Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands
Open accessAbstract
In late December 2019, a cluster of cases of pneumonia of unknown etiology were reported linked to a market in Wuhan, China 1. 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 countries, infected over 2,000,000 people and resulted in over 130,000 deaths 3. 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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Viral genetic diversity, evolution, variable infectivity, or co-pathogenesis might contribute to infectivity and fatality but not much to COVID-19 disease heterogeneity.
“Numerous mutations identified so far by thousands of viral sequences obtained during the first 9 months of the pandemic (Candido et al., 2020; Oude Munnink et al., 2020) suggest that viral genetic diversity, genetic evolution, variable infectivity, or co-pathogenesis might contribute to infectivity and fatality, but not so much to disease heterogeneity observed for COVID-19.”
From COVID-19 and the human innate immune system (2021) · cites this paper as Oude Munnink et al., 2020
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References 35 · Cited by 306
- Authors
- Oude Munnink, B. B., Nieuwenhuijse, D. F., Stein, M., O’Toole, Á., Haverkate, M., Mollers, M., Kamga, S. K., Schapendonk, C., Pronk, M., Lexmond, P., van der Linden, A., Bestebroer, T., Chestakova, I., Overmars, R. J., van Nieuwkoop, S., Molenkamp, R., van der Eijk, A. A., GeurtsvanKessel, C., Vennema, H., Meijer, A., Rambaut, A., van Dissel, J., Sikkema, R. S., Timen, A., Koopmans, M., The Dutch-Covid-19 response team, Oudehuis, G. J. A. P. M., Schinkel, J., Kluytmans, J., Kluytmans-van den Bergh, M., van den Bijllaardt, W., Berntvelsen, R. G., van Rijen, M. M. L., Schneeberger, P., Pas, S., Diederen, B. M., Bergmans, A. M. C., van der Eijk, P. A. V., Verweij, J. J., Buiting, A. G. N., Streefkerk, R., Aldenkamp, A. P., de Man, P., Koelemal, J. G. M., Ong, D., Paltansing, S., Veassen, N., Sleven, J., Bakker, L., Brockhoff, H., Rietveld, A., Slijkerman Megelink, F., Cohen Stuart, J., de Vries, A., van der Reijden, W., Ros, A., Lodder, E., Verspui-van der Eijk, E., Huijskens, I., Kraan, E. M., van der Linden, M. P. M., Debast, S. B., Naiemi, N. A., Kroes, A. C. M., Damen, M., Dinant, S., Lekkerkerk, S., Pontesilli, O., Smit, P., van Tienen, C., Godschalk, P. C. R., van Pelt, J., Ott, A., van der Weijden, C., Wertheim, H., Rahamat-Langendoen, J., Reimerink, J., Bodewes, R., Duizer, E., van der Veer, B., Reusken, C., Lutgens, S., Schneeberger, P., Hermans, M., Wever, P., Leenders, A., ter Waarbeek, H., & Hoebe, C.
- Affiliations
- Erasmus MC (NL)
- National Institute for Public Health and the Environment (NL)
- University of Edinburgh (GB)
- Maastricht University Medical Centre (NL)
- Amphia Ziekenhuis (NL)
- Dienst Gezondheid & Jeugd (NL)
- Ziekenhuis Bernhoven (NL)
- PAMM (NL)
- Sint Franciscus Gasthuis (NL)
- Regio Gooi en Vechtstreek (NL)
- Stichting Haaglanden Medisch Centrum (NL)
- GGD Hart voor Brabant (NL)
- IJsselland Ziekenhuis (NL)
- Isala (NL)
- Leiden University Medical Center (NL)
- Maasstad Ziekenhuis (NL)
- Meander Medisch Centrum (NL)
- Radboud University Medical Center (NL)
- Jeroen Bosch Ziekenhuis (NL)
- Corresponding author
- Koopmans, Marion
- ORCID
- Oude Munnink, Bas B.
- Nieuwenhuijse, David F.
- Stein, Mart
- O’Toole, Áine
- Haverkate, Manon
- Overmars, Ronald J.
- Molenkamp, Richard
- GeurtsvanKessel, Corine
- Vennema, Harry
- Meijer, Adam
- Rambaut, Andrew
- Sikkema, Reina S.
- Timen, Aura
- Koopmans, Marion
- Schinkel, Janke
- Kluytmans, Jan
- Pas, Suzan
- Bergmans, Anneke M. C.
- Verweij, Jaco J.
- Ong, D.
- Rietveld, Ariene
- Naiemi, N. Al
- Kroes, A. C. M.
- Smit, Pieter
- Wertheim, Heiman
- Rahamat-Langendoen, Janette
- Reimerink, Johan
- Bodewes, Rogier
- Duizer, Erwin
- Reusken, Chantal
- Wever, P.
- Leenders, A.
- Hoebe, Christian
- Venue
- Nature Medicine
- Published
- 2020-07-16
- Volume
- 26
- Issue
- 9
- Pages
- 1405-1410
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- OpenAlex
- W3043746245
- Cited by
- 306
- References
- 35
- Citations by year
- 2026: 9 · 2025: 14 · 2024: 21 · 2023: 33 · 2022: 73 · 2021: 122 · 2020: 34
- FWCI
- 8.58
- Type
- journal article
- Language
- en
- Update notices
- correction (2020-10-20)
- Open access
- bronze
- doi.org
- Locations
- Nature Medicine (publishedVersion)
- PubMed (publishedVersion)
- Research Publications (Maastricht University) (publishedVersion, other-oa)
- Pure Amsterdam UMC (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Rivm Repository (Netherlands National Institute for Public Health and the Environment) (submittedVersion)
- Rivm (National Institute for Public Health and the Environment) (submittedVersion)
- Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, cc-by)
- Rivm (National Institute for Public Health and the Environment) (submittedVersion, other-oa)
- Research Publications (Maastricht University) (submittedVersion, other-oa)
- Funders
- EC | Horizon 2020 Framework Programme (874735, 848096, 101003589)
- European Joint Programme One Health EJP under the grant agreement
- U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (HHSN272201400008C)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Keywords
- SARS-CoV-2, COVID-19 pandemic, whole genome sequencing, public health decision-making, epidemic control, Netherlands, community transmission
- MeSH terms
- Clinical Decision-Making, Whole Genome Sequencing, Betacoronavirus, COVID-19, SARS-CoV-2, Humans, Netherlands, Pneumonia, Viral, Public Health, Genome, Viral, Coronavirus Infections, Pandemics
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