SARS-CoV-2 Basel phylogeny paper is published! 22 March 2021
During the first wave of SARS-CoV-2 in Switzerland, we aimed to sequence all positive cases from Basel-City, the core of a larger metropolitan region with a commuter catchment area, and successfully did so for 63% of all detected cases. The first case of SARS-CoV-2 in Basel, Switzerland was detected on February 26th 2020.
We set up a COVID-19 Analysis Pipeline (COVGAP) to QC raw reads, assemble whole-genomes, and call mutations from Illumina sequencing data (freely available on our github).
We analysed viral genetic diversity using PANGOLIN taxonomic lineages and performed phylogenetic analyses to infer spread within the city.
We found that a particular variant, B.1-C15324T, accounted for 68% of cases in Basel. Some of the cases could be linked via epidemiological data to a known super-spreading event in the Alsace suggesting a local spreading event in the larger Basel area.
This study demonstrates the strength of molecular surveillance of SARS-CoV-2 in a city, especially when being linked with epidemiological data.