SARS-CoV-2 Variants of Concern in Switzerland

We use data form our Swiss SARS-CoV-2 Sequencing Consortium combined with genomic screening data to determine the increase in relative and absolute numbers of B.1.1.7. In addition, based on the whole genome sequencing data from our consortium, we provide results for Swiss regions and further track the variant 501Y.V2. We note that due to the delay between infection and swab collection, the numbers for a particular day reflect the epidemic situation around 8-11 days earlier.

A subset of our figures is shown on the website of the Swiss National COVID-19 Science Task Force. The ISPM in Bern, Switzerland set up a complementary webpage tracking the dynamics of all 501Y mutations jointly in Switzerland (link).

The methods employed for the plots below are described in a pre-print (not peer-reviewed). In particular, in this manuscript, we additionally provide estimates on the transmission fitness advantage of B.1.1.7 for Switzerland and the Swiss regions. All contributors are listed as authors in the manuscript. Our code and data is available on Github.

Data collection: In the Swiss SARS-CoV-2 Sequencing Consortium, we currently perform whole genome sequencing of around 4-5% of all confirmed cases on a weekly basis (Viollier dataset below). These sequences are further tagged with a geographic location. Through the work of the Consortium, we identified the first 501Y.V2 variant (on Dec. 26, 2020) and the first P.1 variant (on Feb. 08, 2021) in Switzerland. In addition, we assembled a dataset of a surveillance effort screening for the B.1.1.7 (501Y.V1) variant. Here, samples are first screened with targeted PCR and proposed B.1.1.7 variants are then confirmed through sequencing (Risch dataset below). Taken together, this leads to a characterization of around 11.5% of all confirmed cases since mid-December.

Important: the most recent estimates may be based on incomplete data and may thus be corrected later.

This website was updated from mid-January until mid-April. For current information, please visit our new website CoV-Spectrum.

B.1.1.7 (or S.501Y.V1) Variant

First we show the estimated proportion of B.1.1.7 cases through time (vertical bars) together with the fitted logistic growth curve:

Based on the estimated proportions of B.1.1.7, we provide the estimated expected absolute number of B.1.1.7 cases through time:

Other parametrizations can be directly tried out in our web tool:

International Comparison

Finally, we show the relative frequency of B.1.1.7 for different countries.

Sources: CoV-Spectrum using data from GISAID

Acknowledgements:

Viollier: Samples are provided by Viollier AG. Whole genome sequenicing is performed through the Swiss SARS-CoV-2 Sequencing Consortium lead by ETH Z├╝rich.

Risch: Samples are provided and screened by Labor Risch. Genomic characterization is performed by Labor Risch, the University Hospital Basel (Clinical Mircobiology) and the University Hospitals of Geneva (Group Eckerle and Group Kaiser).