Global disparities in SARS-CoV-2 genomic surveillance.
Brito AF., Semenova E., Dudas G., Hassler GW., Kalinich CC., Kraemer MUG., Ho J., Tegally H., Githinji G., Agoti CN., Matkin LE., Whittaker C., Danish Covid-19 Genome Consortium None., COVID-19 Impact Project None., Network for Genomic Surveillance in South Africa (NGS-SA) None., GISAID core curation team None., 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.
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.