swine with some but not all segments from pH1N1

[gsgs]

.
.

308 >A/******/index/2009-02-01

ommmmmmm
325:501,  0,  0,  4,  2,  2,  3,  2   A/Sw/QLD/09-02865-07/2009(H1N1/08/24

mmmmmomm
226:  3,  3,  6, 16,  0,462,  0,  3   A/Sw/Korea/4940/2010(H1N2/04/
328:  4,  2,  2,  5,  6,479,  6,  7   A/Sw/Italy/116114/2010(H1N2/06/01
340:  2,  3,  1,  4,  4, 99,  6,  3   A/Sw/Thailand/CU-SA412/2010(H1N1/04/
341:  2,  1,  4, 12,  6, 99,  6,  6   A/Sw/Thailand/CU-SA433/2010(H1N1/06/
342:  2,  2,  0,  4,  4,101,  3,  3   A/Sw/Thailand/CU-SA43/2010(H1N1/02/
343:  2,  3,  3,  4,  5,100,  5,  3   A/Sw/Thailand/CU-SA432/2010(H1N1/04/

mmmomomm
  6:  4,  3,  8,471,  4,468,  6,  5   A/Sw/Quebec/1265553/2010(H3N2/12/22
158:  3,  1,  4,248,  6,482,  3,  2   A/Sw/Argentina/CIP051-StaFeN2/2010(H1N2/05/
159:  4,  1,  1,236,  3,485,  7,  4   A/Sw/England/1382/2010(H1N2/04/13
227:  1,  0,  3,138,  0,469,  0,  3   A/Sw/Korea/4382/2009(H1N2/11/
306:  3,  1,  2,239,  3,220,  4,  1   A/Sw/Argentina/CIP051-BsAs76/2009(H1N1/10/

momomomm
128:  5, 58,  3,241,  4,466,  3,  4   A/Sw/Minnesota/239106/2010(H1N2/05/05

mmmooomm
224:  2,  3,  2, 99, 50,474,  3,  3   A/Sw/Indiana/240218/2010(H1N2/02/21
225:  3,  0,  3, 12, 52,472,  0,  3   A/Sw/Korea/4941/2010(H1N2/04/

oomomomm
 76: 69, 38, 11, 69, 19,201,  3,  4   A/Sw/Minnesota/226128/2010(H1N1/09/08

ommooomo
157: 58,  3,  1,239, 50,474,  3, 51   A/Sw/North Carolina/239108/2010(H1N2/04/21

oomomomo
  8: 57, 63,  1,469,  2,474,  3, 54   A/Sw/Minnesota/239105/2009(H3N2/11/24

oooomomm
233: 55, 60, 96,244,  8,473,  4,  7   A/Sw/North Carolina/226125/2010(H1N2/09/08
234: 55, 59, 65,244,  8,474,  4,  7   A/Sw/North Carolina/226126/2010(H1N2/09/08
235: 55, 60, 65,244,  8,474,  4,  7   A/Sw/North Carolina/226124/2010(H1N2/09/08

oooomoom
228: 68, 58, 62,109,  4,462,100,  3   A/Sw/Korea/4456/2009(H1N2/11/

oooooomm
230: 68, 58, 62,109, 52,462,  0,  3   A/Sw/Korea/5008/2010(H1N2/05/

ooooomoo
168: 53, 55, 56,258, 48,  2,127, 63   A/Sw/Hong Kong/201/2010(H1N1/01/07

ooooooom
231: 68, 58, 62,109, 52,462,100,  3   A/Sw/Korea/4383/2009(H1N2/11/
232: 68, 54, 62,134, 73,462,118,  3   A/Sw/Korea/4779/2010(H1N2/03/

omoooooo
216: 66,  3, 68,134, 73,469,100, 70   A/Sw/Korea/4381/2009(H1N2/11/

???o?om?
  9:---,---,---,469,---,473,  6,---   A/Sw/Iowa/A0109034/2010(H3N2/11/16
 10:---,---,---,469,---,473,  6,---   A/Sw/Iowa/A0109035/2010(H3N2/11/16
 74:---,---,---, 68,---,205,  5,---   A/Sw/South Dakota/7/2011(H1N1/02/28
 75:---,---,---, 65,---,201,  5,---   A/Sw/Minnesota/A0109101/2010(H1N1/11/17
129:---,---,---,240,---,469,  5,---   A/Sw/South Dakota/2/2010(H1N2/11/23
130:---,---,---,242,---,469,  5,---   A/Sw/Iowa/A0109071/2010(H1N2/11/16
132:---,---,---,242,---,471,  3,---   A/Sw/South Dakota/4/2010(H1N2/12/28
134:---,---,---,240,---,469,  5,---   A/Sw/South Dakota/3/2010(H1N2/11/23
135:---,---,---,247,---,467,  5,---   A/Sw/South Dakota/5/2011(H1N2/02/25
136:---,---,---,243,---,466,  3,---   A/Sw/South Dakota/6/2011(H1N2/02/25

???o??mm
  5:---,---,---,465,---,---,  7,  5   A/Sw/Quebec/1259260/2010(H3N2/12/20

mmmomo?m
131:  5,  7,  5,242, 14,469,---,  9   A/Sw/Minnesota/A01047604/2010(H1N2/12/07

???o?mm?
315:---,---,---, 73,---,  2,  3,---   A/Sw/Iowa/44837-1/2009(H1N1/11/08
.
.

 

[gsgs]

Re: swine with some but not all segments from pH1N1

Transmission of the (avian) H1N1 virus was achieved through a chain of six pairs of naïve piglets and through four pairs of vaccinated animals. Transmission occurred with minimal clinical signs and, in vaccinates, at antibody levels higher than previously reported to protect against infection.

http://www.ncbi.nlm.nih.gov/pubmed/21668691




two novel swine influenza viruses (SIVs) in pigs in Argentina.
two independent reassortment events between H1N1pdm and human-like SIVs

http://www.ncbi.nlm.nih.gov/pubmed/21668680



Isolation of novel triple-reassortant swine H3N2 influenza viruses possessing the hemagglutinin
and neuraminidase genes of a seasonal influenza virus in Vietnam in 2010.


--------------------------
swchi3 m=63,10.6.2011 China
swgea3 , m=47 , 1.6.2011
sweu5 , m=564 , 1.6.2011 Europe
swjia1 , m=34 , 1.6.2011 Jiangsu etc.
sweue , m=14 , 29.5.2011 Europe
swh1b , 1084 HAs , 25.5.2011
swab1011 , m=66 , 25.5.2011
swus4 , m=36 , 25.5.2011 USA
swgef , m=532 , 23.4.2011 all
swjp3 , m=56 , 20.5.2011 Japan
swam3 , m=81 , 14.5.2011 , America
swh1n2b , m=456 , 3.5.2011
swav21 , m=151 , 3.5.2011 , characteristic avian and swine (and human) genomes
swtha4 , m=64 , 20.4.2011 , Thailand
swtha3 , m=241 , 19.4.2011
swv21 , m=150 , 10.4.2011 , swine,birds
swgee , m=488 , 14.4.2011 , big swine genome
sw00hk , m=233 , 13.4.2011 , Hong Kong HA only
sw77us , m=12 , 13.4.2011 , 1977 USA HA only
swea3 , m=125 , 13.4.2011 , early swine
swh1c , m=374 , 13.4.2011 , HA only
sw10b , m=168 , 6.4.2011
sw11b , m=45 , 6.4.2011 ,
swif2 , m=149 , 31.3.2011 , segment 2
swav4 , m=127 , 27.1.2011 , segment 1?

 

[gsgs]

Re: swine with some but not all segments from pH1N1

USA swine H1
normalized to
A/Sw/Iowa/24297/1991(H1N1)
(classical swine bottleneck in 1991)

http://magictour.free.fr/panflu/ussw3.GIF

the dark area in the lower part is (human) H1N2

http://magictour.free.fr/panflu/ussw1b2.GIF

 

[gsgs]

Re: swine with some but not all segments from pH1N1

http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002077
This study utilizes an expansive data set of hemagglutinin (HA1) sequences (n = 1516) from
swine influenza viruses collected in North America during the period 2003-2010
two separate human-to-swine transmission events around 2003
the Midwest serves primarily as an ecological sink for swine influenza in the US

41 : ******
327 : human H1, two clusters 138+187=327

human-->swine in October 2002–March 2003

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

http://www.ncbi.nlm.nih.gov/pubmed/21697484
Characterization of H1N1 swine influenza viruses circulating in Canadian pigs in 2009
Canadian pigs from May 2009 were comprised of HA and NA genes of classical SIV
origin in combination with the North American triple reassortant internal gene (TRIG)
cassette hereby termed contemporary SIV (conSIV) H1N1. These conSIV H1N1
viruses were contiguous with the North American αH1 cluster which was distinct
from the pH1N1 isolates which were antigenically more related to the γH1 cluster.

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

http://www.ncbi.nlm.nih.gov/pubmed/21680507
Reassortment between seasonal H1N1 and pandemic (H1N1) 2009 influenza viruses is restricted
by limited compatibility among polymerase subunits.
Octaviani CP, Goto H, Kawaoka Y.
J Virol. 2011 Jun 15. [Epub ahead of print]

Here, using reverse genetics and a replicon assay, we demonstrated that a mixed polymerase complex containing a pandemic (H1N1) 2009 influenza virus PB2 on a seasonal H1N1 virus background has reduced polymerase activity, leading to impaired virus viability. Adaptation of viruses containing the mixed polymerase complex resulted in compensatory mutations in PB1. Taken together, our results identify the cooperation between PB2 and PB1 as an important restricting factor for reassortment of influenza viruses.

------------------------------------------------------------
http://www.ncbi.nlm.nih.gov/pubmed/21668680
Evidence of reassortment of pandemic H1N1 influenza virus in swine in Argentina: are we facing
the expansion of potential epicenters of influenza emergence?
2 independent reassortment events between the H1N1 pandemic influenza virus (H1N1pdm)
and human-like SIVs
--------------------------------------------------------------
http://www.ncbi.nlm.nih.gov/pubmed/21651738
Analysis of influenza A viruses of subtype H1 from wild birds, turkeys and pigs in Germany reveals interspecies transmission events.
The recovery of a swine influenza H1N1 virus from a turkey flock in Germany in 2009
viruses from distinct H1 subgroups co-circulate among domestic animals and wild birds.
avian-like porcine H1N1 influenza viruses circulating in Europe since the late 1970s
-------------------------------------------------------------

 

[gsgs]

Re: swine with some but not all segments from pH1N1

momomomo A/turkey/Ontario/FAV-9/2011/02/24(H3N2)
momomomo A/turkey/Ontario/FAV-10/2011/07/21(H3N2)

(2,4,6,8 from triple reassortant, 2005 Canadian variant)

 

[gsgs]

Re: swine with some but not all segments from pH1N1

http://www.info.gov.hk/gia/general/201202/14/P201202140252.htm

1500 pig-samples tested 2011710/15 - 2012/01/30
1 ******
27 (2*H3N2+25*H1N2) swine+****** segment(s)

 

[gsgs]

Re: swine with some but not all segments from pH1N1

11 swine from Saraburi,Thailand today at genbank
6* HA and NA , 5* full genome

the 6 HA+NA are classical swine (1918) H1 in HA and
European swine (1978) in NA

2 of the genomes are classical swine in HA and euoswine in all other segments

then 1 * ****** in all segments

then 2* euroswine(1978) in segments 1,2,3,7 and human H3N2(~1997)
in segment 4,6 classical swine in segment 5,8

 

[gsgs]

Re: swine with some but not all segments from pH1N1

genotypes (a la flugenome.org) of all swine sequences since 2009

,,,,,,,,2009,1
,,,,,,,81D,2010,1
,,,,,,7A,,2011,2
,,,,,,7A,81D,2009,1
,,,,,,7F,,2011,2
,,,,,61B,7A,,2010,1
,,,,,61B,7A,,2011,1
,,,,,61B,7F,,2010,1
,,,,,61B,7F,,2011,1
,,,,,61F,,,2009,1
,,,,,61F,,,2011,1
,,,,,61F,7F,,2009,1
,,,,,62A,,,2010,1
,,,,,62A,,,2011,1
,,,,,62A,7A,,2011,2
,,,,,62A,7F,,2011,4
,,,,,62C,,,2010,1
,,,,5F,,,,2009,2
,,,,5H,61F,7F,,2009,2

,,,41A,,,,,2009,21
,,,41A,,,,,2010,15
,,,41A,,,,,2011,1
,,,41A,,61B,,,2009,7
,,,41A,,61B,,,2010,1
,,,41A,,61B,7A,,2009,41
,,,41A,,61B,7A,,2010,17
,,,41A,,61B,7A,,2011,15
,,,41A,,61B,7F,,2010,3
,,,41A,,61B,7F,,2011,11
,,,41A,,61B,7F,81D,2010,1

,,,41A,,61F,,,2009,41
,,,41A,,61F,,,2010,1
,,,41A,,61F,7A,,2011,1
,,,41A,,61F,7F,,2009,14
,,,41A,,61F,7F,,2010,37
,,,41A,,61F,7F,,2011,9
,,,41A,,61F,7F,81D,2009,1
,,,41A,5H,61F,7F,,2009,5
,,,41B,,,,,2009,16
,,,41B,,,,,2010,35
,,,41B,,,,,2011,6
,,,41B,,62A,,,2009,6
,,,41B,,62A,,,2011,1
,,,41B,,62A,7A,,2009,4
,,,41B,,62A,7A,,2010,8
,,,41B,,62A,7A,,2011,10
,,,41B,,62A,7F,,2009,2
,,,41B,,62A,7F,,2010,7
,,,41B,,62A,7F,,2011,26
,,,41B,,62F,,,2009,1
,,,41B,,62F,,,2010,1
,,,41B,5H,61A,,,2009,1
,,,41C,,,,,2009,1
,,,41C,,61F,,,2010,1
,,,43A,,,,,2009,3
,,,43A,,,,,2010,7
,,,43A,,,7F,81D,2010,1
,,,43A,,62A,,,2009,1
,,,43A,,62A,7A,,2009,10
,,,43A,,62A,7A,,2010,15
,,,43A,,62A,7A,,2011,9
,,,43A,5H,62A,7A,,2009,1
,2D,3E,41A,5H,61F,7F,81D,2009,1
,2G,,41B,,62A,,,2009,2
,2G,,41B,,62A,,,2010,1

1C,,,41A,,61F,,81D,2009,1
1C,,,41A,,61F,7F,,2010,1
1C,2D,3E,,5F,,,81D,2010,1
1C,2D,3E,,5H,,,81D,2010,1
1C,2D,3E,,5H,,,81D,2011,1
1C,2D,3E,,5H,,7A,81D,2010,1
1C,2D,3E,,5H,,7A,81D,2011,1
1C,2D,3E,,5H,,7A,81D,2012,1
1C,2D,3E,41A,,61F,7F,81D,2010,1
1C,2D,3E,41A,5H,61B,,81D,2010,1
1C,2D,3E,41B,5H,62A,,81D,2010,1
1F,2D,3E,41A,,61F,7F,81D,2010,1



1B ,2B ,3C ,41A,5H ,61B,7A ,81D, ,>A/New Jersey/11/1976(H1N1)
1B ,2B ,3C ,41A,5H ,61B,7A ,81D, ,>A/Sw/Tennessee/25/1977(H1N1)
1B ,2B ,3C ,41A,5H ,61B,7A ,81D, ,>A/Sw/Minnesota/27/1976(H1N1///
1B ,2B ,3C ,41A,5A ,61B,7A ,81D, ,>A/swine/Shanghai/1/2005(H1N1/07//
1B ,2B ,3C ,41A,5H ,61B,7A ,81D, ,>A/Sw/Guangdong/34/2006(H1N1)
1B ,2B ,3C ,41A,5H ,62F,7A ,81D, ,>A/swine/Miyazaki/1/2006(H1N2)


full genomes
-----------------

----------------1.)classical swine -----------------------------
1B,2B,3A,41A,5A,61B,7A,81D, ,>A/Index/early swine
1B,2B,3C,41A,5H,61B,7A,81D, ,>A/swine/Iowa/24297/1991(H1N1)
1B,2B,3A,41A,5A,61B,7A,81D,2009,1
1B,2B,3C,41A,5H,61B,7A,81D,2009,4,1,1

-----------------2.) triple-----------------------------
1C,2D,3E,43A,5H,62A,7A,81D, ,>A/Sw/Index/triple-reassortant/1998(H3N2)
1C,2D,3E,43A,5H,62A,7A,81D, ,>A/swine/Ontario/33853/2005(H3N2)
1C,2D,3E,41A,5H,61F,7F,81D, ,>A/******/index/2009/02/01
1A,2E,3A,43A,5A,62F,7B,81A, ,>1968//,182,CHN,A/Beijing/1/68
1C,2D,3E,41A,5A,61B,7A,81D,2009,2
1C,2D,3E,41A,5A,62A,7A,81D,2009,1,1
1C,2D,3E,41A,5A,62A,7B,81D,2009,2
1C,2D,3E,41A,5A,62A,7B,81F,2009,1
1C,2D,3E,41A,5E,62A,7A,81D,2009,1
1C,2D,3E,41A,5F,61B,7A,81D,2009,1,0,1
1C,2D,3E,41A,5H,61B,7A,81D,2009,8
1C,2D,3E,41A,5H,62A,7A,81D,2009,7,0,1
1C,2D,3E,41A,5H,62A,7B,81D,2010,1
1C,2D,3E,41B,5A,62A,7A,81D,2010,0,1
1C,2D,3E,41B,5H,61A,7A,81D,2009,1
1C,2D,3E,41C,5H,61F,7A,81D,2010,0,1
1C,2D,3E,43A,5A,62A,7A,81D,2009,1,1
1C,2D,3E,43A,5F,62A,7A,81D,2009,1,2
1C,2D,3E,43A,5H,62A,7A,81D,2009,7,13,3

------------------3.) mex--------------
1C,2D,3E,41A,5H,61F,7F,81D, ,>A/******/index/2009/02/01
1C,2D,3E,43A,5H,62A,7A,81D, ,>A/swine/Ontario/33853/2005(H3N2)
1B,2B,3A,41A,5A,61B,7A,81D, ,>A/Index/early swine
1C,2D,3E,41A,5A,61B,7F,81D,2009,1
1C,2D,3E,41A,5A,61F,7F,81D,2009,1,4
1C,2D,3E,41A,5A,62A,7F,81D,2009,1,1
1C,2D,3E,41A,5E,62A,7F,81D,2009,1
1C,2D,3E,41A,5H,61F,7F,81D,2009,66,38,2
1C,2D,3E,41A,5H,62A,7F,81D,2009,3,5
1C,2D,3E,41A,5H,62A,7F,81E,2009,1
1C,2D,3E,41B,5H,61A,7F,81D,2010,0,1
1C,2D,3E,41B,5H,62A,7F,81D,2009,3,4
1C,2D,3E,41B,5H,62C,7F,81D,2010,0,1
1C,2D,3E,41C,5H,61F,7F,81D,2010,0,10
1C,2D,3E,43A,5A,62A,7F,81D,2010,0,1,1
1C,2D,3E,43A,5F,62A,7F,81D,2010,0,1
1C,2D,3E,43A,5H,62A,7F,81D,2009,5,6,14

--------------4.) euroswine--------------
1F,2G,3I,41C,5F,61F,7F,81E, ,>A/swine/Germany/2/1981(H1N1)=1578 
1B,2B,3C,41A,5H,61B,7A,81D, ,>A/swine/Iowa/24297/1991(H1N1)
1A,2E,3A,43A,5A,62F,7B,81A, ,>1968//,182,CHN,A/Beijing/1/68
1F,2E,3I,41A,5F,61F,7F,81E,2009,1
1F,2E,3I,41A,5F,62A,7F,81D,2009,1
1F,2E,3I,41A,5F,62A,7F,81E,2009,1
1F,2E,3I,41C,5F,61F,7F,81D,2009,1,8,1
1F,2E,3I,41C,5F,61F,7F,81E,2009,2
1F,2E,3I,41C,5F,62A,7F,81E,2009,1,1
1F,2G,3I,41A,5F,61F,7F,81D,2009,1,1
1F,2G,3I,41A,5F,62A,7F,81E,2010,0,4
1F,2G,3I,41B,5F,62A,7F,81E,2009,2
1F,2G,3I,41B,5H,62A,7F,81E,2009,1
1F,2G,3I,41C,5F,61F,7F,81D,2009,10,2
1F,2G,3I,41C,5F,61F,7F,81E,2009,20,2,1
1F,2G,3I,41C,5F,62A,7F,81E,2009,1
1F,2G,3I,43A,5H,62A,7F,81D,2009,1
1F,2H,3I,41A,5F,61F,7F,81E,2009,2

 ----------------5.) H6N6---------------------
1K,2G,3E,46A,5F,66C,7F,81D,2009,1  




1A ,2A ,3A ,41B,5A ,61A,7B ,81A, ,>A/Kansas/UR06-0068/2007(H1N1)
1A ,2A ,3A ,41B,5A ,61A,7B ,81A, ,>A/Index/1977(H1N1)
1A ,2A ,3A ,41B,5A ,61A,7B ,81A, ,>A/Denver/1957(H1N1)
1C ,2A ,3A ,41B,5A ,61A,7E ,81D, ,>A/Index/early human
1C ,2B ,3A ,41B,5A ,61C,7E ,81D, ,>A/Brevig Mission/1/1918(H1N1)
1B ,2B ,3A ,41A,5A ,61B,7E ,81D, ,>A/swine/Jamesburg/1942(H1N1)
1A ,2A ,3A ,41B,5A ,61A,7B ,81D, ,>A/Taiwan/01/1986///
1A ,2A ,3A ,41B,5A ,61A,7B ,81A, ,>A/Beijing/262/1995///
1A ,2A ,3A ,41B,5A ,61A,7B ,81D, ,>A/New Caledonia/20/1999///
---,---,---,41B,---,61A,7B ,---, ,>A/Solomon Islands/3/2006/08/21/
---,---,---,41B,---,61A,7B ,---, ,>A/Brisbane/59/2007/07/01/
1C ,2D ,3E ,41A,5H ,61F,7F ,81D, ,>A/******-match/1-2/07(H3N2)
1A ,2A ,3A ,41B,5A ,61A,7E ,81D, ,>A/UK/1/1933(H1N1)
1A ,2A ,3A ,41B,5A ,61A,7B ,81D, ,>A/Puerto Rico/8-1/1934(H1N1)
1A ,2A ,3A ,41B,5A ,61A,7B ,81D, ,>A/Texas/36/1991(H1N1)
1A ,2A ,3A ,41B,5A ,61A,7B ,81A, ,>A/Chile/1/1983(H1N1)
1A ,2A ,3A ,41B,5A ,61A,7B ,81A, ,>A/Brisbane/59/2007/07/01(H1N1)
---,---,---,41A,---,---,---,---, ,>A/swine/New Jersey/11/76(H1N1///
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>1972//,1643,RUS,A/Udorn/307/72
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>1979//,4199,THA,A/Bangkok/01/79
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>1983//,5660,HKG,A/HK/14/83
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>1989//,7852,CHN,A/Beijing/353/89
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>1997/11/29,10924,USA,A/NY/503/97
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>2003/04/23,12897,USA,A/NY/214/03
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>A/Wisconsin/67/2005/08/
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>2007/02/06,14278,AUS,A/Brisbane/10/07
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>Index/Brisbane-like/2007
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>Index/Perth-like/2009
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>Index/2009/Egypt/Iowa
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>Index/USA-2007
1A ,2E ,3A ,43A,5A ,62F,7B ,81A, ,>A/Index/1968(H3N2)
1A ,2E ,3A ,42A,5A ,62C,7B ,81A, ,>A/Index/1957(H2N2)
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>A/Index_Fujian/2002(H3N2)
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>A/Index_Fujian/USA/2003(H3N2)
1A ,2D ,3B ,43A,5A ,62A,7B ,81A, ,>A/Index_Fujian_reass./2003/06(H3N2)

 

[gsgs]

Re: swine with some but not all segments from pH1N1

new swine virus from Thailand at genbank
segments 1,2,3,5,7,8 are ******
segments 4 and 6 are human H3N2
but not similar to anything currently circulating.
They are most similar to human H3N2 viruses from ~1996




HA:

   0    0 1701 2306 >A/swine/Chonburi/NIAH106952-028/2011(H3N2)
   5    1 1701 2305 >A/swine/Chonburi/NIAH106952-026/2011(H3N2)
 577   19  329  768 >D13583,A/Ibaraki/1/1990,1990//,H3N2,Japan,:ES,Human,4,.43A.,.433_89.,07-NOV-1992,Contact:Yoshinobu Okuno Res. Inst. for
 607   60  987  146 >AF180624,A/Caracas/465/96,1996//,H3N2,Venezuela,4SA,Human,4,.43A.,.433_97.,26-AUG-1999,Influenza Branch? Centers for Disease
 641   83 1294  951 >CY117808,A/Malaysia/13990/1997,1997/10/17,mixed?H3,Malaysia,:ES,Human,4,.43A.,.433_97.,21-MAY-2012,on behalf of JCVI/University Malaya/NCBI?
 656   85 1294  877 >CY112565,A/Madrid/G102/1993,1993//,H3N2,Spain,5EU,Human,4,.43A.,.433_89.,03-APR-2012,on behalf of JCVI/Erasmus Medical
 658  112 1701 2302 >1997/11/29,10924,USA,A/NY/503/97
 659   72 1091  105 >AY661197,A/Brisbane/8/96,1996//,H3N2,Australia,8OZ,Human,4,.43A.,.433_97.,21-JUN-2004,Virology? Erasmus Medical Center? Dr.
 669   73 1091  460 >AY661195,A/Geneva/3958/1996,1996//,H3N2,Switzerland,5EU,Human,4,.43A.,.433_97.,21-JUN-2004,Virology? Erasmus Medical Center? Dr.
 669   73 1091 2262 >AY661190,A/Wuhan/359/1995,1995//,H3N2,China,:ES,Human,4,.43A.,.433_97.,21-JUN-2004,Virology? Erasmus Medical Center? Dr.

NA:

   0    0 1410 10297 >A/swine/Chonburi/NIAH106952-026/2011(H3N2)
   0    0 1410 10298 >A/swine/Chonburi/NIAH106952-028/2011(H3N2)
 599   78 1302 10226 >AY377569,A/Wuhan/359/1995,1995//,H3N2,China,:ES,Human,6,.62A.,.623_97.,01-SEP-2003,Department of Microbiology? National Public
 602   85 1410 2201 >EF584346,A/Christchurch/1/1996,1996//,H3N2,New Zealand,8OZ,Human,6,.62A.,.623_97.,21-MAR-2007,Professional Genetics Laboratory? Uppsala
 602   85 1410 6387 >CY009902,A/New York/584/1996,1996/12/31,H3N2,USA,2NA,Human,6,.62A.,.623_97.,15-MAR-2006,on behalf of TIGR/Wadsworth-NYSDOH/NCBI?
 602   85 1410 6388 >CY009702,A/New York/585/1997,1997/01/22,H3N2,USA,2NA,Human,6,.62A.,.623_97.,15-MAR-2006,on behalf of TIGR/Wadsworth-NYSDOH/NCBI?
 602   85 1410 6397 >CY009910,A/New York/593/1996,1996/12/09,H3N2,USA,2NA,Human,6,.62A.,.623_97.,15-MAR-2006,on behalf of TIGR/Wadsworth-NYSDOH/NCBI?
 606   79 1302 5651 >AY377570,A/Nanchang/933/95,1995//,H3N2,China,:ES,Human,6,.62A.,.623_97.,01-SEP-2003,Department of Microbiology? National Public
 609   86 1410  639 >CY114479,A/Brisbane/8/1996,1996//,H3N2,Australia,8OZ,Human,6,.62A.,.623_97.,04-APR-2012,on behalf of JCVI/Erasmus Medical
 617   87 1410  914 >EF584350,A/Canada/318/1996,1996//,H3N2,Canada,2NA,Human,6,.62A.,.623_97.,21-MAR-2007,Professional Genetics Laboratory? Uppsala
 617   87 1410 5649 >CY112791,A/Nanchang/933/1995,1995//,H3N2,China,:ES,Human,6,.62A.,.623_97.,03-APR-2012,on behalf of JCVI/Erasmus Medical
 617   87 1410 6364 >CY009998,A/New York/562/1996,1996/12/13,H3N2,USA,2NA,Human,6,.62A.,.623_97.,27-MAR-2006,on behalf of TIGR/Wadsworth-NYSDOH/NCBI?
 624   88 1410 10227 >CY112823,A/Wuhan/359/1995,1995//,H3N2,China,:ES,Human,6,.62A.,.623_97.,03-APR-2012,on behalf of JCVI/Erasmus Medical
 624   88 1410 5650 >AJ457945,A/Nanchang/933/95,1995//,H3N2,China,:ES,Human,6,.62A.,.623_97.,19-APR-2002,Lin Y.? Virology? National Institute for
 624   88 1410 6359 >CY009646,A/New York/558/1997,1997/01/06,H3N2,USA,2NA,Human,6,.62A.,.623_97.,15-MAR-2006,on behalf of TIGR/Wadsworth-NYSDOH/NCBI?
 624   88 1410 6716 >AF038262,A/Niigata/137/96,1996//,H3N2,Japan,:ES,Human,6,.62A.,.623_97.,12-DEC-1997,Virology I? National Institute for
 631   30  475 7902 >AY060077,A/SW/MN/3128/00,2000//,H1N2,USA,2NA,Swine,6,.62A.,.623*.,25-OCT-2001,Clinical and Population Sciences? College
 631   89 1410 2294 >EF584353,A/Delaware/4/1997,1997//,H3N2,USA,2NA,Human,6,.62A.,.623_97.,21-MAR-2007,Professional Genetics Laboratory? Uppsala
 631   89 1410 4794 >CY118428,A/Malaysia/07831/1995,1995/09/27,H3N2,Malaysia,:ES,Human,6,.62A.,.623_97.,21-MAY-2012,on behalf of JCVI/University Malaya/NCBI?
 631   89 1410 5488 >EF584377,A/Montevideo/318/1996,1996//,H3N2,Uruguay,4SA,Human,6,.62A.,.623_97.,21-MAR-2007,Professional Genetics Laboratory? Uppsala
 634   30  473 8851 >AY052779,A/Swine/Minnesota/1713/2000,2000//,H1N2,USA,2NA,Swine,6,.62A.,.623*.,28-AUG-2001,Veterinary Medicine? University of
 637   83 1302 3332 >AY377568,A/Finland/364/1995,1995//,H3N2,Finland,5EU,Human,6,.62A.,.623_97.,01-SEP-2003,Department of Microbiology? National Public
 638   90 1410 6441 >CY011818,A/New York/652/1996,1996/04/01,H3N2,USA,2NA,Human,6,.62A.,.623_97.,14-FEB-2007,on behalf of TIGR/Wadsworth-NYSDOH/NCBI?
 640   21  328 10203 >CY121044,A/Wisconsin/15/2009,2009//,H3N2,USA,2NA,Human,6,.62A.,.62_P9.,20-JUN-2012,on behalf of JCVI/New York Medical
 645   91 1410  652 >AF533995,A/Buenos Aires/4459/96,1996//,H3N2,Argentina,4SA,Human,6,.62A.,.623_97.,02-AUG-2002,Virology? National Institute of Infectious
 645   91 1410 2291 >EF584352,A/Delaware/1/1997,1997//,H3N2,USA,2NA,Human,6,.62A.,.623_97.,21-MAR-2007,Professional Genetics Laboratory? Uppsala

 

[gsgs]

Re: swine with some but not all segments from pH1N1

http://www.ncbi.nlm.nih.gov/nuccore/AB704807

http://www.ncbi.nlm.nih.gov/pubmed/22906589


so we have a new swine virus circulating in Thailand,
that presumably went from humans to swine in ~1996
and since then circulated in swine undetected.
And now it reassorted (4,6) with ****** .
So segments 1,2,3,5,7,8 of that virus are still unknown.

The genetic distance to viruses from 1996 matches
the distance of current human H3H2 to viruses from 1996

 

[gsgs]

Re: swine with some but not all segments from pH1N1

genetical distance to current (2007-index) human H3 in % :

2007:00.00
2002:02.05
1997:04.64
1989:07.11
1983:08.28
1979:09.23
1972:11.22
1968:12.81

triple reassortant swine,1998:07.81
H3N2v,2010:09.28
swine,Chonburi,2011:09.87
equine H3N8,1963:24.67
equine H3N8,2008:25.32