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., Kantardjiev T., Korsun N., Stoitsova S., Dimitrova R., Trifonova I., Dobrinov V., Grigorova L., Stoykov I., Grigorova I., Gancheva A., Jennison A., Leong L., Speers D., Baird R., Cooley L., Kennedy K., de Ligt J., Rawlinson W., van Hal S., Williamson D., Singh R., Nathaniel-Girdharrie S., Edghill L., Indar L., St. John J., Gonzalez-Escobar G., Ramkisoon V., Brown-Jordan A., Ramjag A., Mohammed N., Foster JE., Potter I., Greenaway-Duberry S., George K., Belmar-George S., Lee J., Bisasor-McKenzie J., Astwood N., Sealey-Thomas R., Laws H., Singh N., Oyinloye A., McMillan P., Hinds A., Nandram N., Parasram R., Khan-Mohammed Z., Charles S., Andrewin A., Johnson D., Keizer-Beache S., Oura C., Pybus OG., Faria NR., Stegger M., Albertsen M., Fomsgaard A., Rasmussen M., Khouri R., Naveca F., Graf T., Miyajima F., Wallau G., Motta F., Khare S., Freitas L., Schiavina C., Bach G., Schultz MB., Chew YH., Makheja M., Born P., Calegario G., Romano S., Finello J., Diallo A., Lee RTC., Xu YN., Yeo W., Tiruvayipati S., Yadahalli S., Wilkinson E., Iranzadeh A., Giandhari J., Doolabh D., Pillay S., Ramphal U., San JE., Msomi N., Mlisana K., von Gottberg A., Walaza S., Ismail A., Mohale T., Engelbrecht S., Van Zyl G., Preiser W., Sigal A., Hardie D., Marais G., Hsiao M., Korsman S., Davies M-A., Tyers L., Mudau I., York D., Maslo C., Goedhals D., Abrahams S., Laguda-Akingba O., Alisoltani-Dehkordi A., Godzik A., Wibmer CK., Martin D., Lessells RJ., Bhiman JN., Williamson C., de Oliveira T., Chen C., Nadeau S., du Plessis L., Beckmann C., Redondo M., Kobel O., Noppen C., Seidel S., de Souza NS., Beerenwinkel N., Topolsky I., Jablonski P., Fuhrmann L., Dreifuss D., Jahn K., Ferreira P., Posada-Céspedes S., Beisel C., Denes R., Feldkamp M., Nissen I., Santacroce N., Burcklen E., Aquino C., de Gouvea AC., Moccia MD., Grüter S., Sykes T., Opitz L., White G., Neff L., Popovic D., Patrignani A., Tracy J., Schlapbach R., Dermitzakis E., Harshman K., Xenarios I., Pegeot H., Cerutti L., Penet D., Stadler T., 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., Branda B., 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.
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.