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 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; 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; Danish Covid-19 Genome Consortium

doi:10.1101/2021.08.21.21262393

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 de Oliveira, Raymond T P Lin, Marilda Mendonça SiqueiraPaola 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, 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, Danish Covid-19 Genome Consortium

Afdeling for Epidemiologi

Publikation: Working paper › Preprint

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Abstract

Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in 167 countries. Most countries submit genomes >21 days after sample collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness.

Originalsprog	Engelsk
DOI	https://doi.org/10.1101/2021.08.21.21262393
Status	Udgivet - 2022

Navn	medRxiv

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10.1101/2021.08.21.21262393

Global disparities in SARS-CoV-2 genomic surveillanceAccepteret manuskript, 3,43 MBLicens: CC BY-NC-ND

Citationsformater

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., Blankenship, H. M., de Oliveira, T., Lin, R. T. P., ... Danish Covid-19 Genome Consortium (2022). Global disparities in SARS-CoV-2 genomic surveillance. medRxiv https://doi.org/10.1101/2021.08.21.21262393

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, 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 & Danish Covid-19 Genome Consortium 2022 'Global disparities in SARS-CoV-2 genomic surveillance' medRxiv. https://doi.org/10.1101/2021.08.21.21262393

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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

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AU - Ivanov, Ivan N

AU - Philipova, Ivva

AU - Carrington, Christine V F

AU - Sahadeo, Nikita S D

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AU - Perkins, Mark D

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AU - Hill, Sarah C

AU - Sabino, Ester C

AU - Pybus, Oliver G

AU - Dye, Christopher

AU - Bhatt, Samir

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