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Abstract

Background

Tracking person-to-person SARS-CoV-2 transmission in the population is important to understand the epidemiology of community transmission and may contribute to the containment of SARS-CoV-2. Neither contact tracing nor genomic surveillance alone, however, are typically sufficient to achieve this objective.

Aim

We demonstrate the successful application of the integrated genomic surveillance (IGS) system of the German city of Düsseldorf for tracing SARS-CoV-2 transmission chains in the population as well as detecting and investigating travel-associated SARS-CoV-2 infection clusters.

Methods

Genomic surveillance, phylogenetic analysis, and structured case interviews were integrated to elucidate two genetically defined clusters of SARS-CoV-2 isolates detected by IGS in Düsseldorf in July 2021.

Results

Cluster 1 (n = 67 Düsseldorf cases) and Cluster 2 (n = 36) were detected in a surveillance dataset of 518 high-quality SARS-CoV-2 genomes from Düsseldorf (53% of total cases, sampled mid-June to July 2021). Cluster 1 could be traced back to a complex pattern of transmission in nightlife venues following a putative importation by a SARS-CoV-2-infected return traveller (IP) in late June; 28 SARS-CoV-2 cases could be epidemiologically directly linked to IP. Supported by viral genome data from Spain, Cluster 2 was shown to represent multiple independent introduction events of a viral strain circulating in Catalonia and other European countries, followed by diffuse community transmission in Düsseldorf.

Conclusion

IGS enabled high-resolution tracing of SARS-CoV-2 transmission in an internationally connected city during community transmission and provided infection chain-level evidence of the downstream propagation of travel-imported SARS-CoV-2 cases.

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This work is licensed under a Creative Commons Attribution 4.0 International License.
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/content/10.2807/1560-7917.ES.2022.27.43.2101089
2022-10-27
2024-04-26
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2022.27.43.2101089
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References

  1. World Health Organization (WHO). COVID-19 Weekly Epidemiological Update, Edition 106, published 24 August 2022. Geneva: WHO; 2022.
  2. Pung R, Chiew CJ, Young BE, Chin S, Chen MI, Clapham HE, et al. , Singapore 2019 Novel Coronavirus Outbreak Research Team. Investigation of three clusters of COVID-19 in Singapore: implications for surveillance and response measures. Lancet. 2020;395(10229):1039-46.  https://doi.org/10.1016/S0140-6736(20)30528-6  PMID: 32192580 
  3. Kang J, Jang YY, Kim J, Han SH, Lee KR, Kim M, et al. South Korea’s responses to stop the COVID-19 pandemic. Am J Infect Control. 2020;48(9):1080-6.  https://doi.org/10.1016/j.ajic.2020.06.003  PMID: 32522606 
  4. Peak CM, Kahn R, Grad YH, Childs LM, Li R, Lipsitch M, et al. Individual quarantine versus active monitoring of contacts for the mitigation of COVID-19: a modelling study. Lancet Infect Dis. 2020;20(9):1025-33.  https://doi.org/10.1016/S1473-3099(20)30361-3  PMID: 32445710 
  5. Kretzschmar ME, Rozhnova G, Bootsma MCJ, van Boven M, van de Wijgert JHHM, Bonten MJM. Impact of delays on effectiveness of contact tracing strategies for COVID-19: a modelling study. Lancet Public Health. 2020;5(8):e452-9.  https://doi.org/10.1016/S2468-2667(20)30157-2  PMID: 32682487 
  6. Miller JS, Bonacci RA, Lash RR, Moonan PK, Houck P, Van Meter JJ, et al. COVID-19 Case Investigation and Contact Tracing in Central Washington State, June-July 2020. J Community Health. 2021;46(5):918-21.  https://doi.org/10.1007/s10900-021-00974-5  PMID: 33689116 
  7. Lane CR, Sherry NL, Porter AF, Duchene S, Horan K, Andersson P, et al. Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study. Lancet Public Health. 2021;6(8):e547-56.  https://doi.org/10.1016/S2468-2667(21)00133-X  PMID: 34252365 
  8. COVID-19 Genomics UK (COG-UK) [email protected]. An integrated national scale SARS-CoV-2 genomic surveillance network. Lancet Microbe. 2020;1(3):e99-100.  https://doi.org/10.1016/S2666-5247(20)30054-9  PMID: 32835336 
  9. Callaway E. The coronavirus is mutating - does it matter? Nature. 2020;585(7824):174-7.  https://doi.org/10.1038/d41586-020-02544-6  PMID: 32901123 
  10. Walker A, Houwaart T, Finzer P, Ehlkes L, Tyshaieva A, Damagnez M, et al. , German COVID-19 OMICS Initiative (DeCOI). Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Clusters Based on Integrated Genomic Surveillance, Outbreak Analysis and Contact Tracing in an Urban Setting. Clin Infect Dis. 2022;74(6):1039-46. PMID: 34181711 
  11. Hjorleifsson KE, Rognvaldsson S, Jonsson H, Agustsdottir AB, Andresdottir M, Birgisdottir K, et al. Reconstruction of a large-scale outbreak of SARS-CoV-2 infection in Iceland informs vaccination strategies. Clin Microbiol Infect. 2022;28(6):852-8.  https://doi.org/10.1016/j.cmi.2022.02.012  PMID: 35182757 
  12. Popa A, Genger JW, Nicholson MD, Penz T, Schmid D, Aberle SW, et al. Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2. Sci Transl Med. 2020;12(573):eabe2555.  https://doi.org/10.1126/scitranslmed.abe2555  PMID: 33229462 
  13. Douglas J, Geoghegan JL, Hadfield J, Bouckaert R, Storey M, Ren X, et al. Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand. Emerg Infect Dis. 2021;27(9):2361-8.  https://doi.org/10.3201/eid2709.211097  PMID: 34424164 
  14. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772-80.  https://doi.org/10.1093/molbev/mst010  PMID: 23329690 
  15. 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 
  16. Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403-7.  https://doi.org/10.1038/s41564-020-0770-5  PMID: 32669681 
  17. Robert Koch Institute (RKI). Informationen zur Ausweisung internationaler Risikogebiete, 23. Juli 2021. [Information on the Risk Classification of Regions outside Germany, 23 July 2021]. Berlin: RKI; 2021. Available from: https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Transport/Archiv_Risikogebiete/Risikogebiete_2021-07-23.pdf?__blob=publicationFile
  18. Walker A, Houwaart T, Wienemann T, Vasconcelos MK, Strelow D, Senff T, et al. Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020. Euro Surveill. 2020;25(22).  https://doi.org/10.2807/1560-7917.ES.2020.25.22.2000746  PMID: 32524946 
  19. Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44(W1):W242-5.  https://doi.org/10.1093/nar/gkw290  PMID: 27095192 
  20. Gansner ER, North SC. An open graph visualization system and its applications to software engineering. Softw Pract Exper. 2000;30(11):1203-33.  https://doi.org/10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.0.CO;2-N 
  21. Campbell EM, Boyles A, Shankar A, Kim J, Knyazev S, Cintron R, et al. MicrobeTrace: Retooling molecular epidemiology for rapid public health response. PLOS Comput Biol. 2021;17(9):e1009300.  https://doi.org/10.1371/journal.pcbi.1009300  PMID: 34492010 
Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Torsten+Houwaart&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Houwaart Torsten</a>, <a href="/search?value1=Samir+Belhaj&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Belhaj Samir</a>, <a href="/search?value1=Emran+Tawalbeh&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Tawalbeh Emran</a>, <a href="/search?value1=Dirk+Nagels&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Nagels Dirk</a>, <a href="/search?value1=Yara+Fr%C3%B6hlich&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Fröhlich Yara</a>, <a href="/search?value1=Patrick+Finzer&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Finzer Patrick</a>, <a href="/search?value1=Pilar+Ciruela&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Ciruela Pilar</a>, <a href="/search?value1=Aurora+Sabri%C3%A0&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Sabrià Aurora</a>, <a href="/search?value1=Merc%C3%A8+Herrero&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Herrero Mercè</a>, <a href="/search?value1=Cristina+Andr%C3%A9s&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Andrés Cristina</a>, <a href="/search?value1=Andr%C3%A9s++Ant%C3%B3n&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Antón Andrés </a>, <a href="/search?value1=Assia+Benmoumene&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Benmoumene Assia</a>, <a href="/search?value1=Dounia+Asskali&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Asskali Dounia</a>, <a href="/search?value1=Hussein+Haidar&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Haidar Hussein</a>, <a href="/search?value1=Janina+von+Dahlen&option1=author&noRedirect=true" class="nonDisambigAuthorLink">von Dahlen Janina</a>, <a href="/search?value1=Jessica+Nicolai&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Nicolai Jessica</a>, <a href="/search?value1=Mygg+Stiller&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Stiller Mygg</a>, <a href="/search?value1=Jacqueline+Blum&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Blum Jacqueline</a>, <a href="/search?value1=Christian+Lange&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lange Christian</a>, <a href="/search?value1=Carla+Adelmann&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Adelmann Carla</a>, <a href="/search?value1=Britta+Schroer&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Schroer Britta</a>, <a href="/search?value1=Ute+Osmers&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Osmers Ute</a>, <a href="/search?value1=Christiane+Grice&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Grice Christiane</a>, <a href="/search?value1=Phillipp+P.+Kirfel&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kirfel Phillipp P.</a>, <a href="/search?value1=Hassan+Jomaa&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Jomaa Hassan</a>, <a href="/search?value1=Daniel+Strelow&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Strelow Daniel</a>, <a href="/search?value1=Lisanna+H%C3%BClse&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Hülse Lisanna</a>, <a href="/search?value1=Moritz+Pigulla&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Pigulla Moritz</a>, <a href="/search?value1=Pascal+Kreuzer&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kreuzer Pascal</a>, <a href="/search?value1=Alona+Tyshaieva&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Tyshaieva Alona</a>, <a href="/search?value1=Jonas+Weber&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Weber Jonas</a>, <a href="/search?value1=Tobias+Wienemann&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Wienemann Tobias</a>, <a href="/search?value1=Malte+Kohns+Vasconcelos&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kohns Vasconcelos Malte</a>, <a href="/search?value1=Katrin+Hoffmann&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Hoffmann Katrin</a>, <a href="/search?value1=Nadine+L%C3%BCbke&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lübke Nadine</a>, <a href="/search?value1=Sandra+Hauka&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Hauka Sandra</a>, <a href="/search?value1=Marcel+Andree&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Andree Marcel</a>, <a href="/search?value1=Claus+J%C3%BCrgen+Scholz&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Scholz Claus Jürgen</a>, <a href="/search?value1=Nathalie+Jazmati&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Jazmati Nathalie</a>, <a href="/search?value1=Klaus+G%C3%B6bels&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Göbels Klaus</a>, <a href="/search?value1=Rainer+Zotz&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Zotz Rainer</a>, <a href="/search?value1=Klaus+Pfeffer&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Pfeffer Klaus</a>, <a href="/search?value1=J%C3%B6rg+Timm&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Timm Jörg</a>, <a href="/search?value1=Lutz+Ehlkes&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Ehlkes Lutz</a>, <a href="/search?value1=Andreas+Walker&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Walker Andreas</a>, <a href="/search?value1=Alexander+T.+Dilthey&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Dilthey Alexander T.</a>, <a href="/search?value1=German+COVID-19+OMICS+Initiative+%28DeCOI%29&option1=author&noRedirect=true" class="nonDisambigAuthorLink">German COVID-19 OMICS Initiative (DeCOI)</a></span>. Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021. <a href="/content/ecdc">Euro Surveill.</a> 2022;27(43):pii=2101089. <a href="https://doi.org/10.2807/1560-7917.ES.2022.27.43.2101089" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2022.27.43.2101089</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 19 Nov 2021;&nbsp;&nbsp; <span class="generated">Accepted</span>: 16 Sept 2022 </span> </p>
/content/10.2807/1560-7917.ES.2022.27.43.2101089
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