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Full-genome deep sequencing and phylogenetic analysis of novel human...
An analysis of the sequence of the first UK case including deep sequencing of within-patient diversity can be found here:Cotten M, Lam TT, Watson SJ, Palser AL, Petrova V, Grant P, Pybus OG, Rambaut A,...
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MERS-CoV potential animal reservoirs and related bat coronaviruses
What is the nearest non-human host relative?A recent paper describes a new coronavirus isolated from a bat that represents the closest phylogenetic relative of the MERS-CoV virus:Ithete NL, Stoffberg...
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Real-time characterization of the molecular epidemiology of an influenza...
We have a new paper out in Biology Letters showing what you might be able to learn about an emerging epidemic from viral sequences if they are made available in close to real-time:Hedge J, Lycett SJ...
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How to read a phylogenetic tree
This is work-in-progress prompted by some enquiries about how to interpret the trees of viruses published in this website and elsewhere. There are some gaps that I hope to fill in soon. How to read a...
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MERS-CoV-like fragment in bat in Saudia Arabia
BackgroundA paper published on Aug 22nd reports a short fragment (182 nucleotides in length) of coronavirus sequence recovered from a sample from an individual Taphozous perforatus or Egyptian tomb bat...
View ArticleReconsiling Flutrackers MERS-CoV case list with epidemic's.
I have gone through the Flutrackers case list and highlighted descrepancies from my list. As the Flutrackers list do not cite sources, I will give data from published literature precidence over media...
View ArticleRough Analysis of MERS-CoV case data to date
This analysis is done using the case data presented on this page. The same caveats on that page applies - the data is rough, gleaned from various sources both official and not and contains errors and...
View ArticleSpatial phylogenetic visualisation of MERS-CoV
Visualization of the spatial phylogeny from Cotten et al (2013) The Lancet. The visualization package, Pandemix, developed by Justs Zarins & Andrew Rambaut. This uses the representative tree...
View ArticleH9N2 Avian Influenza Phylogeography
Visualization of the spatial phylogeny of each of the internal gene segments of the H9N2 avian lineages that comprise the direct ancestors of the H7N9 epidemic. The visualization package, Pandemix,...
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MERS-CoV and the hypothesis of a camel source
In the abscence of any other hypotheses I think it is interesting to explore the idea that camels are the primary source of MERS-CoV and whether it can explain the known facts. I should add that these...
View ArticleCamel as reservoir evidence list
List of sources of evidence for the hypothesis of dromedary camels as a source of MERS-CoV in humans.These tables are for reference and are the basis of some of the arguments made in this page.Serology...
View ArticleNew MERS-CoV case with known camel contact
The WHO have just released a bulletin describing a new case of MERS-CoV in a 66 year old man living in Abu Dhabi, UAE. Interestingly it reports he owns camels and had visited Oman where he had been in...
View ArticleEmerging viruses: the phylodynamics of host jumps
Emerging viruses: the phylodynamics of host jumpsFunded PhD studentship at the University of Edinburgh, Institute of Evolutionary Biology. Interested individuals should email their CV and statement of...
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