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 Matkin, Charles Whittaker, Bulgarian SARS-CoV-2 sequencing group, Todor Kantardjiev, Nelly Korsun, Savina Stoitsova, Reneta Dimitrova, Ivelina Trifonova, Veselin Dobrinov, Lubomira Grigorova, Ivan Stoykov, Iliana Grigorova, Anna Gancheva, Communicable Diseases Genomics Network (Australia and New Zealand), Amy V. Jennison, Lex E.X. Leong, David Speers, Robert Baird, Louise Cooley, Karina Kennedy, Joep de Ligt, William D. Rawlinson, Sebastiaan J. van Hal, Deborah A. Williamson, COVID-19 Impact Project, Risha Singh, Sue-Min Nathaniel-Girdharrie, Lisa Edghill, Lisa Indar, Joy St. John, Gabriel González-Escobar, Vernie Ramkisoon, Arianne Brown Jordan, Anushka Ramjag, Nicholas Mohammed, J. E. Foster, Irad Potter, Sharra Greenaway-Duberry, Kenneth George, Sharon Belmar-George, John Lee, Jacqueline Bisasor-McKenzie, Nadia Astwood, Rhonda Sealey-Thomas, Hazel Laws, Narine Singh, Ayoola Oyinloye, Pearl McMillan, Avery Hinds, Naresh Nandram, Roshan Parasram, Zobida Khan-Mohammed, Shawn Charles, Aisha Andrewin, D. Barrie Johnson, Simone Keizer-Beache, Chris Oura, Oliver G. Pybus, Nuno R. Faria, Marc Stegger, Mads Albertsen, Anders Fomsgaard, Morten Rasmussen, Fiocruz COVID-19 Genomic Surveillance Network, Ricardo Khouri, Felipe Gomes Naveca, Tiago Gräf, Fábio Miyajima, Gabriel Luz Wallau, Fernando Couto Motta, GISAID core curation team, Shruti Khare, Lucas Freitas, Constanza Schiavina, Gunter Bach, Mark B. Schultz, Yi Hong Chew, Meera Makheja, Priscila Born, Gabriela Calegário, Sofia Romano, Juan Finello, Amadou Diallo, Raphael Tze Chuen Lee, Ya Ni Xu, Winston Yeo, Suma Tiruvayipati, Shilpa Yadahalli, Network for Genomic Surveillance in South Africa (NGS-SA), Eduan Wilkinson
Abstract
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.