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interesting recent avian viruses

gsgs

gsgs

Registered User
interesting recent avian viruses with differences to the bird-index in the 8 segments

06,17,11,--,24,--,05,17,A/Dk/LA/17G/1987(H3N8) {new lineage}
03,05,02,--,02,--,00,03_2,A/Pelican/Zambia/01/2006(H3N6) {full genome from Africa}
A/anas crecca/Spain/1384/2007(H1N1) {closest to 1918-HA}
11,15,12,--,27,--,10,40,A/mallard/South Dakota/Sg-00125/2007/09/19(H3N2) {swine virus in wild birds,9y preserved}
11,09,10,--,07,--,02,04_2,A/red-winged tinamou/Argentina/MP1/2008/04(H1N1) {full genome from SA, new species}
04,04,--,--,00,13_8,00,04_2,A/Tk/Canada/1963(H6N8) {early, 1963}
00,02,01,--,01,--,01,00,A/mallard/Netherlands/2/2005(H5N2) {close to index , 2009/12/16}



genomes from 2009 with type of the 8 segments (flugenome.org)

A/bar-headedGs/Mongolia/X53/2009,K,G,D,5J,F,1J,F,1E,Mongolia,Avian,H5N1,2009
A/beanGs/Tyva/10/2009,K,G,D,5J,F,1J,F,1E,Russia,Avian,H5N1,2009
A/Ck/Israel/184/2009,G,G,D,9B,F,2E,F,1E,Israel,Avian,H9N2,2009
A/common_goldeneye/Mongolia/X60/2009,K,G,D,5J,F,1J,F,1E,Mongolia,Avian,H5N1,2009
A/goose/Czech Republic/1848/2009,G,G,D,7A,F,9A,F,1E,Czech_Republic,Avian,H7N9,2009
A/grebe/Tyva/3/2009,K,G,D,5J,F,1J,F,1E,Russia,Avian,H5N1,2009
A/mallard/Hokkaido/24/2009,K,G,D,5H,F,1H,E,2A,Japan,Avian,H5N1,2009


I keep editing this
 
Re: interesting recent avian viruses

A/chicken/Beijing/1/1994(H9N2)

several strains (~5 ?) of H9N2 are circulating in Asian poultry
presumably from different introductions from wild birds.
From 2002 on there were several reassortments with H5N1 and
H5N1 acquired segments from H9N2 and H6N1, although the
"genotype Z" dominant since 2003 presumably got it from
wild birds with H9N2, not poultry. (Not so HK 1997)

When and how these introductions happened (and how to prevent them)
is an intereting question.

The Beijing chicken is the earliest record so far from one of the strains.

It already has 19,15,18,-,15,-,19,17 amino-acid differences from the index.
So I assume the introduction happened in the 80s or 70s or even
earlier.

To compare:
the related A/chicken/Yokohama/aq45/2002(H9N2) has 22,21,19,-,15,-,14,21 differences
(apparantly another segment 7 through reassortment)

genotype Z/2002(H5N1) has 3,6,7,-,5,-,12,11 differences
the descendent A/bar-headed goose/Mongolia/X53/2009(H5N1) has 11,7,6,-,7,-,13,23 differences
A/Ck/Egypt/0891/2008(H5N1) has 15,13,15,-,11,-,15,20 differences

10 differences in 8 years in segments 1,2,3,5 in chicken
11 differences in 7 years in segments 1,2,3,5 in wild birds
26 differences in 6 years in segments 1,2,3,5 in chicken
 
Re: interesting recent avian viruses

38 new genomes from Netherlands,Sweden !

not yet available through the main genbank search page, maybe tomorrow...

A/common teal/Netherlands/10/2000(H1N1)
A/common teal/Netherlands/9/2000(H11N9)
A/common teal/Sweden/1/2003(H3N3)
A/greylag goose/Netherlands/4/1999(H6N1)
A/mallard/Netherlands/1/1999(H4N6)
A/mallard/Netherlands/1/2002(H4N6)
A/mallard/Netherlands/10/1999(H1N8)
A/mallard/Netherlands/12/2001(H4N2)
A/mallard/Netherlands/15/1999(H11N9)
A/mallard/Netherlands/2/1999(H3N5)
A/mallard/Netherlands/5/2001(H3N6)
A/mallard/Sweden/110/2002(H11N7)
A/mallard/Sweden/24/2002(H8N4)
A/mallard/Sweden/25/2002(H11N3)
A/mallard/Sweden/3/2002(H1N2)
A/mallard/Sweden/4/2002(H10N2)
A/mallard/Sweden/41/2002(H10N6)
A/mallard/Sweden/45/2002(H11N8)
A/mallard/Sweden/46/2002(H4N3)
A/mallard/Sweden/48/2002(H11N9)
A/mallard/Sweden/50/2002(H3N8)
A/mallard/Sweden/52/2003(H6N2)
A/mallard/Sweden/55/2002(H11N2)
A/mallard/Sweden/57/2003(H1N1)
A/mallard/Sweden/58/2003(H11N1)
A/mallard/Sweden/6/2002(H2N3)
A/mallard/Sweden/62/2003(H4N6)
A/mallard/Sweden/65/2002(H10N9)
A/mallard/Sweden/7/2003(H10N8)
A/mallard/Sweden/8/2003(H8N4)
A/mallard/Sweden/81/2002(H6N1)
A/mallard/Sweden/86/2003(H12N5)
A/mallard/Sweden/88/2002(H2N1)
A/mallard/Sweden/98/2002(H1N6)
A/northern pintail/Sweden/1/2003(H2N3)
A/northern shoveler/Netherlands/18/1999(H11N9)
A/whitefronted goose/Netherlands/1/1999(H6N1)
A/whitefronted goose/Netherlands/2/1999(H6N2)
 
Re: interesting recent avian viruses

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.
Unfortunately there are only few examples from other continents

eubi3p4.GIF
 
Re: interesting recent avian viruses

new genomes with protein differences to the bird-index:
A/mallard/NL/3/1999/10/09(H5N2) 1,1,2,-,8,-,5,*16
A/mallard/NL/5/1999/10/18(H2N9) 1,0,4,-,0,-,5,5
 
Re: interesting recent avian viruses

rosy billed pochard from Argentina

apparantly South American avian flu evolves separately in segments
1,3,5 at least since >100 years

the equine flu H3N8 since 1983 is closest to
South American flu in segments 3,5


~20 avian genomes from South America and Africa would be useful.
And of course anything from before 1960
 
Re: interesting recent avian viruses

pig with H11N6 !

CY073449 Swine 1 H11N6 South Korea 2001 2341 Influenza A virus (A/swine/KU/2/2001(H11N6)) yes
 
Re: interesting recent avian viruses

flu from surface water

http://www.ncbi.nlm.nih.gov/nuccore/306022255?report=genbank
A/surface water/Minnesota/NW1-T/2006(H4N6)
TITLE Direct Submission
JOURNAL Submitted (03-SEP-2010) Department of Veterinary Population
Medicine, University of Minnesota, 1354 Eckles Avenue, Saint Paul,
MN 55108, USA

http://www.ncbi.nlm.nih.gov/nuccore/306022281?report=genbank
A/surface water/Minnesota/W07-2241/2007(H3N8)
Yang,M., Wang,P., Enomoto,S., Ramakrishnan,M.A., Lebarbenchon,C.,
Stallknecht,D.E. and Sreevatsan,S.

------------------------------------------------------------------------------
0 0 2280 2363 >A/surface water/Minnesota/NW1-T/2006(H4N6)
114 26 2280 1963 >A/blue-winged teal/Manitoba/13436/05(H3N8),2005,8,4,0
135 31 2280 1827 >A/mallard/Ohio/1851/05(H11N1),2005,3,4,0
135 31 2280 1846 >A/blue-winged teal/Ohio/1387/05(H6N2),2005,8,4,0
135 31 2280 1976 >A/snow Gs/Maryland/410/05(H6N1),2005,15,4,0
144 33 2280 1977 >A/snow Gs/Maryland/353/05(H6N1),2005,15,4,0
149 34 2280 1978 >A/snow Gs/Maryland/364/05(H6N1),2005,15,4,0
171 39 2280 1584 >A/mallard/Minnesota/249/00(H11N9),2000,3,4,0
175 40 2280 1586 >A/mallard/Minnesota/31/00(H2N9),2000,3,4,0
175 40 2280 2075 >A/blue-winged teal/Minnesota/Sg-00229/06(H4N6),2006,8,4,0

0 0 2274 2675 >A/surface water/Minnesota/NW1-T/2006(H4N6)
285 65 2274 1614 >A/pintail/ALB/275/96(H4N6)08,1996,6,4,0
330 75 2267 1020 >A/guillemot/Sweden/3/00(H6N2),2000,0,3,0
386 88 2274 1748 >A/mallard/MN/42/00(H11N9),2000,3,4,0

0 0 2151 2948 >A/surface water/Minnesota/NW1-T/2006(H4N6)
93 20 2135 2618 >A/mallard Dk/Minnesota/Sg-00100/07(H3N3)09/14, 2007 , 3 , 4 , 0
102 22 2151 2781 >A/mallard/Minnesota/Sg-00627/08(H1N1)07/29, 2008 , 3 , 0 , 0
102 22 2151 2782 >A/mallard/Minnesota/Sg-00628/08(H1N1)07/29, 2008 , 3 , 0 , 0
106 23 2151 2805 >A/N.shoveler/Minnesota/Sg-00651/08(H1N1)07/31, 2008 , 11 , 0 , 0
106 23 2151 2809 >A/N.shoveler/Minnesota/Sg-00655/08(H1N1)07/31, 2008 , 11 , 0 , 0


0 0 1497 2595 >A/surface water/Minnesota/NW1-T/2006(H4N6)
100 15 1497 2463 >A/mallard/Interior Alaska/2/07(H4N6)09/10, 2007 , 3 , 4 , 0
100 15 1497 2467 >A/mallard/Interior Alaska/7MP1050R1/07(H4N6)09/10, 2007 , 3 , 4 , 0
100 15 1497 2481 >A/American widgeon/CA/HKWF42/07(H6N1)10/21, 2007 , 16 , 4 , 0
106 16 1497 2445 >A/mallard/Interior Alaska/1/07(H4N5)09/03, 2007 , 3 , 4 , 0
106 16 1497 2471 >A/mallard/Interior Alaska/7MP1718/07(H4N5)09/16, 2007 , 3 , 4 , 0
113 17 1497 2444 >A/N.shoveler/Interior Alaska/1/07(H4N6)09/01, 2007 , 11 , 4 , 0
113 17 1497 2526 >A/green winged teal/CA/AKS1370/08(H7N3)01/27, 2008 , 8 , 4 , 0
126 19 1497 2396 >A/mallard/Quebec/11063/06(H2N3)08/19, 2006 , 3 , 4 , 0


0 0 759 2724 >A/surface water/Minnesota/NW1-T/2006(H4N6)
26 2 759 2253 >A/mallard/Ohio/363/03(H2N1),2003,3,4,0
26 2 759 2304 >A/mallard/Ohio/793/04(H11N2),2004,3,4,0
26 2 759 2493 >A/N.pintail/Illinois/464067-4/06(H5N9),2006,6,4,0
26 2 759 2503 >A/Muscovy Dk/NY/62095-1/06(H5N2)05/15,2006,10,4,0
26 2 759 2534 >A/mallard/Quebec/11247/06(H3N2)08/24,2006,3,4,0
39 3 759 2319 >A/american black Dk/Ohio/1823/05(H11N9),2005,10,4,0
39 3 759 2463 >A/mallard/Maryland/182/06(H5N2),2006,3,4,0
39 3 759 2527 >A/mallard/Quebec/11111/06(H11N9)08/20,2006,3,4,1
39 3 759 2533 >A/American black Dk/Quebec/11235/06(H3N2)08/24,2006,10,4,0
39 3 759 2605 >A/American widgeon/CA/HKWF41/07(H6N1)10/21,2007,16,4,1
39 3 759 2615 >A/American widgeon/CA/HKWF296/07(H6N1)10/31,2007,16,4,1
52 4 759 2235 >A/mallard/Maryland/750/02(H4N6)08/27,2002,3,4,0

0 0 838 3259 >A/surface water/Minnesota/NW1-T/2006(H4N6)
35 3 838 3064 >A/mallard/Quebec/11063/06(H2N3)08/19,2006,3,4,0
35 3 838 3077 >A/mallard/Quebec/11281/06(H2N3)08/25,2006,3,4,0
59 5 838 2841 >A/pintail/Alberta/49/03(H12N5)07/25,2003,6,4,0

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

0 0 2280 2364 >A/surface water/Minnesota/W07-2241/2007(H3N8)
175 40 2280 1574 >A/mallard/MN/109/00(H11N9),2000,3,4,0
179 41 2280 1579 >A/mallard/MN/479/00(H5N3),2000,3,4,0
188 43 2280 2185 >A/N.shoveler/CA/HKWF1026/07(H7N3),2007,11,4,0
206 47 2280 1673 >A/mallard/MD/403/02(H1N1),2002,3,4,0
228 52 2280 1580 >A/mallard/MN/113/00(H5N2),2000,3,4,0
228 52 2280 1940 >A/mallard/Alberta/11527/05(H3N8),2005,3,4,0
241 55 2280 1944 >A/pintail/Alaska/53/05(H3N6),2005,6,4,0

0 0 2274 2676 >A/surface water/Minnesota/W07-2241/2007(H3N8)
162 37 2274 2387 >A/N.pintail/CA/HKWF151/07(H6N1)10/24,2007,6,4,0
171 39 2274 2383 >A/American widgeon/CA/HKWF41/07(H6N1)10/21,2007,16,4,0
171 39 2274 2393 >A/American widgeon/CA/HKWF296/07(H6N1)10/31,2007,16,4,0

0 0 2151 2949 >A/surface water/Minnesota/W07-2241/2007(H3N8)
60 13 2142 2560 >A/blue-winged teal/Minnesota/Sg-00043/07(H4N6)08/03, 2007 , 8 , 4 , 0
60 13 2151 2540 >A/mallard/Minnesota/Sg-00230/06(H7N3)09/30, 2006 , 3 , 4 , 0
61 13 2130 2565 >A/mallard Dk/Minnesota/Sg-00053/07(H4N6)08/03, 2007 , 3 , 4 , 0
61 13 2131 2559 >A/blue-winged teal/Minnesota/Sg-00030/07(H4N6)08/03, 2007 , 8 , 4 , 0


0 0 1497 2596 >A/surface water/Minnesota/W07-2241/2007(H3N8)
33 5 1497 2440 >A/mallard/Interior Alaska/7MP0372/07(H4N6)08/17, 2007 , 3 , 4 , 0
40 6 1497 2431 >A/N.pintail/Interior Alaska/1/07(H4N6)08/08, 2007 , 6 , 4 , 0
40 6 1497 2436 >A/N.pintail/Alaska/7MP1393/07(H4N6)08/14, 2007 , 6 , 4 , 0
73 11 1497 2502 >A/American green-winged teal/CA/HKWF609/07(H5N2)11/10, 2007 , 8 , 4 , 0
100 15 1497 2479 >A/American widgeon/CA/HKWF371/07(H6N5)10/07, 2007 , 16 , 4 , 0
113 17 1497 2387 >A/shorebird/Delaware/249/06(H9N2)05/22, 2006 , 12 , 4 , 0
120 18 1497 2330 >A/snow Gs/Maryland/364/05(H6N1)12/13, 2005 , 15 , 4 , 0
120 18 1497 2500 >A/American widgeon/CA/HKWF541/07(H6N5)11/07, 2007 , 16 , 4 , 0
126 19 1497 1889 >A/blue-winged teal/Ohio/31/99(H3N2)10/16, 1999 , 8 , 4 , 0
146 22 1497 1867 >A/mallard/MN/160/99(H4N6), 1999 , 3 , 4 , 0
153 23 1497 1830 >A/mallard/Minnesota/114/98(H4N8), 1998 , 3 , 4 , 0


0 0 759 2725 >A/surface water/Minnesota/W07-2241/2007(H3N8)
52 4 759 2135 >A/mallard/Alberta/156/01(H3N8)08/06,2001,3,4,0
65 5 759 2003 >A/mallard/Alberta/125/99(H11N6)08/04,1999,3,4,0
92 7 759 1897 >A/mallard/MN/7/98(H11N2),1998,3,4,0
92 7 759 1928 >A/mallard/Minnesota/153/98(H9N2),1998,3,4,0
92 7 759 2274 >A/blue-winged teal/Alberta/293/03(H4N6)08/13,2003,8,4,0
92 7 759 2577 >A/N.shoveler/Interior Alaska/4/07(H3N8)09/05,2007,11,4,0
105 8 759 1841 >A/mallard/ALB/206/96(H6N8)08,1996,3,4,0
105 8 759 2271 >A/mallard/Alberta/209/03(H10N7)08/07,2003,3,4,0
105 8 759 2421 >A/mallard/Alberta/11527/05(H3N8)08/03,2005,3,4,0
105 8 759 2726 >A/bird/Alaska/Index/2006(H3N8)

0 0 838 3260 >A/surface water/Minnesota/W07-2241/2007(H3N8)
59 5 838 2980 >A/N.pintail/Alberta/11701/05(H3N8)08/05,2005,6,4,0
59 5 838 3114 >A/N.shoveler/Interior Alaska/1/07(H4N6)09/01,2007,11,4,0
71 6 838 3128 >A/mallard/Interior Alaska/4/07(H4N6)09/07,2007,3,4,0
83 7 838 3157 >A/N.pintail/CA/HKWF151/07(H6N1)10/24,2007,6,4,0


differences from the bird-index:

A/surface water/Minnesota/W07-2241/2007(H3N8)
6,5,13,6,2,9,1,3

>A/surface water/Minnesota/NW1-T/2006(H4N6)
3,2,5,-,2,-,2,2


paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197669/?tool=pubmed
 
Re: interesting recent avian viruses

They found H4N6 in a wild raccoon last year

We surveyed the wildlife inhabiting a poultry farm with recent H3N6 and H4N6 avian influenza virus exposure in Pennsylvania, U.S.A. One raccoon (Procyon lotor) tested positive for H4N6 antibodies. This is the first recorded incident of avian influenza exposure in a wild raccoon. We suggest that raccoons may play a role in the transmission of avian influenza viruses and in compromising biosecurity efforts at poultry operations.
Click to expand...

http://www.bioone.org/doi/abs/10.1637/8459-082708-ResNote.1?journalCode=avdi
 
Re: interesting recent avian viruses

several Hongkong poultry H6N1,H6N2 genomes from 2001-2003 were released.
e.g. A/Ck/HK/SF3/2001(H6N1)
It is similar in 7 segments to HK-flu from 1997, so apparantly reassorted
with H5N1 by exchanging HA.
Did this reassortment happen before the 1997 outbreak in Hongkong,
is it the reassortment which led to that outbreak ?
It seems so. E.g. the PB1 of SF3 is closer to A/Dk/HK/562/1979(H10N9),
the best matching PB1 from the 70s, than A/H//156/1997.
But I'm not so sure yet since we had these periods of low mutation
in China which can corrupt normal molecular-clock analyis.

Anyway, I think that probably there was H6N1 in HK poultry all the time
before 1997 and then it just picked up the HA from A/Gs/Gd/1996(H5N1),
so to form a strain much more virulent to chickens.

They should have deep-frozen some sick-chicken/duck-tissues from HK
from the 80s or 90s. We do have some HK-sequences from the 70s,
but almost nothing from 1980-1996.

The 2004 tree-sparrows study shoud be redone.
Find the places,species in China where flu
survives without mutating.
 
Re: interesting recent avian viruses

A/Pekin duck/CA/P30/2006/03/06(H4N2)


Code: 
 13 >A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151 1692 1497 1414  982  838   
  1:135,111,142,483,146,512, 83,123   A/Brevig Mission/1/1918                                  2280 2274 2151 1701 1497 1410  982  838
  2:128,115,115,486,150, 74, 78,286   A/blue goose/WI/711/1975                                 2280 2274 2151 1695 1497 1414  982  838
  3: 39, 49, 47,322, 52,485, 31, 33   A/duck/LA/17G/1987                                       2280 2274 2151 1710 1497 1410  982  838
 14: 26,  8,  7,123, 59, 11,  4,  9   A/mallard/CA/J-808/2006/12/06                             412 1008 1000  516  185 1238  982  838

 14 >A/mallard/CA/J-808/2006/12/06                             412 1008 1000  516  185 1238  982  838   
  1:121,101,139,478,102,512, 85,122   A/Brevig Mission/1/1918                                  2280 2274 2151 1701 1497 1410  982  838
  2: 96,107,110,470,102, 74, 76,286   A/blue goose/WI/711/1975                                 2280 2274 2151 1695 1497 1414  982  838
  3: 36, 32, 42,323,102,485, 33, 30   A/duck/LA/17G/1987                                       2280 2274 2151 1710 1497 1410  982  838
 13: 26,  8,  7,123, 59, 11,  4,  9   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151 1692 1497 1414  982  838

  3 >A/duck/LA/17G/1987                                       2280 2274 2151 1710 1497 1410  982  838   
  1:124, 98,135,490,146,390, 87,110   A/Brevig Mission/1/1918                                  2280 2274 2151 1701 1497 1410  982  838
  2:124,105, 98,484,159,479, 77,290   A/blue goose/WI/711/1975                                 2280 2274 2151 1695 1497 1414  982  838
 13: 39, 49, 47,322, 52,485, 31, 33   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151 1692 1497 1414  982  838
 14: 36, 32, 42,323,102,485, 33, 30   A/mallard/CA/J-808/2006/12/06                             412 1008 1000  516  185 1238  982  838

  1 >A/Brevig Mission/1/1918                                  2280 2274 2151 1701 1497 1410  982  838   
  2:105, 81,129,310,124,505, 52,278   A/blue goose/WI/711/1975                                 2280 2274 2151 1695 1497 1414  982  838
  3:124, 98,135,490,146,390, 87,110   A/duck/LA/17G/1987                                       2280 2274 2151 1710 1497 1410  982  838
 13:135,111,142,483,146,512, 83,123   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151 1692 1497 1414  982  838
 14:121,101,139,478,102,512, 85,122   A/mallard/CA/J-808/2006/12/06                             412 1008 1000  516  185 1238  982  838

  2 >A/blue goose/WI/711/1975                                 2280 2274 2151 1695 1497 1414  982  838   
  1:105, 81,129,310,124,505, 52,278   A/Brevig Mission/1/1918                                  2280 2274 2151 1701 1497 1410  982  838
  3:124,105, 98,484,159,479, 77,290   A/duck/LA/17G/1987                                       2280 2274 2151 1710 1497 1410  982  838
 13:128,115,115,486,150, 74, 78,286   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151 1692 1497 1414  982  838
 14: 96,107,110,470,102, 74, 76,286   A/mallard/CA/J-808/2006/12/06                             412 1008 1000  516  185 1238  982  838


 16 >A/northern pintail/CA/HKWF792/2007/11/28                 2293 2274 2209    3 1520    3 1002  864   
  1:127,149,142,---,148,---, 52,122   A/Brevig Mission/1/1918                                  2280 2274 2151    3 1497    3  982  838
  2: 65,154,115,---,148,---, 47,288   A/blue goose/WI/711/1975                                 2280 2274 2151    3 1497    3  982  838
  3:125,154,130,---, 57,---, 88, 34   A/duck/LA/17G/1987                                       2280 2274 2151    3 1497    3  982  838
 11:164,107, 88,---,148,---, 66,115   A/mallard/New Zealand/527-11/2005                        2280  931 2151    3 1497    3  982  838
 15: 41, 28, 19,---,160,---, 25,289   A/N.shoveler/Int.Alaska/8BM3671/2008/09/25   1844  424 1115    3 1161    3  982  838
 13:135,159,136,---, 15,---, 84,  5   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151    3 1497    3  982  838
 14:125,140,137,---, 48,---, 84, 13   A/mallard/CA/JN808/2006/12/06                             412 1008 1000    3  185    3  982  838


Code: 
  1 >A/Brevig Mission/1/1918                                  2280 2274 2151    0 1497    0  982  838   
  2:105, 81,129,---,124,---, 52,278   A/blue goose/WI/711/1975                                 2280 2274 2151    0 1497    0  982  838
  3:124, 98,135,---,146,---, 87,110   A/duck/LA/17G/1987                                       2280 2274 2151    0 1497    0  982  838
 13:135,111,142,---,146,---, 83,123   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151    0 1497    0  982  838
 14:121,101,139,---, 59,---, 85,122   A/mallard/CA/J-808/2006/12/06                             412 1008 1000    0  185    0  982  838
 15:111, 96,129,---,135,---, 51,281   A/northern shoveler/Interior Alaska/8BM3671/2008/09/25   1844  424 1115    0 1161    0  982  838
 16:127,149,142,---,148,---, 52,122   A/northern pintail/CA/HKWF792/2007/11/28                 2293 2274 2209    0 1520    0 1002  864
 17:137,117,142,---,146,---, 84,122   A/cinnamon teal/CA/44287-325/2007/01/27(H3N8)            2301 2101 2196    0 1507    0  989  851

  2 >A/blue goose/WI/711/1975                                 2280 2274 2151    0 1497    0  982  838   
  1:105, 81,129,---,124,---, 52,278   A/Brevig Mission/1/1918                                  2280 2274 2151    0 1497    0  982  838
  3:124,105, 98,---,159,---, 77,290   A/duck/LA/17G/1987                                       2280 2274 2151    0 1497    0  982  838
 13:128,115,115,---,150,---, 78,286   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151    0 1497    0  982  838
 14: 96,107,110,---, 64,---, 76,286   A/mallard/CA/J-808/2006/12/06                             412 1008 1000    0  185    0  982  838
 15: 61,101,107,---, 84,---, 42, 36   A/northern shoveler/Interior Alaska/8BM3671/2008/09/25   1844  424 1115    0 1161    0  982  838
 16: 65,154,115,---,148,---, 47,288   A/northern pintail/CA/HKWF792/2007/11/28                 2293 2274 2209    0 1520    0 1002  864
 17:134,117,114,---,147,---, 77,284   A/cinnamon teal/CA/44287-325/2007/01/27(H3N8)            2301 2101 2196    0 1507    0  989  851

  3 >A/duck/LA/17G/1987                                       2280 2274 2151    0 1497    0  982  838   
  1:124, 98,135,---,146,---, 87,110   A/Brevig Mission/1/1918                                  2280 2274 2151    0 1497    0  982  838
  2:124,105, 98,---,159,---, 77,290   A/blue goose/WI/711/1975                                 2280 2274 2151    0 1497    0  982  838
 10: 96, 74,129,---,156,---, 94,103   A/mallard/New Zealand/223-31/2005                         476  336 2151    0 1497    0  982  838
 13: 39, 49, 47,---, 52,---, 31, 33   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151    0 1497    0  982  838
 14: 36, 32, 42,---, 91,---, 33, 30   A/mallard/CA/JN808/2006/12/06                             412 1008 1000    0  185    0  982  838
 15:123,103,116,---,166,---, 86,289   A/northern shoveler/Interior Alaska/8BM3671/2008/09/25   1844  424 1115    0 1161    0  982  838
 16:125,154,130,---, 57,---, 88, 34   A/northern pintail/CA/HKWF792/2007/11/28                 2293 2274 2209    0 1520    0 1002  864
 17: 46, 49, 50,---, 54,---, 32, 32   A/cinnamon teal/CA/44287-325/2007/01/27(H3N8)            2301 2101 2196    0 1507    0  989  851

 10 >A/mallard/New Zealand/223-31/2005                         476  336 2151    0 1497    0  982  838   
  1: 94, 80,140,---,140,---, 73, 76   A/Brevig Mission/1/1918                                  2280 2274 2151    0 1497    0  982  838
  2: 85, 86,111,---,109,---, 64,286   A/blue goose/WI/711/1975                                 2280 2274 2151    0 1497    0  982  838
  3: 96, 74,129,---,156,---, 94,103   A/duck/LA/17G/1987                                       2280 2274 2151    0 1497    0  982  838
  6:  8, 15, 24,---, 58,---, 16, 27   A/mallard/New Zealand/449-33/2004                        2280  748 2151    0 1497    0  982  838
 11:  2,  2, 26,---, 48,---, 41, 20   A/mallard/New Zealand/527-11/2005                        2280  931 2151    0 1497    0  982  838
 13: 94, 80,140,---,152,---, 94,119   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151    0 1497    0  982  838
 14: 96, 86,134,---, 59,---, 92,117   A/mallard/CA/J-808/2006/12/06                             412 1008 1000    0  185    0  982  838
 15: 90, 65, 79,---,142,---, 70,278   A/northern shoveler/Interior Alaska/8BM3671/2008/09/25   1844  424 1115    0 1161    0  982  838
 16:104, 74, 91,---,157,---, 69,117   A/northern pintail/CA/HKWF792/2007/11/28                 2293 2274 2209    0 1520    0 1002  864
 17: 96, 89,139,---,154,---, 93,117   A/cinnamon teal/CA/44287-325/2007/01/27(H3N8)            2301 2101 2196    0 1507    0  989  851

 13 >A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151    0 1497    0  982  838   
  1:135,111,142,---,146,---, 83,123   A/Brevig Mission/1/1918                                  2280 2274 2151    0 1497    0  982  838
  2:128,115,115,---,150,---, 78,286   A/blue goose/WI/711/1975                                 2280 2274 2151    0 1497    0  982  838
  3: 39, 49, 47,---, 52,---, 31, 33   A/duck/LA/17G/1987                                       2280 2274 2151    0 1497    0  982  838
 10: 94, 80,140,---,152,---, 94,119   A/mallard/New Zealand/223-31/2005                         476  336 2151    0 1497    0  982  838
 14: 26,  8,  7,---, 26,---,  4,  9   A/mallard/CA/J-808/2006/12/06                             412 1008 1000    0  185    0  982  838
 15:131,120,128,---,171,---, 83,289   A/northern shoveler/Interior Alaska/8BM3671/2008/09/25   1844  424 1115    0 1161    0  982  838
 16:135,159,136,---, 15,---, 84,  5   A/northern pintail/CA/HKWF792/2007/11/28                 2293 2274 2209    0 1520    0 1002  864
 17: 23, 15,  7,---, 11,---,  3, 10   A/cinnamon teal/CA/44287-325/2007/01/27(H3N8)            2301 2101 2196    0 1507    0  989  851

 14 >A/mallard/CA/JN808/2006/12/06                             412 1008 1000    0  185    0  982  838   
  1:121,101,139,---, 59,---, 85,122   A/Brevig Mission/1/1918                                  2280 2274 2151    0 1497    0  982  838
  2: 96,107,110,---, 64,---, 76,286   A/blue goose/WI/711/1975                                 2280 2274 2151    0 1497    0  982  838
  3: 36, 32, 42,---, 91,---, 33, 30   A/duck/LA/17G/1987                                       2280 2274 2151    0 1497    0  982  838
 13: 26,  8,  7,---, 26,---,  4,  9   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151    0 1497    0  982  838
 15:116,115,147,---,117,---, 83,289   A/northern shoveler/Interior Alaska/8BM3671/2008/09/25   1844  424 1115    0 1161    0  982  838
 16:125,140,137,---, 32,---, 84, 13   A/northern pintail/CA/HKWF792/2007/11/28                 2293 2274 2209    0 1520    0 1002  864
 17:  7,  2,  7,---, 26,---,  3,  1   A/cinnamon teal/CA/44287-325/2007/01/27(H3N8)            2301 2101 2196    0 1507    0  989  851

 15 >A/northern shoveler/Interior Alaska/8BM3671/2008/09/25   1844  424 1115    0 1161    0  982  838   
  1:111, 96,129,---,135,---, 51,281   A/Brevig Mission/1/1918                                  2280 2274 2151    0 1497    0  982  838
  2: 61,101,107,---, 84,---, 42, 36   A/blue goose/WI/711/1975                                 2280 2274 2151    0 1497    0  982  838
  3:123,103,116,---,166,---, 86,289   A/duck/LA/17G/1987                                       2280 2274 2151    0 1497    0  982  838
 13:131,120,128,---,171,---, 83,289   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151    0 1497    0  982  838
 14:116,115,147,---,117,---, 83,289   A/mallard/CA/J-808/2006/12/06                             412 1008 1000    0  185    0  982  838
 16: 42, 28, 19,---,160,---, 25,289   A/northern pintail/CA/HKWF792/2007/11/28                 2293 2274 2209    0 1520    0 1002  864
 17:131,115,126,---,162,---, 82,288   A/cinnamon teal/CA/44287-325/2007/01/27(H3N8)            2301 2101 2196    0 1507    0  989  851

 16 >A/northern pintail/CA/HKWF792/2007/11/28                 2293 2274 2209    0 1520    0 1002  864   
  1:127,149,142,---,148,---, 52,122   A/Brevig Mission/1/1918                                  2280 2274 2151    0 1497    0  982  838
  2: 65,154,115,---,148,---, 47,288   A/blue goose/WI/711/1975                                 2280 2274 2151    0 1497    0  982  838
  3:125,154,130,---, 57,---, 88, 34   A/duck/LA/17G/1987                                       2280 2274 2151    0 1497    0  982  838
 13:135,159,136,---, 15,---, 84,  5   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151    0 1497    0  982  838
 14:125,140,137,---, 32,---, 84, 13   A/mallard/CA/J-808/2006/12/06                             412 1008 1000    0  185    0  982  838
 15: 42, 28, 19,---,160,---, 25,289   A/northern shoveler/Interior Alaska/8BM3671/2008/09/25   1844  424 1115    0 1161    0  982  838
 17:134,162,134,---,  5,---, 82, 14   A/cinnamon teal/CA/44287-325/2007/01/27(H3N8)            2301 2101 2196    0 1507    0  989  851

 17 >A/cinnamon teal/CA/44287-325/2007/01/27(H3N8)            2301 2101 2196    0 1507    0  989  851   
  1:137,117,142,---,146,---, 84,122   A/Brevig Mission/1/1918                                  2280 2274 2151    0 1497    0  982  838
  2:134,117,114,---,147,---, 77,284   A/blue goose/WI/711/1975                                 2280 2274 2151    0 1497    0  982  838
  3: 46, 49, 50,---, 54,---, 32, 32   A/duck/LA/17G/1987                                       2280 2274 2151    0 1497    0  982  838
 13: 23, 15,  7,---, 11,---,  3, 10   A/pekin Dk/CA/P30/2006/03/06                             2280 2274 2151    0 1497    0  982  838
 14:  7,  2,  7,---, 26,---,  3,  1   A/mallard/CA/J-808/2006/12/06                             412 1008 1000    0  185    0  982  838
 15:131,115,126,---,162,---, 82,288   A/northern shoveler/Interior Alaska/8BM3671/2008/09/25   1844  424 1115    0 1161    0  982  838
 16:134,162,134,---,  5,---, 82, 14   A/northern pintail/CA/HKWF792/2007/11/28                 2293 2274 2209    0 1520    0 1002  864




http://www.flutrackers.com/forum/showthread.php?t=7400
http://www.flutrackers.com/forum/showthread.php?t=34185


A/duck/LA/17G/1987(H3N8)

A/Northern pintail/California/HKWF792/2007(H3N8),
which is a bit similar in segments 4,5,6,8, clearly reassorted.

segment 2 but not the others is closest to Brevig/1918.

the 1889 pandemic is assumed to have been H3N8
__________________

H3N8 was also in recent outbreaks in horses and dogs.
H3N8 is quite frequent in birds too, but birds have many
different serotypes.

However this H3N8 from 1987 is quite different to any other
known H3N8.
It gave segments 5,8 to the shoveler (edit:also 4,6)
__________________
nucleotide differences of A/duck/LA/17G/1987(H3N8) to other viruses
in 0/00 for the 8 segments:

A/Northern pintail/California/HKWF792/2007(H3N8) : 124,151,128,043,057,047,088,033
A/Brevig Mission/1918(H1N1) : 124,098,135,492,146,428,087,110
A/Kansas.../2007(H1N1) : 152,132,152,500,184,435,123,152
A/fowl plague/Rostock/1934(H7N1) : 143,156,103,441,152,413,095,110



Most recent common anchestor of 17G/1987 in PB1 with Brevig/1918 is ~1915
Most recent common anchestor in PB1 with Dk/Memphis/546/1974 is ~1945
 
Re: interesting recent avian viruses

AT-scores (high-->mammalean)

Code: 
5614  5592,5760,5708,5778,5357,5716,5213,5453,  -  >A/Index/early human/~1935(H1N1)
5574  5561,5659,5620,5802,5310,5751,5152,5465,  -  >A/Brevig Mission/1/1918(H1N1)
5611  5592,5703,5685,5837,5317,5829,5152,5465,  -  >A/Index/early swine/~1935(H1N1)

5505  5531,5659,5674,----,5220,----,5150,----,  -  >A/duck/Memphis/546/1974(H11N9)
5720  ----,----,----,5767,----,5652,----,----,  -  >A/Anas crecca/Spain/1384/2007(H1N1)
5506  5472,5642,5723,----,5214,----,5170,5584,  -  >A/Index/7 birds similar to BM18/~1975
5556  5417,5756,5535,5830,5285,5770,5110,5543,  -  >A/pintail/Alaska/20/2005(H12N5)
5569  5574,5753,5620,5696,5258,5594,5121,5719,  -  >A/mallard/Interior Alaska/2/2007(H4N6)
5560  5510,5732,5655,5655,5234,5659,5183,5649,  -  >A/pintail/Alaska/279/2005(H3N8)
5570  5547,5742,5656,5649,5226,5665,5216,5649,  -  >A/mallard/Alaska/715/2005(H3N8)
5737  5729,5798,5797,5821,5519,5986,5309,5745,  -  >A/duck/LA/17G/1987(H3N8)
5719  5692,5844,5885,5839,5524,5693,5295,5668   -  >A/Pekin duck/CA/P30/2006/03/06(H4N2)
5696  5697,5844,5878,----,5507,----,5288,5663  -     >A/cinnamon teal/CA/44287-325/2007/01/27(H3N8)

6087  6073,6167,6270,6199,5850,6176,5483,6187,  -  >A/equine/Lexington/1-1/1966(H7N7)
6016  ----,----,----,----,5814,6152,----,6150,  -  >A/equine/Prague/1-3/1956(H7N7)
5978  6091,5533,----,6216,5814,6713,5530,6191,  -  >A/equine/Prague/1-1/1956(H7N7)
5897  ----,----,----,----,5725,6142,5550,6191,  -  >A/equine/Prague/1-2/1956(H7N7)
5733  5594,5606,5735,6203,5267,6184,5570,5777,  -  >A/equine/Kentucky/1a/1975(H7N7)
5548  5526,5540,5652,5797,5272,5624,5131,5710,  -  >A/equine/Uruguay/1/1963(H3N8)
5733  5681,5728,5893,5959,5444,5890,5248,5849,  -  >A/swine/Chibi/01/2005/12/15(H3N8)

5621  5723,5743,5741,5543,5384,5687,5236,5627,  -  >1968//,182,CHN,A/Beijing/1/68
5615  5666,5751,5741,5584,5357,5673,5226,5675,  -  >1972//,1643,RUS,A/Udorn/307/72
5641  5710,5769,5788,5617,5357,5695,5241,5663,  -  >1979//,4199,THA,A/Bangkok/01/79
5643  5706,5756,5783,5673,5344,5702,5224,5675,  -  >1983//,5660,HKG,A/HK/14/83
5654  5701,5783,5783,5667,5384,5677,5259,5722,  -  >1989//,7852,CHN,A/Beijing/353/89
5665  5736,5773,5778,5720,5364,5702,5248,5746,  -  >1997/11/29,10924,USA,A/NY/503/97
5674  5728,5760,5736,5784,5437,5687,5243,5817,  -  >2007/02/06,14278,AUS,A/Brisbane/10/07

6087  6073,6167,6270,6199,5850,6176,5483,6187,  -  >A/equine/Lexington/1-1/1966(H7N7)
5990  6071,6179,6166,5774,5765,5746,6138,5964,  -  >B/Mississippi/UR06-0031/2007

5574  5561,5659,5620,5802,5310,5751,5152,5465,  -  >A/Brevig Mission/1/1918(H1N1)
5587  5578,5681,5639,5778,5310,5808,5142,5477,  -  >A/swine/Jamesburg/1942(H1N1)
5663  5684,5839,5741,5753,5370,5817,5158,5596,  -  >A/Denver/57(H1N1)
5691  5614,5848,5792,5978,5357,5851,5244,5489,  -  >A/New Jersey/1976(H1N1)
5669  5671,5826,5750,5843,5283,5810,5274,5584,  -  >A/Index/1977(H1N1)
5742  5820,5897,5834,5812,5384,5866,5366,5596,  -  >A/Kansas/UR06-0068/2007(H1N1)
5632  5526,5800,5578,5920,5377,5794,5285,5608,  -  >A/******/index/2009-02-01(H1N1)


this makes you wonder whether that virus evolves in mammals
3 samples known now, all from ducks : duck,Pekin duck,mallard
LA,CA,CA,1987,2006,2006


Code: 
avian genomes with highest AT-score (out of 3131 genomes from genbank,Jan.2012)
---------------------------------------------------------------------------------------------------------------------------------

5732,5725,5657,5884,5350,5735,5050,5692, = 5641   >A/duck/Fujian/3193/2005//(H6N2)
5675,5831,5732,5729,5477,5475,5376,5525, = 5642   >A/rufous-necked stint/Japan/6KS0279/2006/09/09(H4N8)
5671,5822,5746,5736,5464,5489,5376,5525, = 5643   >A/slaty-backed gull/Japan/6KS0185/2006/07/26(H4N8)
5675,5831,5741,5747,5457,5489,5376,5525, = 5644   >A/rufous-necked stint/Japan/6KS0242/2006/09/02(H4N8)
5609,5809,5708,5837,5337,5765,5305,5572, = 5650   >A/duck/NY/13822/1995//(H3N8)
5714,5778,5736,5765,5397,5863,5193,5584, = 5668   >A/duck/Victoria/5384/2002//(H4N8)
5697,5778,5774,5778,5490,5957,5254,5704, = 5706   >A/duck/LA/17G/1987//(H3N8)
5723,5835,5862,5896,5384,5851,5234,5536, = 5714 *  >A/turkey/Kansas/4880/1980//(H1N1)
5728,5839,5862,5902,5384,5851,5244,5536, = 5717 *  >A/Ck/PA/35154/1991//(H1N1)
5684,5842,5862,5808,5490,5879,5264,5632, = 5719   >A/cinnamon teal/California/44287-325/2007/01/27(H3N8)
5692,5844,5885,5842,5524,5695,5295,5668, = 5719   >A/pekin duck/California/P30/2006/03/06(H4N2)
5666,5875,5853,5972,5424,5829,5264,5584, = 5727 *  >A/turkey/IA/21089-3/1992//(H1N1)
5697,5861,5853,5961,5410,5872,5274,5608, = 5734 *  >A/turkey/NC/19762/1988//(H1N1)
5697,5861,5853,5967,5430,5865,5264,5620, = 5736 *  >A/turkey/NC/17026/1988//(H1N1)

(* : poultry that caught a swine virus)


average AT-score of avian genomes
serotype,score,number of genomes

H9N2 5575 173
H6N2 5575 205
H5N1 5572 533
H6N1 5565 160
H5N2 5560 173
H7N2 5560 124
H1N1 5542 93
H3N8 5523 304
H4N6 5519 212
H7N3 5514 108
rest 5534 1049

score of H5N1-genomes by year:
2011 5578 12
2010 5582 25
2009 5579 21
2008 5582 40
2007 5579 79
2006 5579 95
2005 5569 143
2004 5561 75
2003 5550 19
2002 5543 11
2001 5548 6
2000 5557 1
1997 5537 3
1996 5556 1

AT-score by species:
chicken,duck,guinea fowl,gull,goose,mallard,pintail duck,quail,shorebird,shoveler,
swan,turkey,teal,turnstone,wigeon,rest
Ck 5570 513
Dk 5564 448
GF 5560 17
Gl 5540 19
Gs 5558 35
Ml 5534 804
Pt 5531 127
Qa 5552 30
Sb 5531 98
Sv 5527 120
Sw 5578 32
Tk 5547 107
Tl 5525 209
Ts 5532 92
Wg 5554 34
-- 5550 449


Sw 5578 32
Ck 5570 513

Dk 5564 448
GF 5560 17
Gs 5558 35
Wg 5554 34
Qa 5552 30
-- 5550 449
Tk 5547 107

Gl 5540 19

Ml 5534 804
Ts 5532 92
Pt 5531 127
Sb 5531 98
Sv 5527 120
Tl 5525 209
 
Re: interesting recent avian viruses

With your approval.. a few comments about this from our recent chat:

Sterten : i just found a new interesting avian virus
Sterten : A/Pekin Duck/California/2006
Sterten : http://www.ncbi.nlm.nih.gov/nuccore/CY053821?
Sterten: hmm, known since Dec.2009
Sterten: so, shortly after my last cloud-analysis

Sterten: it's similar to the 1984 17g virus ...A/Duck/LA/17G/1987
Sterten: which was thought to be a "singleton"
mixin: it must have been a domestic duck; were there more with it in the flock?
mixin: pekin ducks are raised for food?
Sterten: wild Pekin Ducks in CA ?
mixin: don't know
Sterten: http://www.ncbi.nlm.nih.gov/nuccore/EU871828? A/Duck/LA/17G/1987
mixin: Around 95% of duck meat consumed in the United States is Pekin duck
Sterten: LA=Louisiana ?
Sterten: that strain may give hints about 1918
Sterten: I thought it was extinct
Sterten: only 2 viruses, LA 1987 and CA 2006
mixin: LA probably does mean Louisiana
Sterten: so, in what species may the virus have hidden and survived for >100 years
Sterten: HA and NA are still reassorting

Sterten: 3rd one is: A/mallard/CA/J808/2006/12/06
Sterten: only partial
mixin177: Pekin is our very popular white duck
Sterten: domesticated ?
mixin: yes, domesticated

Sterten: A/mallard/CA/JN808/2006/12/06
Sterten: http://www.ncbi.nlm.nih.gov/nuccore/CY076830.1
Sterten: /host="mallard; gender M; age After hatch year"
Sterten: so,wild duck ?
Sterten: /country="USA: Gridley, CA"
Sterten: /note="has low uni-directional coverage"
Sterten: http://en.wikipedia.org/wiki/Gridley,_California, not on the coast
Sterten: so what does a mallard in Gridley
mixin: mallards like lakes and marshy areas, too
mixin: they don't need big bodies of water
Sterten: not mixing with other ducks ? for 100 years
mixin: I think they do associate with other ducks and geese; they may all swim together

Sterten: http://www.ncbi.nlm.nih.gov/nuccore/CY076830.1
http://www.ncbi.nlm.nih.gov/nuccore/EU871828?
http://www.ncbi.nlm.nih.gov/nuccore/CY053821?

Sterten: /country="USA: Perris, CA". that was the Pekin duck
mixin1: Gridley is in Butte County
Sterten: distant from Gridley
Sterten: so presumably the strain is still prevalent in the common duck=mallard population
Sterten: but very rare

Sterten: 1987,2006,2006...but one in LA in 1987
Sterten: 3 out of thousands
Sterten: many mallard-flu-sequences from CA
Sterten: pacific flyway; CA--Alaska

mixin: so I've lost the point...
mixin: do you think it's old and rare?
mixin: or new and rare?
mixin: or just interesting?
Sterten: yes to all
Sterten: evolution ...first old then new
Sterten: the common ancestor
Sterten: in segment 2
Sterten: -say-
Sterten: with any other current flu-A
Sterten: is ~1900 or 1850; I haven't yet examined

Sterten: other current avian flu is more distant to 1918 in segment 2
Sterten: and probably other segments
Sterten: we had 7 voruses in the 70s from that close 1918-strain now extinct
Sterten: that 7-bird-70s segment 2 is still different from gridley-flu
Sterten: common anchestor <1900
Sterten (12:39:20 AM): 13 >A/pekin Dk/CA/P30/2006/03/06 2280 2274 2151 1692 1497 1414 982 838
1:135,111,142,483,146,512, 83,123 A/Brevig Mission/1/1918 2280 2274 2151 1701 1497 1410 982 838
2:128,115,115,486,150, 74, 78,286 A/blue goose/WI/711/1975 2280 2274 2151 1695 1497 1414 982 838
3: 39, 49, 47,322, 52,485, 31, 33 A/duck/LA/17G/1987 2280 2274 2151 1710 1497 1410 982 838
 
Re: interesting recent avian viruses

segments from that new (mammalean ?) strain
(I currently call it the 17g-strain, better names ?)
are found in 18 viruses from genbank


Code: 
>A/Dk/LA/17G/1987,1987//,H3N8,USA

---------1-----------
 364   15  412 5312 >A/mallard/CA/JN808/2006,2006/12/06,H4N2,USA
 394   90 2280 6406 >A/pekin Dk/CA/P30/2006,2006/03/06,H4N2,USA
 460  105 2280 4569 >A/cinnamon teal/CA/44287-325/2007,2007/01/27,H3N8,USA
------------2-----------
 327   33 1008 5241 >A/mallard/CA/JN808/2006,2006/12/06,H4N2,USA
 490  103 2100 7268 >A/cinnamon teal/CA/44287-325/2007,2007/01/27,Avian,H3N8,USA
 492  112 2274 6376 >A/pekin Dk/CA/P30/2006,2006/03/06,H4N2,USA
---------3----------------
 430   43 1000 5223 >A/mallard/CA/JN808/2006,2006/12/06,H4N2,USA
 478  103 2151 6362 >A/pekin Dk/CA/P30/2006,2006/03/06,H4N2,USA
 502  108 2151 4481 >A/cinnamon teal/CA/44287-325/2007,2007/01/27,H3N8,USA
 675   27  400 5318 >A/mallard/Interior Alaska/8BM3100/2008,2008/08/18,H8N4,USA
--------------4--------------
 429   73 1701  659 >A/mallard/Mississippi/386/2010,2010/01/17,H3N8,USA
 429   73 1701  660 >A/mallard/Mississippi/390/2010,2010/01/17,H3N8,USA
 429   73 1701  761 >A/northern pintail/CA/HKWF792/2007,2007/11/28,H3N8,USA
 435   74 1701  192 >A/cinnamon teal/CA/44287-325/2007,2007/01/27,H3N8,USA
 435   74 1701  657 >A/mallard/Mississippi/354/2010,2010/01/16,H3N8,USA
 435   74 1701  658 >A/mallard/Mississippi/360/2010,2010/01/16,H3N8,USA
 440   75 1701   18 >A/American green-winged teal/Mississippi/285/2010,2010/01/14,H3N8,USA
 452   77 1701   12 >A/American coot/Oregon/20589-007/2007,2007/12/17,H3N8,USA
 482   82 1700   38 >A/Anas strepera/Arizona/A00271503/2009,2009/01/18,H3N8,USA
----------------5-----------------
 527   79 1497 6163 >A/pekin Dk/CA/P30/2006,2006/03/06,H4N2,USA
 547   82 1497 4455 >A/cinnamon teal/CA/44287-325/2007,2007/01/27,H3N8,USA
 554   78 1406 5927 >A/northern pintail/CA/44291-259/2007,2007/03/18,H10N3,USA
 561   84 1497 3911 >A/American coot/Oregon/20589-007/2007,2007/12/17,H3N8,USA
 574   86 1497 5948 >A/northern pintail/CA/HKWF792/2007,2007/11/28,H3N8,USA
 581   87 1497 3908 >A/American coot/CA/20181-006/2007,2007/03/02,H10N3,USA
 581   87 1497 5555 >A/mallard/Mississippi/360/2010,2010/01/16,H3N8,USA
 581   87 1497 5556 >A/mallard/Mississippi/386/2010,2010/01/17,H3N8,USA
 587   88 1497 3909 >A/American coot/Illinois/3405/2009,2009/10/31,H10N3,USA
 587   88 1497 5557 >A/mallard/Mississippi/390/2010,2010/01/17,H3N8,USA
 594   89 1497 3910 >A/American coot/Mississippi/09OS615/2009,2009/01/24,H10N3,USA
 594   89 1497 5554 >A/mallard/Mississippi/354/2010,2010/01/16,H3N8,USA
 607   91 1497 3940 >A/American green-winged teal/Mississippi/285/2010,2010/01/14,H3N8,USA
-------------------6----------------
 460   65 1413    9 >A/American coot/Oregon/20589-007/2007,2007/12/17,H3N8,USA
 467   66 1413  139 >A/cinnamon teal/CA/44287-325/2007,2007/01/27,H3N8,USA
 467   66 1413  492 >A/mallard/Mississippi/360/2010,2010/01/16,H3N8,USA
 467   66 1413  493 >A/mallard/Mississippi/386/2010,2010/01/17,H3N8,USA
 474   67 1413  491 >A/mallard/Mississippi/354/2010,2010/01/16,H3N8,USA
 474   67 1413  567 >A/northern pintail/CA/HKWF792/2007,2007/11/28,H3N8,USA
 481   68 1413  494 >A/mallard/Mississippi/390/2010,2010/01/17,H3N8,USA
 484   67 1383  507 >A/mallard/Ohio/2039/2009,2009/08/03,mixed,N8,USA
 502   71 1413   16 >A/American green-winged teal/Mississippi/285/2010,2010/01/14,H3N8,USA
---------------7----------------
 149    1   67 3782 >A/Ck/Rostock/8/1934,1934//,H7N1,Germany
 315   31  982 6890 >A/pekin Dk/CA/P30/2006,2006/03/06,H4N2,USA
 325   32  982 4982 >A/cinnamon teal/CA/44287-325/2007,2007/01/27,H3N8,USA
 336   33  982 5746 >A/mallard/CA/JN808/2006,2006/12/06,H4N2,USA
 360    7  194 3422 >A/silky Ck/HK/WF266/2002,2002//,H9N2,HK
 438   11  251 7502 >A/Tk/CA/6889/1980,1980//,H9N2,USA
 442   10  226 7456 >A/shorebird/Delaware/275/2001,2001//,H9N7,USA
 443   14  316 7432 >A/shorebird/Delaware/141/2002,2002//,H9N9,USA
 462   16  346 6267 >A/mallard/Missouri/303/2006,2006//,H6N2,USA
------------8------------
 310   26  838 4077 >A/mallard/CA/JN808/2006,2006/12/06,H4N2,USA
 322   27  838 3781 >A/cinnamon teal/CA/44287-325/2007,2007/01/27,H3N8,USA
 322   27  838 4262 >A/mallard/Mississippi/354/2010,2010/01/16,H3N8,USA
 322   27  838 4265 >A/mallard/Mississippi/390/2010,2010/01/17,H3N8,USA
 334   28  838 3591 >A/American coot/CA/20181-006/2007,2007/03/02,H10N3,USA
 334   28  838 3608 >A/American green-winged teal/Mississippi/285/2010,2010/01/14,H3N8,USA
 334   28  838 5726 >A/pekin Dk/CA/P30/2006,2006/03/06,H4N2,USA
 346   29  838 3594 >A/American coot/Oregon/20589-007/2007,2007/12/17,H3N8,USA
 346   29  838 4263 >A/mallard/Mississippi/360/2010,2010/01/16,H3N8,USA
 346   29  838 5693 >A/northern pintail/CA/HKWF792/2007,2007/11/28,H3N8,USA
 357   30  838 3593 >A/American coot/Mississippi/09OS615/2009,2009/01/24,H10N3,USA
 357   30  838 4264 >A/mallard/Mississippi/386/2010,2010/01/17,H3N8,USA
 387   26  671 4440 >A/northern pintail/CA/44291-259/2007,2007/03/18,H10N3,USA
 393   33  838 3592 >A/American coot/Illinois/3405/2009,2009/10/31,H10N3,USA


closest neighbors in the 8 segments outside the 17g-group:
sequences with a "*" are only small partials, so that doesn't mean so much
it would be useful to get full sequences of these partials with "*"


columns are:
differences in 1/100 percent
nucleotide-differences in total
nucleotides available in the coding region
number in my bits?-files
sequence-name,collection date,serotype,country


Code: 
---------1-----------
 1070  244 2280 7012 >A/Tk/Canada/1963,1963//,H6N8,Canada
 1100  251 2280 6008 >A/mallard/Wisconsin/34/1975,1975//,H5N6,USA
 1114  254 2280 4601 >A/Dk/Memphis/546/1974,1974//,H11N9,USA
------------2-----------
* 833   28  336 7181 >A/mallard/New Zealand/223-31/2005,2005//,H4N6,New Zealand
  985  224 2274    1 >A/Human/Brevig Mission/1/1918,1918//,H1N1,USA
* 996   25  251 7177 >A/mallard/New Zealand/1440-365/2005,2005//,H11N9,New Zealand
*1026   31  302 3560 >A/mute swan/France/06631a/2006,2006//,H5N1,France
*1030   24  233 3559 >A/mute swan/France/06484b/2006,2006//,H5N1,France
*1037   44  424 6323 >A/northern shoveler/Interior Alaska/8BM3671/2008,2008/09/25,H4N1,USA
*1040   23  221 3618 >A/tufted Dk/France/06256/2006,2006//,H5N1,France
*1049   32  305 3349 >A/common pochard/France/06292a/2006,2006//,H5N1,France
*1050   27  257 3638 >A/Tk/France/06222-1.1/2006,2006//,H5N1,France
 1051  239 2274 3995 >A/blue Gs/WI/711/1975,1975//,H5N2,USA
*1055   23  218 3556 >A/mute swan/France/06299/2006,2006//,H5N1,France
 1064  242 2274   14 >A/Human/Index/early human/1935,1935//,H1N1,USA
 1064  242 2274 4532 >A/Dk/Memphis/546/1974,1974//,H11N9,USA
*1070   29  271 3428 >A/great crested grebe/France/06348a/2006,2006//,H5N1,France
*1072  244 2274 7060 >A/Tk/Ontario/6213/1966,1966/06/11,mixed,Canada
*1086  247 2274 5144 >A/mallard/Alberta/663/1979,1979/08/13,H3N5,Canada
---------3----------------
*483    3   62   25 >A/Ck/Egypt/F3/2006,2006/06/01,H5N1,Egypt
 502  108 2151 4481 >A/cinnamon teal/CA/44287-325/2007,2007/01/27,H3N8,USA
*675   27  400 5318 >A/mallard/Interior Alaska/8BM3100/2008,2008/08/18,H8N4,USA
 897  193 2151  232 >A/whiskered tern/Egypt/04/2004,2004/12/05,H6N2,Egypt
 897  193 2151 6996 >A/Tk/Massachusetts/3740/1965,1965//,H6N2,USA
 901  194 2151  163 >A/Dk/Egypt/053/2005,2005/02/05,H6N2,Egypt
---------4--------------
*1239   77  621  254 >A/Dk/Italy/01/2008,2008/09/21,H3,Italy
*1256   78  621   79 >A/Teal/Norway/10_1037/2010,2010//,H3N2,Norway
*1258   78  620   80 >A/Teal/Norway/10_1575/2007,2007//,H3N8,Norway
*1258   78  620  255 >A/Dk/Italy/02/2008,2008/09/21,H3,Italy
----------------5-----------------
 810   15  185 5142 >A/mallard/CA/JN808/2006,2006/12/06,H4N2,USA
1298   63  485 3132 >A/shorebird/Korea/S105/2006,2006//,H6N1,South Korea
1308   50  382 3184 >A/swan/Shimane/42/1999,1999//,H7N8,Japan
1310   46  351 1896 >A/Dk/Hokkaido/18/00,2000//,H10N4,Japan
-------------------6----------------
1650   86  521  174 >A/Dk/Hokkaido/W95/2006,2006//,H10N8,Japan
1667  223 1337  774 >A/Tk/Canada/1963,1963//,H6N8,Canada
1719  243 1413  695 >A/rosy-billed pochard/Argentina/CIP051-269/2007,2007/05/13,H6N8,Argentina
---------------7----------------
*149    1   67 3782 >A/Ck/Rostock/8/1934,1934//,H7N1,Germany
*360    7  194 3422 >A/silky Ck/HK/WF266/2002,2002//,H9N2,HK
*438   11  251 7502 >A/Tk/CA/6889/1980,1980//,H9N2,USA
*442   10  226 7456 >A/shorebird/Delaware/275/2001,2001//,H9N7,USA
*443   14  316 7432 >A/shorebird/Delaware/141/2002,2002//,H9N9,USA
*462   16  346 6267 >A/mallard/Missouri/303/2006,2006//,H6N2,USA
*487    4   82 6888 >A/northern waterthrush/Maine/CTR-AIV21/2006,2006/08/05,,USA
*489    7  143 4039 >A/muscovy Dk/Hungary/1/1975,1975//,H5,Hungary
*489    7  143 4148 >A/Tk/Hungary/1/1985,1985//,H7,Hungary
*559    8  143 3832 >A/Dk/Hungary/1/1970,1970//,H6N2,Hungary
*560   18  321 7513 >A/Tk/MN/511/78,1978//,H9N2,USA
*596   22  369 7434 >A/shorebird/Delaware/18/2002,2002//,H9N9,USA
*611   23  376 5133 >A/Gs/MN/5733-1243/80,1980//,H9N2,USA
*659    6   91 5266 >A/hermit thrush/Washington/CTR-AIV08/2006,2006/06/16,,USA
*674    6   89 5131 >A/golden-crowned Kinglet/Washington/CTR-AIV26/2006,2006/08/02,,USA
*699   10  143 3899 >A/guinea fowl/Hungary/2/1975,1975//,H7,Hungary
*714    7   98 4399 >A/MacGillivray's warbler/Washington/CTR-AIV23/2006,2006/08/04,,USA
*740    8  108 4297 >A/American robin/Washington/CTR-AIV17/2006,2006/07/02,,USA
*740    8  108 7614 >A/western wood-pewee/Washington/CTR-AIV09/2006,2006/07/26,,USA
 743   73  982 5337 >A/mallard Dk/ALB/25/1976,1976/08/11,H3N1,Canada
*744    7   94 4338 >A/Bewick's wren/Oregon/CTR-AIV28/2006,2006/08/01,,USA
 763   75  982 4351 >A/Canada Gs/Wisconsin/902/1975,1975//,H5N2,USA
 763   75  982 4578 >A/blue-winged teal/Alberta/580/1979,1979/08/11,H4N2,Canada
 763   75  982 5160 >A/green-winged teal/ALB/438/1979,1979/08/10,H3N8,Canada
 763   75  982 5352 >A/mallard Dk/ALB/564/1979,1979/08/11,H3N8,Canada
 763   75  982 5599 >A/mallard/Alberta/31/2001,2001/07/27,H3N9,Canada
 763   75  982 7569 >A/Tk/Ontario/6118/1968,1968//,H8N4,Canada
------------8------------
*  747   27  361 3104 >A/swan/Shimane/42/1999,1999//,H7N8,Japan
*  819    5   61   43 >A/Ck/Egypt/F3/2006,2006/06/01,H5N1,Egypt
...
*  864   32  370  629 >A/Ck/Cambodia/022LC3b/2005,2005/02/09,H5N1,Cambodia
*  909   24  264 2428 >A/Dk/Vietnam/OIE-2334/2010,2010//,H9N6,Viet Nam
   978   82  838 5071 >A/mallard/New Zealand/479-8/2005,2005//,H6N2,New Zealand
   990   83  838 5059 >A/mallard/New Zealand/1440-365/2005,2005//,H11N9,New Zealand
...
*1002   84  838 1925 >A/Dk/HK/24/1976,1976//,H4N2,HK
*1002   84  838 3452 >A/mallard/Sweden/74/2003,2003//,H5N2,Sweden
*1014   85  838 5027 >A/Ck/Victoria/1/1985,1985/05/31,H7N7,Australia
*1014   85  838 5101 >A/starling/Victoria/1985,1985//,H7N7,Australia
 
Re: interesting recent avian viruses

A/swan/Czech/5416/2011/04/06(H7N7) 0,2,2,-,2,-0,0
A/mallard/Czech/143331K/2011/09/16(H3N8) 2,2,5,11,0,58,0,6*
 
Re: interesting recent avian viruses

more from above link:

Conclusions

We showed that similar viruses were simultaneously prevalent in a local pig population when a child was infected with an avian-like A (H1N1) SIV. Specifically, isolation of avian-like SIV from a family farm provides direct evidence for the origin of the human infection. No further spread of the Sw/JS/40/2011-like swine strain occurred, according to the limited information available; however, the incident aroused interest in influenza in animals, especially in pigs. Antigenic analysis showed that this avian-like A (H1N1) SIV was antigenically divergent from classical A (H1N1) and human-like A (H1N1) SIVs currently circulating in China, which was further reinforced by the heterogeneity of their genetic relationships. Since early avian-like A (H1N1) SIV isolates in humans, amino acid mutations in the antigenic sites and PGS changes might have altered the antigenic properties in the avian-like A (H1N1) SIV cluster. Our data highlight the need to characterize circulating strains antigenically and genetically through regular influenza virus surveillance.

Pigs can serve as intermediate hosts for influenza viruses to evolve toward efficient replicability in humans. The classical A (H1N1) SIVs and European avian-like A (H1N1) SIVs have circulated worldwide in pigs since 1930 and 1979, respectively, and a classical A (H1N1) SIV emerged in humans as a triple reassortant, causing the 2009 influenza pandemics (15). Although the virulence and transmissibility of the avian-like A (H1N1) SIVs remain to be evaluated, recurrent human infections with avian-like A (H1N1) SIVs suggest that after long-term adaptation in pigs, the avian-like A (H1N1) SIVs already can replicate in humans. After further whole-genome adaptation to the human host or reassortment with other viruses, novel strains bearing the avian-like swine subtype H1N1 HA gene are highly likely to be generated with pandemic potential. Continued surveillance of swine and systemic analysis of swine influenza isolates are clearly needed.
 
Re: interesting recent avian viruses

13 wild bird sequences H10 from Korea, all close to the index
1041 is also close (5) in N8 (the H3N8 in the index is from Alaska ducks
which seemed to be the most canonical when I created it)

some viruses are a bit more distant in PA (segment 3)
(are there maybe 2 bird index PAs ? )

Code: 
  only M1 and NS1                                 1   2   3   4   5   6   7   8
-------------------------------------------------------------------------------
 1 >A/Index/birds/2000(H3N8a)                     0,  0,  0,  0,  0,  0,  0,  0
 3 >A/Brevig Mission/1/1918(H1N1)                 8,  7, 10,308,  9,213,  7,  5
 4 >A/mallard/Korea/1041/2010,2010/11/,H10N8      1,  2,  6,160,  4,  5,  0,  2
 5 >A/mallard/Korea/1203/2010,2010/12/,H10N8      3,  5,  6,269,  2, 50,  1,  2
 6 >A/mallard/Korea/1242/2010,2010/12/,H10N6      2,  2, 10,266,  2,258,  1,  1
 7 >A/pintail/Korea/188/2009,2009/03/,H10N4       2,  3,  9,243,  0,202,  0,  1
 8 >A/wild bird/Korea/A01/2009,2009/02/,H10N6     2,  2, 12,197,  0,258,  0,  1
 9 >A/wild bird/Korea/A01/2011,2011/02/,H10N4     3,  1,  1,268,  4,205,  1,  1
10 >A/wild bird/Korea/A02/2011,2011/02/,H10N4     3,  1,  1,269,  4,205,  1,  1
11 >A/wild bird/Korea/A12/2010,2010/02/,H10N1     3,  2,  1,267,  0,212,  0,  1
12 >A/wild bird/Korea/A13/2010,2010/02/,H10N1     2,  1,  3,267,  0,212,  0,  1
13 >A/wild bird/Korea/A323/2009,2009/11/,H10N1    1,  0,  2,268,  1,213,  0, *5
14 >A/wild bird/Korea/A43/2009,2009/03/,H10N4     4,  2,  2,241,  0,201,  0,  1
15 >A/wild bird/Korea/L110-2/2008,2008/12/,H10N4  2,  3,  0,267,  1,204,  0,  1
16 >A/wild bird/Korea/L110-3/2008,2008/12/,H10N4  2,  5,  2,267,  1,203,  2,  1
 
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