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Incidence Trends for SARS-CoV-2 Alpha and Beta Variants, Finland, Spring 2021

Ravi Kant et al. Emerg Infect Dis. 2021 Dec.

Abstract

Severe acute respiratory syndrome coronavirus 2 Alpha and Beta variants became dominant in Finland in spring 2021 but had diminished by summer. We used phylogenetic clustering to identify sources of spreading. We found that outbreaks were mostly seeded by a few introductions, highlighting the importance of surveillance and prevention policies.

Keywords: Alpha variant; Beta variant; COVID-19; Finland; SARS-CoV-2; coronavirus disease; epidemiology; infectious disease transmission; phylogeny; public health surveillance; respiratory infections; severe acute respiratory syndrome coronavirus 2; vaccination; vaccines; viruses.

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Figures

Figure 1
Figure 1
Phylogenetic tree of severe acute respiratory syndrome coronavirus 2 Alpha (B.1.1.7) variant clusters from Finland and sequence distribution. The tree (A) shows 86 clusters with ≥5 sequences (red circles), of which 84 contain 5,270 sequences sampled in Finland using TreeCluster, and 32 Finland singletons (white circles). The tree was constructed by using IQ-TREE 2 (10) with 1,000 ultrafast bootstraps. Each row in subsequent graphs is equivalent to a cluster and shows the number of sequences from Finland (B) and the proportion of sequences per region of Finland (C). Regions of Finland: 1, Åland Islands; 2, Central Finland Health Care District; 3, Central Ostrobothnia Hospital District; 4, East Savo Hospital District; 5, Hospital District of Helsinki and Uusimaa; 6, Hospital District of South Ostrobothnia; 7, Hospital District of Southwest Finland; 8, Kainuu Social and Health Care Joint Authority; 9, Kanta-Häme Hospital District; 10, Länsi-Pohja Healthcare District; 11, Lapland Hospital District; 12, North Karelia Hospital District; 13, North Ostrobothnia Hospital District; 14, North Savo Hospital District; 15, Päijät-Häme Hospital District; 16, Pirkanmaa Hospital District; 17, Satakunta Hospital District; 18, Social and Health Services in Kymenlaakso; 19, South Karelia Social and Health Care District; 20, South Savo Hospital District; 21, Vaasa Hospital District.
Figure 2
Figure 2
Phylogenetic trees of severe acute respiratory syndrome coronavirus 2 Beta (B1.351) variant clusters from Finland and sequence distribution. The tree (A) shows 76 clusters with ≥5 sequences (red circles), of which 48 contain 898 sequences sampled in Finland using TreeCluster (11), and 23 Finland singletons (white circles) from 33. The tree was constructed by using IQ-TREE 2 (10) with 1,000 ultrafast bootstraps. Each row in subsequent panels is equivalent to a cluster and shows the number of sequences from Finland (B) and the proportion of sequences per region of from Finland (C). Regions of Finland: 1, Central Finland Health Care District; 2, East Savo Hospital District; 3, Hospital District of Helsinki and Uusimaa; 4, Hospital District of South Ostrobothnia; 5, Hospital District of Southwest Finland; 6, Kainuu Social and Health Care Joint Authority; 7, Kanta-Häme Hospital District; 8, Länsi-Pohja Healthcare District; 9, Lapland Hospital District; 10, North Karelia Hospital District; 11, North Ostrobothnia Hospital District; 12, North Savo Hospital District; 13, Päijät-Häme Hospital District; 14, Pirkanmaa Hospital District; 15, Satakunta Hospital District; 16, Social and Health Services in Kymenlaakso; 17, South Karelia Social and Health Care District; 18, South Savo Hospital District; 19, Vaasa Hospital District,
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