Real-time analysis of MERS-CoV evolution
Legend
Data subsets
Variable positions
Mouse over variable positions to color by amino acid at this site.
Feature explanation

Phylogenetic tree

Use the date slider to highlight viruses within the specified time interval. Both ends of the slider can be manipulated with the mouse.

Use the drop down menu to color viruses geographic region, host, sampling date, or local branching index.

Use the input box to specify positions to color viruses by the nucleotide at a specific position. Equivalently, click on a bar in variability graph.

Mouse over a tip to show virus name, location and features.

Mouse over a branch to display the mutations associated with the branch.

Rationale and details

The local branching index is the exponentially weighted tree length surrounding a node, which is associated with rapid branching and expansion of clades. A more detailed explanation is available here. Retrospective analysis has shown that LBI correlates with clade growth.

Acknowledgements
Acknowledgement of investigators at the following institutions for early release MERS-CoV sequences:

College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia (KSA/WTSI) Somily et al. (2015)
Epidemiology section, Command and Control Center, Ministry of Health, Jeddah (KSA/WTSI) Somily et al. (2015)
King Fahad General Hospital, Jeddah (KSA/WTSI) Somily et al. (2015)
Wellcome Trust Sanger Institute, Hinxton, United Kingdom (KSA/WTSI) Somily et al. (2015)
China CDC, National Institute for Viral Disease Control and Prevention (ChinaCDC) Lu et al. (2015)
Korea National Institute of Health, Korea CDC, South Korea (KNIH) Kim et al. (2015)
Division of Viral Diseases, Centers for Disease Control and Prevention (CDC)
The links on the right provide additional information on the contributed sequences. Special thanks to Matt Cotten for putting together the sequences and help with meta data, as well as to Andrew Rambaut and Paul Wikramaratna for curating the case numbers.

Built by Trevor Bedford and Richard Neher. Give us a shout at @trvrb or @richardneher with questions or comments. All source code is freely available under the terms of the GNU Affero General Public License. Data updated and processed with commit .

© 2015 Trevor Bedford and Richard Neher