Nature Communications (Nov 2022)
Global disparities in SARS-CoV-2 genomic surveillance
- 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. Matkin,
- Charles Whittaker,
- 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,
- Benjamin P. Howden,
- Vitali Sintchenko,
- Neta S. Zuckerman,
- Orna Mor,
- Heather M. Blankenship,
- Tulio de Oliveira,
- Raymond T. P. Lin,
- Marilda Mendonça Siqueira,
- Paola Cristina Resende,
- Ana Tereza R. Vasconcelos,
- Fernando R. Spilki,
- Renato Santana Aguiar,
- Ivailo Alexiev,
- Ivan N. Ivanov,
- Ivva Philipova,
- Christine V. F. Carrington,
- Nikita S. D. Sahadeo,
- Ben Branda,
- Céline Gurry,
- Sebastian Maurer-Stroh,
- Dhamari Naidoo,
- Karin J. von Eije,
- Mark D. Perkins,
- Maria van Kerkhove,
- Sarah C. Hill,
- Ester C. Sabino,
- Oliver G. Pybus,
- Christopher Dye,
- Samir Bhatt,
- Seth Flaxman,
- Marc A. Suchard,
- Nathan D. Grubaugh,
- Guy Baele,
- Nuno R. Faria
Affiliations
- Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Elizaveta Semenova
- Department of Computer Science, University of Oxford
- Gytis Dudas
- Institute of Biotechnology, Life Sciences Center, Vilnius University
- Gabriel W. Hassler
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles
- Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Moritz U. G. Kraemer
- Department of Biology, University of Oxford
- Joses Ho
- GISAID Global Data Science Initiative
- Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal
- George Githinji
- KEMRI-Wellcome Trust Research Programme
- Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme
- Lucy E. Matkin
- Department of Biology, University of Oxford
- Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London
- 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
- Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
- Vitali Sintchenko
- Sydney Institute for Infectious Diseases, The University of Sydney
- Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center
- Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center
- Heather M. Blankenship
- Michigan Department of Health and Human Services, Bureau of Laboratories
- Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal
- Raymond T. P. Lin
- National Centre for Infectious Diseases
- Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ
- Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz, FIOCRUZ
- Ana Tereza R. Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica
- Fernando R. Spilki
- Feevale University, Institute of Health Sciences
- Renato Santana Aguiar
- Laboratório de Biologia Integrativa, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais
- 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
- Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies
- Nikita S. D. Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, 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
- Dhamari Naidoo
- Health Emergencies Programme, World Health Organization Regional Office for South-East Asia
- Karin J. von Eije
- Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, University of Groningen, University Medical Center Groningen
- Mark D. Perkins
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization
- Maria van Kerkhove
- Emerging Diseases and Zoonoses Unit, Health Emergencies Programme, World Health Organization
- Sarah C. Hill
- Royal Veterinary College
- Ester C. Sabino
- Instituto Todos pela Saúde
- Oliver G. Pybus
- Department of Biology, University of Oxford
- Christopher Dye
- Department of Biology, University of Oxford
- Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London
- Seth Flaxman
- Department of Computer Science, University of Oxford
- Marc A. Suchard
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles
- Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health
- Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Nuno R. Faria
- Department of Biology, University of Oxford
- DOI
- https://doi.org/10.1038/s41467-022-33713-y
- Journal volume & issue
-
Vol. 13,
no. 1
pp. 1 – 13
Abstract
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.
