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

Oude Munnink BB, Nieuwenhuijse DF, Stein M, O'Toole Á, Haverkate M, Mollers M, Kamga SK, Schapendonk C, Pronk M, Lexmond P, van der Linden A, Bestebroer T, Chestakova I, Overmars RJ, van Nieuwkoop S, Molenkamp R, van der Eijk AA, GeurtsvanKessel C, Vennema H, Meijer A, Rambaut A, van Dissel J, Sikkema RS, Timen A, Koopmans M, Oudehuis GJAPM, Schinkel J, Kluytmans J, Kluytmans-van den Bergh M, van den Bijllaardt W, Berntvelsen RG, van Rijen MML, Schneeberger P, Pas S, Diederen BM, Bergmans AMC, van der Eijk PAV, Verweij J, Buiting AGN, Streefkerk R, Aldenkamp AP, de Man P, Koelemal JGM, 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 EM, van der Linden MPM, Debast SB, Naiemi NA, Kroes ACM, Damen M, Dinant S, Lekkerkerk S, Pontesilli O, Smit P, van Tienen C, Godschalk PCR, 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 & The Dutch-Covid-19 response team

(2020) Nature Medicine 26, 1405-1410.

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 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. ? 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.

 
Andrew Rambaut, 2007