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

Abstract

In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now coined B.1.1.7. Based on the UK data and later additional data from other countries, a transmission advantage of around 40-80% was estimated for this variant. In Switzerland, since spring 2020, we perform whole genome sequencing of SARS-CoV-2 samples obtained from a large diagnostic lab (Viollier AG) on a weekly basis for genomic surveillance. The lab processes SARS-CoV-2 samples from across Switzerland. Based on a total of 7631 sequences obtained from samples collected between 14.12.2020 and 11.02.2021 at Viollier AG, we determine the relative proportion of the B.1.1.7 variant on a daily basis. In addition, we use data from a second lab (Dr Risch) screening all their samples for the B.1.1.7 variant. These two datasets represent 11.5 % of all SARS-CoV-2 confirmed cases across Switzerland during the considered time period. They allow us to quantify the transmission advantage of the B.1.1.7 variant on a national and a regional scale. Taking all our data and estimates together, we propose a transmission advantage of 49-65% of B.1.1.7 compared to the other circulating variants. Further, we estimate the effective reproductive number through time for B.1.1.7 and the other variants, again pointing to a higher transmission rate of B.1.1.7. In particular, for the time period 01.01.2021-17.01.2021, we estimate an average reproductive number for B.1.1.7 of 1.28 [1.07-1.49] while the estimate for the other variants is 0.83 [0.63-1.03], based on the total number of confirmed cases and our Viollier sequencing data. Switzerland tightened measures on 18.01.2021. A comparison of the empirically confirmed case numbers up to 20.02.2021 to a very simple model using the estimates of the reproductive number from the first half of January provides indication that the rate of spread of all variants slowed down recently. In summary, the dynamics of increase in frequency of B.1.1.7 is as expected based on the observations in the UK. Our plots are available online and constantly updated with new data to closely monitor the changes in absolute numbers.

Estimating the strength of selection for new SARS-CoV-2 variants

“…Several studies using other methods have similarly found D614G and B.1.1.7 to each have a selective advantage over other variants circulating contemporaneously [10, 19, 3, 12, 2]. In contrast, however, van Dorp et al [35] found no support for a selective advantage of any of the variants they tested, including D614G.…”

“…Although phylogenetic replication is an appropriate requirement in many situations, it is too conservative for identifying variants of concern on the timescale at which they emerge. Instead, to test for a selective advantage of variants that have arisen only once, power can be obtained from fitting explicitly epidemiological models within one location (e.g., our stochastic model, and others [19, 3, 12, 2]) or looking for consistent effects in multiple locations with largely-distinct conditions (e.g., our isotonic regression and population genetic models, and Korber et al [10]).…”

Estimating the elevated transmissibility of the B.1.1.7 strain over previously circulating strains in England using GISAID sequence frequencies

“…Washington et al estimated a 35–45% increase using data from the United States of America using Volz’s method (Washington et al, 2021). Chen et al estimated 49–65% increase in reproduction number using data from Switzerland also under the constant R assumption (Chen et al, 2021). Due to the high transmissibility the B.1.1.7 strain, strong control measure such as lockdown was taken when the strain was introduced (Davies et al, 2021).…”

“…Volz et al estimated a 50-100% increase in using data from England (Volz et al 2021), while Washington et al estimated a 35-45% increase using data from the United States using Volz's method (Washington et al 2021). As well, Chen et al estimated a 49-65% increase using data from Switzerland (Chen et al 2021). Strong control measures including movement restrictions and ban on meeting and event were taken to respond to the introduction of a strain with high transmissibility.…”

A non-coding A-to-T Kozak site change related to the transmissibility of Alpha, Delta and Omicron VOCs

“…The frequencies of B.1.1.7 associated mutations reached quickly up to 76.92% (4). The B.1.1.7 strains not only have high transmissibility (2), quickly spread to many countries (5)(6)(7)(8), but also increase risk of death (9,10). It has been documented that S:p.N501Y (11,12) and S:p.D614G (13,14) increase the viral transmissibility, and S:p.P681H occurs on the spike S1/S2 cleavage site (15).…”