1 School of Medicine, Örebro University, Örebro, Sweden
2 Department of Laboratory Medicine, Clinical Microbiology, Örebro University hospital, Örebro
3 Faculty of Medicine and Health, Örebro University, Örebro
4 County Medical Officer for Communicable Diseases, Region Örebro County, Örebro
Bakgrund: On March 4, 2020, the first case of covid-19 was identified in Örebro County, Sweden. The aim of this study was to map the introduction of SARS-CoV-2 into Örebro County through demographic and genetic information, enabling a deeper understanding of the pandemic on a regional level.
Metod: The initial 506 laboratory PCR-confirmed cases of COVID-19 in Örebro County (dated 2020-03-04 – 2020-04-15) were analysed regarding demographic aspects and of those cases the first 13 underwent whole genome sequencing through AmpliSeq, Ion Torrent targeted Next Generation Sequencing (Folkhälsomynidgheten, Solna) and the sequences were analysed using Nextclade (www.nextstrain.org).
Resultat: The 13 sequenced cases of SARS-CoV-2 in Örebro County represented three genetic clades of the virus (Clade G n=3, Clade GH n=9, Clade GR n=1). All 13 strains of SARS-CoV-2 carried the D614G spike mutation. The 506 laboratory confirmed cases were found in multiple municipalities in the county, with a significantly higher incidence in the largest municipality, Örebro, as compared to the whole county (OR 2.194 (1.806- 2.665), p<0.001). Three out of five high incidence areas in Örebro were located in districts known to have a higher proportion of foreign born.
Slutsats: SARS-CoV-2 were introduced to Region Örebro through multiple introductions of genetically diverse strains. The cases were unevenly distributed throughout the county during the first six weeks. The presence of D614G spike mutation indicates introduction to Örebro county from Europe rather from other parts of the world. Sequence analysis of more samples collected during this time is ongoing.