Thursday, 29 May 2014

Updated MERS-CoV full genome tree...

With thanks to @arambaut for some tips, and for tying my home computer up for 2-days running PHYML on the sequences (super-computer it ain't) - this is a slightly more robust tree of the MERS-CoV complete (or near-complete) genome nucleotide sequences published to date. This follows from my previous post and tree here.

Very little from 2014 despite the majority of MERS-CoV variants circulating then. But of course we have to wait because next generation sequencing is the main way we roll with MERS-CoV.

Alignment of 56 complete or near complete MERS-CoV genomes and an Egyptian divergent variant from a camel. Alignment made using Geneious v6.1.7. The PHYML v2.2.0 plug-in was added to make this tree, using 1000 bootstraps. Red stars indicate 
virus which is reportedly from the same patient (seems doubtful). Vertical bars to the right indicate Clade A (dark blue) and B (pale blue). Sequences from the the 2013 Al-Ahsa hospital outbreak are boxed in pink; from the Jeddah 2014 hospital outbreak in blue; from  the Hafr Al-Batin community cluster in green. Camel icons indicate genomes from camel variants for MERS-CoV. GenBank accession numbers are indicated at the end of each sequence name which also includes region of detection, host (human if not specified) and year of sample collection.
Click on image to enlarge.

The tree really highlights how remarkably interwoven the camel and human MERS-CoV genome sequences are; remembering that these 30,000nt genomes don't differ from each other by more than 1% at the nucleotide level.

Some new sequence analyses from the Netherlands cases should be coming out in the next issue of Eurosurveillance so get a tab ready and keep hitting refresh. Or, ya know, go get a life or something (I'm hitting refresh).