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Abstract

Background

Despite the unprecedented measures implemented globally in early 2020 to prevent the spread of SARS-CoV-2, Sweden, as many other countries, experienced a severe first wave during the COVID-19 pandemic.

Aim

We investigated the introduction and spread of SARS-CoV-2 into Sweden.

Methods

We analysed stored respiratory specimens (n = 1,979), sampled 7 February–2 April 2020, by PCR for SARS-CoV-2 and sequenced PCR-positive specimens. Sequences generated from newly detected cases and stored positive specimens February–June 2020 (n = 954) were combined with sequences (Sweden: n = 730; other countries: n = 129,913) retrieved from other sources for Nextstrain clade assignment and phylogenetic analyses.

Results

Twelve previously unrecognised SARS-CoV-2 cases were identified: the earliest was sampled on 3 March, 1 week before recognised community transmission. We showed an early influx of clades 20A and 20B from Italy (201/328, 61% of cases exposed abroad) and clades 19A and 20C from Austria (61/328, 19%). Clade 20C dominated the first wave (20C: 908/1,684, 54%; 20B: 438/1,684, 26%; 20A: 263/1,684, 16%), and 800 of 1,684 (48%) Swedish sequences formed a country-specific 20C cluster defined by a spike mutation (G24368T). At the regional level, the proportion of clade 20C sequences correlated with an earlier weighted mean date of COVID-19 deaths.

Conclusion

Community transmission in Sweden started when mitigation efforts still focused on preventing influx. This created a transmission advantage for clade 20C, likely introduced from ongoing cryptic spread in Austria. Therefore, pandemic preparedness should have a comprehensive approach, including capacity for large-scale diagnostics to allow early detection of travel-related cases and community transmission.

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2024-10-10
2024-11-14
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2024.29.41.2400021
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References

  1. Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD, Althaus CL, et al. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature. 2021;595(7869):707-12.  https://doi.org/10.1038/s41586-021-03677-y  PMID: 34098568 
  2. Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, et al. The emergence of SARS-CoV-2 in Europe and North America. Science. 2020;370(6516):564-70.  https://doi.org/10.1126/science.abc8169  PMID: 32912998 
  3. Tegnell A, Bessö A, Björkholm B, Byfors S, Carlson J, Tegmark Wisell K. Implementation of a broad public health approach to COVID-19 in Sweden, January 2020 to May 2022. Euro Surveill. 2023;28(41):2300063.  https://doi.org/10.2807/1560-7917.ES.2023.28.41.2300063  PMID: 37824250 
  4. da Silva Filipe A, Shepherd JG, Williams T, Hughes J, Aranday-Cortes E, Asamaphan P, et al. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nat Microbiol. 2021;6(1):112-22.  https://doi.org/10.1038/s41564-020-00838-z  PMID: 33349681 
  5. Babiker A, Martin MA, Marvil C, Bellman S, Petit Iii RA, Bradley HL, et al. Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic. Virus Evol. 2022;8(1):veac011.  https://doi.org/10.1093/ve/veac011  PMID: 35317348 
  6. Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang M-L, et al. Cryptic transmission of SARS-CoV-2 in Washington state. Science. 2020;370(6516):571-5.  https://doi.org/10.1126/science.abc0523  PMID: 32913002 
  7. Borges V, Isidro J, Trovão NS, Duarte S, Cortes-Martins H, Martiniano H, et al. SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal. Commun Med (Lond). 2022;2(1):10.  https://doi.org/10.1038/s43856-022-00072-0  PMID: 35603268 
  8. Saguti F, Magnil E, Enache L, Churqui MP, Johansson A, Lumley D, et al. Surveillance of wastewater revealed peaks of SARS-CoV-2 preceding those of hospitalized patients with COVID-19. Water Res. 2021;189:116620.  https://doi.org/10.1016/j.watres.2020.116620  PMID: 33212338 
  9. La Rosa G, Mancini P, Bonanno Ferraro G, Veneri C, Iaconelli M, Bonadonna L, et al. SARS-CoV-2 has been circulating in northern Italy since December 2019: Evidence from environmental monitoring. Sci Total Environ. 2021;750:141711.  https://doi.org/10.1016/j.scitotenv.2020.141711  PMID: 32835962 
  10. Fongaro G, Stoco PH, Souza DSM, Grisard EC, Magri ME, Rogovski P, et al. The presence of SARS-CoV-2 RNA in human sewage in Santa Catarina, Brazil, November 2019. Sci Total Environ. 2021;778:146198.  https://doi.org/10.1016/j.scitotenv.2021.146198  PMID: 33714813 
  11. Davis JT, Chinazzi M, Perra N, Mu K, Pastore Y Piontti A, Ajelli M, et al. Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave. Nature. 2021;600(7887):127-32.  https://doi.org/10.1038/s41586-021-04130-w  PMID: 34695837 
  12. du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, et al. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science. 2021;371(6530):708-12.  https://doi.org/10.1126/science.abf2946  PMID: 33419936 
  13. 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;382(24):2302-15.  https://doi.org/10.1056/NEJMoa2006100  PMID: 32289214 
  14. Bluhm A, Christandl M, Gesmundo F, Ravn Klausen F, Mančinska L, Steffan V, et al. SARS-CoV-2 transmission routes from genetic data: A Danish case study. PLoS One. 2020;15(10):e0241405.  https://doi.org/10.1371/journal.pone.0241405  PMID: 33119657 
  15. Muenchhoff M, Graf A, Krebs S, Quartucci C, Hasmann S, Hellmuth JC, et al. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020. Euro Surveill. 2021;26(43):2002066.  https://doi.org/10.2807/1560-7917.ES.2021.26.43.2002066  PMID: 34713795 
  16. Aksamentov I, Roemer C, Hodcroft EB, Neher RA. Nextclade: clade assignment, mutation calling and quality control for viral genomes. J Open Source Softw. 2021;6(67):3773.  https://doi.org/10.21105/joss.03773 
  17. 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 
  18. Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, et al. Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. J Open Source Softw. 2021;6(57):2906.  https://doi.org/10.21105/joss.02906  PMID: 34189396 
  19. De Maio N, Kalaghatgi P, Turakhia Y, Corbett-Detig R, Minh BQ, Goldman N. Maximum likelihood pandemic-scale phylogenetics. Nat Genet. 2023;55(5):746-52.  https://doi.org/10.1038/s41588-023-01368-0  PMID: 37038003 
  20. Sagulenko P, Puller V, Neher RA. TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evol. 2018;4(1):vex042.  https://doi.org/10.1093/ve/vex042  PMID: 29340210 
  21. McBroome J, Thornlow B, Hinrichs AS, Kramer A, De Maio N, Goldman N, et al. A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees. Mol Biol Evol. 2021;38(12):5819-24.  https://doi.org/10.1093/molbev/msab264  PMID: 34469548 
  22. The Public Health Agency of Sweden (PHAS). Bekräftade fall av covid-19 i Sverige. [Confirmed cases of covid-19 in Sweden]. Solna: PHAS; 2 Feb 2024. Swedish. Available from: https://www.folkhalsomyndigheten.se/smittskydd-beredskap/utbrott/aktuella-utbrott/covid-19/statistik-och-analyser/bekraftade-fall-i-sverige/
  23. Díez-Fuertes F, Iglesias-Caballero M, García-Pérez J, Monzón S, Jiménez P, Varona S, et al. A founder effect led early SARS-CoV-2 transmission in Spain. J Virol. 2021;95(3):e01583-20.  https://doi.org/10.1128/JVI.01583-20  PMID: 33127745 
  24. Tsui JL, McCrone JT, Lambert B, Bajaj S, Inward RPD, Bosetti P, et al. Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1. Science. 2023;381(6655):336-43.  https://doi.org/10.1126/science.adg6605  PMID: 37471538 
  25. Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, et al. Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science. 2021;371(6529):eabe3261.  https://doi.org/10.1126/science.abe3261  PMID: 33303686 
  26. Truong Nguyen P, Kant R, Van den Broeck F, Suvanto MT, Alburkat H, Virtanen J, et al. The phylodynamics of SARS-CoV-2 during 2020 in Finland. Commun Med (Lond). 2022;2(1):65.  https://doi.org/10.1038/s43856-022-00130-7  PMID: 35698660 
  27. Murall CL, Fournier E, Galvez JH, N’Guessan A, Reiling SJ, Quirion PO, et al. A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada. Genome Med. 2021;13(1):169.  https://doi.org/10.1186/s13073-021-00986-9  PMID: 34706766 
  28. 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 
  29. Stange M, Mari A, Roloff T, Seth-Smith HM, Schweitzer M, Brunner M, et al. SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. PLoS Pathog. 2021;17(3):e1009374.  https://doi.org/10.1371/journal.ppat.1009374  PMID: 33740028 
  30. Correa-Martínez CL, Kampmeier S, Kümpers P, Schwierzeck V, Hennies M, Hafezi W, et al. A pandemic in times of global tourism: Superspreading and exportation of COVID-19 cases from a ski area in Austria. J Clin Microbiol. 2020;58(6):e00588-20.  https://doi.org/10.1128/JCM.00588-20  PMID: 32245833 
  31. Li Q, Wu J, Nie J, Zhang L, Hao H, Liu S, et al. The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity. Cell. 2020;182(5):1284-1294.e9.  https://doi.org/10.1016/j.cell.2020.07.012  PMID: 32730807 
  32. Ling J, Hickman RA, Li J, Lu X, Lindahl JF, Lundkvist Å, et al. Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic. Viruses. 2020;12(9):1026.  https://doi.org/10.3390/v12091026  PMID: 32937868 
  33. The Public Health Agency of Sweden (PHAS). Påvisning av antikroppar mot SARS-CoV-2 hos blodgivare. [Detection of antibodies to SARS-CoV-2 in blood donors]. Solna: PHAS; 28 Oct 2021. Swedish. Available from: https://www.folkhalsomyndigheten.se/publikationer-och-material/publikationsarkiv/p/pavisning-av-antikroppar-efter-genomgangen-covid-19-hos-blodgivare-delrapport-2/#:~:text=Unders%C3%B6kningar%20p%C3%A5g%C3%A5r%20f%C3%B6r%20p%C3%A5visning%20av,p%C3%A5g%C3%A5ende%20pandemi%202020%20och%202021
Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Robert+Dyrdak&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Dyrdak Robert</a>, <a href="/search?value1=Emma+B+Hodcroft&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Hodcroft Emma B</a>, <a href="/search?value1=Sandra+Broddesson&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Broddesson Sandra</a>, <a href="/search?value1=Malin+Grabbe&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Grabbe Malin</a>, <a href="/search?value1=Hildur+Franklin&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Franklin Hildur</a>, <a href="/search?value1=Magnus+Gissl%C3%A9n&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Gisslén Magnus</a>, <a href="/search?value1=Maricris+E+Holm&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Holm Maricris E</a>, <a href="/search?value1=Magnus+Lindh&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lindh Magnus</a>, <a href="/search?value1=Joanna+Nederby-%C3%96hd&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Nederby-Öhd Joanna</a>, <a href="/search?value1=Johan+Ringlander&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Ringlander Johan</a>, <a href="/search?value1=Martin+Sundqvist&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Sundqvist Martin</a>, <a href="/search?value1=Richard+A+Neher&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Neher Richard A</a>, <a href="/search?value1=Jan+Albert&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Albert Jan</a></span>. Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020. <a href="/content/ecdc">Euro Surveill.</a> 2024;29(41):pii=2400021. <a href="https://doi.org/10.2807/1560-7917.ES.2024.29.41.2400021" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2024.29.41.2400021</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 03 Jan 2024;&nbsp;&nbsp; <span class="generated">Accepted</span>: 30 May 2024 </span> </p>
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