SARS-CoV-2 phylogeny during the early outbreak in the Basel area, Switzerland: import and spread dominated by a single B.1 lineage variant (C15324T)

Stange, M.; Mari, A.; Roloff, T.; Seth-Smith, H. M. B.; Schweitzer, M.; Brunner, M.; Leuzinger, K.; Sogaard, K. K.; Gensch, A.; Tschudin-Sutter, S.; Fuchs, S.; Bielicki, J. A.; Pargger, H.; Siegemund, M.; Nickel, C. H.; Bingisser, R.; Osthoff, M.; Bassetti, S.; Schneider-Sliwa, R.; Battegay, M.; Hirsch, H. H.; Egli, A.

Background: The first local case of SARS-CoV-2 in Basel, Switzerland, was detected on February 26th 2020. We present a phylogenetic cross-sectional study and explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26th until March 23rd. Methods: We sequenced SARS-CoV-2 samples from naso-oropharyngeal swabs and generated 468 high quality genomes and called variants with our COVID-19 Genome Analysis Pipeline (COVGAP). We analysed viral genetic diversity using PANGOLIN taxonomic lineages. For identification of introduction and dissemination events across the Basel area a time-calibrated phylogeny was inferred including global SARS-CoV-2 genomes. Findings: Our samples exhibit low lineage diversity compared to neighbouring countries. Lineage B.1 (82.7%), detected from March 2nd, dominated infections in Basel. A large clade within B.1 contains 69.1% of our samples, all of which carry the SNP C15324T, suggesting local transmission in spreading events. We have located the geographic origin of this mutation in our tri-national region. The remaining genomes map broadly over the global phylogenetic tree, evidencing several events of introduction from and/or dissemination to other regions of the world. Further, we have identified several transmission events within families. Interpretation: Molecular surveillance of SARS-CoV-2 by phylogenetic reconstruction in the Basel area provides important insights into local transmission (spreading events and family transmission). This phylogenetic analysis enriches epidemiological and contact tracing data, allowing connection of seemingly unconnected events and drawing conclusions, which can be used to inform public health interventions. Funding: No dedicated funding was used for this work.