Rhiza Labs FluTracker Forum

and now to segment 7, which is the most bird-index
friendly of all.
1048 out of 2723 available full M1 protein sequences
are identical to the index !

This involves wild birds from distant places and times like:

0 0 244 51 Dk/HK/34/1976(H3N2), 1976 , 10 , 3 , 0
0 0 250 1381 gadwall/Altai/1328/07(H3N8)09, 2007 , 0 , 0 , 0
0 0 251 1373 mallard/Czech Republic/12652/07(H4N6)08/06, 2007 , 3 , 0 , 0
0 0 251 1957 mallard/MN/195/99(H4N6), 1999 , 3 , 0 , 0
0 0 252 2341 pintail/Barrow/38/05(H8N4), 2005 , 6 , 0 , 0
0 0 253 3 ostrich/South Africa/1991(H7N1), 1991 , 21 , 2 , 0
0 0 253 33 pelican/Zambia/01/06(H3N6)08, 2006 , 0 , 3 , 0
0 0 253 1102 Dk/England/1962(H4N8), 1962 , 10 , 0 , 0
0 0 253 1152 Dk/Altai/1285/1991(H5N3)08/15, 1991 , 10 , 0 , 0
0 0 253 1389 mallard/Czech Republic/14884-34/07(H9N2)09/24, 2007 , 3 , 0 , 0
0 0 253 1427 Dk/Memphis/546/1974(H11N9), 1974 , 10 , 0 , 0
0 0 253 1430 arctic tern/Alaska/300/1975(H5N3), 1975 , 4 , 0 , 0
0 0 253 1442 murre/Alaska/305/1976(H1N6)01/01, 1976 , 0 , 0 , 0
0 0 253 2664 Dk/NZL/31/1976(H4N6)01/01, 1976 , 10 , 0 , 0
0 0 253 2667 shearwater/AUS/405/1978(H3N8)10/29, 1978 , 0 , 0 , 0
0 0 253 2715 mallard/New Zealand/1615-17/04(H4N6), 2004 , 3 , 0 , 0
0 0 253 2716 Dk/Tasmania/277/07(H7N2), 2007 , 10 , 0 , 0
0 0 253 2719 Ck/Chile/4322/02(H7N3), 2002 , 1 , 0 , 0



(1) promille out of (2) samples from species (3) have
their M1 amino-acid sequence identical to the index.

(1) (2) (3)
---------------------
955 45 shoveler
823 119 turnstone
817 115 teal
773 485 mallard
666 72 pintail
650 20 shorebird
642 14 widgeon
615 52 gull
400 5 tern
341 428 Dk
338 201 rest
300 150 /Tk/
285 7 avian
200 15 pheasant
200 5 ostrich
197 76 Gs
186 43 fowl
114 35 swan
62 688 Ck/
17 116 /Qa
0 12 stint
0 21 stork


in poultry (and mammals) the virus slowly amino-mutates away from the index
in wild birds apparantly the M1-index is so much advantageous that even
small changes rarely survive.

But there is one variation with 7 amino-acid mutations found in 35 wild birds in
Minnessota/1998
Ohio/1988
Alberta/1985


nucleotide-mutations (=black pixels) of the 1048 amino-acid identical
avian M1-regions is the first attached picture

the 2nd picture is our M1-cloud

_________________
no patents on genes, publish the GISAID sequences !

H5N1 in poultry vs. wild birds

--------------------------------------------------------------------------------

looking at the index-distances ...

the 1997 Hongkong outbreak was caused by a poultry virus in most segments.
The virus had proably evolved since decades in poultry as LP in H6N1 or H9N2.
Hard to say where HA and NA came from - poultry or wild birds.
There is few index-like behaviour in HA.

The 1959 H5N1 outbreak in Scotland was from a much wilder virus.

Then H5N1 reassorted in 2002,2004 with wild viruses and all our modern
H5N1 in Vietnam,Japan,Indonesia,Qinghai is caused by wilder viruses,
still not as wild as 1959.
As ancestor of modern H5N1 I would consider A/Ck/Henan/16/2004. The HP H5-HA
is still from the early poultry outbreak, but inner segments are wilder.

Prevent the mixing of poultry viruses with wild bird viruses.
I.e. in China ducks and geese.
Same for swine.
Keep poultry and swine away from wild birds with flu.
We would still have the old adapted viruses, but no reassortment and refreshment
from outside.

Make regular reassortment tests of poultry viruses with the index-virus.

Test whether amino-identical index-viruses with entirely different
nucleotide-sequence show different reassortment behaviour.

_________________
no patents on genes, publish the GISAID sequences !

I finally completed my "cloud" pictures for the 8 segments

16 for segment 4, 9 for segment 6, 2 for segment 8,
so 32 in total.
Maybe we should (at least) further separate
the American and Eurasian lineages for each of
those 32 - that would make 64 and thus 64 index-strains.
For the inner segments at the protein level the American
and Eurausian inices should be very similar.


each pixel is one pair of segments
horizontal:synonymous differences
vertical:nonsynonymous differences

http://img46.yfrog.com/gal.php?g=sepp8.gif

1: http://img682.yfrog.com/img682/9668/sepp1.gif
2: http://img130.yfrog.com/img130/1489/sepp2.gif
3: http://img697.yfrog.com/img697/6522/sepp3.gif
4: http://img32.yfrog.com/img32/1519/sepp4.gif
5: http://img10.yfrog.com/img10/3641/sepp5.gif
6: http://img97.yfrog.com/img97/1118/sepp6.gif
7: http://img69.yfrog.com/img69/2358/sepp7.gif
8: http://img46.yfrog.com/img46/5748/sepp8.gif


the upper cloud usually consists of pairs with one
component Eurasian, the other North-American

index-like evolution is seen, when on these pictures the
clouds approach the y-axis high above the center

some signs of this in H1,H2,H3,N1 - but not as well
seen as in segments 1,2,3,5,7,8

_________________
no patents on genes, publish the GISAID sequences !

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0008935
> Conclusions
> This study showed that in mallards
> (1) a mild transient increase in body temperature may occur during LPAIV infection
> (2) infection by a LPAIV is limited by prior infection with a homologous strain and
> (3) may be prevented by prior infection with a heterologous strain
> (4) individual heterogeneity exists, both in the susceptibility to infection and the ability
> to develop heterosubtypic immunity.
> (5) viral RNA intermittent shedding occurs
> (6) the daily shedding pattern differs among sample types (water, feces, cloacal and oral swabs).
(hattip mixin at: http://www.flutrackers.com/forum/showthread.php?t=140379 )


-------------------------------------------------

the sequences
A/mallard/Sweden/7206/2004 (H7N7)
A/mallard/Sweden/6566/2004 (H5N2)
are apparantly not available at genbank.
This would be unusual, even for the bio-people, and you may speculate why.
Maybe because they are preparing another paper about the
involved genetics.
It is also only mentioned once, in "virus preparation", not in results,discussion
Other Swedish mallard-sequences were remarcably close to the index in segments 1,2,3,5,7,8 -
in 4,6 we usually have increased amino-acid mutation, even in mallards.

So I assume that the heterosubtypic immunity exists because those 6 other
segments were very similar.
This may not be usually the case for poultry, so the same experiment
for two different H9N2 chicken viruses should provide fewer protection,
although they both are H9N2.

The route of infection - fecal-oral through water - is different from what we have in poultry,pigs,humans.
I speculate that it's this route of infection which makes mallard-viruses gather near the index
while poultry and mammalean viruses mutate away from it.
There is not so much genetical flexibility in water-transmission-flu, the index-virus
is pretty optimal for this type. While for other types of transmissions modifications
in all 8 segments are of advantage.

Flu-A probably originates in mallards and/or other waterfowl and waterborne infections are
original. It is just only a lucky(for the virus) side-effect, that repiratory infections seem
to work in poultry and mammals. (and gulls,geese,.. ?), but those viruses usually die
earlier or later and are replaced by other original index-near viruses from waterfowl.
Replaced through host immuntity attacks against "competing" flu-A strains.

_________________
no patents on genes, publish the GISAID sequences !

Well segment 7 is the champion score!
However I recall segment 8 was somewhat bird-index friendly too!
Does the segment 8 have a comparable score of slow evolution in birds?

I am still checking the sepp8.gif. I understand that label “81” on picture stands for gene non structural #1 cloud, right?
We briefly discussed high S/N rates on paper correlating NP avian genes and 1918 sequences (1)


I also recalled from one of your first tables on this thread, that the [your ref.] A/avian/Alaska/Index(47H3N8,seg8verb.)/2006(H3N8)
had 44 differences [promile] compared with BM-18.

I compared segment 8, nonstructural protein 1 from /Brevig_Mission/1/18 (2) and isolate sequence A/mallard/Interior Alaska/3/2007.

Score =  464 bits (1195),  Expect = 5e-136, Method: Compositional matrix adjust.
 Identities = 225/230 (97%), Positives = 230/230 (100%), Gaps = 0/230 (0%)

Query  1    MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDQKSLRGRGSTLGLDIETATRA  60
            MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDQKSLRGRG+TLGLDIETATRA
Sbjct  1    MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDQKSLRGRGNTLGLDIETATRA  60
.
Query  61   GKQIVERILKEESDEALKMTIASVPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIRMD  120
            GKQIVERIL+EESDEALKMTIASVPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIRMD
Sbjct  61   GKQIVERILEEESDEALKMTIASVPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIRMD  120
.
Query  121  QAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTDEDVKNAVGV  180
            QAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTDEDVKNA+GV
Sbjct  121  QAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTDEDVKNAIGV  180
.
Query  181  LIGGLEWNDNTVRVSETLQRFAWRSSNENGRPPLPPKQKRKMARTIKSEV  230
            LIGGLEWNDNTVRVSETLQRFAWRSSNE+GRPPLPPKQKRKMARTI+SEV
Sbjct  181  LIGGLEWNDNTVRVSETLQRFAWRSSNEDGRPPLPPKQKRKMARTIESEV  230

I hope this sequence is a passable example of an index-like North American segment 8.

If so, is there any Eurasian candidate sequence resembling mallard/Interior Alaska/3/2007 at
amino acid level [NA-EA] with a nonstructural protein 1 [segment 8], differently coded
across the ocean as observed earlier on some other segments?

From the alignement, there are 5 amino acid differences, and 42 nucleotide differences
Identities = 797/839 (94%), Gaps = 2/839 (0%)

[Nucleotide changes]/[amino acid changes] = 8.4
I think it is reasonable suppose that a number of amino acids are just differently coded by silent differences:
Synonym differences : 37= (42-5)
Non synonym differences = 5. {O.K. ?}


(1) Novel Origin of the 1918 Pandemic Influenza Virus Nucleoprotein Gene
Ann H. Reid, Thomas G. Fanning, Thomas A. Janczewski, Raina M. Lourens, and Jeffery K. Taubenberger
http://jvi.asm.org/cgi/content/full/78/22/12462

(2) Sequence of the 1918 pandemic influenza virus nonstructural gene (NS) segment and characterization
of recombinant viruses bearing the 1918 NS genes
Christopher F. Basler, Ann H. Reid, Jody K. Dybing, Thomas A. Janczewski, Thomas G. Fanning, Hongyong Zheng, Mirella Salvatore,
Michael L. Perdue, David E. Swayne, Adolfo Garcıa-Sastre, Peter Palese, and Jeffery K. Taubenberger
PNAS February 27, 2001 vol. 98 no. 5 [2746–2751]
http://www.pnas.orgycgiydoiy 10.1073ypnas.031575198

I wish I had a Bablefish I could shove in my ear that would attach to my optic nerve.

segment 8 sometimes mutates quite a lot in poultry
and mammals but there are examples of low mutation too.
Well, that segment is short and has some overlap
(as for segment 7)

81,82 is for the different types of segment 8 and not NS1,NS2.

NS1 and NS2 are concatenated in my analysis now
and treated as one amino-acid sequence.
(most since Jan.), also M1 and M2

There are 16(well, I'd make it 15) sorts of HA, 9 sorts of NA
and 2 sorts of NS, but most authors omit the NS-type
in the characterisation e.g. (H3N8) instead of (H3N8NS1)
most NS (~90%) and all mammalean NS is of type 1,
maybe also all poultry , I should check

_________________
no patents on genes, publish the GISAID sequences !

146 out of 2630 avian flu viruses in my list
23 from Asia,21 from Europe,102 from America
are equal to the bird-index in segment 81
and 226 have only one amino-acid difference.


links to cloud-pictures

http://img46.yfrog.com/gal.php?g=sepp8.gif

1: http://img682.yfrog.com/img682/9668/sepp1.gif
2: http://img130.yfrog.com/img130/1489/sepp2.gif
3: http://img697.yfrog.com/img697/6522/sepp3.gif
4: http://img32.yfrog.com/img32/1519/sepp4.gif
5: http://img10.yfrog.com/img10/3641/sepp5.gif
6: http://img97.yfrog.com/img97/1118/sepp6.gif
7: http://img69.yfrog.com/img69/2358/sepp7.gif
8: http://img46.yfrog.com/img46/5748/sepp8.gif


you see how the upper cloud in 81 (but not 82) touches the Y-axis
high above zero.
Remember, segment 8 is short, multiply the height and width by ~2.5
when you compare with PB2


I get 42 nucleotide- and 6 amino-acid differences between BM18 and
mallard/int.AK/3/07(H4N6) in the coding regions of segment 8

_________________
no patents on genes, publish the GISAID sequences !

>146 out of 2630 avian flu viruses in my list
>23 from Asia,21 from Europe,102 from America
>are equal to the bird-index in segment 81
>and 226 have only one amino-acid difference.

OK, so there are 146+226=372 avian flu segment 8 type#1 with either 1 or 0
amino acids differences from the index!

I compared segment 8, nonstructural protein 1 from /Brevig_Mission/1/18 and isolate sequence (A/mallard/Netherlands/29/2006(H7N2)).
At the nucleotide level, BM18 NS1 alternates codes: identical to Alaska 2007 mallard, synonym code in 2006 Eurasian mallard or vice versa.
I hope this sequence is a passable index-like EurAsian segment 8. Protein alignment almost replicates previous A/mallard/Interior Alaska/3/2007.

>you see how the upper cloud in 81 (but not 82) touches the Y-axis
>high above zero.
>Remember, segment 8 is short, multiply the height and width by ~2.5
>when you compare with PB2

Segment 8 type#1 effectivelly shows an “upper cloud”, with an “offset” centered at aprox. 50 nucleotides.
Actually there is a second parallel cloud, farther from Y axis, and with and “offset” of aprox. 40 nucleotides.
The normalizing factor should be taken into account to comparison with PB2 [since lengths are different!].
I suspect that at least type#1 segement 8 has high percentage 4-fold degeracies similar to found on PB2.

now 110 genomes from Netherlands and Sweden are availabe at genbank.

These are mainly mallards from 1999-2007.

American mallards (plus pintails,shovelers,turnstones) are also
available (1975-2008) give a similar result, maybe I can post it later.
(see also the first post here in this thread at page 28)
Unfortunately there are only few examples from other continents

_________________
no patents on genes, publish the GISAID sequences !