Brito AF
Semenova E
Dudas G
Hassler GW
Kalinich CC
Kraemer MUG
Ho J
Tegally H
Githinji G
Agoti CN
Matkin LE
Whittaker C
Bulgarian Sars-CoV-sequencing group
Communicable Diseases Genomics Network
Covid- Impact Project
Danish Covid-19 Genome Consortium
Fiocruz Covid-Genomic Surveillance Network
Gisaid core curation team
Network for Genomic Surveillance in South Africa
Swiss Sars-CoV-Sequencing Consortium
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
Nat Commun. 2022;137003
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.
