Abstract

Global disparities in SARS-CoV-2 genomic surveillance

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-sequencing group Communicable Diseases Genomics, Network Covid- Impact Project Danish Covid-19 Genome, Consortium Fiocruz, Covid-Genomic Surveillance Network Gisaid core curation team Network for Genomic Surveillance in South, Africa Swiss, Sars-CoV-Sequencing Consortium Howden, B. P. Sintchenko, V. Zuckerman, N. S. Mor, O. 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. Branda, B. 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.
Nat Commun. 2022; 137003

Permanent descriptor

https://doi.org/10.1038/s41467-022-33713-y

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.