The phylodynamics of SARS-CoV-2 during 2020 in Finland

• Published in: Communications medicine 2022-06, Vol.2 (1), p.65-65, Article 65
• Main Authors: Truong Nguyen, Phuoc, Kant, Ravi, Van den Broeck, Frederik, Suvanto, Maija T., Alburkat, Hussein, Virtanen, Jenni, Ahvenainen, Ella, Castren, Robert, Hong, Samuel L., Baele, Guy, Ahava, Maarit J., Jarva, Hanna, Jokiranta, Suvi Tuulia, Kallio-Kokko, Hannimari, Kekäläinen, Eliisa, Kirjavainen, Vesa, Kortela, Elisa, Kurkela, Satu, Lappalainen, Maija, Liimatainen, Hanna, Suchard, Marc A., Hannula, Sari, Ellonen, Pekka, Sironen, Tarja, Lemey, Philippe, Vapalahti, Olli, Smura, Teemu
• Format: Article
• Language: English
• Subjects: 45; 45/91; 631/326/596/2562; 631/326/596/4130; Medicine; Medicine & Public Health
• ISSN: 2730-664X; 2730-664X
• DOI: 10.1038/s43856-022-00130-7

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections and fatalities globally since its emergence in late 2019. The virus was first detected in Finland in January 2020, after which it rapidly spread among the populace in spring. However, compared to other European nations, Finland has had a low incidence of SARS-CoV-2. To gain insight into the origins and turnover of SARS-CoV-2 lineages circulating in Finland in 2020, we investigated the phylogeographic and -dynamic history of the virus. Methods The origins of SARS-CoV-2 introductions were inferred via Travel-aware Bayesian time-measured phylogeographic analyses. Sequences for the analyses included virus genomes belonging to the B.1 lineage and with the D614G mutation from countries of likely origin, which were determined utilizing Google mobility data. We collected all available sequences from spring and fall peaks to study lineage dynamics. Results We observed rapid turnover among Finnish lineages during this period. Clade 20C became the most prevalent among sequenced cases and was replaced by other strains in fall 2020. Bayesian phylogeographic reconstructions suggested 42 independent introductions into Finland during spring 2020, mainly from Italy, Austria, and Spain. Conclusions A single introduction from Spain might have seeded one-third of cases in Finland during spring in 2020. The investigations of the original introductions of SARS-CoV-2 to Finland during the early stages of the pandemic and of the subsequent lineage dynamics could be utilized to assess the role of transboundary movements and the effects of early intervention and public health measures. Plain language summary The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths since it began spreading globally in late 2019. Unlike other European countries, during early pandemics Finland had relatively few coronavirus cases. We investigated how and from where SARS-CoV-2 arrived in Finland in early 2020. Viruses mutate over time and SARS-CoV-2 viruses with different mutations are described as variants. We assessed the proportions of different SARS-CoV-2 variants over time by studying the different mutations occurring combined with travel history data. We found that the first epidemic wave was seeded by 42 viral introductions (mainly from Spain, Italy and Austria), including one that caused a third of all COVID-19 infections. Our results sho