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, Madlen; Mari, Alfredo; Roloff, Tim; Seth-Smith, Helena M. B.; Schweitzer, Michael; Brunner, Myrta; Leuzinger, Karoline; Søgaard, Kirstine Kobberøe; Gensch, Alexander; Tschudin‐Sutter, Sarah; Fuchs, Simon; Bielicki, Julia; Pargger, Hans; Siegemund, Martin; Nickel, Christian H.; Bingisser, Roland; Osthoff, Michael; Bassetti, Stefano; Schneider-Sliwa, Rita; Battegay, Manuel; Hirsch, Hans H.; Egli, Adrian

doi:10.1101/2020.09.01.20186155

Cited by 9 publications

(22 citation statements)

References 37 publications

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“…To characterize the epidemic over the complete period, we generate 1,439 sequences from our nation-wide sequencing project, representing 3-7% of all laboratory-confirmed cases per week across Switzerland. We couple these data with 675 additional sequences from the early epidemic collected by labs in Basel ( 3 ), Geneva and Zurich to represent in total 5% of all laboratory-confirmed cases in Switzerland until Aug. 31 st . We combine this Swiss dataset with additional sequences from across the globe to address five main goals:…”

Section: Main Textmentioning

confidence: 99%

Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data

Nadeau

Beckmann²,

Topolsky

et al. 2020

Preprint

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Pathogen genomes provide insights into their evolution and epidemic spread. We sequenced 1,439 SARS-CoV-2 genomes from Switzerland, representing 3-7% of all confirmed cases per week. Using these data, we demonstrate that no one lineage became dominant, pointing against evolution towards general lower virulence. On an epidemiological level, we report no evidence of cryptic transmission before the first confirmed case. We find many early viral introductions from Germany, France, and Italy and many recent introductions from Germany and France. Over the summer, we quantify the number of non-traceable infections stemming from introductions, quantify the effective reproductive number, and estimate the degree of undersampling. Our framework can be applied to quantify evolution and epidemiology in other locations or for other pathogens based on genomic data.

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Section: Main Textmentioning

confidence: 99%

Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data

Nadeau

Beckmann²,

Topolsky

et al. 2020

Preprint

Self Cite

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“…We inferred the lineage identity 24 and observed 29 viral lineages in Basel-City ( Figure S8), with 247 genomes (60.0%) belonging to a viral variant that we henceforth refer to as B.1-C15324T 23 ( Figure 1A, B). Applying a genetic divergence threshold, a total of 128 phylogenetic clusters, and 70 clusters that belong to lineage B.1-C15324T ( Figure 1C) were determined.…”

Section: Sars-covmentioning

confidence: 99%

“…Phylogenetic inference and cluster analysis. Whole-SARS-CoV-2-genomes from Basel-City patients were assembled using our custom analysis pipeline COVGAP 23 (github.com/appliedmicrobiologyresearch CoV-2/). Global sequences and metadata were downloaded from GISAID 47,48 (as of October…”

Section: Geographicmentioning

confidence: 99%

“…The copyright holder for this this version posted December 17, 2020. ; https://doi.org/10.1101/2020.12.15.20248130 doi: medRxiv preprint CoV-2 whole genomes from unique patients (54.8% of all cases). Of these, 247 (247/411, 60%) could be attributed to contain the C15324T mutation in the B.1 lineage (and therefore called B.1-C15324T) characteristic to the virus variant that originated in this tri-national area 23 . Figure 2A).…”

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Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area

Brueningk

Klatt

Stange

et al. 2020

Preprint

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Transmission chains within cities provide an important contribution to case burden and economic impact during the ongoing COVID-19 pandemic, and should be a major focus for preventive measures to achieve containment. Here, at very high spatio-temporal resolution, we analysed determinants of SARS-CoV-2 transmission in a medium-sized European city. We combined detailed epidemiological, mobility, and socioeconomic data-sets with whole genome sequencing during the first SARS-CoV-2 wave. Both phylogenetic clustering and compartmental modelling analysis were performed based on the dominating viral variant (B.1-C15324T; 60% of all cases). Here we show that transmissions on the city population level are driven by the socioeconomically weaker and highly mobile groups. Simulated vaccination scenarios showed that vaccination of a third of the population at 90% efficacy prioritising the latter groups would induce a stronger preventive effect compared to vaccinating exclusively senior population groups first. Our analysis accounts for both social interaction and mobility on the basis of molecularly related cases, thereby providing high confidence estimates of the underlying epidemic dynamics that may readily be translatable to other municipal areas.

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“…Each center used individual bioinformatic pipelines to check for sequencing quality and generate the consensus sequences details are shared in GISAID (e.g. 37 ;…”

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 N501Y introductions and transmissions in Switzerland from beginning of October 2020 to February 2021 – implementation of Swiss-wide diagnostic screening and whole genome sequencing

Cabecinhas

Roloff

Stange

et al. 2021

Preprint

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The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations by the European Center for Disease Prevention and Control (ECDC) and World Health Organization (WHO) for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological definitions based on travel history and the S gene dropout in certain diagnostic systems. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 3492 VoCs have been identified since the detection of the first Swiss case in October 2020, with 1370 being B1.1.7, 61 B.1.351, and none P.1. The remaining 2061 cases of VoCs have been described without further lineage specification. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.

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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)

Cited by 9 publications

References 37 publications

Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data

Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data

Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area

SARS-CoV-2 N501Y introductions and transmissions in Switzerland from beginning of October 2020 to February 2021 – implementation of Swiss-wide diagnostic screening and whole genome sequencing

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