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Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands
Bas B. Oude Munnink, David F. Nieuwenhuijse, Mart Stein, Áine O’Toole, Manon Haverkate, Madelief Mollers, Sandra K. Kamga, Claudia Schapendonk, Mark Pronk, Pascal Lexmond, Anne van der Linden, Theo Bestebroer, Irina Chestakova, Ronald J. Overmars, Stefan van Nieuwkoop, Richard Molenkamp, Annemiek van der Eijk, Corine GeurtsvanKessel, Harry Vennema, Adam Meijer, Andrew Rambaut, Jaap van Dissel, Reina S. Sikkema, Aura Timen, Marion Koopmans, on behalf of the Dutch-Covid-19 response team
doi: https://doi.org/10.1101/2020.04.21.050633
Bas B. Oude Munnink
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
David F. Nieuwenhuijse
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Mart Stein
2Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
Áine O’Toole
3University of Edinburgh
Manon Haverkate
2Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
Madelief Mollers
2Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
Sandra K. Kamga
2Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
Claudia Schapendonk
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Mark Pronk
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Pascal Lexmond
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Anne van der Linden
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Theo Bestebroer
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Irina Chestakova
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Ronald J. Overmars
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Stefan van Nieuwkoop
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Richard Molenkamp
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Annemiek van der Eijk
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Corine GeurtsvanKessel
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Harry Vennema
2Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
Adam Meijer
2Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
Andrew Rambaut
3University of Edinburgh
Jaap van Dissel
2Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
Reina S. Sikkema
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands
Aura Timen
2Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
Marion Koopmans
1ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, the Netherlands

Abstract
SARS-CoV-2 is a novel coronavirus that has rapidly spread across the globe. In the Netherlands, the first case of SARS-CoV-2 has been notified on the 27th of February. Here, we describe the first three weeks of the SARS-CoV-2 outbreak in the Netherlands, which 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 timely generation of whole genome sequences combined with epidemiological investigations facilitated early decision making in an attempt to control local transmission of SARS-CoV-2 in the Netherlands.
Competing Interest Statement
The authors have declared no competing interest.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Posted April 25, 2020.
Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands
Bas B. Oude Munnink, David F. Nieuwenhuijse, Mart Stein, Áine O’Toole, Manon Haverkate, Madelief Mollers, Sandra K. Kamga, Claudia Schapendonk, Mark Pronk, Pascal Lexmond, Anne van der Linden, Theo Bestebroer, Irina Chestakova, Ronald J. Overmars, Stefan van Nieuwkoop, Richard Molenkamp, Annemiek van der Eijk, Corine GeurtsvanKessel, Harry Vennema, Adam Meijer, Andrew Rambaut, Jaap van Dissel, Reina S. Sikkema, Aura Timen, Marion Koopmans, on behalf of the Dutch-Covid-19 response team
bioRxiv 2020.04.21.050633; doi: https://doi.org/10.1101/2020.04.21.050633
Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands
Bas B. Oude Munnink, David F. Nieuwenhuijse, Mart Stein, Áine O’Toole, Manon Haverkate, Madelief Mollers, Sandra K. Kamga, Claudia Schapendonk, Mark Pronk, Pascal Lexmond, Anne van der Linden, Theo Bestebroer, Irina Chestakova, Ronald J. Overmars, Stefan van Nieuwkoop, Richard Molenkamp, Annemiek van der Eijk, Corine GeurtsvanKessel, Harry Vennema, Adam Meijer, Andrew Rambaut, Jaap van Dissel, Reina S. Sikkema, Aura Timen, Marion Koopmans, on behalf of the Dutch-Covid-19 response team
bioRxiv 2020.04.21.050633; doi: https://doi.org/10.1101/2020.04.21.050633
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