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Global disparities in SARS-CoV-2 genomic surveillance

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; Brito, AF; Semenova, E; Dudas, G; Hassler, GW; Kalinich, CC; Kraemer, MUG; Ho, J; Tegally, H; Githinji, G; Agoti, CN; Matkin, LE; Whittaker, C; 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; 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


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

AF Brito

E Semenova

G Dudas

GW Hassler

CC Kalinich

MUG Kraemer

J Ho

H Tegally

G Githinji

CN Agoti

LE Matkin

C Whittaker

BP Howden

V Sintchenko

NS Zuckerman

O Mor

HM Blankenship

T de Oliveira


MM Siqueira

PC Resende

ATR Vasconcelos

FR Spilki

RS Aguiar

I Alexiev

IN Ivanov

I Philipova

CVF Carrington

NSD Sahadeo

C Gurry

S Maurer-Stroh

D Naidoo

KJ von Eije

MD Perkins

M van Kerkhove

SC Hill

EC Sabino

OG Pybus

C Dye

S Bhatt

S Flaxman

MA Suchard

ND Grubaugh

G Baele

NR Faria


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.


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, …Faria, N. (2022). Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications, 13(1),

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
Publisher Nature Research
Peer Reviewed Peer Reviewed
Volume 13
Issue 1


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