interesting recent avian viruses

[gsgs]

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

>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

---------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

[gsgs]

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*

[gsgs]

Re: interesting recent avian viruses

Human Infection from Avian-like Influenza A (H1N1) Viruses in Pigs, China.

http://wwwnc.cdc.gov/eid/article/18/7/12-0009_article.htm

A/swine/Jiangsu/40/2011

> European avian-like swine A (H1N1) lineage (Figure 1

oops, so swine and not avian , since >30 years in swine

[sharon sanders]

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.

[gsgs]

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 ? )

  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

[gsgs]

Re: interesting recent avian viruses

http://www.ncbi.nlm.nih.gov/nuccore/KC693640

14.Dec.2007, (5 years ago) , Upo-Wetland South Korea
A/white-fronted goose/Korea/20-36/2007(H9N2)
36Eurasian,124578American
10,7,4,-,4,-2,5* , i_bird
26,11,--,--,10,--,13,06, A/snow goose/Montana/466771-4/2006,2006//,H5N2

39 9 2280 5928 >A/northern shoveler/Interior Alaska/8BM3470/2008,2008/09/01,H9N2
48 11 2274 4142 >A/snow goose/Montana/466771-4/2006,2006//,H5N2
51 11 2151 4780 >A/aquatic bird/Korea/w217/2007,2007/11/,H5N2
83 14 1683 1068 >A/northern shoveler/Interior Alaska/8BM3470/2008,2008/09/01,H9N2
46 7 1497 5784 >A/northern shoveler/Interior Alaska/8BM3470/2008,2008/09/01,H9N2
70 10 1410 5357 >A/duck/Korea/A14/2008,2008/10/04,H5N2
30 3 982 3923 >A/ruddy turnstone/Delaware Bay/262/2006,2006/05/22,H7N3
71 6 838 814 >A/snow goose/Montana/466771-4/2006,2006//,H5N2

[gsgs]

Re: interesting recent avian viruses

an avian H10N7 genome from 1953 from Manitoba,Canada !

A/duck/Manitoba/1953(H10N7)

http://www.ncbi.nlm.nih.gov/nuccore/KF435062

http://www.ncbi.nlm.nih.gov/nuccore/J02110

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349324/

 >A/duck/Manitoba_KF/1953(H10N7)
----------segment 1------------- 
 381   87 2280 4684 >A/turkey/Canada/1963,1963//,H6N8
 382   87 2275 6036 >A/turkey/Canada/1963,1963//,H6N8
 431   54 1252 4708 >A/chicken/Pakistan/447/1995,1995//,H7N3
 433   54 1247 4707 >A/chicken/Pakistan/1369-CR2/1995,1995//,H7N3
 465   13  279 8889 >A/turkey/Oregon/1/1971,1971//,H7N3
 468   56 1196 4705 >A/chicken/Chile/184240-5/2002,2002//,H7N3
 522  111 2123 8882 >A/turkey/Ontario/6118/1968,1968/06/11,H8N4
 539  123 2279  697 >A/turkey/Ontario/6118/1968,1968//,H8N4
 565  129 2280 4073 >A/whiskered tern/Egypt/04/2004,2004/12/05,H6N2
----------segment 2------------- 
 386   88 2274 6144 >A/turkey/Ontario/6213/1966,1966/06/11,mixed
 413   94 2274 1147 >A/turkey/Ontario/7732/1966,1966//,H5N9
 470  107 2274 3809 >A/duck/Memphis/546/1974,1974//,H11N9
 470  107 2274 8360 >A/turkey/Ontario/6118/1968,1968//,H8N4
 492  112 2274  597 >A/mallard/Alberta/663/1979,1979/08/13,H3N5
 518  118 2274 3443 >A/blue goose/WI/711/1975,1975//,H5N2
 518  118 2274 6053 >A/turkey/Wisconsin/1/1968,1968/06/11,H5N9
 527  120 2274  551 >A/pintail duck/ALB/628/1979,1979/08/13,H6N8
 527  120 2274  595 >A/blue-winged teal/ALB/286/1977,1977/08/10,H3N6
----------segment 3------------- 
 609  131 2151  541 >A/mallard/Alberta/46/1977,1977/08/08,H1N1
 609  131 2151 1058 >A/turkey/Massachusetts/3740/1965,1965//,H6N2
 609  131 2151 3873 >A/whiskered tern/Egypt/04/2004,2004/12/05,H6N2
 609  131 2151 5884 >A/turkey/Ontario/6213/1966,1966/06/11,mixed
 609  131 2151 8293 >A/turkey/Massachusetts/3740/1965,1965//,H6N2
 613  132 2151  700 >A/mallard/Alberta/106/1979,1979/08/07,H4N2
 613  132 2151 6206 >A/duck/Egypt/053/2005,2005/02/05,H6N2
 613  132 2151 7803 >A/turkey/Oregon/1971,1971//,H7N3
 618  133 2151  699 >A/mallard/Alberta/354/1978,1978/08/10,H4N2
----------segment 4------------- 
 865  146 1686 2306 >A/mallard duck/Minnesota/19/1979,1979/08/01,H10N7,USA
 883  149 1686 4880 >A/turkey/MN/3/1979,1979//,H10N7,USA
 907  153 1686  415 >A/bluewinged teal/ALB/778/1978,1978/08/08,H10N3,Canada
 913  154 1686 2283 >A/mallard duck/ALB/302/1977,1977/08/31,H10N7,Canada
 919  155 1686 4110 >A/pintail duck/ALB/303/1977,1977/09/03,H10N7,Canada
 931  157 1686 2285 >A/mallard duck/ALB/40/1984,1984/08/,H10N6,Canada
 931  157 1686 4112 >A/pintail duck/ALB/584/1984,1984/07/31,H10N6,Canada
 948  160 1686 2086 >A/greenwinged teal/LA/169GW/1988,1988//,H10N7,USA
 948  160 1686 4383 >A/ruddy turnstone/Delaware Bay/2763/1987,1987/05/20,H10N7,USA
 958  161 1680 4391 >A/ruddy turnstone/Delaware Bay/2813/1987,1987/05/19,mixedÞN7,USA
 960  162 1686 2537 >A/mallard/Alberta/553/1986,1986/08/19,H10N7,Canada
 966  163 1686 2218 >A/knot/Delaware Bay/2561/1987,1987/05/19,H10N5,USA
 966  163 1686 4294 >A/ruddy turnstone/DE/2764/1987,1--- 
----------segment 5------------- 
 253    8  315 7932 >A/pintail/Alberta/480/1986,1986/08/16,H6N2
 300   45 1497 1356 >A/turkey/Ontario/7732/1966,1966//,H5N9
 351    9  256 7930 >A/mallard/Alberta/372/1986,1986/08/14,H6N2
 360   54 1497  736 >A/mallard/ALB/1151/1979,1979/08/22,H6N9
 360   54 1497  766 >A/pintail/ALB/219/1977,1977/09/03,H1N1
 360   54 1497  785 >A/pintail/ALB/159/1977,1977/08/31,H4N6
 360   54 1497  967 >A/blue-winged teal/ALB/778/1978,1978/08/08,H10N3
 360   54 1497 4411 >A/mallard/Wisconsin/428/1975,1975//,H5N1
 360   54 1497 5946 >A/turkey/Ontario/6213/1966,1966/06/11,mixed
 363   54 1484 1985 >A/mallard/Minnesota/1979,1979//,H3N1
 367   55 1497 3005 >A/mallard/WI/42/1975,1975//,H5N2
 382   57 1491   71 >A/turkey/California/189/66,1966//,H9N2
----------segment 6------------- 
 743  105 1413 1168 >A/mallard/ALB/302/1977,1977/08/31,H10N7
 757  107 1413 1107 >A/pintail/ALB/303/1977,1977/09/03,H10N7
 813  115 1413 1560 >A/mallard/Minnesota/19/1979,1979/08/01,H10N7
 813  115 1413 5556 >A/turkey/MN/3/1979,1979//,H10N7
 835  118 1413 1027 >A/redhead duck/ALB/767/1984,1984/08/11,H10N7
 835  118 1413 1028 >A/ruddy turnstone/DE/2764/1987,1987/05/27,H10N7
 856  121 1413 3684 >A/green-winged teal/LA/169GW/1988,1988//,H10N7
 863  122 1413 1159 >A/ruddy turnstone/DE/2378/1988,1988/05/31,H7N7
 905  128 1413 1932 >A/mallard/Ohio/99/1989,1989/10/19,H10N7
 905  128 1413 2205 >A/mallard/Ohio/122/1989,1989/10/19,H10N7
 905  128 1413 7476 >A/mallard/Ohio/65/1989,1989/10/19,mixed_N7
 927  131 1413 3802 >A/duck/Alaska/712/1991,1991//,H10N7
----------segment 7------------- 
 204    2   98 5945 >A/MacGillivray's warbler/Washington/CTR-AIV23/2006,2006/08/04,
 219    2   91 5930 >A/hermit thrush/Washington/CTR-AIV08/2006,2006/06/16,
 239    6  251  934 >A/turkey/California/6889/1980,1980//,H9N2
 260    9  346 7154 >A/mallard/Missouri/303/2006,2006//,H6N2
 264   26  982 5128 >A/turkey/Canada/1963,1963//,H6N8
 265    6  226  949 >A/shorebird/Delaware/275/2001,2001//,H9N7
 277    3  108 5931 >A/western wood-pewee/Washington/CTR-AIV09/2006,2006/07/26,
 277    3  108 5939 >A/American robin/Washington/CTR-AIV17/2006,2006/07/02,
 280    9  321  933 >A/turkey/MN/511/78,1978//,H9N2
 284    9  316  946 >A/shorebird/Delaware/141/2002,2002//,H9N9
 295   29  981 4201 >A/turkey/Canada/1963,1963//,H6N8
 298    2   67   18 >A/chicken/Rostock/8/1934,1934//,H7N1
 305   30  982 1165 >A/mallard/ALB/564/1979,1979/08/11,H3N8
 305   30  982 1187 >A/green-winged teal/ALB/438/1979,1979/08/10,H3N8
----------segment 8------------- 
 226   19  838 5143 >A/turkey/Ontario/6213/1966,1966/06/11,mixed
 262   22  838  552 >A/duck/PA/69,1969//,H6
 262   22  838  846 >A/mallard/ALB/676/1979,1979/08/13,H3N6
 262   22  838 1279 >A/turkey/Ontario/7732/1966,1966//,H5N9
 262   22  838 2780 >A/duck/PA/486/1969,1969//,H6N1
 298   25  838 1235 >A/turkey/Ontario/6118/1968,1968//,H8N4
 298   25  838 1258 >A/black duck/New York/184/1988,1988//,H5N2
 298   25  838 1563 >A/mallard/Ohio/99/1989,1989/10/19,H10N7
 298   25  838 1742 >A/mallard/Ohio/122/1989,1989/10/19,H10N7
 298   25  838 1746 >A/mallard/Ohio/129/1989,1989//,H4N6
 298   25  838 3487 >A/whiskered tern/Egypt/04/2004,2004/12/05,H6N2
 298   25  838 3924 >A/chicken/New Jersey/15906-9/1996,1996//,H11N1

this gives a new best avian match to 1918flu in segments 2,7

212,166,272,732,186,626,043,033 mutations away from A/Brevig Mission/1/1918(H1N1)
092,072,126,444,124,460,043,039 in promille

087,088,131,146,045,105,026,019 mutations away from the next best match
38,39,61,87,30,74,26,23 in promille

it has 2,5,7,-,4,-,4,3 amino-differences to the bird index.
That is pretty close, yet not quite close enough for a wild mallard.
So I wonder whether this was a domestic duck in Manitoba 1953
and if the 1953-virus may as well have been circulating and adapted
in domestic ducks (and/or swine) in the 10-20 years before 1918

segments 2,7,8 are so close to 1918 Spainflu, that the common ancester
could well be in ~1915 (+-5) ; segment 1 in ~1910 ; segments 3 and 5 in ~1903

this also confirms once again, that 1918 Spainflu was mainly an American avian virus
at least in the inner segments. Where HA and NA came from is not so clear

amino acid mutations shared with 1918flu : E383D(2),S400QL(3),V105M(5)

[gsgs]

Re: interesting recent avian viruses

http://wwwnc.cdc.gov/eid/article/20/5/13-1707_article.htm

KF609524–KF609531).
A/tree sparrow/Shanghai/01/2013 (H7N9).

During April 10–May 15, a total of 2,198 fecal, tissue, cloacal swab,
and tracheal swab samples were collected from wild birds in Shanghai.


This record has not yet been released. Please contact info@ncbi.nlm.nih.gov with the publication
details if the accession has been published.

----------------edit------------
now available:

http://www.ncbi.nlm.nih.gov/nuccore/KF609524

mutations relative to the index with the new MP:

18,>A/Tree sparrow/Shanghai/01/2013,2013/05/09,H7N9,
G273T(1),A963G(1),C1601T(1),
A11C(2),T12A(2),C13T(2),A1729G(2),
C802T(3),
A339G(4),A1413G(4),T1675G(4),
C8T(5),
C1185T(6),
C36A(7),T327C(7),C615T(7),C760T(7),
G174A(8),

goes into this group:
>A/Taiwan/T02081/2013,2013/04/22,Taiwan,H7N9
>A/Taiwan/S02076/2013,2013/04/22,Taiwan,H7N9
>A/homing pigeon/Jiangsu/SD184/2013,2013/04/20,China,H7N9
>A/pigeon/Shanghai/S1423/2013,2013/04/03,China,H7N9
>A/Tree sparrow/Shanghai/01/2013,2013/05/09,H7N9

[gsgs]

Re: interesting recent avian viruses

A/quail/California/K1400794/2014/04/,H5N8
(American virus, has nothing to do with H5N8 in Asia or Europe)

has a deletion of 63 nucleotides=21 amino-acids in NA
the only other such deletion in N8 was in
A/turkey/Canada/1963,H6N8 with 69 nucleotides



reminds to the deletion of 60 nucleotides in NA of H5N1

deletion of 15 nucleotides in NA of H7N9

[gsgs]

http://www.ncbi.nlm.nih.gov/pubmed/16791426

not a recent virus (2002) , but it looks like one of these absurd combinations of genes
--> contaminations. Again the Harbin lab

long preservation, unexpected similarities

See comment in PubMed Commons below
Virus Genes. 2006 Aug;33(1):117-22.
Characterization of an avian influenza virus of subtype H7N2 isolated from chickens in northern China.
Li Y1, Li C, Liu L, Wang H, Wang C, Tian G, Webster RG, Yu K, Chen H.
An H7N2 avian influenza virus was isolated from chickens during routine surveillance in
northern China in 2002. To understand the origin of this virus, we completely sequenced
its genome. The PB1, PA, HA, and M genes of this virus were highly homologous with
those of the wild bird virus A/Africa starling/Eng-Q/983/79 (H7N1). The NP and NS genes
were closely related to those of two other wild bird viruses isolated 30 years ago.
The closest relatives of the PB2 and NA genes of the virus were those of the
A/swine/Germany/2/81 (H1NI) and A/Leningrad/134/57 (H2N2), respectively.
Animal inoculation tests showed that the virus cannot replicate efficiently in chickens.
However, after intranasal inoculation, the virus induced 20% weight loss and replicated
well in the lungs of mice. The virus was also recovered from the hearts and brains of the mice.

[FONT=Arial][SIZE=10px]>AY724251,A/chicken/Hebei/1/2002,2002//,China,H7N2,Avian

----------segment 1-------------
  48   11 2280   76 >EU627685,A/turkey/England/N28/73,1973//,United Kingdom,H5N2,Avian,1
  87   20 2280   74 >CY014716,A/duck/Germany/1215/1973,1973//,Germany,H2N3,Avian,1
342   78 2280   38 >CY130157,A/turkey/England/1963,1963//,United Kingdom,H7N3,Avian,1
364   83 2280   41 >CY005800,A/quail/Italy/1117/1965,1965//,Italy,H10N8,Avian,1
368   84 2280   24 >CY014686,A/duck/England/1/1956,1956//,United Kingdom,H11N6,Avian,1
372   85 2280   71 >CY087767,A/shearwater/Australia/2/1972,1972/06/11,Australia,H10N8,Avian,1
447  102 2280   31 >GU052525,A/chicken/Scotland/1959,1959//,United Kingdom,H5N1,Avian,1
456  104 2280  103 >CY005559,A/duck/Hong Kong/7/1975,1975//,Hong Kong,H3N2,Avian,1
473  108 2280   61 >GU052282,A/turkey/England/1969,1969//,United Kingdom,H3N2,Avian,1
473  108 2280  162 >CY005631,A/duck/Hong Kong/24/1976,1976//,Hong Kong,H4N2,Avian,1
478  108 2258  163 >EF597466,A/duck/Hong Kong/23/1976,1976//,Hong Kong,H5N3,Avian,1
495  113 2280  188 >CY178934,A/common murre/Alaska/305/1976,1976//,USA,H1N6,Avian,1
508  116 2280  287 >CY005646,A/duck/Hong Kong/147/1977,1977//,Hong Kong,H9N6,Avian,1
517  118 2280  279 >CY005562,A/goose/HK/10/1976,1976/11/11,Hong Kong,H3N2,Avian,1
526  120 2280  434 >CY005652,A/duck/Hong Kong/562/1979,1979//,Hong Kong,H10N9,Avian,1
526  120 2280 2252 >AY585523,A/duck/Zhejiang/11/2000,2000//,China,H5N1,Avian,1
526  120 2280 4062 >DQ835807,A/slaty-backed gull/Shandong/38/04,2004//,China,H5N1,Avian,1
----------segment 2-------------
  39    9 2274  488 >AY724255,A/African starling/England-Q/983/1979,1979//,United Kingdom,H7N1,Avian,2
250   57 2274  721 >CY116865,A/mallard/Potsdam/177-4/1983,1983//,Germany,H2N1,Avian,2
312   71 2274  284 >CY005595,A/duck/Hong Kong/205/1977,1977//,Hong Kong,H5N3,Avian,2
351   75 2135 2136 >GU396949,A/duck/Taiwan/M18/1999,1999/07/,Taiwan,H4N6,Avian,2
404   92 2274  525 >CY117065,A/mallard/Berlin/452-6/1980,1980//,Germany,H2N3,Avian,2
404   92 2274  528 >CY116739,A/mallard/Berlin/453-4/1980,1980//,Germany,mixed,Avian,2
439  100 2274  527 >CY081272,A/duck/Potsdam/15/1980,1980//,Germany,H7N7,Avian,2
448  102 2274  529 >CY116748,A/mallard/Rugen/27-6/1980,1980//,Germany,mixed,Avian,2
----------segment 3-------------
  69   15 2151  485 >AY724254,A/African starling/England-Q/983/1979,1979//,United Kingdom,H7N1,Avian,3
306   66 2151  164 >CY005602,A/duck/Hong Kong/d73/1976,1976//,Hong Kong,H6N1,Avian,3
357   77 2151   72 >CY014714,A/duck/Germany/1215/1973,1973//,Germany,H2N3,Avian,3
413   89 2151  435 >CY031258,A/duck/Hong Kong/702/1979,1979//,Hong Kong,H9N2,Avian,3
430   90 2091 2141 >GU396928,A/duck/Taiwan/M18/1999,1999/07/,Taiwan,H4N6,Avian,3
450   97 2151   74 >EU636683,A/turkey/England/N28/73,1973//,United Kingdom,H5N2,Avian,3
----------segment 4-------------
  29    5 1683   62 >AF202232,A/African starling/England-Q/983/1979,1979//,United Kingdom,H7N1,Avian,4
106   18 1683   57 >AF202235,A/turkey/Israel/Ramon/79,1979//,Israel,H7N2,Avian,4
279   47 1683  129 >AF202248,A/gull/Italy/692-2/93,1993//,Italy,H7N2,Avian,4
285   48 1683  116 >AF202242,A/psittacine/Italy/1/91,1991//,Italy,H7N2,Avian,4
415   70 1683  101 >U20465,A/duck/Heinersdorf/S495/6/86,1986//,Germany,H7N7,Avian,4
427   72 1683  103 >U20469,A/chicken/Jena/1816/87,1987//,Germany,H7N7,Avian,4
459   75 1633  111 >AF202239,A/chicken/Ireland/1733/89,1989//,Ireland,H7N7,Avian,4
534   90 1683   38 >AF202247,A/turkey/England/647/77,1977//,United Kingdom,H7N7,Avian,4
----------segment 5-------------
   0    0 1482   90 >CY030994,A/turkey/England/N28/1973,1973//,United Kingdom,H5N2,Avian,5
327   49 1497  617 >CY116754,A/mallard/Stralsund/40-6/1981,1981//,Germany,H1,Avian,5
327   49 1497  624 >CY117118,A/duck/Rugen/88-4/1981,1981//,Germany,H2N3,Avian,5
327   49 1497  625 >CY117126,A/duck/Rugen/88-6/1981,1981//,Germany,H2N3,Avian,5
327   49 1497  626 >CY117134,A/mallard/Stralsund/55-4/1981,1981//,Germany,H2N3,Avian,5
327   49 1497  627 >CY117142,A/mallard/Stralsund/55-6/1981,1981//,Germany,H2N3,Avian,5
327   49 1497  902 >CY117150,A/Peking duck/Wagun/1689-4/1985,1985//,Germany,H2N3,Avian,5
327   49 1497  903 >CY117158,A/Peking duck/Wagun/1688-4/1985,1985//,Germany,H2N3,Avian,5
327   49 1497  904 >CY117166,A/Peking duck/Wagun/1689-6/1985,1985//,Germany,H2N3,Avian,5
330   49 1484  180 >EF597326,A/duck/Hong Kong/23/1976,1976//,Hong Kong,H5N3,Avian,5
334   50 1497  620 >CY116762,A/duck/Rugen/78-6/1981,1981//,Germany,H2N3,Avian,5
334   50 1497  622 >CY117086,A/mallard/Stralsund/45-6/1981,1981//,Germany,H2N3,Avian,5
334   50 1497  623 >CY117110,A/duck/Rugen/79-6/1981,1981//,Germany,H2N3,Avian,5
334   50 1497  933 >GQ176117,A/fowl/Hampshire/PD378/1985,1985//,United Kingdom,H10N4,Avian,5
334   50 1497  934 >GQ176125,A/mallard/Gloucestershire/PD374/1985,1985//,United Kingdom,H10N4,Avian,5
340   51 1497  179 >CY005627,A/duck/Hong Kong/24/1976,1976//,Hong Kong,H4N2,Avian,5
347   52 1497  309 >CY005642,A/duck/Hong Kong/147/1977,1977//,Hong Kong,H9N6,Avian,5
354   53 1497   41 >CY014987,A/tern/South Africa/1961,1961//,South Africa,H5N3,Avian,5
----------segment 6-------------
  14    2 1410    3 >AY968677,A/turkey/Canada/63,1963//,Canada,H6N2,Avian,6
  14    2 1410   22 >AJ574905,A/turkey/England/N28/73,1973//,United Kingdom,H5N2,Avian,6
375   53 1410  257 >CY005778,A/duck/Potsdam/1402-6/1986,1986//,Germany,H5N2,Avian,6
384   51 1326 3978 >CY077096,A/mallard/Potsdam/178-4/1983-quail-chicken-adapted,NON//,LAB,H2N2,Avian,6
390   55 1410    2 >CY116845,A/mallard/MT/Y61 ,//,Russia,H2N2,Avian,6
397   56 1410  199 >CY116853,A/mallard/Potsdam/176/1983,1983//,Germany,H2N2,Avian,6
397   56 1410  200 >CY116869,A/mallard/Potsdam/177-6/1983,1983//,Germany,H2N2,Avian,6
397   56 1410  201 >CY116877,A/mallard/Potsdam/178-6/1983,1983//,Germany,H2N2,Avian,6
397   56 1410  202 >CY116885,A/mallard/Potsdam/179/1983,1983//,Germany,H2N2,Avian,6
397   56 1410  204 >DQ017487,A/mallard/Postdam/178-4/1983,1983//,Germany,H2N2,Avian,6
404   57 1410   31 >CY005554,A/duck/Hong Kong/7/1975,1975//,Hong Kong,H3N2,Avian,6
404   57 1410  205 >DQ017496,A/mallard/Postdam/178-4/1983,1983//,Germany,H2N2,Avian,6
418   59 1410  198 >CY067274,A/mallard/Postdam/178-CIP046-qa6rnd2/1983,1983//,Germany,H2N2,Avian,6
439   62 1410  232 >CY116725,A/Peking duck/Wagun/1827-6/1984,1984//,Germany,H11N2,Avian,6
----------segment 7-------------
101   10  982  566 >AY724262,A/African starling/England-Q/983/1979,1979//,United Kingdom,H7N1,Avian,7
149    1   67   16 >J02113,A/chicken/Rostock/8/1934,1934//,Germany,H7N1,Avian,7
234   23  981   87 >GQ404592,A/duck/Germany/1972,1972//,Germany,H2N9,Avian,7
244   24  982 1148 >DQ376656,A/chicken/Taiwan/G23/87,1987//,Taiwan,H6N1,Avian,7
254   25  982   90 >DQ376654,A/duck/Taiwan/0526/72,1972//,Taiwan,H6N1,Avian,7
254   25  982 1147 >DQ376655,A/chicken/Taiwan/G2/87,1987//,Taiwan,H6N1,Avian,7
264   26  982    4 >CY116844,A/mallard/MT/Y61 ,//,Russia,H2N2,Avian,7
264   26  982 1833 >DQ997124,A/chicken/Hubei/wk/1997,1997//,China,H5N1,Avian,7
274   27  982  197 >CY005598,A/duck/Hong Kong/d73/1976,1976//,Hong Kong,H6N1,Avian,7
275   27  981  420 >GQ404608,A/duck/Slovakia/2/1978,1978//,Slovakia,H3,Avian,7
281   27  959 1664 >AF508684,A/ostrich/South Africa/9508103/95,1995//,South Africa,H9N2,Avian,7
285   28  981  196 >EF597270,A/duck/Hong Kong/23/1976,1976//,Hong Kong,H5N3,Avian,7
285   28  981  342 >GQ404597,A/mallard/Slovakia/9/1977,1977//,Slovakia,H3N6,Avian,7
285   28  981  363 >GQ404605,A/gull/36/1977,1977//,unknown,H3N6,Avian,7
----------segment 8-------------
184    6  325 13022 >KC599273,A/mallard/Czech Republic/15902-3K/2009,2009/09/30,Czech Republic,N9,Avian,8
214   18  838 10818 >M55467,A/turkey/Bethlehem-Glilit/1492-B/1982,1982//,Israel,H1N1,Avian,8
238   20  838 10706 >CY005615,A/duck/Hong Kong/d134/1977,1977//,Hong Kong,H6N2,Avian,8
262   22  838 10632 >M55466,A/tern/Turkmenia/18/1972,1972//,Turkmenistan,H3N3,Avian,8
265   16  602 10748 >GU052918,A/pintail/Alberta/21/1979,1979//,Canada,H7,Avian,8
274   23  838 10629 >CY014706,A/duck/Chabarovsk/1610/1972 ,1972//,Russia,H3N8,Avian,8
274   23  838 10840 >CY005773,A/duck/Potsdam/2216-4/1984,1984//,Germany,H5N6,Avian,8
276    9  325 13016 >KC599287,A/mallard/Czech Republic/15902-12K/2009,2009/09/30,Czech Republic,H11N2,Avian,8
276    9  325 13020 >KC599294,A/mallard/Czech Republic/15902-14K/2009,2009/09/30,Czech Republic,H6N2,Avian,8
286   24  838 10702 >CY004321,A/mallard duck/ALB/57/1976,1976/08/12,Canada,H5N2,Avian,8
286   24  838 10703 >CY004580,A/pintail duck/ALB/86/1976,1976/08/13,Canada,H3N2,Avian,8
286   24  838 10749 >CY015043,A/goose/Leipzig/187-7/1979,1979//,Germany,H7N7,Avian,8
298   25  838 10612 >CY116847,A/mallard/MT/Y61 ,//,Russia,H2N2,Avian,8
298   25  838 10891 >DQ376763,A/chicken/Taiwan/G2/87,1987//,Taiwan,H6N1,Avian,8[/SIZE][/FONT]

[with the arrival of Asian flu in America I was examining how American and Eurasian strains
mixed in the past. Particularly interesting is segment 2 (PB1) which was newly introduced
from birds in the human pandemics of 1957 and 1968.
European and American PB1 had a common ancester in ~1952 and Australian and American
PB1 had a common ancester in ~1969]