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Global disparities in SARS-CoV-2 genomic surveillance

Author

Listed:
  • Anderson F. Brito

    (Yale School of Public Health
    Instituto Todos pela Saúde)

  • Elizaveta Semenova

    (University of Oxford)

  • Gytis Dudas

    (Vilnius University)

  • Gabriel W. Hassler

    (University of California Los Angeles)

  • Chaney C. Kalinich

    (Yale School of Public Health
    Yale University)

  • Moritz U. G. Kraemer

    (University of Oxford)

  • Joses Ho

    (GISAID Global Data Science Initiative
    Agency for Science Technology and Research)

  • Houriiyah Tegally

    (University of KwaZulu-Natal
    Stellenbosch University)

  • George Githinji

    (KEMRI-Wellcome Trust Research Programme
    Pwani University)

  • Charles N. Agoti

    (KEMRI-Wellcome Trust Research Programme
    Pwani University)

  • Lucy E. Matkin

    (University of Oxford)

  • Charles Whittaker

    (Imperial College London
    Imperial College London)

  • Benjamin P. Howden

    (The University of Melbourne at The Peter Doherty Institute for Infection and Immunity)

  • Vitali Sintchenko

    (The University of Sydney
    NSW Health Pathology)

  • Neta S. Zuckerman

    (Israel Ministry of Health, Sheba Medical Center)

  • Orna Mor

    (Israel Ministry of Health, Sheba Medical Center)

  • Heather M. Blankenship

    (Bureau of Laboratories)

  • Tulio Oliveira

    (University of KwaZulu-Natal
    Stellenbosch University
    Centre for the AIDS Programme of Research in South Africa (CAPRISA)
    University of Washington)

  • Raymond T. P. Lin

    (National Centre for Infectious Diseases)

  • Marilda Mendonça Siqueira

    (Instituto Oswaldo Cruz, FIOCRUZ)

  • Paola Cristina Resende

    (Instituto Oswaldo Cruz, FIOCRUZ)

  • Ana Tereza R. Vasconcelos

    (Laboratório Nacional de Computação Científica)

  • Fernando R. Spilki

    (Feevale University, Institute of Health Sciences)

  • Renato Santana Aguiar

    (Universidade Federal de Minas Gerais
    Instituto D’Or de Pesquisa e Ensino (IDOR))

  • Ivailo Alexiev

    (National Center of Infectious and Parasitic Diseases)

  • Ivan N. Ivanov

    (National Center of Infectious and Parasitic Diseases)

  • Ivva Philipova

    (National Center of Infectious and Parasitic Diseases)

  • Christine V. F. Carrington

    (The University of the West Indies)

  • Nikita S. D. Sahadeo

    (The University of the West Indies)

  • Ben Branda

    (GISAID Global Data Science Initiative)

  • Céline Gurry

    (GISAID Global Data Science Initiative)

  • Sebastian Maurer-Stroh

    (GISAID Global Data Science Initiative
    Agency for Science Technology and Research
    National Centre for Infectious Diseases)

  • Dhamari Naidoo

    (World Health Organization Regional Office for South-East Asia)

  • Karin J. Eije

    (University of Groningen, University Medical Center Groningen
    World Health Organization)

  • Mark D. Perkins

    (World Health Organization)

  • Maria Kerkhove

    (World Health Organization)

  • Sarah C. Hill

    (Royal Veterinary College)

  • Ester C. Sabino

    (Instituto Todos pela Saúde
    Faculdade de Medicina da Universidade de São Paulo)

  • Oliver G. Pybus

    (University of Oxford
    Royal Veterinary College)

  • Christopher Dye

    (University of Oxford)

  • Samir Bhatt

    (Imperial College London
    Imperial College London
    University of Copenhagen)

  • Seth Flaxman

    (University of Oxford)

  • Marc A. Suchard

    (University of California Los Angeles
    University of California Los Angeles
    University of California Los Angeles)

  • Nathan D. Grubaugh

    (Yale School of Public Health
    Yale University)

  • Guy Baele

    (Rega Institute, KU Leuven)

  • Nuno R. Faria

    (University of Oxford
    Imperial College London
    Imperial College London
    Faculdade de Medicina da Universidade de São Paulo)

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

Suggested Citation

  • Anderson F. Brito & Elizaveta Semenova & Gytis Dudas & Gabriel W. Hassler & Chaney C. Kalinich & Moritz U. G. Kraemer & Joses Ho & Houriiyah Tegally & George Githinji & Charles N. Agoti & Lucy E. Matk, 2022. "Global disparities in SARS-CoV-2 genomic surveillance," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33713-y
    DOI: 10.1038/s41467-022-33713-y
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    References listed on IDEAS

    as
    1. Yang Ye & Qingpeng Zhang & Xuan Wei & Zhidong Cao & Hsiang-Yu Yuan & Daniel Dajun Zeng, 2022. "Equitable access to COVID-19 vaccines makes a life-saving difference to all countries," Nature Human Behaviour, Nature, vol. 6(2), pages 207-216, February.
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    Cited by:

    1. Benjamin Faucher & Chiara E. Sabbatini & Peter Czuppon & Moritz U. G. Kraemer & Philippe Lemey & Vittoria Colizza & François Blanquart & Pierre-Yves Boëlle & Chiara Poletto, 2024. "Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Mark P. Khurana & Jacob Curran-Sebastian & Neil Scheidwasser & Christian Morgenstern & Morten Rasmussen & Jannik Fonager & Marc Stegger & Man-Hung Eric Tang & Jonas L. Juul & Leandro Andrés Escobar-He, 2024. "High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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