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). SARS-CoV-2 phylogeny during the early outbreak in the Basel area, Switzerland

Background. The new coronavirus SARS-CoV-2 was detected on February 26th 2020 in the City of Basel, Switzerland. We present a phylogenetic case 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 the Basel outbreak and generated 462 high quality genomes and called variants with our COVID-19 Genome Analysis Pipeline (COVGAP), and analyzed 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.Results. Our samples exhibit low lineage diversity compared to neighboring countries. The first detected case, a travel returner from Italy, belonged to viral lineage B.1.1. In general, however, lineage B.1 (82.7%) dominated infections in Basel, detected from March 2nd. A large phylogenetic cluster (B.1) contains 71.2% of our samples, all of which carry the SNP C15324T, suggesting local transmission and/or a common source. We locate the geographic origin of this mutation in Switzerland or France. The other genomes map broadly over the global phylogenetic tree, evidencing several events of introduction from and/or dissemination to other regions of the world.Conclusion. Molecular surveillance of SARS-CoV-2 by phylogenetic reconstruction in a global context aids in discerning local transmissions versus introductions and dissemination events, complementing and enriching epidemiology and contact tracing data.