Reproductive number based on confirmed case data

We are quantifying the spread of COVID-​19 through time in Switzerland by quantifying the reproductive number. If this number is above 1, the epidemic is exponentially increasing, if this number is below 1, the epidemic is declining. 

The National COVID-19 Science Taskforce reports our estimates (updated daily) in their situation report. We additionally provide a short report on that website on the current state of the Swiss COVID-19 epidemic and refer to the methods used to obtain the estimates. We further have a dedicated webpage to display estimates of the reproductive number for Switzerland, as well as its Cantons and Greater Regions. 

Finally, on our dedicated webpage, we provide estimates for countries around the world based on published data. For South Africa, this is a great collaboration with team of Prof Tulio de Oliveira. All estimates are updated daily and our code is open source.

Core team: Jeremie Scire, Jana Huisman, Dr Daniel Angst, Prof Sebastian Bonhoeffer, Prof Tanja Stadler.

Transmission patterns based on genome data

We are leading the currently largest SARS-CoV-2 sequencing effort in Switzerland (on Nov 24: 1617/1966 of the Swiss genomes come from our project). The diagnostics company Viollier AG provides to us their SARS-​CoV-2 samples from across Switzerland for genome sequencing. For each sample we additionally know the location where it is stemming from (on a city scale) as well as the date of sampling. The Genomics Facility Basel at D-BSSE, ETHZ performs the sequencing and the V-​pipe team conducts the sequence assembly. We release all sequencing data immediately to GISAID allowing the research community to analyse our data as it comes in.

The NextStrain team set up a website featuring the Swiss-focussed phylogenetic tree. The National COVID-19 Science Taskforce reports the Swiss-based phylogenetic NextStrain tree on their website.

A narrative from June 17, 2020 is available and interested users are encouraged to explore the interactive tree themselves.

A preprint summarizing this effort is available here and a preprint describing a new European variant is available here.

Core team: Sarah Nadeau (phylogenetic analyses), Dr Emma Hodcroft & Prof Richard Neher (NextStrain), Genomic facility Basel (sequencing), V-pipe team (assembly), Viollier AG (providing samples), Prof Tanja Stadler (project lead & phylogenetic analyses).