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 WhittakerBenjamin 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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    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.

    Originele taal-2English
    Artikelnummer7003
    Aantal pagina's13
    TijdschriftNature Communications
    Volume13
    DOI's
    StatusPublished - 16-nov.-2022
    • 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 anderenBlankenship, 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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