Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands

08 May 2020

The Clinical Biological Study team of RECOVER has carried out a rapid SARS-CoV-2 whole genome sequencing combined with epidemiological studies to inform public health decision making in the Netherlands (Oude Munnink et al. 2020). This study was done in liaison with the national outbreak response team of the Netherlands.

Whole genome sequencing is a powerful tool to understand transmission dynamics of viral outbreaks, and can be used to inform outbreak control decisions. It provides a precise understanding of the transmission patterns in various initial phases of the outbreaks. In the Netherlands, the first complete SARS-CoV-2 genome sequencing from the first two patients were generated, analysed, and shared on 29 February.

Using this data, the team was able to understand the genetic diversity, the extent of local and regional clusters, and the transmission patterns within the healthcare professionals groups in different phases (read more in article). This information accompanied the data obtained from more traditional methods such as contact investigation.

Despite the fact that there is limited amount of genomic information available from certain parts of the world, a few observations can be made from the information gathered. Since the emergence of the virus, its global spread led to diversification into lineages that reflect ongoing chains of transmission in specific global geographic regions, in Europe, and in the Netherlands. Given the widespread circulation, most likely scenario is that SARS-CoV-2 will (sporadically) re-emerge. In addition, due to genomic mutations, the phenotype and the transmission dynamics of the virus might change during time.

Sharing of metadata is needed within a country and on a global level. Countries are urged to share sequence information to combine efforts in understanding the spread of SARS-CoV-2. In order to fully realise the potential added value of whole genome sequencing for public health decision making, systems for combined analysis of data are needed that are in agreement with general data protection rules.


Read the full preprint article here.

Authors: 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.

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