Re: Origins of the April Jeddah MERS-CoV outbreak (Andrew Rambaut's Epidemic Blog, April 28 2014)
I haven't been doing MERS-sequence analysis yet
"Christian's" webpage just goes to
http://www.virology-bonn.de/
there is no possibility of commenting or discussion, afaics
it would be nice to have a computer-readable file with all the aligned
MERS-sequences, locations and dates and patient-data.
that everyone can easily check and discuss
are all sequences at genbank or do the MERS-people have some
GISAID-like semi-secret database ?
do we have the one MERS-index sequence ?
what's the mutation rate
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Rambaut (U.of Edinburgh) has threads and comments, but requires log in
and there is no button for registering, so that seems to be a closed group
http://epidemic.bio.ed.ac.uk/node/63
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http://epidemic.bio.ed.ac.uk/
> This is a website for collaborative analysis and discussion about the emergence,
> evolution and epidemiology of novel human viral pathogens. The site is divided into
> sections for different viruses. The aim is to present new analyses as data becomes
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> entries is restricted to account holders.
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Rambaut wrote at
http://epidemic.bio.ed.ac.uk/node/58 :
> KSA has been consistently less forthcoming with details of individual cases
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for the 3 sequences at Bonn I get: (ignoring positions behind ~26000)
29915 nucleotides when aligned with MAFFT, 29133-29705 filled nucleotides
index = average of the 3 , starting with CTTCCCCTCGTT...
>MERS-CoV/Jeddah_2014_C7770,2014/04/07,6,1-29748
C1657T,C1759T,C18498T
>MERS-CoV/Jeddah_2014_C7569,2014/04/05,167,1-29915,167,
>MERS-CoV/Jeddah_2014_C7149,2014/04/03,213,1-29750,213,
G6745A
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I get 289 hits at genbank for middle east respiratory syndrome
http://www.ncbi.nlm.nih.gov/nuccore/?term=middle+east+respiratory+syndrome
OK, I figured you can click "send to" and make a fasta-file from them
289 sequences , 204 - 30177 nucleotides , 2.2MB
aligning now ... allocation error ...splitting the big file ... still very slow with MAFFT
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http://epidemic.bio.ed.ac.uk/coronavirus_analysis
Fri, 2013-06-14 10:26
There are now >70 published complete or partial genome sequences from MERS-CoV cases
both of humans and, recently, camels
http://epidemic.bio.ed.ac.uk/MERS_sequences
rate of molecular evolution : 1.12*10^(-3) subst/site/year (flu-A has ~ double that)
most recent common ancestor : mid-2011
28 complete or partial genomes sampled from April 2012 to late 2013
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