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I made this for my own benefit as a quick look at changes in the H5N1 HA cleavage site. It is NOT definitive and is based only on a fairly random set of sequences I had but has enough data to give a qualatative feel for the sites in circulation.
I post it here so I can have a quick look while reading posts and incase anyone else finds it useful. If I get around to updating it I will repost.
PM me if you would like the XLS to add to yourself.
Great table. It looks like most of the cleavage site sequences that deviate from SE Asia consensus and from Quinghai consensus are human cases - is that correct ? If so this could be very relvant.
Originally posted by JJackson
I made this for my own benefit as a quick look at changes in the H5N1 HA cleavage site. It is NOT definitive and is based only on a fairly random set of sequences I had but has enough data to give a qualatative feel for the sites in circulation.
I post it here so I can have a quick look while reading posts and incase anyone else finds it useful. If I get around to updating it I will repost.
PM me if you would like the XLS to add to yourself.
I have had a couple of PMs and the sheet is not as clear as I hoped.
I have pasted below a bit more detail.
All I have done is search the Los Alamos data base with the CGAT sequence taken form a typical example of the cleavage change to see which sequences included it. I use BioEdit to align sequences, find anomalous cleavage sites in the AA view and toggle to get the residues that created them and then use this as the search input. The problem is that more than one codon can code for a given AA and I will only find those that have an exact match for the residue sequence and there may be other residue strings that produce an identical AA string. The KERRRKKR is an example of this the Vietnam '05 and Egypt '06 needed different probes.
Re the coloured bit at the top. Once I have aligned the bases the cleavage site lies between position 323 to 330 along the Amino Acid chain. So reading down the second column you have a RERRRKKR cleavage site, when I searched the data base for the sequence of bases that created it I found 435 instances in H5N1 and the section below shows the countries, and years, that those sequence occurred in. The letters in the coloured area denoted the AA found at that position, the colours are just there to make it easier to see changes from the consensus sequence (X denoted a gap in the sequence - this presents a problem when searching as the raw data does not have gaps they only 'appear' when you align samples). I divided the sites into two blocks headed SE Asia and
Qinghai because they have - up till know - followed separate evolutionary paths.
BioEdit and all the links and methods used are to be found in Mingus' Lab.
I hope it helps,
Jonathan.
Henry:
What is the basis for classifying the SE Asia sequences as Qinghai?
Sorry my mistake in the version I 'cleaned up' to post I split into blocks and forgot to move two of the columns REKRRKKR & RERKRKKR should have been dragged into the SE Asian block.
As to the Egyptian sequences I listed three different sites all in 2006 and have pasted an example of each below.
Great table. It looks like most of the cleavage site sequences that deviate from SE Asia consensus and from Quinghai consensus are human cases - is that correct ? If so this could be very relevant.
As you will see from the Egypt sequences the 'straight Qinghai' and the two variants are in Chickens. I was not very methodical when I originally did this and should have made a note of the sequences' No. so I could check. It was just rough and ready for my own use initially.
I have had a couple of PMs and the sheet is not as clear as I hoped.
I have pasted below a bit more detail.
Henry:
Sorry my mistake in the version I 'cleaned up' to post I split into blocks and forgot to move two of the columns REKRRKKR & RERKRKKR should have been dragged into the SE Asian block.
As to the Egyptian sequences I listed three different sites all in 2006 and have pasted an example of each below.
Great table. It looks like most of the cleavage site sequences that deviate from SE Asia consensus and from Quinghai consensus are human cases - is that correct ? If so this could be very relvant.
No there are a large number of bird sequences that have either dropper one R or one K. There are also novel sequences in Ian Brown's presentation on Qinghai in Europe (which are all bird sequences). There are also novel swine HA cleavage sites China and Indonesia.
3 synonymous,3 nonsynonymous which is a relatively high proportion of
nonsynonymous=amino-relevant changes.
Looks as if the humans don't get it from the chickens and that there are different,separated sources from which humans and chickens get it.
And also that these changes are part of an adaption of H5N1
to other species. I can't remember that we saw this before ?!?
The cleavage site is the red button that allow the virus to "shoot his gene" inside our cells.
A high pathogenic cleavage site like the one H5N1 have will be more "sensible" than a low path does.
JJackson try to record every variant of this feature in the virus.
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