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.
ABSTRACT
The recent outbreak of a new coronavirus that causes a Severe Acute Respiratory Syndrome in humans (SARS-CoV-2) has developed into a global pandemic with over 6 million reported cases and more than 375,000 deaths worldwide. Many countries have faced a shortage of diagnostic kits as well as a lack of infrastructure to perform necessary testing. Due to these limiting factors, only patients showing symptoms indicating infection were subjected to testing, whilst asymptomatic individuals, who are widely believed to be responsible for the fast dispersion of the virus, were largely omitted from the testing regimes. The inability to implement high throughput diagnostic and contact tracing strategies has forced many countries to institute lockdowns with severe economic and social consequences. The World Health Organization (WHO) has encouraged affected countries to increase testing capabilities to identify new cases, allow for a well-controlled lifting of lockdown measures, and prepare for future outbreaks. Here, we propose HiDRA-seq, a rapidly implementable, high throughput, and scalable solution that uses NGS lab infrastructure and reagents for population-scale SARS-CoV-2 testing. This method is based on the use of indexed oligo-dT primers to generate barcoded cDNA from a large number of patient samples. From this, highly multiplexed NGS libraries are prepared targeting SARS-CoV-2 specific regions and sequenced. The low amount of sequencing data required for diagnosis allows the combination of thousands of samples in a sequencing run, while reducing the cost to approximately 2 CHF/EUR/USD per RNA sample. Here, we describe in detail the first version of the protocol, which can be further improved in the future to increase its sensitivity and to identify other respiratory viruses or analyze individual genetic features associated with disease progression.