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 - Communicable Diseases Genomics Network (Australia and New Zealand)
AU - COVID-19 Impact Project
AU - Danish Covid-19 Genome Consortium
AU - Fiocruz COVID-19 Genomic Surveillance Network
AU - GISAID core curation team
AU - Network for Genomic Surveillance in South Africa (NGS-SA)
AU - Swiss SARS-CoV-2 Sequencing Consortium
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
AU - Williamson, Deborah
N1 - Funding: E.S. and S.F. acknowledge the EPSRC (EP/V002910/1). G.B. acknowledges support from the Internal Funds KU Leuven (Grant No. C14/18/094) and the Research Foundation—Flanders (“Fonds voor Wetenschappelijk Onderzoek—Vlaanderen,” G0E1420N, G098321N). G.W.H. acknowledges support from NIH F31 AI154824. M.A.S. acknowledges support from grants NIH R01 AI153044 and NIH U19 AI135995. M.U.G.K. acknowledges funding from the Oxford Martin School, EUH2020 project MOOD, Branco Weiss Fellowship and grants from The Rockefeller Foundation and Google.org. N.D.G. acknowledges support from Fast Grant from Emergent Ventures at the Mercatus Center at George Mason University and CDC Contract # 75D30120C09570. O.G.P. acknowledges support from the Oxford Martin School. N.R.F. acknowledges support by a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z); acknowledges funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/R015600/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 programme supported by the European Union; and acknowledges funding by Community Jameel. N.R.F. and E.C.S. acknowledge support by the Medical Research Council-São Paulo Research Foundation (FAPESP) CADDE partnership award (MR/S0195/1 and FAPESP 18/14389-0) (http://caddecentre.org/) and Bill & Melinda Gates Foundation (INV-034540 and INV-034652). Rede Corona-ômica BR MCTI/FINEP is affiliated to RedeVírus/MCTI (awards FINEP = 01.20.0029.000462/20, CNPq = 404096/2020-4). B.P.H. and V.S. acknowledge the contribution of SARS-CoV-2 genomes by members of the Communicable Diseases Genomics Network of Australia. C.C.K. acknowledges support from the US Public Health Service Ruth L. Kirschstein National Research Service Award (5T35HL007649-35). R.S.A. acknowledges funding from CNPq: 312688/2017-2 and 439119/2018-9; MEC/CAPES: 14/2020—23072.211119/2020-10; FINEP: 0494/20 01.20.0026.00 and UFMG-NB3 1139/20 and FAPERJ: 202.922/2018. A.T.R.V. acknowledges the Corona-ômica-RJ (FAPERJ E-26/210.179/2020 and E-26/211.107/2021) and CNPq (307145/2021-2 and 440931/2020-7). I.A., I.N.I. and I.P. acknowledge a grant from the Ministry of Education and Science, Bulgaria (contract: KП‐06‐H43/1-27.11.2020). S.C.H. acknowledged support by a Wellcome Trust Sir Henry Wellcome Fellowship (220414/Z/20/Z).
PY - 2022/11/16
Y1 - 2022/11/16
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 - Humans
KW - SARS-CoV-2/genetics
KW - Genome, Viral/genetics
KW - COVID-19/epidemiology
KW - Pandemics
KW - Genomics
UR - https://www.scopus.com/pages/publications/85142128821
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
SP - 1
EP - 13
JO - Nature Communications
JF - Nature Communications
M1 - 7003
ER -
