Rhiza Labs FluTracker Forum

You really don't understand evolution. The phylogenetic analysis clearly shows branches with MANY polymorphisms that ONLY have human sequences.

It really doesn't get much more basic than clusters in phylogenetic analysis.

This is NOT your field, and you just post one nonsense post after another.

When the CDC released these sequences, it was game, set, match for H2H of swine sequences and evolution by recombination (which was demonstrated in triple REASSORTANTS!).

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www.twitter.com/hniman

I did a quick estimate :

nucleotide mutation-rate in segments 1,2,3 or 5
--------------------------------------------
nucleotide mutation rate in segment 4



human : 0.58
swine : 0.79
equine : 0.74

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no patents on genes, publish the GISAID sequences !

The human sequences on this thread are TRIPLE REASSORTANTS, not seasonal flu. You are posting utter nonsense. Your lack of understanding is at the MOST basic level.

The internal genes in H3N2 have seasonal HA from the 1990's, in pH1N1 the HA is swine, in trH1N1 they are different swine, yet they have related internal genes. The evolution rate is NOT based on seasonal HA.

You really don't have a clue in this area (or any other area related to sequences).

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www.twitter.com/hniman

mexflu has 35 nucleotide mutations in the genome per year, rate 2.67e-3 /position/year
in HA it has 9.86 mutations per year or 5.8e-3 ,mutations per position per year
more than twice as much

triple reasortant swine has almost the same mutation rate
in HA as in the polymerases

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no patents on genes, publish the GISAID sequences !

Here is a quick summary to define the key issue in the recent triple reassortments in humans. There have been five trH3N2 human isolates in the US and all have appeared in just over a year. The internal genes have the saame constellation as other H1N2 and H1N1 triple reassortants, but they all have evolved. As a result, four of the five H3N2's (Kansas, Minnesota, Wisconsin, Pennsylvania) form a cluster for most of the internal genes, and this cluster creates a branch devoid of swine sequences (or at least recent swine sequences).

These patterns demonstrate that the human sequences are evolving separately from swine, and the H3N2 sequences even link back to the H1N2 and H1N1 sequences. However, these human versions can jump back to swine, as was seen in pH1N1 sequences, where local swine picked up pH1N1 infections with regional markers found in human cases in the area, so the species delineation can become less clear.

However, the release of the human sequences left little doubt that the evolution was happening in humans, not swine.

There are MANY more swine sequences in swine than in humans, so the absence swine isolates matching these evolving humans sequences (which have markers that go back to 2007), indicates the evolution is not happening in swine.

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www.twitter.com/hniman

I ran some of these sequences through gs's program, comparing them to A/swine/Ontario/33853/2005(H3N2). Here are the differences in each of the 8 segments

   
  1:  0,  0,  0,  0,  0,  0,  0,  0   A/swine/Ontario/33853/2005(H3N2)    
  2: 20, 19, 23, 65, 20, 40, 16, 13   A/Sw/Index/triple-reassortant/1998(H3N2) 
  3: 20, 17, 18, 26, 24, 21, 15, 19   A/Wisconsin/12/2010/11/02(H3N2)    
  4: 19, 17, 18, 18, 25, 36, 15, 20   A/PA/14/2010/10/26(H1N1)      
  5: 12, 11, 13,461, 20, 17,  0, 19   A/Michigan/09/2007/08/19(H1N2)      
.

Why would you use swine in Ontario as an index? You really don't understand what is in the database and just generate data that have little meaning (and simply create confusion). The only thing that is clear, is that like GSGS, you don't have a clue. PA/14 is H3N2, not H1N1.

As has been noted, four of five H3N2's are closely related to the Huron fair sequences (human or swine).

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www.twitter.com/hniman

You are living in a parallel universe. Like GSGS, you take very clear data and post very confusing garbage. Like GSGS, you continue to post nonsense. Do you share a computer with GSGS?

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www.twitter.com/hniman

No, we each have our own computer; but we are joined at the hip

Actually, he gives me his programs to use and I ask for his suggestions as to what to compare with.

And yes, we all know I'm clueless beyond belief.

GSGS has a VERY unique outlook on sequences and data analysis, and your approach and results look remarkably similar to his.

I have put up commentaries which have identified which sequences are closely related to each other.

Like GSGS, you pick and choose VERY odd selections and then post nonsense data that just confuses.

You can download free software to do phylogenetic analysis, and if you trim down sequence so they start and stop at the same place you can very quickly see what is related to what.

Here is a link for a free download of a viewer

http://www.clcbio.com/index.php?id=479

Your selections and posts, like GSGS's just create confusion.

The human and swine sequneces from the Huron fair are VERY closely related to each other, as well as the Illinois case (all were from August 2007) and all are trH1N1.

Four of the five trH3N2's are also closely related. You have ignored the VERY clear story, and instead post utter nonsense, just like GSGS.

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www.twitter.com/hniman