Global disparities in SARS-CoV-2 genomic surveillance

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; 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 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

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
, 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 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

Research output: Contribution to journal › Article › Academic › peer-review

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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
DOIs	https://doi.org/10.1038/s41467-022-33713-y
Publication status	Published - 16-Nov-2022

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Global disparities in SARS-CoV-2 genomic surveillance
Danish Covid-19 Genome Consortium, COVID-19 Impact Project, Network for Genomic Surveillance in South Africa (NGS-SA), GISAID core curation team, 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., Howden, B. P., Sintchenko, V., Zuckerman, N. S. & Mor, O. & 29 others, Blankenship, H. M., de Oliveira, T., Lin, R. T. P., Siqueira, M. M., Resende, P. C., Vasconcelos, A. T. R., Spilki, F. R., Aguiar, R. S., Alexiev, I., Ivanov, I. N., Philipova, I., Carrington, C. V. F., Sahadeo, N. S. D., Gurry, C., Maurer-Stroh, S., Naidoo, D., von Eije, K. J., Perkins, M. D., van Kerkhove, M., Hill, S. C., Sabino, E. C., Pybus, O. G., Dye, C., Bhatt, S., Flaxman, S., Suchard, M. A., Grubaugh, N. D., Baele, G. & Faria, N. R., 9-Dec-2021, MedRxiv.
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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, 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., ... Faria, N. R. (2022). Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications, 13, Article 7003. https://doi.org/10.1038/s41467-022-33713-y

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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.",

author = "\{Bulgarian SARS-CoV-2 sequencing group\} and \{Communicable Diseases Genomics Network (Australia and New Zealand)\} and \{COVID-19 Impact Project\} and \{Danish Covid-19 Genome Consortium\} and \{Fiocruz COVID-19 Genomic Surveillance Network\} and \{GISAID core curation team\} and \{Network for Genomic Surveillance in South Africa (NGS-SA)\} and \{Swiss SARS-CoV-2 Sequencing Consortium\} and 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 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\}",

note = "{\textcopyright} 2022. The Author(s).",

year = "2022",

month = nov,

day = "16",

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

language = "English",

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journal = "Nature Communications",

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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, Brito, AF, Semenova, E, Dudas, G, Hassler, GW, Kalinich, CC, Kraemer, MUG, Ho, J, Tegally, H, Githinji, G, Agoti, CN, Matkin, LE, Whittaker, C, 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, 7003. https://doi.org/10.1038/s41467-022-33713-y

TY - JOUR

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

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 - 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 - 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 - 2022/11/16

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.

U2 - 10.1038/s41467-022-33713-y

DO - 10.1038/s41467-022-33713-y

M3 - Article

C2 - 36385137

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

M1 - 7003

ER -

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 et al. Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications. 2022 Nov 16;13:7003. doi: 10.1038/s41467-022-33713-y

Global disparities in SARS-CoV-2 genomic surveillance

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Global disparities in SARS-CoV-2 genomic surveillance

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