Global disparities in SARS-CoV-2 genomic surveillance
Authors: Brito Anderson F. , Semenova Elizaveta , Dudas Gytis , Hassler Gabriel W. , Kalinich Chaney C. , Kraemer Moritz U. G. , Ho Joses , Tegally Houriiyah , Githinji George , Agoti Charles N. , Matkin Lucy E. , Whittaker Charles ,   Bulgarian SARS-CoV-2 sequencing group, Kantardjiev Todor , Korsun Nelly , Stoitsova Savina , Dimitrova Reneta , Trifonova Ivelina , Dobrinov Veselin , Grigorova Lubomira , Stoykov Ivan , Grigorova Iliana , Gancheva Anna ,   Communicable Diseases Genomics Network (Australia and New Zealand), Jennison Amy , Leong Lex , Speers David , Baird Rob , Cooley Louise , Kennedy Karina , de Ligt Joep , Rawlinson William , van Hal Sebastiaan , Williamson Deborah ,   COVID-19 Impact Project, Singh Risha , Nathaniel-Girdharrie SueMin , Edghill Lisa , Indar Lisa , St. John Joy , Gonzalez-Escobar Gabriel , Ramkisoon Vernie , Brown-Jordan Arianne , Ramjag Anushka , Mohammed Nicholas , Foster Jerome E. , Potter Irad , Greenaway-Duberry Sharra , George Kenneth , Belmar-George Sharon , Lee John , Bisasor-McKenzie Jacqueline , Astwood Nadia , Sealey-Thomas Rhonda , Laws Hazel , Singh Narine , Oyinloye Ayoola , McMillan Pearl , Hinds Avery , Nandram Naresh , Parasram Roshan , Khan-Mohammed Zobida , Charles Shawn , Andrewin Aisha , Johnson David , Keizer-Beache Simone , Oura Chris , Pybus Oliver G. , Faria Nuno R. ,   Danish Covid-19 Genome Consortium, Stegger Marc , Albertsen Mads , Fomsgaard Anders , Rasmussen Morten ,   Fiocruz COVID-19 Genomic Surveillance Network, Khouri Ricardo , Naveca Felipe , Graf Tiago , Miyajima Fábio , Wallau Gabriel , Motta Fernando ,   GISAID core curation team, Khare Shruti , Freitas Lucas , Schiavina Constanza , Bach Gunter , Schultz Mark B. , Chew Yi Hong , Makheja Meera , Born Priscila , Calegario Gabriela , Romano Sofia , Finello Juan , Diallo Amadou , Lee Raphael T. C. , Xu Ya Ni , Yeo Winston , Tiruvayipati Suma , Yadahalli Shilpa ,   Network for Genomic Surveillance in South Africa (NGS-SA), Wilkinson Eduan , Iranzadeh Arash , Giandhari Jennifer , Doolabh Deelan , Pillay Sureshnee , Ramphal Upasana , San James E. , Msomi Nokukhanya , Mlisana Koleka , von Gottberg Anne , Walaza Sibongile , Ismail Arshad , Mohale Thabo , Engelbrecht Susan , Van Zyl Gert , Preiser Wolfgang , Sigal Alex , Hardie Diana , Marais Gert , Hsiao Marvin , Korsman Stephen , Davies Mary-Ann , Tyers Lynn , Mudau Innocent , York Denis , Maslo Caroline , Goedhals Dominique , Abrahams Shareef , Laguda-Akingba Oluwakemi , Alisoltani-Dehkordi Arghavan , Godzik Adam , Wibmer Constantinos K. , Martin Darren , Lessells Richard J. , Bhiman Jinal N. , Williamson Carolyn , de Oliveira Tulio ,   Swiss SARS-CoV-2 Sequencing Consortium, Chen Chaoran , Nadeau Sarah , du Plessis Louis , Beckmann Christiane , Redondo Maurice , Kobel Olivier , Noppen Christoph , Seidel Sophie , de Souza Noemie Santamaria , Beerenwinkel Niko , Topolsky Ivan , Jablonski Philipp , Fuhrmann Lara , Dreifuss David , Jahn Katharina , Ferreira Pedro , Posada-Céspedes Susana , Beisel Christian , Denes Rebecca , Feldkamp Mirjam , Nissen Ina , Santacroce Natascha , Burcklen Elodie , Aquino Catharine , de Gouvea Andreia Cabral , Moccia Maria Domenica , Grüter Simon , Sykes Timothy , Opitz Lennart , White Griffin , Neff Laura , Popovic Doris , Patrignani Andrea , Tracy Jay , Schlapbach Ralph , Dermitzakis Emmanouil , Harshman Keith , Xenarios Ioannis , Pegeot Henri , Cerutti Lorenzo , Penet Deborah , Stadler Tanja , Howden Benjamin P. , Sintchenko Vitali , Zuckerman Neta S. , Mor Orna , Blankenship Heather M. , de Oliveira Tulio , Lin Raymond T. P. , 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 V. F. , Sahadeo Nikita S. D. , Branda Ben , 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. 
Published: November 2022

AbstractGenomic 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.