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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
general
Global disparities in SARS-CoV-2 genomic surveillance
Nature Communications, Volume 13, No. 1, Article 7003, Year 2022
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Description
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. © 2022, The Author(s).
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC9667854/bin/41467_2022_33713_MOESM1_ESM.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC9667854/bin/41467_2022_33713_MOESM2_ESM.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC9667854/bin/41467_2022_33713_MOESM3_ESM.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC9667854/bin/41467_2022_33713_MOESM4_ESM.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC9667854/bin/41467_2022_33713_MOESM5_ESM.pdf
Authors & Co-Authors
Brito, Anderson Fernandes
United States, New Haven
Yale University
Brazil, Sao Paulo
Instituto Todos Pela Saúde
Semenova, Elizaveta
United Kingdom, Oxford
University of Oxford
Dudas, Gytis
Lithuania, Vilnius
Vilniaus Universitetas
Hassler, Gabriel W.
United States, Los Angeles
University of California, Los Angeles
Kalinich, Chaney C.
United States, New Haven
Yale University
Kraemer, Moritz U.G.
United Kingdom, Oxford
University of Oxford
Ho, Joses Wei Hao
Germany, Munich
Gisaid Global Data Science Initiative Gisaid
Singapore, Singapore City
Agency for Science, Technology and Research, Singapore
Tegally, Houriiyah
South Africa, Durban
University of Kwazulu-natal
South Africa, Stellenbosch
Stellenbosch University
Githinji, George
Kenya, Nairobi
Wellcome Trust Research Laboratories Nairobi
Kenya, Kilifi
Pwani University
Agoti, Charles N.
Kenya, Nairobi
Wellcome Trust Research Laboratories Nairobi
Kenya, Kilifi
Pwani University
Matkin, Lucy E.
United Kingdom, Oxford
University of Oxford
Whittaker, Charles A.
United Kingdom, London
Medical Research Council
United Kingdom, London
Imperial College London
Kantardjiev, Todor V.
Bulgaria, Sofia
National Center of Infectious and Parasitic Diseases Bulgaria
Stoitsova, Savina O.
Bulgaria, Sofia
National Center of Infectious and Parasitic Diseases Bulgaria
Leong, Lex
Australia, Melbourne
University of Melbourne
Kennedy, Karina J.
Australia, Melbourne
University of Melbourne
de Ligt, Joep
Australia, Melbourne
University of Melbourne
Rawlinson, William D.
Australia, Melbourne
University of Melbourne
van Hal, Sebastiaan J.M.
Australia, Melbourne
University of Melbourne
Williamson, Deborah A.
Australia, Melbourne
University of Melbourne
Brown-Jordan, Arianne
Trinidad and Tobago, St Augustine
The University of the West Indies, St. Augustine Campus
Oura, Christopher A.L.
Trinidad and Tobago, St Augustine
The University of the West Indies, St. Augustine Campus
Pybus, Oliver George
United Kingdom, Oxford
University of Oxford
United Kingdom, London
Royal Veterinary College University of London
Faria, Nuno R.
United Kingdom, Oxford
University of Oxford
United Kingdom, London
Medical Research Council
United Kingdom, London
Imperial College London
Brazil, Sao Paulo
Universidade de São Paulo
Stegger, Marc
Denmark, Aalborg
Aalborg University
Albertsen, Mads
Denmark, Copenhagen
Statens Serum Institut
Fomsgaard, Anders
Denmark, Copenhagen
Statens Serum Institut
Rasmussen, Morten Arendt Rendt
Denmark, Copenhagen
Statens Serum Institut
Khouri, Ricardo
Brazil, Rio de Janeiro
Fundacao Oswaldo Cruz
Naveca, F. G.
Brazil, Rio de Janeiro
Fundacao Oswaldo Cruz
Gräf, Tiago
Brazil, Rio de Janeiro
Fundacao Oswaldo Cruz
Miyajima, F.
Brazil, Rio de Janeiro
Fundacao Oswaldo Cruz
Wallau, G. L.
Brazil, Rio de Janeiro
Fundacao Oswaldo Cruz
Khare, Shruti
Germany, Munich
Gisaid Global Data Science Initiative Gisaid
Freitas, Lucas A.
Germany, Munich
Gisaid Global Data Science Initiative Gisaid
Bach, Gunter
Germany, Munich
Gisaid Global Data Science Initiative Gisaid
Diallo, Amadou Bailo
Germany, Munich
Gisaid Global Data Science Initiative Gisaid
Lee, Raphael Tze Chuen
Germany, Munich
Gisaid Global Data Science Initiative Gisaid
Yeo, Winston
Germany, Munich
Gisaid Global Data Science Initiative Gisaid
Wilkinson, Eduan
South Africa, Durban
University of Kwazulu-natal
Iranzadeh, Arash
South Africa, Durban
University of Kwazulu-natal
Giandhari, Jennifer
South Africa, Durban
University of Kwazulu-natal
Doolabh, Deelan
South Africa, Durban
University of Kwazulu-natal
Pillay, Sureshnee
South Africa, Durban
University of Kwazulu-natal
Ramphal, Upasana
South Africa, Durban
University of Kwazulu-natal
San, James Emmanuel
South Africa, Durban
University of Kwazulu-natal
Msomi, Nokukhanya
South Africa, Durban
University of Kwazulu-natal
Mlisana, Koleka P.
South Africa, Durban
University of Kwazulu-natal
von Gottberg, Anne M.
South Africa, Durban
University of Kwazulu-natal
Walaza, Sibongile
South Africa, Durban
University of Kwazulu-natal
Ismail, Arshad
South Africa, Durban
University of Kwazulu-natal
Mohale, Thabo
South Africa, Durban
University of Kwazulu-natal
Engelbrecht, Susan
South Africa, Durban
University of Kwazulu-natal
Van Zyl, Gert Uves
South Africa, Durban
University of Kwazulu-natal
Preiser, Wolfgang
South Africa, Durban
University of Kwazulu-natal
Sigal, Alex
South Africa, Durban
University of Kwazulu-natal
Hardie, Diana Ruth
South Africa, Durban
University of Kwazulu-natal
Marais, Gert J.K.
South Africa, Durban
University of Kwazulu-natal
Hsiao, Marvin
South Africa, Durban
University of Kwazulu-natal
Korsman, Stephen N.J.
South Africa, Durban
University of Kwazulu-natal
Davies, Mary Ann
South Africa, Durban
University of Kwazulu-natal
Tyers, Lynn
South Africa, Durban
University of Kwazulu-natal
Mudau, Innocent
South Africa, Durban
University of Kwazulu-natal
York, Denis F.
South Africa, Durban
University of Kwazulu-natal
Maslo, Caroline
South Africa, Durban
University of Kwazulu-natal
Goedhals, Dominique
South Africa, Durban
University of Kwazulu-natal
Abrahams, Shareef
South Africa, Durban
University of Kwazulu-natal
Laguda-Akingba, Oluwakemi
South Africa, Durban
University of Kwazulu-natal
Alisoltani-Dehkordi, Arghavan
South Africa, Durban
University of Kwazulu-natal
Godzik, Adam
South Africa, Durban
University of Kwazulu-natal
Wibmer, Constantinos Kurt
South Africa, Durban
University of Kwazulu-natal
Martin, Darren Patrick
South Africa, Durban
University of Kwazulu-natal
Lessells, Richard John
South Africa, Durban
University of Kwazulu-natal
Bhiman, Jinal N.
South Africa, Durban
University of Kwazulu-natal
Williamson, Carolyn
South Africa, Durban
University of Kwazulu-natal
De Oliveira, Tulio
South Africa, Durban
University of Kwazulu-natal
South Africa, Stellenbosch
Stellenbosch University
South Africa, Congella
Centre for the Aids Programme of Research in South Africa
United States, Seattle
University of Washington
Nadeau, Sarah Ann
Switzerland, Zurich
Eth Zürich
Beisel, Christian
Switzerland, Zurich
Eth Zürich
Aquino, Catharine
Switzerland, Zurich
Eth Zürich
Opitz, Lennart
Switzerland, Zurich
Eth Zürich
Patrignani, Andrea
Switzerland, Zurich
Eth Zürich
Schlapbach, Ralph
Switzerland, Zurich
Eth Zürich
Dermitzakis, Emmanouil Theophilos
Unknown Affiliation
Xenarios, Ioannis
Unknown Affiliation
Stadler, Tanja
Switzerland, Zurich
Eth Zürich
Howden, Benjamin P.
Australia, Melbourne
University of Melbourne
Sintchenko, Vitali G.
Australia, Sydney
The University of Sydney
Australia, Parramatta
Nsw Health Pathology
Zuckerman, Neta S.
Israel, Tel Hashomer Tel Aviv
Chaim Sheba Medical Center Israel
Mor, Orna
Israel, Tel Hashomer Tel Aviv
Chaim Sheba Medical Center Israel
Blankenship, Heather M.
United States, Lansing
Bureau of Laboratories
Lin, Raymond Tzer Pin
Singapore, Singapore City
National Centre for Infectious Diseases
Siqueira, Marilda Mendonça
Brazil, Rio de Janeiro
Fundacao Oswaldo Cruz
Resende, Paola Cristina
Brazil, Rio de Janeiro
Fundacao Oswaldo Cruz
Vasconcelos, Ana Tereza Ribeiro De
Brazil, Petropolis
Laboratorio Nacional de Computacao Cientifica, Petropolis
Spilki, Fernando Rosado
Brazil, Novo Hamburgo
Universidade Feevale
Aguiar, Renato Santana De
Brazil, Belo Horizonte
Universidade Federal de Minas Gerais
Brazil, Rio de Janeiro
Instituto D'or de Pesquisa e Ensino
Alexiev, Ivailo
Bulgaria, Sofia
National Center of Infectious and Parasitic Diseases Bulgaria
Ivanov, Ivan Nikolaev
Bulgaria, Sofia
National Center of Infectious and Parasitic Diseases Bulgaria
Philipova, Ivva
Bulgaria, Sofia
National Center of Infectious and Parasitic Diseases Bulgaria
Carrington, Christine V.F.
Trinidad and Tobago, St Augustine
The University of the West Indies, St. Augustine Campus
Sahadeo, Nikita S.D.
Trinidad and Tobago, St Augustine
The University of the West Indies, St. Augustine Campus
Branda, Ben
Germany, Munich
Gisaid Global Data Science Initiative Gisaid
Gurry, Celine
Germany, Munich
Gisaid Global Data Science Initiative Gisaid
Maurer-Stroh, Sebastian
Germany, Munich
Gisaid Global Data Science Initiative Gisaid
Singapore, Singapore City
Agency for Science, Technology and Research, Singapore
Singapore, Singapore City
National Centre for Infectious Diseases
Naidoo, Dhamari
Switzerland, Geneva
Organisation Mondiale de la Santé
von Eije, Karin Jasmijn
Netherlands, Groningen
Rijksuniversiteit Groningen
Switzerland, Geneva
Organisation Mondiale de la Santé
Perkins, Mark D.
Switzerland, Geneva
Organisation Mondiale de la Santé
van Kerkhove, Maria D.
Switzerland, Geneva
Organisation Mondiale de la Santé
Hill, Sarah Catherine
United Kingdom, London
Royal Veterinary College University of London
Sabino, Ester Cerdeira
Brazil, Sao Paulo
Instituto Todos Pela Saúde
Brazil, Sao Paulo
Universidade de São Paulo
Dye, Christopher
United Kingdom, Oxford
University of Oxford
Bhatt, S. M.
United Kingdom, London
Medical Research Council
United Kingdom, London
Imperial College London
Denmark, Copenhagen
Københavns Universitet
Flaxman, Seth R.
United Kingdom, Oxford
University of Oxford
Suchard, Marc A.
United States, Los Angeles
University of California, Los Angeles
Grubaugh, Nathan D.
United States, New Haven
Yale University
Baele, Guy
Belgium, Leuven
Rega Institute for Medical Research
Statistics
Citations: 53
Authors: 116
Affiliations: 43
Identifiers
Doi:
10.1038/s41467-022-33713-y
ISSN:
20411723
Research Areas
Covid