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Global disparities in SARS-CoV-2 genomic surveillance.

Publication date: 2021-12-09

Author:

Brito, Anderson F
Semenova, Elizaveta ; Dudas, Gytis ; Hassler, Gabriel W ; Kalinich, Chaney C ; Kraemer, Moritz UG ; Ho, Joses ; Tegally, Houriiyah ; Githinji, George ; Agoti, Charles N ; Matkin, Lucy E ; Whittaker, Charles ; Danish Covid-19 Genome Consortium, ; COVID-19 Impact Project, ; Network for Genomic Surveillance in South Africa (NGS-SA), ; GISAID core curation team, ; Howden, Benjamin P ; Sintchenko, Vitali ; Zuckerman, Neta S ; Mor, Orna ; Blankenship, Heather M ; de Oliveira, Tulio ; Lin, Raymond TP ; Siqueira, Marilda Mendonça ; Resende, Paola Cristina ; Vasconcelos, Ana Tereza R ; Spilki, Fernando R ; Aguiar, Renato Santana ; Alexiev, Ivailo ; Ivanov, Ivan N ; Philipova, Ivva ; Carrington, Christine VF ; Sahadeo, Nikita SD ; Gurry, Céline ; Maurer-Stroh, Sebastian ; Naidoo, Dhamari ; von Eije, Karin J ; Perkins, Mark D ; van Kerkhove, Maria ; Hill, Sarah C ; Sabino, Ester C ; Pybus, Oliver G ; Dye, Christopher ; Bhatt, Samir ; Flaxman, Seth ; Suchard, Marc A ; Grubaugh, Nathan D ; Baele, Guy ; Faria, Nuno R

Keywords:

STG/17/003#54272001

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.