TY - JOUR
T1 - Global disparities in SARS-CoV-2 genomic surveillance
AU - Communicable Diseases Genomics Network (Australia and New Zealand)
AU - COVID-19 Impact Project
AU - Danish Covid-19 Genome Consortium
AU - Fiocruz COVID-19 Genomic Surveillance Network
AU - GISAID core curation team
AU - Network for Genomic Surveillance in South Africa (NGS-SA)
AU - Swiss SARS-CoV-2 Sequencing Consortium
AU - Bulgarian SARS-CoV-2 sequencing group
AU - Brito, Anderson F.
AU - Semenova, Elizaveta
AU - Dudas, Gytis
AU - Hassler, Gabriel W.
AU - Kalinich, Chaney C.
AU - Kraemer, Moritz U.G.
AU - Ho, Joses
AU - Tegally, Houriiyah
AU - Githinji, George
AU - Agoti, Charles N.
AU - Matkin, Lucy E.
AU - Whittaker, Charles
AU - Kantardjiev, Todor
AU - Korsun, Nelly
AU - Stoitsova, Savina
AU - Dimitrova, Reneta
AU - Trifonova, Ivelina
AU - Dobrinov, Veselin
AU - Grigorova, Lubomira
AU - Stoykov, Ivan
AU - Grigorova, Iliana
AU - Gancheva, Anna
AU - Jennison, Amy
AU - Leong, Lex
AU - Speers, David
AU - Baird, Rob
AU - Cooley, Louise
AU - Kennedy, Karina
AU - de Ligt, Joep
AU - Rawlinson, William
AU - van Hal, Sebastiaan
AU - Williamson, Deborah
AU - Singh, Risha
AU - Nathaniel-Girdharrie, Sue Min
AU - Edghill, Lisa
AU - Indar, Lisa
AU - St. John, Joy
AU - Gonzalez-Escobar, Gabriel
AU - Ramkisoon, Vernie
AU - Brown-Jordan, Arianne
AU - Ramjag, Anushka
AU - Mohammed, Nicholas
AU - Foster, Jerome E.
AU - Potter, Irad
AU - Greenaway-Duberry, Sharra
AU - George, Kenneth
AU - Belmar-George, Sharon
AU - Lee, John
AU - Bisasor-McKenzie, Jacqueline
AU - Mor, Orna
N1 - Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85142128821&partnerID=8YFLogxK
U2 - 10.1038/s41467-022-33713-y
DO - 10.1038/s41467-022-33713-y
M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???
C2 - 36385137
AN - SCOPUS:85142128821
SN - 2041-1723
VL - 13
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 7003
ER -