1887
  1. Home
  2. Eurosurveillance
  3. Volume 26, Issue 44, 04/Nov/2021
  4. Article
Research Open Access
Like 0
Download

Abstract

Background

Many countries have attempted to mitigate and control COVID-19 through non-pharmaceutical interventions, particularly with the aim of reducing population movement and contact. However, it remains unclear how the different control strategies impacted the local phylodynamics of the causative SARS-CoV-2 virus.

Aim

We aimed to assess the duration of chains of virus transmission within individual countries and the extent to which countries exported viruses to their geographical neighbours.

Methods

We analysed complete SARS-CoV-2 genomes to infer the relative frequencies of virus importation and exportation, as well as virus transmission dynamics, in countries of northern Europe. We examined virus evolution and phylodynamics in Denmark, Finland, Iceland, Norway and Sweden during the first year of the COVID-19 pandemic.

Results

The Nordic countries differed markedly in the invasiveness of control strategies, which we found reflected in transmission chain dynamics. For example, Sweden, which compared with the other Nordic countries relied more on recommendation-based rather than legislation-based mitigation interventions, had transmission chains that were more numerous and tended to have more cases. This trend increased over the first 8 months of 2020. Together with Denmark, Sweden was a net exporter of SARS-CoV-2. Norway and Finland implemented legislation-based interventions; their transmission chain dynamics were in stark contrast to their neighbouring country Sweden.

Conclusion

Sweden constituted an epidemiological and evolutionary refugium that enabled the virus to maintain active transmission and spread to other geographical locations. Our analysis reveals the utility of genomic surveillance where monitoring of active transmission chains is a key metric.

© Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Loading

Article metrics loading...

/content/10.2807/1560-7917.ES.2021.26.44.2001996
2021-11-04
2024-11-22
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2021.26.44.2001996
Loading
Loading full text...

Full text loading...

/deliver/fulltext/eurosurveillance/26/44/eurosurv-26-44-4.html?itemId=/content/10.2807/1560-7917.ES.2021.26.44.2001996&mimeType=html&fmt=ahah

References

  1. Wu F, Zhao S, Yu B, Chen Y-M, Wang W, Song Z-G, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265-9. <jrn10<jrn10<jrn10 https://doi.org/10.1038/s41586-020-2008-3  PMID: 32015508 
  2. Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020;395(10224):565-74.  https://doi.org/10.1016/S0140-6736(20)30251-8  PMID: 32007145 
  3. Ludvigsson JF. The first eight months of Sweden’s COVID-19 strategy and the key actions and actors that were involved. Acta Paediatr. 2020;109(12):2459-71.  https://doi.org/10.1111/apa.15582  PMID: 32951258 
  4. Conyon MJ, He L, Thomsen S. Lockdowns and COVID-19 deaths in Scandinavia. SSRN Electronic Journal.2020; (Preprint).  https://doi.org/10.2139/ssrn.3616969 
  5. Kontis V, Bennett JE, Rashid T, Parks RM, Pearson-Stuttard J, Guillot M, et al. Magnitude, demographics and dynamics of the effect of the first wave of the COVID-19 pandemic on all-cause mortality in 21 industrialized countries. Nat Med. 2020;26(12):1919-28.  https://doi.org/10.1038/s41591-020-1112-0  PMID: 33057181 
  6. World Health Organization (WHO). WHO coronavirus (COVID-19) dashboard. Geneva: WHO. [Accessed: 12 May 2021]. Available from https://covid19.who.int
  7. 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 
  8. Ritchie H, Ortiz-Ospina E, Beltekian D, Mathieu E, Hasell J, Macdonald B, et al. Coronavirus pandemic (COVID-19). Our world in data; 2020. Available from: https://ourworldindata.org/coronavirus
  9. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37(5):1530-4.  https://doi.org/10.1093/molbev/msaa015  PMID: 32011700 
  10. Rambaut A, Lam TT, Max Carvalho L, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2(1):vew007.  https://doi.org/10.1093/ve/vew007  PMID: 27774300 
  11. To T-H, Jung M, Lycett S, Gascuel O. Fast dating using least-squares criteria and algorithms. Syst Biol. 2016;65(1):82-97.  https://doi.org/10.1093/sysbio/syv068  PMID: 26424727 
  12. Duchene S, Featherstone L, Haritopoulou-Sinanidou M, Rambaut A, Lemey P, Baele G. Temporal signal and the phylodynamic threshold of SARS-CoV-2. Virus Evol. 2020;6(2):a061.  https://doi.org/10.1093/ve/veaa061  PMID: 33235813 
  13. 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. preprint. medRxiv 2020.10.23.20218446. Preprint. https://doi.org/ https://doi.org/10.1101/2020.10.23.20218446 
  14. Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, et al. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature. 2021;593(7858):266-9.  https://doi.org/10.1038/s41586-021-03470-x  PMID: 33767447 
  15. Minin VN, Suchard MA. Counting labeled transitions in continuous-time Markov models of evolution. J Math Biol. 2008;56(3):391-412.  https://doi.org/10.1007/s00285-007-0120-8  PMID: 17874105 
  16. Minin VN, Suchard MA. Fast, accurate and simulation-free stochastic mapping. Philos Trans R Soc Lond B Biol Sci. 2008;363(1512):3985-95.  https://doi.org/10.1098/rstb.2008.0176  PMID: 18852111 
  17. Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018;4(1):vey016.  https://doi.org/10.1093/ve/vey016  PMID: 29942656 
  18. Dellicour S, Durkin K, Hong SL, Vanmechelen B, Martí-Carreras J, Gill MS, et al. A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages. preprint. Mol Biol Evol. 2021;38(4):1608-13.  https://doi.org/10.1093/molbev/msaa284  PMID: 33316043 
  19. Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 2018;67(5):901-4.  https://doi.org/10.1093/sysbio/syy032  PMID: 29718447 
  20. Hale T, Angrist N, Goldszmidt R, Kira B, Petherick A, Phillips T, et al. A global panel database of pandemic policies (Oxford COVID-19 Government Response Tracker). Nat Hum Behav. 2021;5(4):529-38.  https://doi.org/10.1038/s41562-021-01079-8  PMID: 33686204 
  21. 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 
  22. Flaxman S, Mishra S, Gandy A, Unwin HJT, Mellan TA, Coupland H, et al. Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe. Nature. 2020;584(7820):257-61.  https://doi.org/10.1038/s41586-020-2405-7  PMID: 32512579 
  23. Geoghegan JL, Ren X, Storey M, Hadfield J, Jelley L, Jefferies S, et al. Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nat Commun. 2020;11(1):6351.  https://doi.org/10.1038/s41467-020-20235-8  PMID: 33311501 
  24. Modig K, Ahlbom A, Ebeling M. Excess mortality from COVID-19: weekly excess death rates by age and sex for Sweden and its most affected region. Eur J Public Health. 2021;31(1):17-22.  https://doi.org/10.1093/eurpub/ckaa218  PMID: 33169145 
  25. Kamerlin SCL, Kasson PM. Managing coronavirus disease spread with voluntary public health measures: Sweden as a case study for pandemic control. Clin Infect Dis. 2020;71(12):3174-81.  https://doi.org/10.1093/cid/ciaa864  PMID: 32609825 
  26. Buja A, Paganini M, Cristofori V, Baldovin T, Fusinato R, Boccuzzo G, et al. Opening schools and trends in SARS-CoV-2 transmission in European countries. Public and Global Health. medRxiv 2021.02.26.21252504. Preprint..  https://doi.org/10.1101/2021.02.26.21252504 
  27. Stage HB, Shingleton J, Ghosh S, Scarabel F, Pellis L, Finnie T. Shut and re-open: the role of schools in the spread of COVID-19 in Europe. Preprint. medRxiv 2020.06.24.20139634. Preprint.  https://doi.org/10.1101/2020.06.24.20139634 
  28. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 vaccine against the B.1.351 variant. N Engl J Med. 2021;384(20):1885-98.  https://doi.org/10.1056/NEJMoa2102214  PMID: 33725432 
  29. Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;19(7):409-24.  https://doi.org/10.1038/s41579-021-00573-0  PMID: 34075212 
  30. Del Rio C, Malani PN, Omer SB. Confronting the delta variant of SARS-CoV-2, summer 2021. JAMA. 2021;326(11):1001-2.  https://doi.org/10.1001/jama.2021.14811  PMID: 34406361 
The impact of public health interventions in the Nordic countries during the first year of SARS-CoV-2 transmission and evolution
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Sebastian+Duchene&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Duchene Sebastian</a>, <a href="/search?value1=Leo+Featherstone&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Featherstone Leo</a>, <a href="/search?value1=Birgitte+Freiesleben+de+Blasio&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Freiesleben de Blasio Birgitte</a>, <a href="/search?value1=Edward+C+Holmes&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Holmes Edward C</a>, <a href="/search?value1=Jon+Bohlin&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Bohlin Jon</a>, <a href="/search?value1=John+H-O+Pettersson&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Pettersson John H-O</a></span>. The impact of public health interventions in the Nordic countries during the first year of SARS-CoV-2 transmission and evolution. <a href="/content/ecdc">Euro Surveill.</a> 2021;26(44):pii=2001996. <a href="https://doi.org/10.2807/1560-7917.ES.2021.26.44.2001996" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2021.26.44.2001996</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 25 Nov 2020;&nbsp;&nbsp; <span class="generated">Accepted</span>: 04 Jun 2021 </span> </p>
/content/10.2807/1560-7917.ES.2021.26.44.2001996
/content/10.2807/1560-7917.ES.2021.26.44.2001996
Loading

Data & Media loading...

Supplementary data

Submit comment
Close
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