Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland

Abstract

Background In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.7. Based on initial data from the UK and later data from other countries, this variant was estimated to have a transmission fitness advantage of around 40–80 % (Volz et al., 2021; Leung et al., 2021; Davies et al., 2021). Aim This study aims to estimate the transmission fitness advantage and the effective reproductive number of B.1.1.7 through time based on data from Switzerland. Methods We generated whole genome sequences from 11.8 % of all confirmed SARS-CoV-2 cases in Switzerland between 14 December 2020 and 11 March 2021. Based on these data, we determine the daily frequency of the B.1.1.7 variant and quantify the variant’s transmission fitness advantage on a national and a regional scale. Results We estimate B.1.1.7 had a transmission fitness advantage of 43–52 % compared to the other variants circulating in Switzerland during the study period. Further, we estimate B.1.1.7 had a reproductive number above 1 from 01 January 2021 until the end of the study period, compared to below 1 for the other variants. Specifically, we estimate the reproductive number for B.1.1.7 was 1.24 [1.07–1.41] from 01 January until 17 January 2021 and 1.18 [1.06–1.30] from 18 January until 01 March 2021 based on the whole genome sequencing data. From 10 March to 16 March 2021, once B.1.1.7 was dominant, we estimate the reproductive number was 1.14 [1.00–1.26] based on all confirmed cases. For reference, Switzerland applied more non-pharmaceutical interventions to combat SARS-CoV-2 on 18 January 2021 and lifted some measures again on 01 March 2021. Conclusion The observed increase in B.1.1.7 frequency in Switzerland during the study period is as expected based on observations in the UK. In absolute numbers, B.1.1.7 increased exponentially with an estimated doubling time of around 2–3.5 weeks. To monitor the ongoing spread of B.1.1.7, our plots are available online.

Impact of vaccination and non-pharmaceutical interventions on SARS-CoV-2 dynamics in Switzerland

“…We did not consider potential changes in behaviour among people once they were vaccinated. We only considered variants of concern identified through Swiss genomic surveillance data ( Chen et al, 2021 ); B.1.1.7, the most prevalent VOC in Switzerland as of March 2021, and B.1.351. We did not consider P.1 nor the delta variant, B.1.617.2, for which vaccines may be less efficacious ( Fontanet et al, 2021 , Madhi et al, 2021 ).…”

“…NPI measures data from various public sources were used to compute national- and cantonal-level interpretations of the OCHI ( FOPH, 2020 , FOPH, 2021 , SwissTPH, 2021 ). A subset of model parameters (Appendix Table S.1 ) was calibrated to align model output to six types of epidemiological data, including confirmed cases, patients in hospital, deaths, and prevalence of viral variants ( Chen et al, 2021 ) from 18 February 2020 to 5 March 2021 (see Fig. 2 and Appendix Figure S.1 -S.3).…”

“…We assume the variant with which an individual is infected is inherited from the infector. At the time of analysis, B.1.1.7 was the dominant variant in Switzerland, replacing D614G ( FOPH, 2021 , Chen et al, 2021 ). We modelled three variants in this study: D614G, B.1.1.7, and B.1.351.…”

CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants

“…Second, CoV-Spectrum integrates a model to estimate variant transmission fitness advantages, as described in Chen et al (2021) . Chen et al (2021) presents static results for the Alpha variant in Switzerland, while CoV-Spectrum allows users to explore results for any variants and countries. This enables assessment of VOC property (i) (increased transmissibility).…”

CoV-Spectrum: Analysis of globally shared SARS-CoV-2 data to Identify and Characterize New Variants

“…In addition to presenting the raw data, CoV-Spectrum applies statistical analyses to them. Currently, it integrates a model to estimate the transmission fitness advantage that was described in [9]. While the manuscript presents the results for a selected variant and country, CoV-spectrum allows to explore results for any variants and countries.…”