Rapid communication Open Access
Like 0


We whole-genome sequenced 55 SARS-CoV-2 isolates from Germany to investigate SARS-CoV-2 outbreaks in 2020 in the Heinsberg district and Düsseldorf. While the genetic structure of the Heinsberg outbreak indicates a clonal origin, reflecting superspreading dynamics from mid-February during the carnival season, distinct viral strains were circulating in Düsseldorf in March, reflecting the city’s international links. Limited detection of Heinsberg strains in the Düsseldorf area despite geographical proximity may reflect efficient containment and contact-tracing efforts.


Article metrics loading...

Loading full text...

Full text loading...



  1. Robert Koch Institute (RKI). Coronavirus Disease 2019 (COVID-19) Daily Situation Report 05/03/2020. Berlin: RKI; Mar 2020. Available from: https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Situationsberichte/2020-03-05-en.pdf?__blob=publicationFile
  2. Walker A, Ennker KS, Kaiser R, Lübke N, Timm J. A pan-genotypic Hepatitis C Virus NS5A amplification method for reliable genotyping and resistance testing. J Clin Virol. 2019;113:8-13.  https://doi.org/10.1016/j.jcv.2019.01.012  PMID: 30771598 
  3. Quick, J. ARTIC amplicon sequencing protocol for MinION for nCoV-2019.2020.  https://doi.org/http://dx.doi.org/10.17504/protocols.io.bdp7i5rn 
  4. Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc. 2017;12(6):1261-76.  https://doi.org/10.1038/nprot.2017.066  PMID: 28538739 
  5. Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265-9.  https://doi.org/10.1038/s41586-020-2008-3  PMID: 32015508 
  6. Kreis Heinsberg. Coronavirus im Kreis Heinsberg. [Coronavirus in the district of Heinsberg]. Heinsberg: Kreisverwaltung Heinsberg; 2020. Available from: https://www.kreis-heinsberg.de/aktuelles/aktuelles/?pid=5149
  7. Netherlands National Institute for Public Health and the Environment (RIVM). Duitse coronapatiënt niet ziek tijdens verblijf in Limburg. [German corona patient not ill during stay in Limburg]; 26 Feb 2020. Bilthoven: RIVM. Available from: https://www.rivm.nl/nieuws/duitse-coronapatient-niet-ziek-tijdens-verblijf-in-limburg
  8. Lauer SA, Grantz KH, Bi Q, Jones FK, Zheng Q, Meredith HR, et al. The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Ann Intern Med. 2020;172(9):577-82.  https://doi.org/10.7326/M20-0504  PMID: 32150748 
  9. Pressedienst Landeshauptstadt Düsseldorf. Zwei Düsseldorfer mit Coronavirus infiziert. [Two Düsseldorfers infected with coronavirus]. Düsseldorf: Pressedienst Landeshauptstadt Düsseldorf; 2020. [Accessed 04 Jun 2020]. Available from: https://www.duesseldorf.de/medienportal/pressedienst-einzelansicht/pld/zwei-duesseldorfer-mit-coronavirus-infiziert.html
  10. Pressedienst Landeshauptstadt Düsseldorf. Die Coronazahlen vom 21. April. [Coranavirus case numbers 21 April]. Düsseldorf: Pressedienst Landeshauptstadt Düsseldorf; 2020. https://www.duesseldorf.de/medienportal/pressedienst-einzelansicht/pld/die-coronazahlen-vom-21-april.html
  11. Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, et al. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biol. 2019;20(1):8.  https://doi.org/10.1186/s13059-018-1618-7  PMID: 30621750 
  12. World Health Organization (WHO). Coronavirus disease 2019 (COVID-19) Situation Report – 135. Geneva: WHO; 03 Jun 2020. Available from: https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200603-covid-19-sitrep-135.pdf?sfvrsn=39972feb_2
  13. Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data - from vision to reality. Euro Surveill. 2017;22(13):30494.  https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494  PMID: 28382917 
  14. Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34(23):4121-3.  https://doi.org/10.1093/bioinformatics/bty407  PMID: 29790939 
  15. Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36(4):338-45.  https://doi.org/10.1038/nbt.4060  PMID: 29431738 
  16. Dilthey AT, Jain C, Koren S, Phillippy AM. Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps. Nat Commun. 2019;10(1):3066.  https://doi.org/10.1038/s41467-019-10934-2  PMID: 31296857 
  17. Robert Koch Institute (RKI). Coronavirus Disease 2019 (COVID-19) Daily Situation Report 23/03/2020. Berlin: RKI; Mar 2020. Available from: https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Situationsberichte/2020-03-23-en.pdf?__blob=publicationFile
  18. Gudbjartsson DF, Helgason A, Jonsson H, Magnusson OT, Melsted P, Norddahl GL, et al. Spread of SARS-CoV-2 in the Icelandic Population. N Engl J Med. 2020;NEJMoa2006100.  https://doi.org/10.1056/NEJMoa2006100  PMID: 32289214 
  19. Gonzalez-Reiche AS, Hernandez MM, Sullivan MJ, Ciferri B, Alshammary A, Obla A, et al. Introductions and early spread of SARS-CoV-2 in the New York City area. medRxiv, 2020.04.08.20056929 (preprint).  https://doi.org/10.1126/science.abc1917 
  20. Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, et al. Tracking virus outbreaks in the twenty-first century. Nat Microbiol. 2019;4(1):10-9.  https://doi.org/10.1038/s41564-018-0296-2  PMID: 30546099 
  21. Gardy JL, Loman NJ. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat Rev Genet. 2018;19(1):9-20.  https://doi.org/10.1038/nrg.2017.88  PMID: 29129921 

Data & Media loading...

Supplementary data

Submit comment
Comment moderation successfully completed
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error