The impact of public health interventions in the Nordic countries during the first year of SARS-CoV-2 transmission and evolution

  1. Sebastian Duchene
  2. Leo Featherstone
  3. Birgitte Freiesleben de Blasio
  4. Edward C Holmes
  5. Jon Bohlin
  6. John H-O Pettersson

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Abstract

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.

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  1. Version published to 10.2807/1560-7917.es.2021.26.44.2001996
  2. Version published to 10.1101/2020.11.18.20233767v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.11.18.20233767: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All genome sequences were aligned with Mafft v.
    Mafft
    suggested: (MAFFT, RRID:SCR_011811)
    7.455 (https://mafft.cbrc.jp/alignment/software/) and the ‘auto’ option, whereafter poorly aligned regions were removed using TrimAl (https://github.com/scapella/trimal) employing the ‘automated1’ algorithm.
    TrimAl
    suggested: (trimAl, RRID:SCR_017334)
    Estimating a time-scaled phylogenetic tree: We estimated maximum likelihood phylogenetic trees using IQ-TREE v2.0.614 employing the GTR+ Γ model of nucleotide substitution.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    A root-to-tip regression of genetic divergence against sampling time was performed on the resultant maximum likelihood tree using TempEst v.1.5.315.
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    Inferring virus migration dynamics between Nordic countries: To infer the frequency of importation or exportation events of SARS-CoV-2 between the Nordic countries and from the rest of the world, we employed a Bayesian stochastic mapping approach, also known as a discrete phylogeographic approach, as implemented in BEAST v1.10.418–20 using guidelines from Dellicour et al. for very large genomic data sets8.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    Sufficient sampling from the posterior was assessed using Tracer with all effective sample size values above 200 as estimated in Tracer v.1.721.
    Tracer
    suggested: (Tracer, RRID:SCR_019121)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    During the first six months of the pandemic Sweden never enforced strict community mobility limitations. Instead, social distancing, limiting sizes of social events and moving to distance education for students above 16 years were employed as the main mitigation efforts. Conversely, Denmark, Finland and Norway enforced a relatively strict population movement restrictions of their communities, closure of borders and government run facilities4. Iceland, in a similar manner to South Korea, utilised large-scale testing and contact tracing combined with social distancing and voluntary home-based quarantine without the need to regulate population movement9 (see also Supplementary table S1). Thus, while regulating population movement appears to provide an efficient mode to reduce community transmission10,11, non-population movement-targeted mitigation efforts are also viable options under certain circumstances. Norway experienced relatively low numbers of transmission chains during the first six months of the pandemic, with the bulk of the transmission chains sampled here emerging in mid-April and towards the end of July, although this might in part reflect a delayed start to genome sequencing such results should be interpreted with caution (Figure 1, Panel D). Indeed, we note that the sequencing intensity of Norwegian cases is lower than some of the other Nordic countries with similar case burdens (Table 1). When sample size per country increases with time, the effect of such poten...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

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  4. Version published to 10.1101/2020.11.18.20233767v1 on medRxiv