Mendonça Teixeira de
Resende, Paola Cristina
Vasconcelos, Ana Tereza R.
Spilki, Fernando R.
Aguiar, Renato Santana
Alexiev, Ivailo
Ivanov, Ivan N.
Philipova, Ivva
Carrington, Christine V. F.
Sahadeo, Nikita S. D.
Gurry, Céline
Maurer-Stroh, Sebastian
Naidoo, Dhamari
von Eije, Karin J
Perkins, Mark D.
van Kerkhove, Maria
Hill, Sarah C.
Sabino, Ester C.
Pybus, Oliver G.
Dye, Christopher
Bhatt, Samir
Flaxman, Seth
Suchard5, Marc A.
Grubaugh‡, Nathan D.
Baele, Guy
Faria, Nuno
Semenova, Elizaveta
Dudas, Gytis
Hassler, Gabriel W.
Kalinich, Chaney C.
Kraemer, Moritz U.G.
Ho, Joses
Tegally, Houriiyah
Githinji, George
Agoti, Charles N.
Matkin, Lucy E.
Whittaker, Charles
Howden, Benjamin P.
Sintchenko, Vitali
Zuckerman, Neta S.
Mor, Orna
Blankenship, Heather M.
Oliveira, Tulio de
Lyn, Raymond T. P
Siqueira, Marilda Agudo Mendonça Teixeira de
Resende, Paola Cristina
Vasconcelos, Ana Tereza R.
Spilki, Fernando R.
Aguiar, Renato Santana
Alexiev, Ivailo
Ivanov, Ivan N.
Philipova, Ivva
Carrington, Christine V. F.
Sahadeo, Nikita S. D.
Gurry, Céline
Maurer-Stroh, Sebastian
Naidoo, Dhamari
von Eije, Karin J
Perkins, Mark D.
van Kerkhove, Maria
Hill, Sarah C.
Sabino, Ester C.
Pybus, Oliver G.
Dye, Christopher
Bhatt, Samir
Flaxman, Seth
Suchard5, Marc A.
Grubaugh‡, Nathan D.
Baele, Guy
Faria, Nuno
Affilliation
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA / Instituto Todos pela Saúde, São Paulo, SP, Brasil.
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA / Department of Mathematics, Imperial College London, London, UK.
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA / Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles. Los Angeles, California, USA;
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA / Yale School of Medicine, Yale University, New Haven, Connecticut, USA.
Department of Zoology, University of Oxford, Oxford, United Kingdom.
GISAID Global Data Science Initiative. Munich, Germany / Bioinformatics Institute & ID Labs, Agency for Science Technology and Research. Singapore, Singapore.
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa.
KEMRI-Wellcome Trust Research Programme, Kenya / Department of Biochemistry and Biotechnology, Pwani University. Kenya.
KEMRI-Wellcome Trust Research Programme, Kenya.
Department of Zoology, University of Oxford, Oxford, United Kingdom,
MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom / The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom.
Microbiological 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.
Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia / Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales 2145, Australia.
Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel.
Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel.
Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA.
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa / Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa / Department of Global Health, University of Washington, S 5 eattle, Washington, USA.
National Centre for Infectious Diseases, Singapore.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratório e do Sarampo. Rio de Janeiro, RJ, Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratório e do Sarampo. Rio de Janeiro, RJ, Brasil.
Laboratório Nacional de Computação Científica. Laboratório de Bioinformática. Petrópolis, RJ, Brasil.
Feevale Universidade, Instituto de Ciências da Saúde. Novo Hamburgo, RS, Brasil.
Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Laboratório de Biologia Integrativa. Belo Horizonte, MG, Brasil / Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, RJ, Brasil.
National Center of Infectious and Parasitic Diseases. Sofia, Bulgaria.
National Center of Infectious and Parasitic Diseases. Sofia, Bulgaria.
National Center of Infectious and Parasitic Diseases. Sofia, Bulgaria.
Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago.
Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago.
GISAID Global Data Science Initiative. Munich, Germany.
GISAID Global Data Science Initiative. Munich, Germany / Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore / National Centre for Infectious Diseases, Singapore.
Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India.
Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands / Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.
Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.
Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.
Royal Veterinary College, Hawkshead, United Kingdom.
Universidade de São Paulo. Faculdade de Medicina. Instituto de Medicina Tropical. São Paulo, SP, Brasil.
Department of Zoology, University of Oxford, Oxford, United Kingdom / Royal Veterinary College, Hawkshead, United Kindom.
Department of Zoology, University of Oxford, Oxford, United Kingdom.
MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom / The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom / Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
Department of Computer Science, University of Oxford, Oxford, United Kingdom.
Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA / Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA / Department of Human Genetics, David Geffen School of Medicine, University of California. Los Angeles, Los Angeles, California, USA.
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA / Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
Department of Zoology, University of Oxford, Oxford, United Kingdom / MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom / Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia / Universidade de São Paulo. Faculdade de Medicina. Instituto de Medicina Tropical. São Paulo, SP, Brasil.
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA / Department of Mathematics, Imperial College London, London, UK.
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA / Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles. Los Angeles, California, USA;
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA / Yale School of Medicine, Yale University, New Haven, Connecticut, USA.
Department of Zoology, University of Oxford, Oxford, United Kingdom.
GISAID Global Data Science Initiative. Munich, Germany / Bioinformatics Institute & ID Labs, Agency for Science Technology and Research. Singapore, Singapore.
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa.
KEMRI-Wellcome Trust Research Programme, Kenya / Department of Biochemistry and Biotechnology, Pwani University. Kenya.
KEMRI-Wellcome Trust Research Programme, Kenya.
Department of Zoology, University of Oxford, Oxford, United Kingdom,
MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom / The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom.
Microbiological 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.
Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia / Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales 2145, Australia.
Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel.
Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Israel.
Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA.
KwaZulu–Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa / Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa / Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa / Department of Global Health, University of Washington, S 5 eattle, Washington, USA.
National Centre for Infectious Diseases, Singapore.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratório e do Sarampo. Rio de Janeiro, RJ, Brasil.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Vírus Respiratório e do Sarampo. Rio de Janeiro, RJ, Brasil.
Laboratório Nacional de Computação Científica. Laboratório de Bioinformática. Petrópolis, RJ, Brasil.
Feevale Universidade, Instituto de Ciências da Saúde. Novo Hamburgo, RS, Brasil.
Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Laboratório de Biologia Integrativa. Belo Horizonte, MG, Brasil / Instituto D’Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, RJ, Brasil.
National Center of Infectious and Parasitic Diseases. Sofia, Bulgaria.
National Center of Infectious and Parasitic Diseases. Sofia, Bulgaria.
National Center of Infectious and Parasitic Diseases. Sofia, Bulgaria.
Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago.
Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago.
GISAID Global Data Science Initiative. Munich, Germany.
GISAID Global Data Science Initiative. Munich, Germany / Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore / National Centre for Infectious Diseases, Singapore.
Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India.
Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands / Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.
Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.
Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.
Royal Veterinary College, Hawkshead, United Kingdom.
Universidade de São Paulo. Faculdade de Medicina. Instituto de Medicina Tropical. São Paulo, SP, Brasil.
Department of Zoology, University of Oxford, Oxford, United Kingdom / Royal Veterinary College, Hawkshead, United Kindom.
Department of Zoology, University of Oxford, Oxford, United Kingdom.
MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom / The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, United Kingdom / Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
Department of Computer Science, University of Oxford, Oxford, United Kingdom.
Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA / Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California, USA / Department of Human Genetics, David Geffen School of Medicine, University of California. Los Angeles, Los Angeles, California, USA.
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA / Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
Department of Zoology, University of Oxford, Oxford, United Kingdom / MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom / Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia / Universidade de São Paulo. Faculdade de Medicina. Instituto de Medicina Tropical. São Paulo, SP, Brasil.
Abstract
Genomic sequencing provides critical information to track the evolution and spread of
SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health
responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic
surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on
variant detection in 167 countries. Most countries submit 5 genomes >21 days after sample
collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We
found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for
SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our
ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness.
Keywords in Portuguese
Vigilância genômicaSARS-CoV-2
Disparidades globais
Desigualdades socioeconômicas
Share