Global disparities in SARS-CoV-2 genomic surveillance.
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, Communicable Diseases Genomics Network (Australia and New Zealand), COVID-19 Impact Project, Danish Covid-19 Genome Consortium, Fiocruz COVID-19 Genomic Surveillance Network, GISAID core curation team, Network for Genomic Surveillance in South Africa (NGS-SA), Swiss SARS-CoV-2 Sequencing Consortium, 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
Nature communications · 2022 · PMID 36385137 · 인용 309
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.