Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Sep;26(9):1405-1410.
doi: 10.1038/s41591-020-0997-y. Epub 2020 Jul 16.

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

Collaborators, Affiliations

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

Bas B Oude Munnink et al. Nat Med. 2020 Sep.

Erratum in

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 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.

PubMed Disclaimer

Similar articles

  • Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling.
    Rockett RJ, Arnott A, Lam C, Sadsad R, Timms V, Gray KA, Eden JS, Chang S, Gall M, Draper J, Sim EM, Bachmann NL, Carter I, Basile K, Byun R, O'Sullivan MV, Chen SC, Maddocks S, Sorrell TC, Dwyer DE, Holmes EC, Kok J, Prokopenko M, Sintchenko V. Rockett RJ, et al. Nat Med. 2020 Sep;26(9):1398-1404. doi: 10.1038/s41591-020-1000-7. Epub 2020 Jul 9. Nat Med. 2020. PMID: 32647358
  • Emergence of a Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2: Biology and Therapeutic Options.
    Khan S, Siddique R, Shereen MA, Ali A, Liu J, Bai Q, Bashir N, Xue M. Khan S, et al. J Clin Microbiol. 2020 Apr 23;58(5):e00187-20. doi: 10.1128/JCM.00187-20. Print 2020 Apr 23. J Clin Microbiol. 2020. PMID: 32161092 Free PMC article. Review.
  • A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan.
    Sekizuka T, Itokawa K, Hashino M, Kawano-Sugaya T, Tanaka R, Yatsu K, Ohnishi A, Goto K, Tsukagoshi H, Ehara H, Sadamasu K, Taira M, Shibata S, Nomoto R, Hiroi S, Toho M, Shimada T, Matsui T, Sunagawa T, Kamiya H, Yahata Y, Yamagishi T, Suzuki M, Wakita T, Kuroda M. Sekizuka T, et al. mSphere. 2020 Nov 11;5(6):e00786-20. doi: 10.1128/mSphere.00786-20. mSphere. 2020. PMID: 33177213 Free PMC article.
  • International Expansion of a Novel SARS-CoV-2 Mutant.
    Wang M, Li M, Ren R, Li L, Chen EQ, Li W, Ying B. Wang M, et al. J Virol. 2020 Jun 1;94(12):e00567-20. doi: 10.1128/JVI.00567-20. Print 2020 Jun 1. J Virol. 2020. PMID: 32269121 Free PMC article. No abstract available.
  • Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to animals: an updated review.
    Salajegheh Tazerji S, Magalhães Duarte P, Rahimi P, Shahabinejad F, Dhakal S, Singh Malik Y, Shehata AA, Lama J, Klein J, Safdar M, Rahman MT, Filipiak KJ, Rodríguez-Morales AJ, Sobur MA, Kabir F, Vazir B, Mboera L, Caporale M, Islam MS, Amuasi JH, Gharieb R, Roncada P, Musaad S, Tilocca B, Koohi MK, Taghipour A, Sait A, Subbaram K, Jahandideh A, Mortazavi P, Abedini MA, Hokey DA, Hogan U, Shaheen MNF, Elaswad A, Elhaig MM, Fawzy M. Salajegheh Tazerji S, et al. J Transl Med. 2020 Sep 21;18(1):358. doi: 10.1186/s12967-020-02534-2. J Transl Med. 2020. PMID: 32957995 Free PMC article. Review.

Cited by

References

    1. Zhu, N. et al. A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 382, 727–733 (2020). - PubMed - PMC
    1. Gorbalenya, A. E. et al. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 5, 536–544 (2020). - DOI
    1. Dong, E., Du, H. & Gardner, L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect. Dis. 20, 533–534 (2020). - DOI
    1. Oude Munnink, B. B. et al. Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016–2018. Sci. Rep. 10, 2798 (2020). - DOI
    1. Quick, J. et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228–232 (2016). - DOI

Publication types

MeSH terms

LinkOut - more resources