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; Bulgarian SARS-CoV-2 Sequencing Gr; Communicable Dis Genomics Network; COVID-19 Impact Project; Danish Covid-19 Genome Consortium; Fiocruz COVID-19 Genomic Surveilla; GISAID Core Curation Team; Network Genomic Surveillance South; Swiss SARS-CoV-2 Sequencing Consor; 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, Ben; 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. In this study, the authors provide a global overview of SARS-CoV-2 genome sequencing, and estimate the proportion of cases sequenced and time to genome upload. They identify disparities and highlight the need to strengthen surveillance in lower and middle income countries.

Citation

Brito, A., Semenova, E., Dudas, G., Hassler, G., Kalinich, C., Kraemer, M., Ho, J., Tegally, H., Githinji, G., Agoti, C., Matkin, L., Whittaker, C., Bulgarian SARS-CoV-2 Sequencing Gr, Communicable Dis Genomics Network, COVID-19 Impact Project, Danish Covid-19 Genome Consortium, Fiocruz COVID-19 Genomic Surveilla, GISAID Core Curation Team, Network Genomic Surveillance South, Swiss SARS-CoV-2 Sequencing Consor, …Faria, N. (2022). Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications, 13(1), https://doi.org/10.1038/s41467-022-33713-y

• Journal Article Type: Article
• Acceptance Date: Sep 29, 2022
• Online Publication Date: Nov 16, 2022
• Publication Date: 2022
• Deposit Date: Aug 15, 2023
• Publicly Available Date: Aug 15, 2023
• Journal: Nature Communications
• Electronic ISSN: 2041-1723
• Publisher: Nature Research
• Peer Reviewed: Peer Reviewed
• Volume: 13
• Issue: 1
• DOI: https://doi.org/10.1038/s41467-022-33713-y
• Keywords: VARIANTS; COVID-19