SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event

Abstract

The first case of SARS-CoV-2 in Basel, Switzerland was detected on February 26th 2020. We present a phylogenetic study to explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26th until March 23rd. We sequenced SARS-CoV-2 naso-oropharyngeal swabs from 746 positive tests that were performed at the University Hospital Basel during the study period. We successfully generated 468 high quality genomes from unique patients and called variants with our COVID-19 Pipeline (COVGAP), and analysed viral genetic diversity using PANGOLIN taxonomic lineages. To identify introduction and dissemination events we incorporated global SARS-CoV-2 genomes and inferred a time-calibrated phylogeny. Epidemiological data from patient questionnaires was used to facilitate the interpretation of phylogenetic observations. The early outbreak in Basel was dominated by lineage B.1 (83·6%), detected first on March 2nd, although the first sample identified belonged to B.1.1. Within B.1, 68·2% of our samples fall within a clade defined by the SNP C15324T ('Basel cluster'), including 157 identical sequences at the root of the 'Basel cluster', some of which we can specifically trace to regional spreading events. We infer the origin of B.1-C15324T to mid-February in our tri-national region. The other genomes map broadly over the global phylogenetic tree, showing several introduction events from and/or dissemination to other regions of the world via travellers. Family transmissions can also be traced in our data. A single lineage variant dominated the outbreak in the Basel area while other lineages, such as the first (B.1.1), did not propagate. A mass gathering event was the predominant initial source of cases, with travel returners and family transmissions to a lesser extent. We highlight the importance of adding specific questions to epidemiological questionnaires, to obtain data on attendance of large gatherings and their locations, as well as travel history, to effectively identify routes of transmissions in up-coming outbreaks. This phylogenetic analysis in concert with epidemiological and contact tracing data, allows connection and interpretation of events, and can inform public health interventions. Trial Registration: ClinicalTrials.gov NCT04351503.

Fig 1. Epidemiological curve of the first COVID-19 wave in Basel-City and region, Switzerland.

Positive (red line, dark grey area) and negative (grey line, light grey area) SARS-CoV-2 PCR tests are depicted, from the beginning of the outbreak in February to March 23^rd 2020. Major events and imposed restrictions are marked by horizontal lines. The first confirmed cases in Switzerland and Basel were on February 25^th and February 26^th, respectively.

Fig 2. SARS-CoV-2 lineage diversity in Switzerland and neighbouring countries during the study period from the first detected case on February 26^th to March 23^rd 2020, divided into four weeks (I: February 26^th–March 3^rd, II: March 4^th - 10^th, III: March 11^th - 17^th, IV: March 18^th - 23^rd (6 days)).

A. Daily cases and lineage identity in the Basel area cohort. Low-abundant lineages increased one week after the end of winter school vacation (March 8^th) and were introduced by travel returners. B. SARS-CoV-2 lineage diversity in the Basel area, the rest of Switzerland, and neighbouring countries. Number of genomes per week are represented in the inner margin of the time wheel. Number of lineages (L) per country counted from onset of the epidemic in each country until March 23^rd 2020. Link to the baselayer: https://ec.europa.eu/eurostat/web/gisco/geodata/reference-data/administrative-units-statistical-units/nuts.

Fig 3. SARS-CoV-2 phylogeny of Basel area samples and genetic lineages (PANGOLIN) in a global context.

A. Time tree of SARS-CoV-2 genomes from the Basel area cohort as well as subsampled global genomes (30 genomes per country and month), coloured by continent of origin. Amino acid mutations at internal nodes representing clade defining mutations are shown. B. Mirrored time tree coloured by genetic lineages sensu PANGOLIN v.May19 (https://github.com/cov-lineages/). Each tip with a circle represents a genome from the Basel area cohort, branches without circled tips represent global genomes, showing the global context of the Basel genomes.

Fig 4. Divergence trees plotting nucleotide divergence between 468 genomes and expanded clusters of genomes in selected phylogenetic lineages.

A. Genomes from the Basel area cohort in global context. Tree composition is identical to the time tree from Fig 3. Branches with circles at the tip represent genomes from the present study; branches without circles represent global genomes from GISAID. The major Basel cluster contains genomes with up to five mutations from its ancestral node. B. Detail of a mixed cluster derived from B.1.1 with seven to nine mutations to the root. A single genome assigned to lineage B.1.1.6 has an assumed origin in Austria; two genomes (B.1.1.10) most likely originate from the UK. C. Potential ski-holiday related cluster (C1059T) with seven samples had confirmed associations with skiing destinations. D. Proportion of B.1-C15324T genomes among all publicly available genomes per country from the five countries in which this variant was first registered to March 23^rd. Note: Divergence scale can be translated to number of mutations difference to the root (Wuhan-Hu-1) by multiplication with the SARS-CoV-2 genome size (29903 bases).