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

Ravi Kant,Sari Hannula,Hanna Jarva,Marianne Gunell,Sara Lehtinen,Tarja Sironen,Jonna Ikonen,Pekka Ellonen,Hanna Liimatainen,Teemu Smura,Bruno Luukinen,Satu Kurkela,Maija Lappalainen,Hussein Alburkat,Ilya Plyusnin,Carita Savolainen-Kopra,Mert Erdin,Tytti Vuorinen,Viktor Olander,Veera Salminen,Leena Huhti,Olli Vapalahti,Erika Lindh,Jani Halkilahti,Soile Blomqvist,Phuoc Truong Nguyen,Fathiah Zakham,Otto Helve,Minna Paloniemi,Niina Ikonen,Hannimari Kallio‐Kokko ,Maija T Suvanto

doi:10.3201/eid2712.211631

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.

Highlights

Severe acute respiratory syndrome coronavirus 2 Alpha and Beta variants became dominant in Finland in spring 2021 but had diminished by summer
The Study To assess the temporal epidemiologic dynamics among different variants of concern and identify spreading events and sources of SARS-CoV-2 cases detected in Finland, we began sequencing 400–1,000 virus samples per week collected during December 2020–May 2021 and analyzed the resulting genomes (n = 14,080), which are available in the GISAID database
Each phylogenetic tree was computed from the filtered sequences and a global reference dataset consisting of 5 representative sequences, 1 sequence from the country of origin (England for Alpha, South Africa for Beta) and 4 randomly chosen from other countries containing the same lineage, for each date during December 2020– May 2021

Summary

Introduction

Severe acute respiratory syndrome coronavirus 2 Alpha and Beta variants became dominant in Finland in spring 2021 but had diminished by summer. The Study To assess the temporal epidemiologic dynamics among different variants of concern and identify spreading events and sources of SARS-CoV-2 cases detected in Finland, we began sequencing 400–1,000 virus samples per week collected during December 2020–May 2021 and analyzed the resulting genomes (n = 14,080), which are available in the GISAID We analyzed the resulting dataset (n = 9,160) with Pangolin (https://cov-lineages.org) (8) to identify lineages, from which we filtered Alpha and Beta variants for phylogenetic analyses.

Results

Conclusion