Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands
Oude Munnink, Bas B; Nieuwenhuijse, David F; Stein, Mart; O'Toole, Áine; Haverkate, Manon; Mollers, Madelief; Kamga, Sandra K; Schapendonk, Claudia; Pronk, Mark; Lexmond, Pascal; van der Linden, Anne; Bestebroer, Theo; Chestakova, Irina; Overmars, Ronald J; van Nieuwkoop, Stefan; Molenkamp, Richard; van der Eijk, Annemiek A; GeurtsvanKessel, Corine; Vennema, Harry; Meijer, Adam; Rambaut, Andrew; van Dissel, Jaap; Sikkema, Reina S; Timen, Aura; Koopmans, Marion; Dutch-Covid-19 response team
(2020) Nature Medicine, volume 26, issue 9, pp. 1405 - 1410
(Article)
Abstract
In late December 2019, a cluster of cases of pneumonia of unknown etiology were reported linked to a market in Wuhan, China1. The causative agent was identified as the species Severe acute respiratory syndrome-related coronavirus and was named SARS-CoV-2 (ref. 2). By 16 April the virus had spread to 185 different
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countries, infected over 2,000,000 people and resulted in over 130,000 deaths3. In the Netherlands, the first case of SARS-CoV-2 was notified on 27 February. The outbreak started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also outside, the south of the Netherlands. The combination of near to real-time whole-genome sequence analysis and epidemiology resulted in reliable assessments of the extent of SARS-CoV-2 transmission in the community, facilitating early decision-making to control local transmission of SARS-CoV-2 in the Netherlands. We demonstrate how these data were generated and analyzed, and how SARS-CoV-2 whole-genome sequencing, in combination with epidemiological data, was used to inform public health decision-making in the Netherlands.
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Keywords: General Biochemistry,Genetics and Molecular Biology
ISSN: 1078-8956
Publisher: Nature Publishing Group
Note: Funding Information: We thank the following additional members of the Dutch-Covid-19 response team: staff of the Department of Communicable Disease Control, Public Health Service Amsterdam, MHC Amsterdam, Amsterdam; staff of the Department of Communicable Disease Control, Public Health Service Gelderland-Zuid, MHC Gelderland-Zuid, Tiel; the Laboratorium Medische Microbiologie of JBZ, MHC Hart voor Brabant, Tilburg; staff of the Department of Communicable Disease Control, Public Health Service Utrecht, MHC Regio Utrecht, Utrecht; staff of the Department of Communicable Disease Control, Public Health Service Rotterdam-Rijnmond, MHC Rotterdam-Rijnmond, Rotterdam; staff of the Department of Communicable Disease Control, Public Health Service Zaanstreek-Waterland, MHC Zaanstreek Waterland, Zaandam; staff of the Department of Communicable Disease Control, Public Health Service Brabant Zuidoost, MHC Brabant Zuidoost, Eindhoven. We gratefully acknowledge the originating laboratories, where specimens were first obtained, and the submitting laboratories, where sequence data were generated and submitted to the EpiFlu Database of the GISAID, on which this research is based. All contributors of data may be contacted directly via the GISAID website (http://platform.gisaid.org). We also acknowledge M. de Graaf for her expertise in the interpretation of the early phylogenetic analysis. B.B.O.M., R.S.S., D.F.N., R.M. and M.K. received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement numbers 874735 (VEO), 848096 (SHARP JA) and 101003589 (RECoVER) and C.S., B.B.O.M. and M.K. from the European Joint Programme One Health EJP under the grant agreement number 773830 (METASTAVA). Part of this work was funded by the NIAID/NIH contract HHSN272201400008C for T.B., P.L. and M.P. Publisher Copyright: © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.
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