Global disparities in SARS-CoV-2 genomic surveillance

Anderson F. Brito (), Elizaveta Semenova, Gytis Dudas, Gabriel W. Hassler, Chaney C. Kalinich, Moritz U. G. Kraemer, Joses Ho, Houriiyah Tegally, George Githinji, Charles N. Agoti, Lucy E. Matkin, Charles Whittaker, Benjamin P. Howden, Vitali Sintchenko, Neta S. Zuckerman, Orna Mor, Heather M. Blankenship, Tulio Oliveira, Raymond T. P. Lin, Marilda Mendonça Siqueira, Paola Cristina Resende, Ana Tereza R. Vasconcelos, Fernando R. Spilki, Renato Santana Aguiar, Ivailo Alexiev, Ivan N. Ivanov, Ivva Philipova, Christine V. F. Carrington, Nikita S. D. Sahadeo, Ben Branda, Céline Gurry, Sebastian Maurer-Stroh, Dhamari Naidoo, Karin J. Eije, Mark D. Perkins, Maria Kerkhove, Sarah C. Hill, Ester C. Sabino, Oliver G. Pybus, Christopher Dye, Samir Bhatt, Seth Flaxman, Marc A. Suchard, Nathan D. Grubaugh, Guy Baele and Nuno R. Faria ()
Additional contact information
Anderson F. Brito: Yale School of Public Health
Elizaveta Semenova: University of Oxford
Gytis Dudas: Vilnius University
Gabriel W. Hassler: University of California Los Angeles
Chaney C. Kalinich: Yale School of Public Health
Moritz U. G. Kraemer: University of Oxford
Joses Ho: GISAID Global Data Science Initiative
Houriiyah Tegally: University of KwaZulu-Natal
George Githinji: KEMRI-Wellcome Trust Research Programme
Charles N. Agoti: KEMRI-Wellcome Trust Research Programme
Lucy E. Matkin: University of Oxford
Charles Whittaker: Imperial College London
Benjamin P. Howden: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Vitali Sintchenko: The University of Sydney
Neta S. Zuckerman: Israel Ministry of Health, Sheba Medical Center
Orna Mor: Israel Ministry of Health, Sheba Medical Center
Heather M. Blankenship: Bureau of Laboratories
Tulio Oliveira: University of KwaZulu-Natal
Raymond T. P. Lin: National Centre for Infectious Diseases
Marilda Mendonça Siqueira: Instituto Oswaldo Cruz, FIOCRUZ
Paola Cristina Resende: Instituto Oswaldo Cruz, FIOCRUZ
Ana Tereza R. Vasconcelos: Laboratório Nacional de Computação Científica
Fernando R. Spilki: Feevale University, Institute of Health Sciences
Renato Santana Aguiar: Universidade Federal de Minas Gerais
Ivailo Alexiev: National Center of Infectious and Parasitic Diseases
Ivan N. Ivanov: National Center of Infectious and Parasitic Diseases
Ivva Philipova: National Center of Infectious and Parasitic Diseases
Christine V. F. Carrington: The University of the West Indies
Nikita S. D. Sahadeo: The University of the West Indies
Ben Branda: GISAID Global Data Science Initiative
Céline Gurry: GISAID Global Data Science Initiative
Sebastian Maurer-Stroh: GISAID Global Data Science Initiative
Dhamari Naidoo: World Health Organization Regional Office for South-East Asia
Karin J. Eije: University of Groningen, University Medical Center Groningen
Mark D. Perkins: World Health Organization
Maria Kerkhove: World Health Organization
Sarah C. Hill: Royal Veterinary College
Ester C. Sabino: Instituto Todos pela Saúde
Oliver G. Pybus: University of Oxford
Christopher Dye: University of Oxford
Samir Bhatt: Imperial College London
Seth Flaxman: University of Oxford
Marc A. Suchard: University of California Los Angeles
Nathan D. Grubaugh: Yale School of Public Health
Guy Baele: Rega Institute, KU Leuven
Nuno R. Faria: University of Oxford

Nature Communications, 2022, vol. 13, issue 1, 1-13

Abstract: 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

Date: 2022
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DOI: 10.1038/s41467-022-33713-y

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