Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland; Department of Environmental Systems Science, ETH Zürich, Swiss Federal Institute of Technology, Zurich, Switzerland.
Epidemics. 2021 Dec;37:100480. doi: 10.1016/j.epidem.2021.100480. Epub 2021 Aug 9.
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).
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.
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.
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.
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.
2020 年 12 月，英国（UK）报告了一种关注的 SARS-CoV-2 变体（VoC），现在称为 B.1.1.7。根据英国的初步数据和后来其他国家的数据，该变体的传播适应力估计高出约 40-80%（Volz 等人，2021 年；Leung 等人，2021 年；Davies 等人，2021 年）。
本研究旨在根据瑞士的数据估计 B.1.1.7 的传播适应力优势和有效繁殖数随时间的变化。
我们从 2020 年 12 月 14 日至 2021 年 3 月 11 日期间瑞士所有确诊 SARS-CoV-2 病例中抽取 11.8%的病例生成全基因组序列。基于这些数据，我们确定了 B.1.1.7 变体的日频率，并在国家和地区范围内定量了变体的传播适应力优势。
我们估计，与研究期间在瑞士传播的其他变体相比，B.1.1.7 的传播适应力优势为 43-52%。此外，我们估计，B.1.1.7 的繁殖数从 2021 年 1 月 1 日到研究结束一直高于 1，而其他变体则低于 1。具体而言，我们根据全基因组测序数据估计，从 2021 年 1 月 1 日至 17 日，B.1.1.7 的繁殖数为 1.24[1.07-1.41]，从 1 月 18 日至 3 月 1 日为 1.18[1.06-1.30]。从 2021 年 3 月 10 日至 16 日，当 B.1.1.7 成为主要变体时，我们根据所有确诊病例估计繁殖数为 1.14[1.00-1.26]。作为参考，瑞士于 2021 年 1 月 18 日实施了更多非药物干预措施来对抗 SARS-CoV-2，并于 3 月 1 日再次放宽了一些措施。
根据英国的观察结果，研究期间瑞士 B.1.1.7 频率的增加是预期的。在绝对数量上，B.1.1.7 呈指数级增长，估计倍增时间约为 2-3.5 周。为了监测 B.1.1.7 的持续传播，我们的图表可在线获取。
