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evolutionary stasis

gsgs

gsgs

Registered User
http://www.virologyj.com/content/pdf/1743-422X-8-350.pdf

{partial HAs from Greek equine outbreaks in 2003 and 2007 being identical}

> Endo et al (1992) [29] was the first to describe this phenomenon {frozen evolution}
> A/Eq/Switzerland/07 is an example of frozen evolution

> A/Eq/Cheshire/1/06, which showed 100% similarity to the prototype strain
> A/Eq/Newmarket/1/93 was another evidence of frozen evolution...

> ...contamination [30] ...
> Tu et al [34] .. pigs in China 2005 close to European from 1990


[29] Endo,Pecoraro,Sugia,... 1992 http://www.ncbi.nlm.nih.gov/pubmed/1550498
[a] 1998 http://www.ncbi.nlm.nih.gov/pubmed/9739336
[30] Gupta,Yadav,Uppal,...1987 epizootic India http://www.ncbi.nlm.nih.gov/pubmed/8385602
[31] Manuguerra, ... evolutionary stasis ..., 2000 http://www.ncbi.nlm.nih.gov/pubmed/10799778
[34] Zhou,Yiang,Zhang,Guo,Zou,Chen,Jin, Arch.Virol.2009,154(5),887-90
http://www.ncbi.nlm.nih.gov/pubmed/19396578
[mixin]Characterisation of three equine influenza A H3N8 viruses from Germany (2000 and 2002):
evidence for frozen evolution. http://www.ncbi.nlm.nih.gov/pubmed/15795074



eq38s4a.GIF



eq38g2a.GIF




after some decades since 1963 we do see the effect
that previous mutations are being undone so the
curve usually gets less steep over time

I have a 6BP inclusion in 2004 near the start

> HA gene alignment analysis of the Greek isolates showed no nucleotide
> substitution among them and in comparison with
> A/ equine/ Newmarket/2/93 strain.

as it happens they did use whole virus vax for horses and
A/Eq/Newmarket/2/93 was one of the vaccine strains !
Coincidence ?

http://www.aht.org.uk/equiflunet/equiflunet_vaccines.html



Intervet/Schering-Plough Animal Health
Equilis Resequin
(Resequin NN plus) (Resequin Vet.)
Prague/56 (H7N7),Newmarket/1/93(H3N8; American),Newmarket/2/93(H3N8; European)
used in : Austria ,Belgium ,Switzerland ,Germany ,Denmark ,Greece ,Spain ,Finland ,Hungary
Ireland ,Italy ,Luxembourg ,Netherlands ,Norway ,Sweden ,UK

http://www.msd-animal-health.co.za/products/equilis_resequin/020_product_details.aspx

mutation picture
HAs sorted by date
~270 out of ~280 A/Eq/Newmarket/5/2003 deleted

eq38s4b.GIF


full genomes:
http://magictour.free.fr/panflu/eq38s24.GIF



31 A/Eq/NY/VR-297/1983 is frozen for 10 years

the 2 Chinese swine from early 2006 are close to Eq/Qinghai/1994 , also frozen 12 years

promille difference acquired from 1963-2008 = 45 years in the 8 segments is:

68,72,72,94,65,88,39,39

to compare: human H3N2 from 1972-2009 = 37 years :
56,70,53,115,65,94,43,54
 
Re: evolutionary stasis

slow flu-evolution in Chinese swine H3N2 - HA
mutations per position per year
nucleotides available
mutations in total
------------------------------------------------------------------
1.072151E-03 1698 71 >A/swine/Guangdong/223/2006,2006//
1.102353E-03 1698 73 >A/swine/Guangdong/211/2006,2006//
1.102353E-03 1698 73 >A/swine/Guangdong/423/2006,2006//
1.102353E-03 1698 73 >A/swine/Guangdong/811/2006,2006//
1.131362E-03 1698 73 >A/swine/Heilongjiang/1/05,2005//
1.147655E-03 1698 76 >A/swine/Guangdong/968/2006,2006//
1.161030E-03 1698 69 >A/swine/Guangdong/106/2002,2002//
1.161030E-03 1698 69 >A/swine/Guangdong/111/2002,2002//
1.211509E-03 1698 72 >A/swine/Guangdong/102/2002,2002//
1.211509E-03 1698 72 >A/swine/Guangdong/107/2002,2002//
1.211509E-03 1698 72 >A/swine/Guangdong/110/2002,2002//
1.211509E-03 1698 72 >A/swine/Guangdong/113/2002,2002//
1.284934E-03 1698 72 >A/swine/Heilongjiang/74/2000,2000//
1.405829E-03 1698 74 >A/swine/Guangdong/01/1998,1998//

only 6 mutations in the whole HA when compared to
A/Memphis/105/1976 and others from that time


A/Swine/Guangdong/111/2002
has only one difference to
A/Swine/Colorado/1/1977


let me speculate:

they were using whole virus attenuated live vaccine made from the
1977 Colorado virus or similar in Guangdong from 2002-2006 ?!?

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

http://www.ncbi.nlm.nih.gov/nuccore/GQ422426?
AUTHORS Xu,C., Luo,H. and Cao,Y.
TITLE Genomic characterization of six H3N2 swine influenza viruses
isolated from southeast China
JOURNAL Unpublished

JOURNAL Submitted (29-JUL-2009) Sun Yat-Sen University, Life Science
College, Guangzhou, Guangdong 510006, China

http://www.ncbi.nlm.nih.gov/nuccore/GU086134?
AUTHORS Bi,Y., Wang,J., Guan,J., Gao,H., Fu,G., Pu,J. and Liu,J.
TITLE Genetic Reassortant of H1 and H3 Subtype Swine Influenza A Viruses
in China
JOURNAL Unpublished
Submitted (14-OCT-2009) Department of Veterinary Prevention
Medicine, College of Veterinary Medicine, China Agricultural
University, No.2 Yuan Ming Yuan Western Road, Beijing 100193,
People's Republic of China


differences to Colorado/1977 in the 8 segments in promille:
.(*:partial sequence)

Code: 
.
  1 >CY009307 A/swine/Colorado/1/1977
  1:  0,  0,  0,  0,  0,  0,  0,  0   CY009307 A/swine/Colorado/1/1977 1977//     
  2:  4,  8,  5,  2,  5,  2,  0,  1   AF251394 A/swine/Colorado/1/1977 1977//     
  3:  0,  0,  0,  1,  1,  0, 91,  3   GQ422426 A/swine/Guangdong/102/2002 2002//  
  4:  0,  0,  0,  1,  1,  0, 91,  3   GQ422427 A/swine/Guangdong/106/2002 2002//  
  5:  1,  0,  0,  1,  1,  3, 93,  3   GQ422431 A/swine/Guangdong/107/2002 2002//  
  6:  0,  0,  0,  1,  1,  0, 91,  3   GQ422430 A/swine/Guangdong/110/2002 2002//  
  7:  0,  0,  2,  0,  1,  0, 91,  3   GQ422428 A/swine/Guangdong/111/2002 2002//  
  8:  0,  0,  0,  1,  1,  0, 91,  4   GQ422429 A/swine/Guangdong/113/2002 2002//  
 12:  0,  2,  7,  1,  3,  0, 95,  0  *GU086118 A/swine/Guangdong/211/2006 2006//  
 13: *3,  2,  0,  2,  0,  0, 92,  0   GU086126 A/swine/Guangdong/223/2006 2006//  
 14:  0,  1,  0,  2,  1,  2, 93,  1   GU086134 A/swine/Guangdong/423/2006 2006//  

 16:  3,  5,  3,  1,  1,177, 92,  0  *GU086142 A/swine/Guangdong/811/2006 2006//  
 17:  4,  7,187,  3,  2,  0, 96,  1  *GU086150 A/swine/Guangdong/968/2006 2006//  
 11: 51, 63, 48, 88,  1, 88, 34, 47   EU273805 A/swine/Guangdong/166/06 2006//    
  9: 50, 64, 49, 88, 59, 87, 34, 46   EU273803 A/swine/Guangdong/164/06 2006//    
 10: 49, 62, 48, 87, 59, 88, 35, 46   EU273804 A/swine/Guangdong/165/06 2006//    
 15: 45, 64,199, 88, 58, 85, 36, 46  *GU086086 A/swine/Guangdong/7/2006 2006//
.

http://www.ncbi.nlm.nih.gov/pubmed/19463787
http://www.cnic.org.cn/pdf/2011-2-18/Emergence of novel reassortant H3N2 influenza.pdf
http://www.flutrackers.com/forum/showthread.php?t=122336

A/Swine/Ange-Gardien/150/1990(H3N2)
http://www.ncbi.nlm.nih.gov/nuccore/U07146?
http://www.ncbi.nlm.nih.gov/pubmed/7897358
Of the four pandemic strains of human influenza A virus observed this century,
the 1977 virus strain was very similar in all genes to a 1950 isolate. Since
mammalian influenza A viruses change annually by genetic drift, this reappearance
could only be attributed at that time to conservation of the virus in a frozen state.
We report here the isolation of swine influenza A viruses with haemagglutinin and
nucleoprotein genes which are virtually identical to those of the human virus that
circulated in 1975. We have also found serological evidence that this virus is circulating
extensively in Quebec swine herds. We propose that human-like H3N2 influenza A strains
may remain invariant for long periods in swine, which may serve as a reservoir for
human pandemics

by some strange coincidence, that Ange-Gardien (Canada) virus is also
close to Colorado/77 ...
by another strange coincidence the Guangdong Swine are preserved in segments
1,2,3,4,5,6,8 and almost identical to Colorado/77, but in segment 7 they are
almost identical to A/Sw/Tennessee/25(H1N1) which is the preserved
virus found in the Canadian recombination swine
By another strange coincidence 1976,1977 were the years, when USA was panicking
about swine flu and creating and experimenting with swine flu vaccines
and sequencing lots of swine.


http://www.springerlink.com/content/vl1l482033020316/fulltext.html
http://download.thelancet.com/flatcontentassets/H1N1-flu/virology/virology-7.pdf
 
Re: evolutionary stasis

Code: 
                                                                                                                                                 00000000000000000000000000001111111111111111111111111111111 
                                                                                                                                                 00000001123333445567777778990001111112233344455578888888888 
                                                                                                                                                 23667790852234120370136799261361445551713315858972222233333 
                                                                                                                                                 90361827211710400243227531396472483464675700733774678912345 
-codon-position----------------------------------------------------------------------------------------------------------------------------------2   2 2222  11  21211 211 2 22221212121  2 122211 2 1212 12 
---Index-----------------------------------------------------------------------------------------------------------------------------------------CCCTTCGGTTTTTGTTCTCAGGGCGATACTGGAACTGAATGATCTAAGATGAGTTATTA 
   2 >CY009300,A/swine/Colorado/1/1977,1977//,H3N2,USA,2NA,Swine,4,.43A.,.433_72.,02-MAR-2006,on behalf of TIGR/St. Jude Children's              ...........................................................        0      0 ,      0      0       2:>CY009300,A/swine/Colorado/1/1977,1977//,H3N2,USA,2NA,Swine,4,.43A.,.433_72.,02-MAR-2006,on behalf of TIGR/St. Jude Children's              
   3 >M73774,A/swine/Colorado/1/1977,1977//,H3N2,USA,2NA,Swine,4,.43A.,.433_72.,,                                                                ....C...................TG.............C...G...............        5      5 ,      5      5       3:>M73774,A/swine/Colorado/1/1977,1977//,H3N2,USA,2NA,Swine,4,.43A.,.433_72.,,                                                                
   6 >GQ422437,A/swine/Guangdong/102/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          ................A...........T..............................        2      2 ,      2      2       6:>GQ422437,A/swine/Guangdong/102/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          
  17 >EF569597,A/swine/Guangdong/SGD6,//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,21-APR-2007,College of Veterinary Medicineœ South China           --............GC..............................G.....-------       12     12 ,      3      3      17:>EF569597,A/swine/Guangdong/SGD6,//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,21-APR-2007,College of Veterinary Medicineœ South China           

   8 >GQ422432,A/swine/Guangdong/107/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          .............A......T......................................        2      2 ,      2      2       8:>GQ422432,A/swine/Guangdong/107/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          
   9 >GQ422433,A/swine/Guangdong/110/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          .............A......T......................................        2      2 ,      2      2       9:>GQ422433,A/swine/Guangdong/110/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          
  11 >GQ422434,A/swine/Guangdong/113/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          .............A......C......................................        2      2 ,      2      2      11:>GQ422434,A/swine/Guangdong/113/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          

  14 >GU086137,A/swine/Guangdong/423/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           .............A......T.....C...........G.....G..............        5      5 ,      5      5      14:>GU086137,A/swine/Guangdong/423/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           
  15 >GU086145,A/swine/Guangdong/811/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           ............CA......T......................................        3      3 ,      3      3      15:>GU086145,A/swine/Guangdong/811/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           
  12 >GU086121,A/swine/Guangdong/211/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           ..........CC........T......................................        3      3 ,      3      3      12:>GU086121,A/swine/Guangdong/211/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           
  16 >GU086153,A/swine/Guangdong/968/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           ..AC.TA..A..........T......................................        6      6 ,      6      6      16:>GU086153,A/swine/Guangdong/968/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           

   1 >U07146,A/swine/Ange-Gardien/150/1990,1990//,H3N2,Canada,2NA,Swine,4,.43A.,.433_72.,,                                                       .....................A.........A..TC...........C...........        5      5 ,      5      5       1:>U07146,A/swine/Ange-Gardien/150/1990,1990//,H3N2,Canada,2NA,Swine,4,.43A.,.433_72.,,                                                       
   5 >FJ830855,A/swine/Guangdong/01/1998,1998//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-MAR-2009,Department of Life Scienceœ Sun Yet-san        ............C........A.....G....G....G...........C.........        6      6 ,      6      6       5:>FJ830855,A/swine/Guangdong/01/1998,1998//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-MAR-2009,Department of Life Scienceœ Sun Yet-san        
  19 >DQ021911,A/swine/Heilongjiang/74/2000,2000//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-APR-2005,National Key Laboratory of Biotechnologyœ   --...............C...A.T.....................G....AG-------       15     15 ,      6      6      19:>DQ021911,A/swine/Heilongjiang/74/2000,2000//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-APR-2005,National Key Laboratory of Biotechnologyœ   
  10 >GQ422436,A/swine/Guangdong/111/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          .....................A.....................................        1      1 ,      1      1      10:>GQ422436,A/swine/Guangdong/111/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          
   7 >GQ422435,A/swine/Guangdong/106/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          ..................A..A.....................................        2      2 ,      2      2       7:>GQ422435,A/swine/Guangdong/106/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          
  13 >GU086129,A/swine/Guangdong/223/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           ..................AG.A...................G.................        4      4 ,      4      4      13:>GU086129,A/swine/Guangdong/223/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           
  18 >EU273774,A/swine/Heilongjiang/1/05,2005//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,11-NOV-2007,National Key Laboratory of Veterinary          --......G............A...........G..A...........G...-------       14     14 ,      5      5      18:>EU273774,A/swine/Heilongjiang/1/05,2005//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,11-NOV-2007,National Key Laboratory of Veterinary          
   4 >JN105973,A/swine/Fujian/F2/2007,2007/10/05,H3N2,China,:ES,Swine,4,.43A.,.433_72.,08-JUN-2011,Fujian Academy of Agriculture Sciencesœ       TT...................A............................AGAGATAAT       12     12 ,     12     12       4:>JN105973,A/swine/Fujian/F2/2007,2007/10/05,H3N2,China,:ES,Swine,4,.43A.,.433_72.,08-JUN-2011,Fujian Academy of Agriculture Sciencesœ       
  20 >JX138525,A/swine/Hunan/3/2008,2008/07/,H3N2,China,:ES,Swine,4,.43A.,.433_72.,07-JUN-2012,Dabeinong Research Center for Veterinary          .......A.............AA...................C................        4      4 ,      4      4      20:>JX138525,A/swine/Hunan/3/2008,2008/07/,H3N2,China,:ES,Swine,4,.43A.,.433_72.,07-JUN-2012,Dabeinong Research Center for Veterinary          
  21 >A/swine/HuNan/01/2008(H3N2)                                                                                                                --.....A.............A.......CA.........A...........-------       14     14 ,      5      5      21:>A/swine/HuNan/01/2008(H3N2)                                                                                                                
                                                                                                                                                                                                             
---Index-----------------------------------------------------------------------------------------------------------------------------------------CCCTTCGGTTTTTGTTCTCAGGGCGATACTGGAACTGAATGATCTAAGATGAGTTATTA 
-codon-position----------------------------------------------------------------------------------------------------------------------------------2   2 2222  11  21211 211 2 22221212121  2 122211 2 1212 12 
                                                                                                                                                 00000000000000000000000000001111111111111111111111111111111 
                                                                                                                                                 00000001123333445567777778990001111112233344455578888888888 
                                                                                                                                                 23667790852234120370136799261361445551713315858972222233333 
                                                                                                                                                 90361827211710400243227531396472483464675700733774678912345


with natural evolution we would see ~5 mutations per year in HA

so, maybe these were grown in labs ?


all 8 segments:

Code: 
                                                         0000000111111111111111111111222222 0000000000000000000000001111111111111111111111111111222 0000000000000001111111111111111111122 0000000000000000000000000000111111111111111111 00000000000000000111 00000000000001111111111111 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 0000000000000 
                                                         1344558001112455556666788999011222 0000000122233333345558991112234444566666777778889999011 0001245667888990011122222444555677901 0000001222224455666667888999000000112223344667 00112223335578899023 00344556668990011222233333 0000001111112222222223333333444444444444444444455555555555666666666677777777778888888888888999999999 0012222444667 
                                                         3602550781128825670567479278389667 0113345155526777950034040580341347613579237883881457608 0380389172169021415500115447188439824 3344674177893669024577049149223339591182637590 68781156991936733936 02877154795030369444605556 1467990012882466677890113448001222334456778889914445566799122255667756667778894444445566799124555677 0152356159696 
                                                         7556084108985775970289388399473457 5895685434542589040448187754012227074613070453164804208 5012997010524516272369041069814594027 3618241039321376558642474250261241342477404180 01860955129448002914 68412992965987836178183580 2292392513092314703810280381294039582458780393990132514014815724362850461580131247894703925935235626 7236841719910 
-codon-position------------------------------------------22  1    2  12 1 212 2  2 2    2   2 12  1 12  2  1 12  21  2 1  2121  2  11  2   2 1  1 1 2   2  12 21 2 211 1  12       12   2   2 22    1121 221 221 1    2 2 221  2 12211 2   1    212  21  2112  1  1 1 1   22 2222 1  221                          1   1      1 2  1   11  1          1 1     2121 11 1112112 2222 1112 121  1 1  112  11 11 
---Index-------------------------------------------------GCCCATATCCAGATGAGGTATTGATGAACAGGGT ATTTTTACACATATTCCTTAACAAAGTTCTAAAAAAAATGTGGGGGTAAGTCATT ATTAATAACCATATGAAATAATTGGCAGGTTCACGCG CTTCGGTTTTTGCTCAGGGCGATACTGGAACTGAATGATCTAGATG GAAACGAAGCTAGGCTATGA TAGCCGACGTTAAATCAGGCTATCAG ACACCTAGATGAGATGTATATCGGTAACGGGTACCGTTACCAGTGAGATCGTAGTGGGTTGCGCTTCTACTTTTGGTCCTTATCGCGCCATAGCCATGAG TCTGACGCACGCA 
   1 >A/swine/Colorado/1/1977,1977//,USA,H3N2            .................................. ....................................................... ..................................... .............................................. .................... .......................... .................................................................................................... .............        0      0 ,      0      0       1:>A/swine/Colorado/1/1977,1977//,USA,H3N2            
   2 >A/swine/Colorado/1/1977,1977//,USA,H3N2            .TT.CC.....A..A.AA..C..........AA. ...AG...CAG.G..AT..G..............CT.C.C.AC.AAC.G....C. .C...C..TT........C......TTAAC.T....A ..C.................TG.............C...G...... ...TT.G.CG...A.C.... .C...A...C................ .................................................................................................... .........T...       59     59 ,     59     59       2:>A/swine/Colorado/1/1977,1977//,USA,H3N2            
   3 >A/swine/Guangdong/01/1998,1998//,China,H3N2        .......G.......................... .....................T................................. .........T.........G.C............... ..........C......A.....G....G....G..........C. ..........C...A..... .......T...G....G......... .................................................................................................... .........TA..       18     18 ,     18     18       3:>A/swine/Guangdong/01/1998,1998//,China,H3N2        
   4 >A/swine/HuNan/01/2008,2008/03/10,China,H3N2        ......................A........... .......T...........................................A... ........................A............ .....A...........A.......CA.........A......... -------------------- ..A....................... ............................................................A..............A....C................... .T...A.......       35     35 ,     15     15       4:>A/swine/HuNan/01/2008,2008/03/10,China,H3N2        
   5 >A/swine/Hunan/3/2008,2008/07/,China,H3N2           T..T....T...............CAG....... ..C....T......C...C.G...T......TG.................CA..C ...G..C.......A........T..........AT. .....A...........AA...................C....... .............A...... .............G............ ............................................................A..............A....C................... ....C.A......       34     34 ,     34     34       5:>A/swine/Hunan/3/2008,2008/07/,China,H3N2           
   6 >A/swine/Heilongjiang/1/05,2005//,China,H3N2        ............GC...................A ...........C..........G.......G.......C........C....G.. ...........CG.................C..T... ......G..........A...........G..A..........G.. -------------------- ................G......... ......................................................................................A............. ..C....TG..T.       44     44 ,     24     24       6:>A/swine/Heilongjiang/1/05,2005//,China,H3N2        
   7 >A/swine/Ange-Gardien/150/1990,1990//,Canada,H3N2   ---------------------------------- ------------------------------------------------------- ------------------------------------- .................A.........A..TC..........C... -------------------- -------------------------- ---------------------------------------------------------------------------------------------------- -------------      290    290 ,      5      5       7:>A/swine/Ange-Gardien/150/1990,1990//,Canada,H3N2   
   8 >A/swine/Guangdong/102/2002,2002//,China,H3N2       .................................. ....................................................... ..................................... ............A...........T..................... .............A...... .......................... GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.C.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA .............       93     93 ,     93     93       8:>A/swine/Guangdong/102/2002,2002//,China,H3N2       
   9 >A/swine/Guangdong/106/2002,2002//,China,H3N2       .................................. ....................................................... ..................................... ..............A..A............................ .............A...... .......................... GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.C.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA .............       93     93 ,     93     93       9:>A/swine/Guangdong/106/2002,2002//,China,H3N2       
  10 >A/swine/Guangdong/107/2002,2002//,China,H3N2       .........TT.................Y..... ....................................................... ..................................... ...........A....T............................. .............A...... C..TT.........C......G.... GTGATAGACGAGRGCTCGCGC.AACGGTAACAGATAYC.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA .............      103    103 ,    103    103      10:>A/swine/Guangdong/107/2002,2002//,China,H3N2       
  11 >A/swine/Guangdong/110/2002,2002//,China,H3N2       .................................. ....................................................... ..................................... ...........A....T............................. .............A...... ........A................. GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.C.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA .............       94     94 ,     94     94      11:>A/swine/Guangdong/110/2002,2002//,China,H3N2       
  12 >A/swine/Guangdong/111/2002,2002//,China,H3N2       .................................. ....................................................... ..C.G..G.....Y....................... .................A............................ .............A...... .......................... GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.C.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA .............       96     96 ,     96     96      12:>A/swine/Guangdong/111/2002,2002//,China,H3N2       
  13 >A/swine/Guangdong/113/2002,2002//,China,H3N2       ...............G.................. ....................................................... G.................................... ...........A....C............................. .............A....A. C......................... GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.C.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA ............R       98     98 ,     98     98      13:>A/swine/Guangdong/113/2002,2002//,China,H3N2       
  14 >A/swine/Fujian/F2/2007,2007/10/05,China,H3N2       .................................. ....................................................... ..C.G..G.....Y....................... .................A...........................A .............A....A. --.............T.TAGC.AACA GTGATAGACGAG.GCTCGCGCTAACGGTAACAGATA.C.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA .............      110    110 ,    108    108      14:>A/swine/Fujian/F2/2007,2007/10/05,China,H3N2       
  15 >A/swine/Guangdong/211/2006,2006//,China,H3N2       ------------------.............--- ------------------------............G.......A---------- ----------T.........GAG.------------- ........CC......T............................. .G...A.....GAA...... .......................... GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.CGTTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTGCACA .............      184    184 ,    106    106      15:>A/swine/Guangdong/211/2006,2006//,China,H3N2       
  16 >A/swine/Guangdong/223/2006,2006//,China,H3N2       ------------------C..C.........--- .C....T......C...C...............................A..... ..................................... ..............AG.A...................G........ .............A...... .......................... GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.C.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA .............      123    123 ,    102    102      16:>A/swine/Guangdong/223/2006,2006//,China,H3N2       
  17 >A/swine/Guangdong/423/2006,2006//,China,H3N2       ......G........................... G....C.................G.........G..................... ................C...............G.... ...........A....T.....C...........G.....G..... A............A...C.. ......G...C.G............. GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.C.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA ...A.........      109    109 ,    109    109      17:>A/swine/Guangdong/423/2006,2006//,China,H3N2       
  18 >A/swine/Guangdong/811/2006,2006//,China,H3N2       ------------------.T.........T.--- ------------------------..C.........G...C...A---------- ----------.....G.G......------------- ..........CA....T............................. .............A..G... -------------------------- GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.C.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA .............      207    207 ,    103    103      18:>A/swine/Guangdong/811/2006,2006//,China,H3N2       
  19 >A/swine/Guangdong/968/2006,2006//,China,H3N2       ------------------.....G...G..A--- ------------------------.A.ATC.............A.---------- ------------------------------------- AC.TA..A........T............................. ..G....G.....A.....G .......................... GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.C.TTCACAGACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.TTGGGATTG.ACA C............      203    203 ,    111    111      19:>A/swine/Guangdong/968/2006,2006//,China,H3N2       
  20 >A/swine/Heilongjiang/74/2000,2000//,China,H3N2     ---------------------------------- ------------------------------------------------------- ------------------------------------- .............C...A.T.....................G...A -------------------- -------------------------- ---------------------------------------------------------------------------------------------------- -------------      290    290 ,      5      5      20:>A/swine/Heilongjiang/74/2000,2000//,China,H3N2     
  21 >A/swine/Tennessee/25/77,1977//,USA,H1N1            ---------------------------------- ------------------------------------------------------- ------------------------------------- ---------------------------------------------- -------------------- -------------------------- GTGATAGACGAG.GCTCGCGC.AACGGTAACAGATA.C.TTCACA.ACATAAGACAAACC.TAAACTCGTCCCCA.CTTCCTCGAT.T.GGGATTG.ACA -------------      321    321 ,     90     90      21:>A/swine/Tennessee/25/77,1977//,USA,H1N1            
                                                                                                                                                                                                                                                                                                                                                                                                            
---Index-------------------------------------------------GCCCATATCCAGATGAGGTATTGATGAACAGGGT ATTTTTACACATATTCCTTAACAAAGTTCTAAAAAAAATGTGGGGGTAAGTCATT ATTAATAACCATATGAAATAATTGGCAGGTTCACGCG CTTCGGTTTTTGCTCAGGGCGATACTGGAACTGAATGATCTAGATG GAAACGAAGCTAGGCTATGA TAGCCGACGTTAAATCAGGCTATCAG ACACCTAGATGAGATGTATATCGGTAACGGGTACCGTTACCAGTGAGATCGTAGTGGGTTGCGCTTCTACTTTTGGTCCTTATCGCGCCATAGCCATGAG TCTGACGCACGCA 
-codon-position------------------------------------------22  1    2  12 1 212 2  2 2    2   2 12  1 12  2  1 12  21  2 1  2121  2  11  2   2 1  1 1 2   2  12 21 2 211 1  12       12   2   2 22    1121 221 221 1    2 2 221  2 12211 2   1    212  21  2112  1  1 1 1   22 2222 1  221                          1   1      1 2  1   11  1          1 1     2121 11 1112112 2222 1112 121  1 1  112  11 11 
                                                         0000000111111111111111111111222222 0000000000000000000000001111111111111111111111111111222 0000000000000001111111111111111111122 0000000000000000000000000000111111111111111111 00000000000000000111 00000000000001111111111111 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 0000000000000 
                                                         1344558001112455556666788999011222 0000000122233333345558991112234444566666777778889999011 0001245667888990011122222444555677901 0000001222224455666667888999000000112223344667 00112223335578899023 00344556668990011222233333 0000001111112222222223333333444444444444444444455555555555666666666677777777778888888888888999999999 0012222444667 
                                                         3602550781128825670567479278389667 0113345155526777950034040580341347613579237883881457608 0380389172169021415500115447188439824 3344674177893669024577049149223339591182637590 68781156991936733936 02877154795030369444605556 1467990012882466677890113448001222334456778889914445566799122255667756667778894444445566799124555677 0152356159696 
                                                         7556084108985775970289388399473457 5895685434542589040448187754012227074613070453164804208 5012997010524516272369041069814594027 3618241039321376558642474250261241342477404180 01860955129448002914 68412992965987836178183580 2292392513092314703810280381294039582458780393990132514014815724362850461580131247894703925935235626 7236841719910


http://www.ncbi.nlm.nih.gov/pubmed/21318308
 
Re: evolutionary stasis

http://www.ncbi.nlm.nih.gov/pubmed/25075739
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103053


> Interestingly the IAV, with the H6N9 subtype, was re-detected a year later in a genetically
> unchanged form in the close proximity of the original sampling locality. The almost absolute
> nucleotide sequence identity of all the respective genomic segments between the two H6N9
> viruses indicates frozen evolution as a result of prolonged conservation in the environment.

(I have doubts, so often was this claimed before and turned out to be erraneous)

KC599271-73 A/mallard/Czech Republic/15902-3K/2009(N9)
KC599274-76 A/mallard/Czech Republic/15902-4K/2009(H6)
KC599277-80 A/mallard/Czech Republic/15902-9K/2009
KC599281-87 A/mallard/Czech Republic/15902-12K/2009(H11N2)
KC599288-94 A/mallard/Czech Republic/15902-14K/2009(H6N2)
HQ244427-34 A/mallard/Czech Republic/15902-17K/2009(H6N2)
JF682618-25 A/mallard/Czech Republic/15902-18K/2009(H11N9)
KC599295-302 A/mallard/Czech Republic/15902-18K/2009(H6N9)
KC599309-16 A/mallard/Czech Republic/15902-23K/2009(H6N2)
KC599317-24 A/mallard/Czech Republic/15902-25K/2009(H11N9)
KC599303-08 A/mallard/Czech Republic/15902-18T/2009(H6)
JQ737234-41 A/mallard/Czech Republic/15962-1T/2010(H6N9)
KC599325-32 A/mallard/Czech Republic/15962-4T/2010(H6N9)

http://www.ncbi.nlm.nih.gov/nuccore/KC599309
 
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