Dating the most recent common ancestor (MRCA) of SARS-CoV-2
What's the point?
To estimate the time of COVID-19 emergence we use simple root-to-tip regression (Korber et al. 2000; more complex and powerful phylodynamics methods could certainly be used, but for this data with very low levels of sequence divergence, simpler and faster methods suffice). From the set of all COVID-19 sequences available as of Feb 16, 2020 we obtain an MRCA date of Oct 24, 2019, which is close to other existing estimates Rambaut 2020.
The workflow is used to extract full length sequences of SARS-CoV-2, tidy up their names in FASTA files, produce a multiple sequences alignment and compute a maximum likelihood tree.
The Jupyter notebook is used to correlate branch lengths with collection dates in order to estimate MRCA timing.
One input is required: a comma-separated file containing accession numbers and collection dates:
An up-to-date version of this file can be generated directly from the NCBI Virus resource by
- searching for SARS-CoV-2 (NCBI taxid: 2697049) sequences
- configuring the list of results to display only the
- downloading the
Current table view resultin
The collection dates will be taken from the corresponding GenBank record's
The Galaxy workflow generates a maximum-likelihood phylogenetic tree. This tree and the initial workflow input of accession numbers and collection times are then used in the Jupyter notebook to calculate an estimate of the time to the most recent common ancestor of all samples.
History and workflow
A Galaxy workspace (history) containing the most current analysis can be imported from here.
The publicly accessible workflow can be downloaded and installed on any Galaxy instance. It contains version information for all tools used in this analysis.
Tools used in this analysis are also available from BioConda:
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|4||NCBI Accession Download||toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0|
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Created: 25th Mar 2020 at 10:02
Last updated: 25th Mar 2020 at 11:23
Last used: 14th May 2021 at 12:37