. 2022 Nov 16;13(1):7003.

doi: 10.1038/s41467-022-33713-y.

Global disparities in SARS-CoV-2 genomic surveillance

Anderson F Brito^#^{1

2}, Elizaveta Semenova^#³, Gytis Dudas^#⁴, Gabriel W Hassler⁵, Chaney C Kalinich^{6

7}, Moritz U G Kraemer⁸, Joses Ho^{9

10}, Houriiyah Tegally^{11

12}, George Githinji^{13

14}, Charles N Agoti^{13

15}, Lucy E Matkin⁸, Charles Whittaker^{16

17}; 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 Howden¹⁸, Vitali Sintchenko^{19

20}, Neta S Zuckerman²¹, Orna Mor²¹, Heather M Blankenship²², Tulio de Oliveira^{11

12

23

24}, Raymond T P Lin²⁵, Marilda Mendonça Siqueira²⁶, Paola Cristina Resende²⁶, Ana Tereza R Vasconcelos²⁷, Fernando R Spilki²⁸, Renato Santana Aguiar^{29

30}, Ivailo Alexiev³¹, Ivan N Ivanov³¹, Ivva Philipova³¹, Christine V F Carrington³², Nikita S D Sahadeo³², Ben Branda⁹, Céline Gurry⁹, Sebastian Maurer-Stroh^{9

10

25}, Dhamari Naidoo³³, Karin J von Eije^{34

35}, Mark D Perkins³⁵, Maria van Kerkhove³⁵, Sarah C Hill³⁶, Ester C Sabino^{37

38}, Oliver G Pybus^{8

36}, Christopher Dye⁸, Samir Bhatt^{16

17

39}, Seth Flaxman³, Marc A Suchard^{5

40

41}, Nathan D Grubaugh^{6

42}, Guy Baele⁴³, Nuno R Faria^{44

45

46

47}

Collaborators, Affiliations

Collaborators

Todor Kantardjiev, Nelly Korsun, Savina Stoitsova, Reneta Dimitrova, Ivelina Trifonova, Veselin Dobrinov, Lubomira Grigorova, Ivan Stoykov, Iliana Grigorova, Anna Gancheva, Amy Jennison, Lex Leong, David Speers, Rob Baird, Louise Cooley, Karina Kennedy, Joep de Ligt, William Rawlinson, Sebastiaan van Hal, Deborah Williamson, Risha Singh, SueMin Nathaniel-Girdharrie, Lisa Edghill, Lisa Indar, Joy St John, Gabriel Gonzalez-Escobar, Vernie Ramkisoon, Arianne Brown-Jordan, Anushka Ramjag, Nicholas Mohammed, Jerome E Foster, Irad Potter, Sharra Greenaway-Duberry, Kenneth George, Sharon Belmar-George, John Lee, Jacqueline Bisasor-McKenzie, Nadia Astwood, Rhonda Sealey-Thomas, Hazel Laws, Narine Singh, Ayoola Oyinloye, Pearl McMillan, Avery Hinds, Naresh Nandram, Roshan Parasram, Zobida Khan-Mohammed, Shawn Charles, Aisha Andrewin, David Johnson, Simone Keizer-Beache, Chris Oura, Oliver G Pybus, Nuno R Faria, Marc Stegger, Mads Albertsen, Anders Fomsgaard, Morten Rasmussen, Ricardo Khouri, Felipe Naveca, Tiago Graf, Fábio Miyajima, Gabriel Wallau, Fernando Motta, Shruti Khare, Lucas Freitas, Constanza Schiavina, Gunter Bach, Mark B Schultz, Yi Hong Chew, Meera Makheja, Priscila Born, Gabriela Calegario, Sofia Romano, Juan Finello, Amadou Diallo, Raphael T C Lee, Ya Ni Xu, Winston Yeo, Suma Tiruvayipati, Shilpa Yadahalli, Eduan Wilkinson, Arash Iranzadeh, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Upasana Ramphal, James E San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Arshad Ismail, Thabo Mohale, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Alex Sigal, Diana Hardie, Gert Marais, Marvin Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos K Wibmer, Darren Martin, Richard J Lessells, Jinal N Bhiman, Carolyn Williamson, Tulio de Oliveira, Chaoran Chen, Sarah Nadeau, Louis du Plessis, Christiane Beckmann, Maurice Redondo, Olivier Kobel, Christoph Noppen, Sophie Seidel, Noemie Santamaria de Souza, Niko Beerenwinkel, Ivan Topolsky, Philipp Jablonski, Lara Fuhrmann, David Dreifuss, Katharina Jahn, Pedro Ferreira, Susana Posada-Céspedes, Christian Beisel, Rebecca Denes, Mirjam Feldkamp, Ina Nissen, Natascha Santacroce, Elodie Burcklen, Catharine Aquino, Andreia Cabral de Gouvea, Maria Domenica Moccia, Simon Grüter, Timothy Sykes, Lennart Opitz, Griffin White, Laura Neff, Doris Popovic, Andrea Patrignani, Jay Tracy, Ralph Schlapbach, Emmanouil Dermitzakis, Keith Harshman, Ioannis Xenarios, Henri Pegeot, Lorenzo Cerutti, Deborah Penet, Tanja Stadler

Affiliations

¹ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA. andersonfbrito@gmail.com.
² Instituto Todos pela Saúde, São Paulo, SP, Brazil. andersonfbrito@gmail.com.
³ Department of Computer Science, University of Oxford, Oxford, UK.
⁴ Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
⁵ Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
⁶ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
⁷ Yale School of Medicine, Yale University, New Haven, CT, USA.
⁸ Department of Biology, University of Oxford, Oxford, UK.
⁹ GISAID Global Data Science Initiative, Munich, Germany.
¹⁰ Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore.
¹¹ KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
¹² Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
¹³ KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
¹⁴ Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya.
¹⁵ School of Health and Human Sciences, Pwani University, Kilifi, Kenya.
¹⁶ MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
¹⁷ The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.
¹⁸ 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.
¹⁹ Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.
²⁰ Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia.
²¹ Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel.
²² Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, USA.
²³ Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
²⁴ Department of Global Health, University of Washington, Seattle, WA, USA.
²⁵ National Centre for Infectious Diseases, Singapore, Singapore.
²⁶ Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
²⁷ Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil.
²⁸ Feevale University, Institute of Health Sciences, Novo Hamburgo, RS, Brazil.
²⁹ Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
³⁰ Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil.
³¹ National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria.
³² Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago.
³³ Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India.
³⁴ Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
³⁵ Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.
³⁶ Royal Veterinary College, Hawkshead, UK.
³⁷ Instituto Todos pela Saúde, São Paulo, SP, Brazil.
³⁸ Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
³⁹ Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
⁴⁰ Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA.
⁴¹ Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
⁴² Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
⁴³ Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
⁴⁴ Department of Biology, University of Oxford, Oxford, UK. nfaria@ic.ac.uk.
⁴⁵ MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK. nfaria@ic.ac.uk.
⁴⁶ The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK. nfaria@ic.ac.uk.
⁴⁷ Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil. nfaria@ic.ac.uk.

^# Contributed equally.

PMID: 36385137
PMCID: PMC9667854
DOI: 10.1038/s41467-022-33713-y

Free PMC article

Global disparities in SARS-CoV-2 genomic surveillance

Anderson F Brito et al. Nat Commun. 2022.

Free PMC article

. 2022 Nov 16;13(1):7003.

doi: 10.1038/s41467-022-33713-y.

Authors

Collaborators

Todor Kantardjiev, Nelly Korsun, Savina Stoitsova, Reneta Dimitrova, Ivelina Trifonova, Veselin Dobrinov, Lubomira Grigorova, Ivan Stoykov, Iliana Grigorova, Anna Gancheva, Amy Jennison, Lex Leong, David Speers, Rob Baird, Louise Cooley, Karina Kennedy, Joep de Ligt, William Rawlinson, Sebastiaan van Hal, Deborah Williamson, Risha Singh, SueMin Nathaniel-Girdharrie, Lisa Edghill, Lisa Indar, Joy St John, Gabriel Gonzalez-Escobar, Vernie Ramkisoon, Arianne Brown-Jordan, Anushka Ramjag, Nicholas Mohammed, Jerome E Foster, Irad Potter, Sharra Greenaway-Duberry, Kenneth George, Sharon Belmar-George, John Lee, Jacqueline Bisasor-McKenzie, Nadia Astwood, Rhonda Sealey-Thomas, Hazel Laws, Narine Singh, Ayoola Oyinloye, Pearl McMillan, Avery Hinds, Naresh Nandram, Roshan Parasram, Zobida Khan-Mohammed, Shawn Charles, Aisha Andrewin, David Johnson, Simone Keizer-Beache, Chris Oura, Oliver G Pybus, Nuno R Faria, Marc Stegger, Mads Albertsen, Anders Fomsgaard, Morten Rasmussen, Ricardo Khouri, Felipe Naveca, Tiago Graf, Fábio Miyajima, Gabriel Wallau, Fernando Motta, Shruti Khare, Lucas Freitas, Constanza Schiavina, Gunter Bach, Mark B Schultz, Yi Hong Chew, Meera Makheja, Priscila Born, Gabriela Calegario, Sofia Romano, Juan Finello, Amadou Diallo, Raphael T C Lee, Ya Ni Xu, Winston Yeo, Suma Tiruvayipati, Shilpa Yadahalli, Eduan Wilkinson, Arash Iranzadeh, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Upasana Ramphal, James E San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Arshad Ismail, Thabo Mohale, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Alex Sigal, Diana Hardie, Gert Marais, Marvin Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos K Wibmer, Darren Martin, Richard J Lessells, Jinal N Bhiman, Carolyn Williamson, Tulio de Oliveira, Chaoran Chen, Sarah Nadeau, Louis du Plessis, Christiane Beckmann, Maurice Redondo, Olivier Kobel, Christoph Noppen, Sophie Seidel, Noemie Santamaria de Souza, Niko Beerenwinkel, Ivan Topolsky, Philipp Jablonski, Lara Fuhrmann, David Dreifuss, Katharina Jahn, Pedro Ferreira, Susana Posada-Céspedes, Christian Beisel, Rebecca Denes, Mirjam Feldkamp, Ina Nissen, Natascha Santacroce, Elodie Burcklen, Catharine Aquino, Andreia Cabral de Gouvea, Maria Domenica Moccia, Simon Grüter, Timothy Sykes, Lennart Opitz, Griffin White, Laura Neff, Doris Popovic, Andrea Patrignani, Jay Tracy, Ralph Schlapbach, Emmanouil Dermitzakis, Keith Harshman, Ioannis Xenarios, Henri Pegeot, Lorenzo Cerutti, Deborah Penet, Tanja Stadler

Affiliations

¹ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA. andersonfbrito@gmail.com.
² Instituto Todos pela Saúde, São Paulo, SP, Brazil. andersonfbrito@gmail.com.
³ Department of Computer Science, University of Oxford, Oxford, UK.
⁴ Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
⁵ Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
⁶ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
⁷ Yale School of Medicine, Yale University, New Haven, CT, USA.
⁸ Department of Biology, University of Oxford, Oxford, UK.
⁹ GISAID Global Data Science Initiative, Munich, Germany.
¹⁰ Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore.
¹¹ KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
¹² Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
¹³ KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
¹⁴ Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya.
¹⁵ School of Health and Human Sciences, Pwani University, Kilifi, Kenya.
¹⁶ MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.
¹⁷ The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.
¹⁸ 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.
¹⁹ Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.
²⁰ Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia.
²¹ Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel.
²² Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, MI, USA.
²³ Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa.
²⁴ Department of Global Health, University of Washington, Seattle, WA, USA.
²⁵ National Centre for Infectious Diseases, Singapore, Singapore.
²⁶ Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
²⁷ Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil.
²⁸ Feevale University, Institute of Health Sciences, Novo Hamburgo, RS, Brazil.
²⁹ Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
³⁰ Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil.
³¹ National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria.
³² Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago.
³³ Health Emergencies Programme, World Health Organization Regional Office for South-East Asia, New Delhi, India.
³⁴ Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
³⁵ Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization, Geneva, Switzerland.
³⁶ Royal Veterinary College, Hawkshead, UK.
³⁷ Instituto Todos pela Saúde, São Paulo, SP, Brazil.
³⁸ Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
³⁹ Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
⁴⁰ Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA.
⁴¹ Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
⁴² Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
⁴³ Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
⁴⁴ Department of Biology, University of Oxford, Oxford, UK. nfaria@ic.ac.uk.
⁴⁵ MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK. nfaria@ic.ac.uk.
⁴⁶ The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK. nfaria@ic.ac.uk.
⁴⁷ Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil. nfaria@ic.ac.uk.

^# Contributed equally.

PMID: 36385137
PMCID: PMC9667854
DOI: 10.1038/s41467-022-33713-y

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.

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Update of

Global disparities in SARS-CoV-2 genomic surveillance.
Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C; Danish Covid-19 Genome Consortium; COVID-19 Impact Project; Network for Genomic Surveillance in South Africa (NGS-SA); GISAID core curation team; Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Brito AF, et al. medRxiv [Preprint]. 2021 Dec 9:2021.08.21.21262393. doi: 10.1101/2021.08.21.21262393. medRxiv. 2021. Update in: Nat Commun. 2022 Nov 16;13(1):7003. doi: 10.1038/s41467-022-33713-y. PMID: 34462754 Free PMC article. Updated. Preprint.

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Global disparities in SARS-CoV-2 genomic surveillance

Collaborators

Affiliations

Global disparities in SARS-CoV-2 genomic surveillance

Authors

Collaborators

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Abstract

Update of

References

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