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; Bulgarian SARS-CoV-2 sequencing group; Communicable Diseases Genomics Network (Australia and New Zealand); Lex Leong; Rob Baird; 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. Howden; Vitali Sintchenko; Neta S. Zuckerman; Orna Mor; Heather M. Blankenship; Tulio de 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. von Eije; Mark D. Perkins; Maria van Kerkhove; Sarah C. Hill; Ester C. Sabino; Oliver G. Pybus; Christopher Dye; Samir Bhatt; Seth Flaxman; Marc A. Suchard; Nathan D. Grubaugh; Guy Baele; Nuno R. Faria

doi:10.1038/s41467-022-33713-y

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, Bulgarian SARS-CoV-2 sequencing group, Communicable Diseases Genomics Network (Australia and New Zealand), Lex Leong, Rob Baird, COVID-19 Impact Project, Danish Covid-19 Genome Consortium, Fiocruz COVID-19 Genomic Surveillance Network, GISAID core curation teamNetwork for Genomic Surveillance in South Africa (NGS-SA), Swiss SARS-CoV-2 Sequencing Consortium, Benjamin P. Howden, Vitali Sintchenko, Neta S. Zuckerman, Orna Mor, Heather M. Blankenship, Tulio de 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. von Eije, Mark D. Perkins, Maria van Kerkhove, Sarah C. Hill, Ester C. Sabino, Oliver G. Pybus, Christopher Dye, Samir Bhatt, Seth Flaxman, Marc A. Suchard, Nathan D. Grubaugh, Guy Baele, Nuno R. Faria

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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.

Original language	English
Article number	7003
Number of pages	13
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-33713-y
Publication status	Published - Dec 2022
Externally published	Yes

Keywords

COVID-19 pandemic
Global disparities
SARS-CoV-2 genomic surveillance

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41467-022-33713-yLicence: CC BY

Final published versionFinal published version, 4.16 MBLicence: CC BY

Cite this

Brito, A. F., Semenova, E., Dudas, G., Hassler, G. W., Kalinich, C. C., Kraemer, M. U. G., Ho, J., Tegally, H., Githinji, G., Agoti, C. N., Matkin, L. E., Whittaker, C., Bulgarian SARS-CoV-2 sequencing group, Communicable Diseases Genomics Network (Australia and New Zealand), Leong, L., Baird, R., COVID-19 Impact Project, Danish Covid-19 Genome Consortium, Fiocruz COVID-19 Genomic Surveillance Network, ... Faria, N. R. (2022). Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications, 13(1), Article 7003. https://doi.org/10.1038/s41467-022-33713-y

@article{badeb5a46c274f4791e7b23a1d8ced26,

title = "Global disparities in SARS-CoV-2 genomic surveillance",

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.",

keywords = "COVID-19 pandemic, Global disparities, SARS-CoV-2 genomic surveillance",

author = "Brito, {Anderson F.} and Elizaveta Semenova and Gytis Dudas and Hassler, {Gabriel W.} and Kalinich, {Chaney C.} and Kraemer, {Moritz U.G.} and Joses Ho and Houriiyah Tegally and George Githinji and Agoti, {Charles N.} and Matkin, {Lucy E.} and Charles Whittaker and {Bulgarian SARS-CoV-2 sequencing group} and Todor Kantardjiev and Nelly Korsun and Savina Stoitsova and Reneta Dimitrova and Ivelina Trifonova and Veselin Dobrinov and Lubomira Grigorova and Ivan Stoykov and Iliana Grigorova and Anna Gancheva and {Communicable Diseases Genomics Network (Australia and New Zealand)} and Amy Jennison and Lex Leong and David Speers and Rob Baird and Louise Cooley and Karina Kennedy and {de Ligt}, Joep and William Rawlinson and {van Hal}, Sebastiaan and Deborah Williamson and {COVID-19 Impact Project} and Risha Singh and SueMin Nathaniel-Girdharrie and Lisa Edghill and Lisa Indar and {St. John}, Joy and Gabriel Gonzalez-Escobar and Vernie Ramkisoon and Arianne Brown-Jordan and Anushka Ramjag and Nicholas Mohammed and Foster, {Jerome E.} and Irad Potter and Sharra Greenaway-Duberry and Kenneth George and Sharon Belmar-George and John Lee and Jacqueline Bisasor-McKenzie and Nadia Astwood and Rhonda Sealey-Thomas and Hazel Laws and Narine Singh and Ayoola Oyinloye and Pearl McMillan and Avery Hinds and Naresh Nandram and Roshan Parasram and Zobida Khan-Mohammed and Shawn Charles and Aisha Andrewin and David Johnson and Simone Keizer-Beache and Chris Oura and Pybus, {Oliver G.} and Faria, {Nuno R.} and {Danish Covid-19 Genome Consortium} and Marc Stegger and Mads Albertsen and Anders Fomsgaard and Morten Rasmussen and {Fiocruz COVID-19 Genomic Surveillance Network} and Ricardo Khouri and Felipe Naveca and Tiago Graf and F{\'a}bio Miyajima and Gabriel Wallau and Fernando Motta and {GISAID core curation team} and Shruti Khare and Lucas Freitas and Constanza Schiavina and Gunter Bach and Schultz, {Mark B.} and Chew, {Yi Hong} and Meera Makheja and Priscila Born and Gabriela Calegario and Sofia Romano and Juan Finello and Amadou Diallo and Lee, {Raphael T.C.} and Xu, {Ya Ni} and Winston Yeo and Suma Tiruvayipati and Shilpa Yadahalli and {Network for Genomic Surveillance in South Africa (NGS-SA)} and Eduan Wilkinson and Arash Iranzadeh and Jennifer Giandhari and Deelan Doolabh and Sureshnee Pillay and Upasana Ramphal and San, {James E.} and Nokukhanya Msomi and Koleka Mlisana and {von Gottberg}, Anne and Sibongile Walaza and Arshad Ismail and Thabo Mohale and Susan Engelbrecht and {Van Zyl}, Gert and Wolfgang Preiser and Alex Sigal and Diana Hardie and Gert Marais and Marvin Hsiao and Stephen Korsman and Davies, {Mary Ann} and Lynn Tyers and Innocent Mudau and Denis York and Caroline Maslo and Dominique Goedhals and Shareef Abrahams and Oluwakemi Laguda-Akingba and Arghavan Alisoltani-Dehkordi and Adam Godzik and Wibmer, {Constantinos K.} and Darren Martin and Lessells, {Richard J.} and Bhiman, {Jinal N.} and Carolyn Williamson and {de Oliveira}, Tulio and {Swiss SARS-CoV-2 Sequencing Consortium} and Chaoran Chen and Sarah Nadeau and {du Plessis}, Louis and Christiane Beckmann and Maurice Redondo and Olivier Kobel and Christoph Noppen and Sophie Seidel and {de Souza}, {Noemie Santamaria} and Niko Beerenwinkel and Ivan Topolsky and Philipp Jablonski and Lara Fuhrmann and David Dreifuss and Katharina Jahn and Pedro Ferreira and Susana Posada-C{\'e}spedes and Christian Beisel and Rebecca Denes and Mirjam Feldkamp and Ina Nissen and Natascha Santacroce and Elodie Burcklen and Catharine Aquino and {de Gouvea}, {Andreia Cabral} and Moccia, {Maria Domenica} and Simon Gr{\"u}ter and Timothy Sykes and Lennart Opitz and Griffin White and Laura Neff and Doris Popovic and Andrea Patrignani and Jay Tracy and Ralph Schlapbach and Emmanouil Dermitzakis and Keith Harshman and Ioannis Xenarios and Henri Pegeot and Lorenzo Cerutti and Deborah Penet and Tanja Stadler and Howden, {Benjamin P.} and Vitali Sintchenko and Zuckerman, {Neta S.} and Orna Mor and Blankenship, {Heather M.} and {de Oliveira}, Tulio and Lin, {Raymond T.P.} and Siqueira, {Marilda Mendon{\c c}a} and Resende, {Paola Cristina} and Vasconcelos, {Ana Tereza R.} and Spilki, {Fernando R.} and Aguiar, {Renato Santana} and Ivailo Alexiev and Ivanov, {Ivan N.} and Ivva Philipova and Carrington, {Christine V.F.} and Sahadeo, {Nikita S.D.} and Ben Branda and C{\'e}line Gurry and Sebastian Maurer-Stroh and Dhamari Naidoo and {von Eije}, {Karin J.} and Perkins, {Mark D.} and {van Kerkhove}, Maria and Hill, {Sarah C.} and Sabino, {Ester C.} and Pybus, {Oliver G.} and Christopher Dye and Samir Bhatt and Seth Flaxman and Suchard, {Marc A.} and Grubaugh, {Nathan D.} and Guy Baele and Faria, {Nuno R.}",

year = "2022",

month = dec,

doi = "10.1038/s41467-022-33713-y",

language = "English",

volume = "13",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature",

number = "1",

}

Brito, AF, Semenova, E, Dudas, G, Hassler, GW, Kalinich, CC, Kraemer, MUG, Ho, J, Tegally, H, Githinji, G, Agoti, CN, Matkin, LE, Whittaker, C, Bulgarian SARS-CoV-2 sequencing group, Communicable Diseases Genomics Network (Australia and New Zealand), Leong, L, Baird, R, 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, 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, Branda, B, 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 2022, 'Global disparities in SARS-CoV-2 genomic surveillance', Nature Communications, vol. 13, no. 1, 7003. https://doi.org/10.1038/s41467-022-33713-y

TY - JOUR

T1 - Global disparities in SARS-CoV-2 genomic surveillance

AU - Brito, Anderson F.

AU - Semenova, Elizaveta

AU - Dudas, Gytis

AU - Hassler, Gabriel W.

AU - Kalinich, Chaney C.

AU - Kraemer, Moritz U.G.

AU - Ho, Joses

AU - Tegally, Houriiyah

AU - Githinji, George

AU - Agoti, Charles N.

AU - Matkin, Lucy E.

AU - Whittaker, Charles

AU - Bulgarian SARS-CoV-2 sequencing group

AU - Kantardjiev, Todor

AU - Korsun, Nelly

AU - Stoitsova, Savina

AU - Dimitrova, Reneta

AU - Trifonova, Ivelina

AU - Dobrinov, Veselin

AU - Grigorova, Lubomira

AU - Stoykov, Ivan

AU - Grigorova, Iliana

AU - Gancheva, Anna

AU - Communicable Diseases Genomics Network (Australia and New Zealand)

AU - Jennison, Amy

AU - Leong, Lex

AU - Speers, David

AU - Baird, Rob

AU - Cooley, Louise

AU - Kennedy, Karina

AU - de Ligt, Joep

AU - Rawlinson, William

AU - van Hal, Sebastiaan

AU - Williamson, Deborah

AU - COVID-19 Impact Project

AU - Singh, Risha

AU - Nathaniel-Girdharrie, SueMin

AU - Edghill, Lisa

AU - Indar, Lisa

AU - St. John, Joy

AU - Gonzalez-Escobar, Gabriel

AU - Ramkisoon, Vernie

AU - Brown-Jordan, Arianne

AU - Ramjag, Anushka

AU - Mohammed, Nicholas

AU - Foster, Jerome E.

AU - Potter, Irad

AU - Greenaway-Duberry, Sharra

AU - George, Kenneth

AU - Belmar-George, Sharon

AU - Lee, John

AU - Bisasor-McKenzie, Jacqueline

AU - Astwood, Nadia

AU - Sealey-Thomas, Rhonda

AU - Laws, Hazel

AU - Singh, Narine

AU - Oyinloye, Ayoola

AU - McMillan, Pearl

AU - Hinds, Avery

AU - Nandram, Naresh

AU - Parasram, Roshan

AU - Khan-Mohammed, Zobida

AU - Charles, Shawn

AU - Andrewin, Aisha

AU - Johnson, David

AU - Keizer-Beache, Simone

AU - Oura, Chris

AU - Pybus, Oliver G.

AU - Faria, Nuno R.

AU - Danish Covid-19 Genome Consortium

AU - Stegger, Marc

AU - Albertsen, Mads

AU - Fomsgaard, Anders

AU - Rasmussen, Morten

AU - Fiocruz COVID-19 Genomic Surveillance Network

AU - Khouri, Ricardo

AU - Naveca, Felipe

AU - Graf, Tiago

AU - Miyajima, Fábio

AU - Wallau, Gabriel

AU - Motta, Fernando

AU - GISAID core curation team

AU - Khare, Shruti

AU - Freitas, Lucas

AU - Schiavina, Constanza

AU - Bach, Gunter

AU - Schultz, Mark B.

AU - Chew, Yi Hong

AU - Makheja, Meera

AU - Born, Priscila

AU - Calegario, Gabriela

AU - Romano, Sofia

AU - Finello, Juan

AU - Diallo, Amadou

AU - Lee, Raphael T.C.

AU - Xu, Ya Ni

AU - Yeo, Winston

AU - Tiruvayipati, Suma

AU - Yadahalli, Shilpa

AU - Network for Genomic Surveillance in South Africa (NGS-SA)

AU - Wilkinson, Eduan

AU - Iranzadeh, Arash

AU - Giandhari, Jennifer

AU - Doolabh, Deelan

AU - Pillay, Sureshnee

AU - Ramphal, Upasana

AU - San, James E.

AU - Msomi, Nokukhanya

AU - Mlisana, Koleka

AU - von Gottberg, Anne

AU - Walaza, Sibongile

AU - Ismail, Arshad

AU - Mohale, Thabo

AU - Engelbrecht, Susan

AU - Van Zyl, Gert

AU - Preiser, Wolfgang

AU - Sigal, Alex

AU - Hardie, Diana

AU - Marais, Gert

AU - Hsiao, Marvin

AU - Korsman, Stephen

AU - Davies, Mary Ann

AU - Tyers, Lynn

AU - Mudau, Innocent

AU - York, Denis

AU - Maslo, Caroline

AU - Goedhals, Dominique

AU - Abrahams, Shareef

AU - Laguda-Akingba, Oluwakemi

AU - Alisoltani-Dehkordi, Arghavan

AU - Godzik, Adam

AU - Wibmer, Constantinos K.

AU - Martin, Darren

AU - Lessells, Richard J.

AU - Bhiman, Jinal N.

AU - Williamson, Carolyn

AU - de Oliveira, Tulio

AU - Swiss SARS-CoV-2 Sequencing Consortium

AU - Chen, Chaoran

AU - Nadeau, Sarah

AU - du Plessis, Louis

AU - Beckmann, Christiane

AU - Redondo, Maurice

AU - Kobel, Olivier

AU - Noppen, Christoph

AU - Seidel, Sophie

AU - de Souza, Noemie Santamaria

AU - Beerenwinkel, Niko

AU - Topolsky, Ivan

AU - Jablonski, Philipp

AU - Fuhrmann, Lara

AU - Dreifuss, David

AU - Jahn, Katharina

AU - Ferreira, Pedro

AU - Posada-Céspedes, Susana

AU - Beisel, Christian

AU - Denes, Rebecca

AU - Feldkamp, Mirjam

AU - Nissen, Ina

AU - Santacroce, Natascha

AU - Burcklen, Elodie

AU - Aquino, Catharine

AU - de Gouvea, Andreia Cabral

AU - Moccia, Maria Domenica

AU - Grüter, Simon

AU - Sykes, Timothy

AU - Opitz, Lennart

AU - White, Griffin

AU - Neff, Laura

AU - Popovic, Doris

AU - Patrignani, Andrea

AU - Tracy, Jay

AU - Schlapbach, Ralph

AU - Dermitzakis, Emmanouil

AU - Harshman, Keith

AU - Xenarios, Ioannis

AU - Pegeot, Henri

AU - Cerutti, Lorenzo

AU - Penet, Deborah

AU - Stadler, Tanja

AU - Howden, Benjamin P.

AU - Sintchenko, Vitali

AU - Zuckerman, Neta S.

AU - Mor, Orna

AU - Blankenship, Heather M.

AU - de Oliveira, Tulio

AU - Lin, Raymond T.P.

AU - Siqueira, Marilda Mendonça

AU - Resende, Paola Cristina

AU - Vasconcelos, Ana Tereza R.

AU - Spilki, Fernando R.

AU - Aguiar, Renato Santana

AU - Alexiev, Ivailo

AU - Ivanov, Ivan N.

AU - Philipova, Ivva

AU - Carrington, Christine V.F.

AU - Sahadeo, Nikita S.D.

AU - Branda, Ben

AU - Gurry, Céline

AU - Maurer-Stroh, Sebastian

AU - Naidoo, Dhamari

AU - von Eije, Karin J.

AU - Perkins, Mark D.

AU - van Kerkhove, Maria

AU - Hill, Sarah C.

AU - Sabino, Ester C.

AU - Pybus, Oliver G.

AU - Dye, Christopher

AU - Bhatt, Samir

AU - Flaxman, Seth

AU - Suchard, Marc A.

AU - Grubaugh, Nathan D.

AU - Baele, Guy

AU - Faria, Nuno R.

PY - 2022/12

Y1 - 2022/12

N2 - 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.

AB - 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.

KW - COVID-19 pandemic

KW - Global disparities

KW - SARS-CoV-2 genomic surveillance

UR - http://www.scopus.com/inward/record.url?scp=85142128821&partnerID=8YFLogxK

U2 - 10.1038/s41467-022-33713-y

DO - 10.1038/s41467-022-33713-y

M3 - Article

C2 - 36385137

AN - SCOPUS:85142128821

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 7003

ER -

Global disparities in SARS-CoV-2 genomic surveillance

Abstract

Keywords

UN SDGs

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