Rhiza Labs FluTracker Forum

I have a first human picture here:
http://magictour.free.fr/panflu/sepph1.GIF

830 human PB2s (0.2% filter) , H5N1 and H9N2 and H7* excluded

the main cloud just shows the proportional increase of
amino-acid and nucleotide differences in humans

the smaller clouds should be avian or swine viruses going to humans.
I'll have to check this


we had H1N1 in 1918, since then segment 1 is unchanged in humans,
the 1957,1968 pandemics did not change PB2.

Only now in 2009 we get another PB2 with Mexflu

_________________
no patents on genes, publish the GISAID sequences !

Just wonderfull picture!
Diagram shows just continuous linear change,
no sign of "index", no convergence to stable configuration.
This pattern is the signature of "dead end" scenario.

Are the big scale tics the same as previous pictures? Slope estimates:
scale=(0,100,200,300 ...vert ; 0,10,20,30,40 horiz ), Slope=8 Nuc/Amin
scale=(0,10,20,30 ...vert ; 0,10,20,30,40 horiz ), Slope=0.8 Nuc/Amin

yes, same scale.
I removed 15 swinish viruses or strange ones
from Asia, and only one cloud remains:
http://magictour.free.fr/panflu/sepph2.GIF

The branch towards the right near the bottom (green arrow)
is not so easy to remove/explain


I took all human PB2s from genbank H1N1(without mexflu),H1N2,H3N2
and removed PB2s closer than 0.2% in nucleotides to another
PB2 in the list. That gave 760 PB2s.
From these the 15 following were removed:

>A/TW/872/02(H3N2)
>A/HK/497/97(H3N2)
>A/TW/875/04(H3N2)
>A/Fiji/15899/83(H1N1)
>A/WSN/1933(H1N1)
>A/Wisconsin/301/1976(H1N1)
>A/New Jersey/11/1976(H1N1)
>A/Ontario/RV1273/05(H3N2)
>A/Ohio/3559/1988(H1N1)
>A/Iowa/CEID23/05(H1N1)
>A/Ontario/1252/07(H3N2)
>A/Maryland/12/1991(H1N1)
>A/HK/1774/99(H3N2)
>A/THA/271/05(H1N1)
>A/Philippines/344/04(H1N2)

     

_________________
no patents on genes, publish the GISAID sequences !

scale=(0,100,200,300 ...vert ; 0,10,20,30,40 horiz ),

Slope=8 Nuc/Amin

Does this figure have any simple genetics interpretation?

Supposing sucessive equiprobable random changes
on each nucleotide of a random codon triplet,

plus codon translations rules and degeneracy,

what Nuc/Amin Slope would be expected?
This is the crudest theoretical model I can imagine.
Not sure if reasoning is genetically realist.

This is essentially a genetic "random walk", encoded by codon rules.
The modes does not imply that actual time evolution is random.
It just assumes that on the average, they are random.

about 80% of mutations are synonymous, that's what we estimated earlier.

So: N=S*5, but we have from the picture

N=S*7 in humans

_________________
no patents on genes, publish the GISAID sequences !

gsgs and neuromedia...

The Two-of-You are absolutely amazing !!!
Every once in a while, I tune in and try to follow along... wish that I felt more capable for TheOpportunity. I notice another 29 "lurker guests" on this thread, this morning (along with the 3 of us). Perhaps, one of the same can add that key bit of insight, which might also enable me to keep up with your ping-pong-tournament-of-sequence-deciphering ???

ThankYou... I can't even begin to imagine the gigantic mental intricacies of your combined efforts.

Pfuati'...

we are still in the idea-colecting phase.
Once we see clearer we may make a formulation which
everyone easily understands

(? can it be done ?) We need a better picture for that too.


my summary:
over long periods (decades) flu evolves differently in some segments
in birds than in humans

e.g. in segment 1:
http://magictour.free.fr/panflu/sepph3.GIF

_________________
no patents on genes, publish the GISAID sequences !

Is there a contradiction? Or N=S*7 is a better estimate?

Anyway, the picture clearly shows a single main cluster,
with a constant S/N (Synonimous/Nonsynonimous) rate.

This characterizes human influenza as an avian-like gene "dead end", wiped out after pandemics.
In bird hosts amino acid sequence preservation is likely to be a biological fit.

birds are not able to get what humans have by simple evolution,
no escape from the valley.

What, when they steal it from humans or pigs ?
Will that greatly enhance avian flu dynamics ?

_________________
no patents on genes, publish the GISAID sequences !

Humm Not sure! This is an "untried experiment", and I learned to respect these tricky ortomixoviruses! Imagine the last pandemic was 1918. No more pantemics. I guess seasonal H1N1 would gradually adapt, and not disapear. Hellas, pandemics do happen!

The tendency appears to be on the bird =>mammalian direction.
I think that these genes would tend to be “corrected” to the common “bird index”.