evolution and diversity of avian influenza

gsgs · Oct 6, 2012

I'm planning to show the mutation pictures for all segments
and some different HAs and NAs

for now I have segment 1 , PB2, which is separated between
Eurasia and North-America (and South-America) more than
the other segments.
It evolves separately since ~100 years

while segments 2 and 3 only are separated since ~ 50 years
when an Eurasian variant entered North America and replaced
the American strain which was similar to the 1918 virus

so bad human pandemics did happen, when North-American
and Eurasian strains did mix on a large basis.
An avian epizootic preceded the human pandemics

This could happen again, when/if Eurasian H5N1 establishes
in North America and mixes/reassorts with the American lineages
resulting in enhanced evolution and development of new influenza
viruses with pandemic potential

http://magictour.free.fr/panflu/bitt14c.GIF

3 big groups and some smaller groups.
Eurasia 1, Eurasia 2, North America
(17G,South America,classical swine, )

I should add the continents and years and codon-positions of the
viruses to the graphics. I've done this before with bars to the right,
but maybe a color encoding is better ?!
The sorting is improved now with a TSP-solver

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

it's not so clear to me whether the most recent common ancestor date
between the Eurasian and North-American strains in PB2 is really
~1900 . We have these periods of low-mutation-evolution in non-poultry birds (mallards)
And when I plot the #mutations against the index over time I don't get these
main-diagonal-line-like areas as usual.
The closest that I came to this "line-like" with subgroups of avian PB2s
was with the Australean viruses and HK from the 70s

The early ancestor viruses from 1949,1934,1956,1959,1963 were all not much closer
to the index as recent viruses. So, do those have today-living descendents at all ?
Where did the HK 70s viruses come from ?

gsgs · Feb 22, 2013

Re: evolution and diversity of avian influenza

bitu* now, Feb.2013
m=number of sequences in the file , n=length +2 in the alignment

2013.02.16 , avian sequences from genbank

bitu1: m=8888 n=:2282
bitu2: m=8871 n=:2276
bitu3: m=8824 n=:2153
bitu4: m=14088 n=:1744
bitu5: m=8510 n=:1499
bitu6: m=10610 n=:1395
bitu7: m=9392 n=:984
bitu8: m=9063 n=:1236

bitu41: m= 362 n=:1806
bitu42: m= 373 n=:1781
bitu43: m=1250 n=:1812
bitu44: m= 952 n=:1817
bitu45: m=4943 n=:2047
bitu46: m=1414 n=:1836
bitu47: m=1122 n=:1849
bitu48: m= 111 n=:1762
bitu49: m=2595 n=:1900
bitu4a: m= 334 n=:1783
bitu4b: m= 357 n=:1800
bitu4c: m= 125 n=:1740
bitu4d: m= 87 n=:1782
bitu4e: m= 14 n=:1751
bitu4f: m= 14 n=:1765
bitu4g: m= 35 n=:1785

bitu61: m=3647 n=:1412
bitu62: m=2934 n=:1412
bitu63: m= 675 n=:1412
bitu64: m= 176 n=:1415
bitu65: m= 205 n=:1487
bitu66: m=1203 n=:1488
bitu67: m= 360 n=:1418
bitu68: m=1027 n=:1415
bitu69: m= 380 n=:1415

bitu81: m=7176 n=:840
bitu82: m=1886 n=:840

bitu65a: m= 137 n=:1424
bitu65b: m= 68 n=:1421

bitu68a: m= 872 n=:1415
bitu68b: m= 155 n=:1415

bitu45a: m=4051 n=:1980
bitu45b: m= 892 n=:1847

bitu45a: m=4051 n=:1980
bitu45b: m= 327 n=:1831
bitu45c: m= 556 n=:1794
bitu45d: m= 9 n=:1797

Asian H5N1(1997ff) mutation pictures added below
indexed at A/Ck/Henan/16/2004

we have the 4 classical strains,
Qinghai(2005)
Indonesia(2003)
Vietnam(2003)
Japan,Korea(2003)

and two further groups

===================================================
continued here:
http://www.flutrackers.com/forum/showthread.php?t=206556
merge the threads

gsgs · Sep 10, 2014

Re: evolution and diversity of avian influenza

2014/05/17, avian sequences at genbank

bitsb1f,11371
bitsb2f,11481
bitsb3f,11507
bitsb5f,11441
bitsb7f,12895
bitsb81f,9655
bitsb82f,2820
bitsb00,9890 (123578)

bitsb4,18732
bitsb6,15185
bitsb45,5352
bitsb47,1599
bitsb61,4487

(f for full, >~90% of nucleotides available)

gsgs · Sep 10, 2014

Re: evolution and diversity of avian influenza

differences in pairs of avian segments over isolation-time-difference

Code:

--------------segment 1----------q=9464
d=   0=  0/ 20years,z=2280,pairs: 540-   1   501,>CY004412,A/ruddy turnstone/New Jersey/65/1985,1985/05/29,USA,H7N3,Avian,1    ,    500,>CY004405,A/shorebird/DE/101/2004,2004/05/17,USA,H5N7,Avian,1
d= 163= 26/ 26years,z=2280,pairs: 347-   9   659,>CY005559,A/duck/Hong Kong/7/1975,1975//,Hong Kong,H3N2,Avian,1    ,    372,>AY585523,A/duck/Zhejiang/11/2000,2000//,China,H5N1,Avian,1
d=  13=  2/ 23years,z=2280,pairs: 214-   3   2026,>CY043316,A/bald eagle/Virginia/Sg-00154/2008(mixed),2008//,USA,Mixed,Avian,1    ,    854,>CY017700,A/mallard/Ohio/30/1986,1986/10/20,USA,H2N1,Avian,1
d=   0=  0/  7years,z=2280,pairs: 142-  10   9798,>HM590786,A/chicken/Thailand/ICRC-7356/2010,2010/03/24,Thailand,H5N1,Avian,1    ,    8093,>EF593099,A/chicken/Thailand/vsmu-3-BKK/2004,2004//,Thailand,H5N1,Avian,1
d=  21=  1/  6years,z=2280,pairs: 142-  10   9799,>HM590794,A/chicken/Thailand/ICRC-7372/2010,2010/03/24,Thailand,H5N1,Avian,1    ,    8336,>EU716168,A/brown-headed gull/Thailand/VSMU-28-SPK/2005,2005//,Thailand,H5N1,Avian,1
d= 157=  4/  3years,z=2257,pairs: 126-   6   9773,>HM193839,A/mallard/Alaska/44354-830/2007,2007/09/01,USA,H4N6,Avian,1    ,    4795,>CY136077,A/northern pintail/Interior Alaska/9BM6960R0/2009,2009//,USA,H3N8,Avian,1
d= 196=  5/  3years,z=2280,pairs: 114-   6   2660,>CY079018,A/mallard/Interior Alaska/7MP1835/2007,2007/09/05,USA,H3N8,Avian,1    ,    4802,>CY136130,A/northern pintail/Interior Alaska/9BM7108R2/2009,2009//,USA,H3N8,Avian,1
d= 196=  5/  3years,z=2280,pairs: 114-   6   2795,>CY080198,A/duck/Interior Alaska/7MP1550/2007,2007/09/01,USA,H4N6,Avian,1    ,    4813,>CY136220,A/northern pintail/Interior Alaska/9BM9153R0/2009,2009//,USA,H3N8,Avian,1
d=   0=  0/  5years,z=2280,pairs: 114-  14   8684,>FJ868019,A/chicken/Thailand/ST-351/2008,2008//,Thailand,H5N1,Avian,1    ,    7726,>DQ407243,A/little grebe/Thailand/Phichit-01/2004,2004//,Thailand,H5N1,Avian,1
d= 235=  6/  3years,z=2280,pairs:  87-   6   9756,>HM193822,A/mallard/Alaska/44354-831/2007,2007/10/02,USA,H4N6,Avian,1    ,    4817,>CY136254,A/mallard/Interior Alaska/9BM12748R0/2009,2009//,USA,mixed,Avian,1
d= 304= 58/ 32years,z=2280,pairs:  77-   9   672,>CY005652,A/duck/Hong Kong/562/1979,1979//,Hong Kong,H10N9,Avian,1    ,    10621,>KC986327,A/mallard/Mongolia/1551/2010,2010/09/10,Mongolia,H3N1,Avian,1
d= 228= 40/ 29years,z=2280,pairs:  73-  10   6879,>CY178934,A/common murre/Alaska/305/1976,1976//,USA,H1N6,Avian,1    ,    7778,>DQ835807,A/slaty-backed gull/Shandong/38/04,2004//,China,H5N1,Avian,1
d= 235=  6/  3years,z=2280,pairs:  68-  11   2673,>CY079122,A/northern pintail/Interior Alaska/8BM3582/2008,2008/09/14,USA,H3N8,Avian,1    ,    4780,>CY135954,A/mallard/Interior Alaska/10BM06828R0/2010,2010/07/31,USA,H3N8,Avian,1
d= 275=  7/  3years,z=2273,pairs:  68-  11   9755,>HM193821,A/mallard/Alaska/44421-148/2008,2008/10/13,USA,H3N6,Avian,1    ,    4367,>CY130420,A/northern pintail/Interior Alaska/10BM00303R0/2010,2010/05/14,USA,H3N8,Avian,1

------------------segment 2-------q=11862
d=   0=  0/ 20years,z=2274,pairs: 521-   1   499,>CY004411,A/ruddy turnstone/New Jersey/65/1985,1985/05/29,USA,H7N3,Avian,2    ,    498,>CY004404,A/shorebird/DE/101/2004,2004/05/17,USA,H5N7,Avian,2
d= 169= 15/ 13years,z=2274,pairs: 234-  20   3460,>CY102234,A/blue-winged teal/Alberta/16/1997,1997/07/29,Canada,H2N9,Avian,2    ,    3277,>CY097620,A/northern shoveler/Missouri/196/2009,2009/12/07,USA,H10N3,Avian,2
d= 190= 19/ 15years,z=2274,pairs: 186-  23   440,>CY003966,A/blue-winged teal/Alberta/16/1997,1997/10/24,Canada,H2N9,Avian,2    ,    6586,>CY166895,A/mallard/Wisconsin/11OS3177/2011,2011/09/24,USA,mixed,Avian,2
d= 296= 33/ 17years,z=2274,pairs: 179-   9   3399,>CY101713,A/mallard/Alberta/61/1991,1991/08/09,Canada,H3N8,Avian,2    ,    4269,>CY128617,A/American black duck/New Brunswick/02654/2007,2007/09/24,Canada,mixed,Avian,2
d= 308= 36/ 18years,z=2274,pairs: 179-  15   3400,>CY101721,A/mallard/Alberta/62/1991,1991/08/09,Canada,H3N8,Avian,2    ,    2029,>CY042621,A/mallard/Minnesota/Sg-00574/2008,2008/07/31,USA,H3N8,Avian,2
d= 308= 36/ 18years,z=2242,pairs: 179-  15   3401,>CY101729,A/mallard/Alberta/64/1991,1991/08/09,Canada,H3N8,Avian,2    ,    2030,>CY042625,A/gadwall duck/Minnesota/Sg-00575/2008,2008/07/31,USA,H3N8,Avian,2
d= 317= 37/ 18years,z=2274,pairs: 160-  15   3394,>CY101673,A/mallard/Alberta/12/1991,1991/08/09,Canada,H4N6,Avian,2    ,    2039,>CY042664,A/mallard/Minnesota/Sg-00629/2008,2008/07/31,USA,H3N8,Avian,2
d=  21=  3/ 22years,z=2258,pairs: 150-   1   2120,>CY043317,A/bald eagle/Virginia/Sg-00154/2008(mixed),2008//,USA,Mixed,Avian,2    ,    711,>CY011046,A/green-winged teal/Ohio/430/1987,1987/10/23,USA,H1N1,Avian,2
d=  38=  2/  7years,z=2273,pairs: 135-   6   9880,>HM590787,A/chicken/Thailand/ICRC-7356/2010,2010/03/24,Thailand,H5N1,Avian,2    ,    9226,>GU052439,A/pigeon/Thailand/1B/2004,2004//,Thailand,H5N1,Avian,2
d=  57=  3/  7years,z=2271,pairs: 135-   6   9881,>HM590795,A/chicken/Thailand/ICRC-7372/2010,2010/03/24,Thailand,H5N1,Avian,2    ,    42,>AB450521,A/chicken/NaraThiwat/NIAH1703/2004,2004//,Thailand,H5N1,Avian,2
d=   0=  0/  5years,z=2269,pairs: 122-   6   8618,>FJ868020,A/chicken/Thailand/ST-351/2008,2008//,Thailand,H5N1,Avian,2    ,    377,>AY651661,A/bird/Thailand/3.1/2004,2004//,Thailand,H5N1,Avian,2
d=   0=  0/ 23years,z=2274,pairs: 120-   9   2121,>CY043318,A/bald eagle/Virginia/Sg-00154/2008(mixed),2008//,USA,Mixed,Avian,2    ,    862,>CY017699,A/mallard/Ohio/30/1986,1986/10/20,USA,H2N1,Avian,2
d= 101=  4/  5years,z=2190,pairs: 102-   7   2199,>CY047456,A/chicken/Thailand/CU-354/2008,2008/11/14,Thailand,H5N1,Avian,2    ,    414,>AY770994,A/chicken/Ayutthaya/Thailand/CU-23/04,2004//,Thailand,H5N1,Avian,2
d= 322= 34/ 16years,z=2274,pairs:  99-  15   8322,>EU743119,A/pheasant/MD/4457/1993,1993//,USA,H5N2,Avian,2    ,    2048,>CY042706,A/mallard/Minnesota/Sg-00638/2008,2008/07/31,USA,H3N8,Avian,2
d= 187= 11/  8years,z=2274,pairs:  93-  12   7028,>CY180233,A/widgeon/Wisconsin/541/1976,1976//,USA,H3N8,Avian,2    ,    6903,>CY179233,A/mallard/Wisconsin/1349/1983,1983//,USA,H4N8,Avian,2

--------------segment 3-----------q=15154
d=   0=  0/ 20years,z=2151,pairs: 376-   1   502,>CY004410,A/ruddy turnstone/New Jersey/65/1985,1985/05/29,USA,H7N3,Avian,3    ,    501,>CY004403,A/shorebird/DE/101/2004,2004/05/17,USA,H5N7,Avian,3
d=  20=  3/ 23years,z=2151,pairs: 286-   1   2118,>CY043320,A/bald eagle/Virginia/Sg-00154/2008(mixed),2008//,USA,Mixed,Avian,3    ,    857,>CY017698,A/mallard/Ohio/30/1986,1986/10/20,USA,H2N1,Avian,3
d=   0=  0/  7years,z=2003,pairs: 168-   8   10000,>HM590788,A/chicken/Thailand/ICRC-7356/2010,2010/03/24,Thailand,H5N1,Avian,3    ,    8204,>EF593101,A/chicken/Thailand/vsmu-3-BKK/2004,2004//,Thailand,H5N1,Avian,3
d= 182= 14/ 11years,z=2151,pairs: 139-  28   454,>CY003965,A/blue-winged teal/Alberta/16/1997,1997/10/24,Canada,H2N9,Avian,3    ,    3636,>CY103321,A/mallard/Alberta/156/2007,2007/08/22,Canada,mixed,Avian,3
d= 247= 16/  9years,z=2151,pairs: 139-  23   3500,>CY102233,A/blue-winged teal/Alberta/16/1997,1997/07/29,Canada,H2N9,Avian,3    ,    2963,>CY089554,A/pintail/Alaska/315/2005,2005/08/11,USA,H3N8,Avian,3
d=   0=  0/  5years,z=2151,pairs: 137-   9   8793,>FJ868021,A/chicken/Thailand/ST-351/2008,2008//,Thailand,H5N1,Avian,3    ,    51,>AB450544,A/open-bill stork/Thailand/VSMU-20-AYA/2004,2004//,Thailand,H5N1,Avian,3
d=  92=  3/  4years,z=2151,pairs: 130-  10   1879,>CY039833,A/northern shoveler/Interior Alaska/1/2007,2007/09/01,USA,H4N6,Avian,3    ,    5844,>CY143753,A/northern pintail/Interior Alaska/10CH00003R0/2010,2010/09/04,USA,H4N6,Avian,3
d= 123=  4/  4years,z=2151,pairs: 123-  20   1873,>CY039785,A/mallard/Interior Alaska/4/2007,2007/09/07,USA,H4N6,Avian,3    ,    5855,>CY143841,A/northern pintail/Interior Alaska/10BM10480R0/2010,2010/08/09,USA,H3N8,Avian,3
d= 184=  6/  4years,z=2151,pairs: 123-  15   2766,>CY078976,A/mallard/Interior Alaska/7MP0956/2007,2007/09/07,USA,mixed,Avian,3    ,    4866,>CY135734,A/American green-winged teal/Interior Alaska/10BM05376R0/2010,2010/07/25,USA,H3N8,Avian,3
d= 123=  4/  4years,z=2151,pairs: 121-  15   9964,>HM193753,A/mallard/Alaska/44354-830/2007,2007/09/01,USA,H4N6,Avian,3    ,    4893,>CY135952,A/mallard/Interior Alaska/10BM06828R0/2010,2010/07/31,USA,H3N8,Avian,3
d= 215=  7/  4years,z=2151,pairs: 111-  15   2794,>CY079208,A/mallard/Interior Alaska/7MP1701/2007,2007/09/03,USA,mixed,Avian,3    ,    4894,>CY135960,A/mallard/Interior Alaska/10BM06835R0/2010,2010/07/31,USA,H3N8,Avian,3
d=   0=  0/ 22years,z=2151,pairs: 107-  19   2117,>CY043319,A/bald eagle/Virginia/Sg-00154/2008(mixed),2008//,USA,Mixed,Avian,3    ,    712,>CY011045,A/green-winged teal/Ohio/430/1987,1987/10/23,USA,H1N1,Avian,3
d= 215=  7/  4years,z=2142,pairs:  92-  17   8417,>EU557471,A/northern pintail/Alaska/44244-108/2006,2006/09/01,USA,H3N8,Avian,3    ,    4815,>CY135332,A/northern shoveler/Interior Alaska/9BM2943R1/2009,2009/07/16,USA,H4N6,Avian,3
d= 215=  7/  4years,z=2151,pairs:  92-  17   9970,>HM193759,A/mallard/Alaska/44244-097/2006,2006/09/01,USA,H3N8,Avian,3    ,    4825,>CY135412,A/northern pintail/Interior Alaska/9BM4583R0/2009,2009/07/29,USA,H4N6,Avian,3
d=   0=  0/ 13years,z=2151,pairs:  91-   1   9052,>GU049983,A/duck/Pennsylvania/467189/2006,2006//,USA,H5N9,Avian,3    ,    8484,>EU742949,A/chicken/New York/13142-5/1994,1994//,USA,H7N2,Avian,3

--------------------segment 5------q=7756
d=  25=  1/  5years,z=1497,pairs: 103-  21   8536,>FJ868015,A/chicken/Thailand/ST-351/2008,2008//,Thailand,H5N1,Avian,5    ,    44,>AB450582,A/quail/Phathumthani/NIAH2711/2004,2004//,Thailand,H5N1,Avian,5
d=   0=  0/  4years,z=1481,pairs: 103-  50   9702,>HM590790,A/chicken/Thailand/ICRC-7356/2010,2010/03/24,Thailand,H5N1,Avian,5    ,    7999,>EU233417,A/chicken/Thailand/ICRC-V143/2007,2007//,Thailand,H5N1,Avian,5
d=   0=  0/  4years,z=1497,pairs: 102-  50   9703,>HM590798,A/chicken/Thailand/ICRC-7372/2010,2010/03/24,Thailand,H5N1,Avian,5    ,    8297,>EU875394,A/chicken/Thailand/ICRC-213/2007,2007/08/23,Thailand,H5N1,Avian,5
d=   0=  0/  4years,z=1482,pairs:  83-   5   1787,>CY047458,A/chicken/Thailand/CU-354/2008,2008/11/14,Thailand,H5N1,Avian,5    ,    7557,>DQ989988,A/open-billed stork/Nakhonsawan/BBD1521J/2005,2005//,Thailand,H5N1,Avian,5
d=   0=  0/  4years,z=1474,pairs:  83-   5   1788,>CY047462,A/chicken/Thailand/CU-355/2008,2008/11/14,Thailand,H5N1,Avian,5    ,    7627,>EF112295,A/open-billed stork/Nakhonsawan/BBD1221J/05,2005//,Thailand,H5N1,Avian,5
d=   0=  0/ 23years,z=1497,pairs:  72-   1   1709,>CY043324,A/bald eagle/Virginia/Sg-00154/2008(mixed),2008//,USA,Mixed,Avian,5    ,    987,>CY017696,A/mallard/Ohio/30/1986,1986/10/20,USA,H2N1,Avian,5
d=  39=  1/  3years,z=1497,pairs:  68-  21   10153,>JQ794449,A/duck/Thailand/TS01/2006,2006//,Thailand,H5N1,Avian,5    ,    7493,>DQ407246,A/little grebe/Thailand/Phichit-01/2004,2004//,Thailand,H5N1,Avian,5
d=  39=  1/  3years,z=1497,pairs:  68-  21   10154,>JQ794457,A/chicken/Thailand/TS02/2006,2006//,Thailand,H5N1,Avian,5    ,    7555,>DQ989970,A/open-billed stork/Nakhonsawan/BBD0404F/2004,2004//,Thailand,H5N1,Avian,5
d=  78=  2/  3years,z=1481,pairs:  57-  11   8278,>EU850417,A/chicken/Thailand/NS-341/2008,2008//,Thailand,H5N1,Avian,5    ,    50,>AB450588,A/chicken/Phichit/NIAH606988/2006,2006//,Thailand,H5N1,Avian,5
d=  78=  2/  3years,z=1486,pairs:  57-  11   8279,>EU850425,A/chicken/Thailand/NS-342/2008,2008//,Thailand,H5N1,Avian,5    ,    7612,>DQ999883,A/chicken/Thailand/PC-168/2006,2006//,Thailand,H5N1,Avian,5
d=   0=  0/ 20years,z=1497,pairs:  56-   1   617,>CY004408,A/ruddy turnstone/New Jersey/65/1985,1985/05/29,USA,H7N3,Avian,5    ,    616,>CY004401,A/shorebird/DE/101/2004,2004/05/17,USA,H5N7,Avian,5
d=  50=  2/  5years,z=1497,pairs:  54-   7   8150,>EU676318,A/Kalij pheasant/Thailand/vsmu-1/2008,2008//,Thailand,H5N1,Avian,5    ,    7867,>EF593103,A/chicken/Thailand/vsmu-3-BKK/2004,2004//,Thailand,H5N1,Avian,5
d=  92=  3/  4years,z=1495,pairs:  54-   6   8151,>EU676326,A/brown-head gull/Thailand/vsmu-4/2008,2008//,Thailand,H5N1,Avian,5    ,    8158,>EU716170,A/brown-headed gull/Thailand/VSMU-28-SPK/2005,2005//,Thailand,H5N1,Avian,5

--------------------segment 7---------------q=54436
d=  37=  6/ 26years,z= 982,pairs: 615-   3   1266,>CY015054,A/chicken/Brescia/1902,1902//,Italy,H7N7,Avian,7    ,    12865,>M63526,A/fowl/Dobson/1927,1927//,United Kingdom,H7N7,Avian,7
d=  30=  1/  4years,z= 982,pairs: 530- 168   7686,>CY181274,A/blue-winged teal/Wisconsin/151/1978,1978//,USA,H11N9,Avian,7    ,    1225,>CY014727,A/duck/Minnesota/1525/1981,1981/10/17,USA,H5N1,Avian,7
d=  86= 41/ 94years,z= 982,pairs: 520-   2   1,>xxxxxxxx,A/Brevig Mission/1/1918,1918/10/10,USA,H1N1,Human,0    ,    4938,>CY132002,A/mallard/Ohio/11OS2045/2011,2011/08/17,USA,mixed,Avian,7
d=   0=  0/ 20years,z= 982,pairs: 364-   1   972,>CY004406,A/ruddy turnstone/New Jersey/65/1985,1985/05/29,USA,H7N3,Avian,7    ,    971,>CY004399,A/shorebird/DE/101/2004,2004/05/17,USA,H5N7,Avian,7
d=  50=  8/ 26years,z= 982,pairs: 318-   3   12854,>L37795,A/chicken/Brescia/1902,1902//,Italy,H7N7,Avian,7    ,    4892,>CY130143,A/FPV/Dutch/1927,1927//,United Kingdom,H7N7,Avian,7
d=  79= 16/ 34years,z= 974,pairs: 285-   5   9830,>GQ404592,A/duck/Germany/1972,1972//,Germany,H2N9,Avian,7    ,    9429,>EU819131,A/aquatic bird/Korea/w14/2005,2005//,South Korea,H6N2,Avian,7

-----------------------------segment 81--------q=94770
d=  31=  5/ 26years,z= 838,pairs:1064-   3   641,>CY015056,A/chicken/Brescia/1902,1902//,Italy,H7N7,Avian,8    ,    637,>CY014995,A/fowl/Dobson/1927,1927//,USA,H7N7,Avian,8
d=  76= 35/ 90years,z= 838,pairs:1057-   1   1,>xxxxxxxx,A/Brevig Mission/1/1918,1918/10/10,USA,H1N1,Human,0    ,    6189,>GU183417,A/chicken/Pessel/BPPVRII/2007,2007/03/07,Indonesia,H5N1,Avian,8
d=  22=  3/ 21years,z= 838,pairs: 860- 207   1872,>CY101442,A/pintail/Alberta/128/1987,1987/08/12,Canada,H3N8,Avian,8    ,    1865,>CY101376,A/bufflehead/Alberta/399/2007,2007/08/28,Canada,mixed,Avian,8
d=  34=  2/  8years,z= 838,pairs: 812- 416   4582,>CY180520,A/duck/Minnesota/1/1975,1975//,USA,H6N9,Avian,8    ,    4327,>CY177690,A/mallard/Wisconsin/1102/1982,1982//,USA,H11N9,Avian,8
d=  34=  2/  8years,z= 838,pairs: 812- 416   4592,>CY180624,A/duck/Minnesota/2/1975,1975//,USA,H6N1,Avian,8    ,    4425,>CY178763,A/mallard/Wisconsin/1073/1982,1982//,USA,H11N9,Avian,8
d=  34=  2/  8years,z= 838,pairs: 812- 416   4594,>CY180640,A/duck/Minnesota/56/1975,1975//,USA,H6N1,Avian,8    ,    4480,>CY179255,A/mallard/Wisconsin/1071/1982,1982//,USA,H11N9,Avian,8
d=  12=  2/ 26years,z= 838,pairs: 742-   3   6205,>GU186781,A/chicken/Brescia/1902,1902//,Italy,H7N7,Avian,8    ,    2688,>CY130146,A/FPV/Dutch/1927,1927//,United Kingdom,H7N7,Avian,8
d=  37=  5/ 21years,z= 838,pairs: 685- 187   4581,>CY180512,A/mallard/Wisconsin/793/1976,1976//,USA,H2N3,Avian,8    ,    6070,>GU051920,A/chicken/New Jersey/15906-9/1996,1996//,USA,H11N1,Avian,8
d=  38=  2/  7years,z= 838,pairs: 584- 418   575,>CY005892,A/pheasant/Minnesota/917/1980,1980/08/20,USA,H7N3,Avian,8    ,    498,>CY005224,A/mallard duck/ALB/666/1986,1986/08/22,Canada,H10N7,Avian,8
d=  25=  1/  5years,z= 838,pairs: 564- 418   4423,>CY178747,A/mallard/Wisconsin/1092/1982,1982//,USA,H1N3,Avian,8    ,    3036,>CY136392,A/mallard/Alberta/670/1986,1986/08/22,Canada,mixed,Avian,8
d=  49=  9/ 30years,z= 838,pairs: 530- 287   4595,>CY180656,A/mallard/Wisconsin/438/1979,1979//,USA,H7N3,Avian,8    ,    1139,>CY043330,A/bald eagle/Virginia/Sg-00154/2008(mixed),2008//,USA,Mixed,Avian,8
d=  25=  1/  5years,z= 838,pairs: 527- 328   4360,>CY178058,A/mallard/Wisconsin/2322/1984,1984//,USA,H4N6,Avian,8    ,    626,>CY014876,A/black duck/New York/184/1988,1988//,USA,H5N2,Avian,8
d=  50=  2/  5years,z= 838,pairs: 488- 467   4405,>CY178490,A/mallard/Wisconsin/143/1981,1981//,USA,H7N3,Avian,8    ,    4389,>CY178322,A/duck/Wisconsin/2632/1985,1985//,USA,H10N3,Avian,8
d=  69= 14/ 34years,z= 838,pairs: 474- 236   7644,>U85375,A/mallard/Wisconsin/1975/169,1975//,USA,H5,Avian,8    ,    3403,>CY140463,A/mallard/Minnesota/Sg-00902/2008,2008/09/03,USA,mixed,Avian,8
d=  51=  3/  8years,z= 838,pairs: 467-  77   4525,>CY179687,A/duck/Wisconsin/2627/1985,1985//,USA,H10N3,Avian,8    ,    1899,>CY101793,A/mallard/Alberta/196/1992,1992/08/24,Canada,mixed,Avian,8
d=  61=  2/  4years,z= 838,pairs: 461- 189   4326,>CY177682,A/mallard/Wisconsin/1083/1982,1982//,USA,H11N9,Avian,8    ,    4408,>CY178523,A/duck/Wisconsin/2420/1985,1985//,USA,H2N1,Avian,8

-----------------------segment 82--------------q=67422
d=  39=  5/ 20years,z= 838,pairs:1254-  39   2025,>CY180712,A/green-winged teal/Wisconsin/562/1979,1979//,USA,H9N1,Avian,8    ,    1433,>CY139749,A/mallard/Minnesota/182722/1998,1998/09/01,USA,H11N9,Avian,8
d=  47=  6/ 20years,z= 770,pairs:1157-  52   1985,>CY179943,A/mallard/Wisconsin/73/1979,1979//,USA,H1N1,Avian,8    ,    186,>AY633264,A/mallard/Alberta/295/98,1998//,Canada,H4N6,Avian,8
d=  47=  8/ 28years,z= 838,pairs:1157-  94   1987,>CY180039,A/mallard/Wisconsin/654/1979,1979//,USA,H1N1,Avian,8    ,    1018,>CY103030,A/mallard/Alberta/190/2006,2006/08/04,Canada,mixed,Avian,8
d=  30=  1/  4years,z= 838,pairs: 987- 907   1946,>CY178450,A/duck/Wisconsin/2736/1985,1985//,USA,H4N6,Avian,8    ,    196,>CY004092,A/knot/Delaware Bay/526/1988,1988/05/15,USA,H6N8,Avian,8
d=  30=  1/  4years,z= 838,pairs: 987- 907   1948,>CY178466,A/duck/Wisconsin/2810/1985,1985//,USA,H3N6,Avian,8    ,    1124,>CY126307,A/knot/Delaware Bay/526/1988,1988/05/15,USA,H6N8,Avian,8
d=  54= 10/ 31years,z= 838,pairs: 899- 117   214,>CY004486,A/pintail duck/ALB/238/1979,1979/08/09,Canada,H1N1,Avian,8    ,    2520,>JX080988,A/American green-winged teal/Alaska/44493-527/2009,2009/08/16,USA,H3N8,Avian,8
d=  45=  4/ 13years,z= 838,pairs: 871-  62   212,>CY004409,A/ruddy turnstone/New Jersey/65/1985,1985/05/29,USA,H7N3,Avian,8    ,    189,>AY633344,A/pintail/Alberta/156/97,1997//,Canada,H3N8,Avian,8
d=  48=  4/ 12years,z= 838,pairs: 871- 102   2111,>CY185833,A/ruddy turnstone/New Jersey/65/1985,1985/05/29,USA,H7N3,Avian,8    ,    1333,>CY136940,A/pintail/Alberta/140/1996,1996/08/02,Canada,H1N1,Avian,8
d=  43=  6/ 22years,z= 838,pairs: 867-  76   194,>CY003883,A/mallard duck/Alberta/376/1985,1985/08/18,Canada,H2N3,Avian,8    ,    1029,>CY103141,A/mallard/Alberta/256/2006,2006/08/09,Canada,mixed,Avian,8
d=  55=  8/ 23years,z= 838,pairs: 849-  54   1964,>CY179287,A/mallard/Wisconsin/1636/1983,1983//,USA,H3N8,Avian,8    ,    906,>CY095350,A/mallard/Nova Scotia/14728/2005,2005/09/08,Canada,H3N8,Avian,8
d=  39=  1/  3years,z= 838,pairs: 828- 407   1966,>CY179335,A/mallard/Wisconsin/607/1977,1977//,USA,H4N6,Avian,8    ,    1988,>CY180087,A/mallard/Wisconsin/538/1979,1979//,USA,H11N9,Avian,8
d=  53=  8/ 24years,z= 838,pairs: 817-  88   1945,>CY178442,A/duck/Wisconsin/2731/1985,1985//,USA,H4N6,Avian,8    ,    741,>CY079368,A/American green-winged teal/Wisconsin/08OS3469/2008,2008/11/16,USA,H2N9,Avian,8
d=  55=  8/ 23years,z= 838,pairs: 727- 101   296,>CY017079,A/bufflehead/Ohio/246/1986,1986//,USA,H11N2,Avian,8    ,    1449,>CY140168,A/blue-winged teal/North Dakota/Sg-00750/2008,2008/09/10,USA,H4N6,Avian,8
d=  62=  7/ 17years,z= 838,pairs: 710-  42   250,>CY005267,A/redhead duck/Alberta/357/1983,1983/08/07,Canada,H11N9,Avian,8    ,    1006,>CY102469,A/shorebird/Delaware Bay/204/1999,1999/05/24,USA,mixed,Avian,8
d=  60=  6/ 15years,z= 838,pairs: 708-  42   223,>CY004659,A/mallard duck/Alberta/438/1985,1985/08/20,Canada,H3N4,Avian,8    ,    1007,>CY102595,A/shorebird/Delaware Bay/287/1999,1999/05/24,USA,H6N2,Avian,8
d=  60=  8/ 21years,z= 838,pairs: 602-  90   972,>CY101458,A/mallard/Alberta/140/1987,1987/08/13,Canada,H3N8,Avian,8    ,    1046,>CY103354,A/mallard/Alberta/284/2007,2007/08/04,Canada,mixed,Avian,8
d=  60=  8/ 21years,z= 838,pairs: 602-  90   973,>CY101468,A/mallard/Alberta/144/1987,1987/08/13,Canada,mixed,Avian,8    ,    2484,>JF323808,A/Steller's eider/Alaska/44354-138/2007,2007/09/13,USA,H3N6,Avian,8
d=  67= 10/ 24years,z= 838,pairs: 522-  42   2043,>CY181057,A/mallard/Saskatchewan/1/1982,1982//,Canada,H3N8,Avian,8    ,    907,>CY095358,A/green-winged teal/Nova Scotia/14917/2005,2005/09/14,Canada,H6N1,Avian,8
d=  62= 10/ 26years,z= 838,pairs: 496-  85   234,>CY004834,A/mallard duck/Alberta/630/1984,1984/08/06,Canada,H4N2,Avian,8    ,    926,>CY096966,A/American green-winged teal/Illinois/3443/2009,2009/10/31,USA,mixed,Avian,8

--------------------segments 123578 combined-------------------------
d=  95=  5/  7years,z=9848,pairs: 106-   7   2574,>HM590786,A/chicken/Thailand/ICRC-7356/2010,2010/03/24,Thailand,H5N1,Avian    ,    2589,>EF593099,A/chicken/Thailand/vsmu-3-BKK/2004,2004//,Thailand,H5N1,Avian
d= 152=  6/  5years,z=10013,pairs:  79-   7   2586,>FJ868019,A/chicken/Thailand/ST-351/2008,2008//,Thailand,H5N1,Avian    ,    4664,>DQ407243,A/little grebe/Thailand/Phichit-01/2004,2004//,Thailand,H5N1,Avian
d= 861= 28/  4years,z=9861,pairs:  26-   8   3842,>JQ794453,A/duck/Thailand/TS01/2006,2006//,Thailand,H5N1,Avian    ,    8121,>HM627942,A/openbill stork/Thailand/VSMU-12-BKK/2003,2003/12/30,Thailand,H5N1,Avian
d= 904= 23/  3years,z=9987,pairs:  25-   7   2587,>JQ794461,A/chicken/Thailand/TS02/2006,2006//,Thailand,H5N1,Avian    ,    684,>AY651714,A/Qa/Thailand/57/2004,2004//,Thailand,H5N1,Avian
d=1120= 44/  5years,z=9711,pairs:  22-   7   1289,>EU676322,A/brown-head gull/Thailand/vsmu-4/2008,2008//,Thailand,H5N1,Avian    ,    8197,>AB576199,A/pigeon/Thailand/VSMU-7-NPT/2004,2004//,Thailand,H5N1,Avian
d=  17=  1/  8years,z=10025,pairs:  18-   1   6637,>CY183440,A/mallard/Sweden/124987/2010,2010/11/10,Sweden,H7N7,Avian    ,    6675,>CY184567,A/mallard/Sweden/2027/2003,2003/09/24,Sweden,H7N7,Avian
d= 157=  4/  3years,z=10028,pairs:  15-   1   431,>CY130339,A/American wigeon/Interior Alaska/9BM2501R1/2009,2009/07/11,USA,H3N8,Avian    ,    5401,>CY039839,A/mallard/Interior Alaska/1/2007,2007/09/03,USA,H4N5,Avian
d=1120= 44/  5years,z=9737,pairs:  12-   5   611,>EU676314,A/Kalij pheasant/Thailand/vsmu-1/2008,2008//,Thailand,H5N1,Avian    ,    1334,>AY770993,A/chicken/Ayutthaya/Thailand/CU-23/04,2004//,Thailand,H5N1,Avian
d= 414= 19/  6years,z=9921,pairs:  11-   5   1399,>KF746873,A/chicken/Beijing/243/2010,2010/05/21,China,H9N2,Avian    ,    1401,>EU914197,A/chicken/Beijing/L1/2005,2005//,China,H9N2,Avian
d=1015= 33/  4years,z=10028,pairs:  11-   1   6737,>CY184140,A/mallard/Sweden/50980/2006,2006/10/09,Sweden,H11N9,Avian    ,    6536,>CY184324,A/mallard/Sweden/100687/2009,2009/10/29,Sweden,H11N9,Avian
d= 738= 24/  4years,z=10027,pairs:   9-   7   2330,>CY037751,A/chicken/Pakistan/c1998/1998,1998//,Pakistan,H7N3,Avian    ,    2314,>CY015039,A/chicken/Pakistan/34669/1995,1995//,Pakistan,H7N3,Avian
d= 310= 22/ 10years,z=10025,pairs:   7-   7   1434,>FJ577557,A/chicken/Chakwal/NARC-148/2004,2004//,Pakistan,H7N3,Avian    ,    2076,>FJ577517,A/chicken/Murree/NARC-01/1995,1995//,Pakistan,H7N3,Avian
d= 286= 15/  7years,z=10028,pairs:   7-   7   1435,>FJ577525,A/chicken/Chakwal/NARC-35/2001,2001//,Pakistan,H7N3,Avian    ,    2313,>CY035828,A/chicken/Pakistan/34668/1995,1995//,Pakistan,H7N3,Avian
d=9999= 15/  7years,z=10028,pairs:   7-   0   2575,>EU233413,A/chicken/Thailand/ICRC-V143/2007,2007//,Thailand,H5N1,Avian    ,    2313,>CY035828,A/chicken/Pakistan/34668/1995,1995//,Pakistan,H7N3,Avian


running through all viruses ,one per line, and the pairs that it forms
z is the number of nucleotides available
pairs: is the number of other segments for that line, that have unusually few differences
first name in a line is the virus of that line, second name is the name of the segment with fewest differences per year

d= , others , forgotten (old program, written years ago)


view this as a list of virus-segments with the most unusual preservations  (first names in the rows only)

-----edit--------
I should do other graphs later :
linear,non-logarithmic
at different darknesses,
256-colors greyscale
remove the most preserving viruses 10,20,50,100,
identify groups with low differences
North America only, Eurasia only , Chickens/ducks/mallards only
compare with human(H3N2,H1N1),swine,equine(H3N8)
program : jahr7g.c
H5N1 only, H9N2 only ,
scale
#mutations, %identity
add HA,NA

--------------------------------------
seg1.gif : compares segment1 of human H3N2 with
segment 1, North America, wild birds since 1974.

The birds look different, but the diversity is bigger, the most recent
common anchester dates

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

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001931

they claim that different HA-types of North American mallard viruses
have different durability in water : (figure 5) [38]

H1=09.4d, H2=20.5d, H3=26.0d, H4=12.7d, H5=13.7d, H6=16.1d
H7=25.8d, H9=08.0d, H10=03.7d, H11=05.6d, H12=14.8

++:H3,H7
--:H10,H11

And this depends mainly on HA (and NA ?), the amino-acid diversity
in inner segments of mallard-flu is low.
And since there is frequent reassortment we concentrate on HA
to measure the mutation rate so to compare with durability.

the minimum nucleotide differences in HA in pairs of viruses
isolated 20 years apart see bitsb4m.gif

of H3 is ~50
of H10 is ~100
of H11 is ~70
of H7 is ~100

mallard-H10 spends 5 days in ducks, 2 days in water
mallard-H3 spends 5 days in ducks, 9 days in water

Code:

percentages in HA-subtypes by species

                                                           sequences
HA      ,01,02,03,04,05,06,07,08,09,10,11,12,13,14,15,16  , 10410 
hicken  ,00,01,00,00,47,04,16,00,29,00,00,00,00,00,00,00  ,  1734 
urkey   ,04,00,04,01,19,03,52,02,09,00,00,00,00,00,00,00  ,   242 
gull    ,05,13,01,03,09,08,04,00,04,02,06,00,27,00,00,11  ,   211 
allard  ,06,07,18,24,07,08,05,02,01,07,07,02,00,00,00,00  ,  2772 
duck    ,04,02,11,10,31,22,07,00,02,02,02,01,00,00,00,00  ,  2000 
intail  ,05,01,29,18,03,09,08,06,00,12,03,02,00,00,00,00  ,   598 
urnstone,09,05,11,11,03,06,12,00,04,15,12,08,00,00,00,00  ,   528 
oveler  ,05,03,20,11,03,07,14,05,02,14,07,01,00,01,00,00  ,   235 
horebird,10,02,18,05,01,10,04,00,05,23,13,00,01,00,00,01  ,   268 
teal    ,04,01,29,28,04,11,05,01,00,05,06,00,00,00,00,00  ,   792 
laska   ,07,01,33,24,01,01,07,06,00,10,00,02,00,00,00,00  ,  1030

I would expect turnstone,shorebird,shoveler to be species who preferrably get
(from mallards) flu that lasts long in water, so H3,H7, but to the contrary they preferrable
get the short duration strains H10 and H11

pres.gif : all inner segments together, differences in 6317*6316/2
pairs over time in months. picture at 3 intensities (#pairs to make one pixel)

evolution and diversity of avian influenza

gsgs

Registered User

gsgs

Registered User

Attachments

gsgs

Registered User

gsgs

Registered User

Attachments