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. 2024 Oct;29(41):2400021.
doi: 10.2807/1560-7917.ES.2024.29.41.2400021.

Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020

Robert Dyrdak  1   2 , Emma B Hodcroft  3   4 , Sandra Broddesson  2 , Malin Grabbe  1   2 , Hildur Franklin  5 , Magnus Gisslén  6   7   8 , Maricris E Holm  9 , Magnus Lindh  6   9 , Joanna Nederby-Öhd  10   11 , Johan Ringlander  6   9 , Martin Sundqvist  12   5 , Richard A Neher  13   4 , Jan Albert  1   2
Affiliations

Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020

Robert Dyrdak et al. Euro Surveill. 2024 Oct.

Abstract

BackgroundDespite 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.AimWe investigated the introduction and spread of SARS-CoV-2 into Sweden.MethodsWe 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.ResultsTwelve 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.ConclusionCommunity 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.

Keywords: COVID-19 pandemic; SARS-CoV-2; epidemiology; phylogenetics; viral respiratory tract infection.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Sources of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences and number of sequences included, Sweden (n = 1,684) and other countries (n = 129,913), December 2019–June 2020
Figure 2
Figure 2
Retrospective PCR testing of stored respiratory specimens for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), by date and exposure, Stockholm Region, Sweden, February–April 2020 (n = 1,979)
Figure 3
Figure 3
Number of sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), by region, Sweden, January–June 2020 (n = 1,684)
Figure 4
Figure 4
Sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), by genetic clade and patient exposure, Sweden, February–June 2020 (n = 1,675)a
Figure 5
Figure 5
Phylogenetic tree of sequences and selected clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Sweden (n = 1,684) and other countries (n = 1,199), January–June 2020
Figure 6
Figure 6
Registered deaths of patients with a COVID-19 diagnosis (n = 4,867), by the proportion of clade 20C severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among domestic cases (A) and cumulative number of registered deaths of patients with a COVID-19 diagnosis, by mean date of registered deaths of patients with a COVID-19 diagnosis (B), Sweden, January–June 2020
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