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First Novel trH3N2 In New York Swine

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Mon Nov 21, 2011 10:14 pm

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

Slide 7 has an HA tree of the 2010 trH3N2 cases showing clear clustering for A/Pennsylvanai/40/2010, A/Wisconsin/12/2010, A/Minnesota/11/2010

http://www.google.com/url?sa=t&rct=j&q= ... Q8C92QA5KQ

The 2011 HA sequences, including the NY swine evolved from these 2010 sequences.

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Mon Nov 21, 2011 10:30 pm

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

niman wrote:

This clustering gave rise to 2011 HA and multiple additional gene segments (PB2, PB1, PA, NP, NS). The 2011 NA is from A/Pennsylvania/14/2010, which is highlighted in slide 8 of NA sequences. The MP is from H1N1pdm09. All eight of these lineages are in the NY swine.

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Tue Nov 22, 2011 6:23 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

niman wrote:

Slide 4 lists the swine "exposure" for the first seven trH3N2 cases (not included is the daughter of the Minnesota cluster index case, A/Minnesota/11/2010):

A/Kansas/13/2009 Visit local animal fair (July)
A/Iowa/16/2009 No reported exposure (Sept)
A/Minnesota/09/2010 Visit live animal market (May)
A/Wisconsin/12/2010 Visit local animal fair (Sept)
A/Pennsylvania/14/2010 No direct exposure (Oct)
A/Pennsylvania/40/2010 Visit local animal fair (Sept)
A/Minnesota/11/2010 Visited live animal market (Nov)

The above list, from the Nancy Cox presentation at the Feb 2011 FDA advisory committee meeting on vaccines summarizes the swine "expsoure", which is a long way from "close contact" used by ProMed to describe the 2011 trH3N2 cases, which using the same criteria as above would read something like this:
A/Indiana/08/2011 No direct exposure (July)
A/Pennsylvania/09/2011 Visit county fair (Aug)
A/Pennsylvania/10/2011 Exhibited market hogs at local animal fair (Aug)
A/Pennsylvania/11/2011 Visit local animal fair (Aug)
A/Maine/06/2011 Visit local animal fair (Oct)
A/Indiana/10/2011 Veterinarian visit local swine (Oct)
A/Maine/07/2011 Local swine exposure (on farm?) (Oct)

Note that only PA/10 (and possibly ME/07) had close contact with swine and in both cases swine were asymptomatic. Since the all swine associated with veterinarian (IN/10) were asymptomatic, the "contact" with swine is unclear (visit were unlikely to be due to ILI in swine).

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Tue Nov 22, 2011 6:47 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

niman wrote:

Slide 4 lists the swine "exposure" for the first seven trH3N2 cases (not included is the daughter of the Minnesota cluster index case, A/Minnesota/11/2010):

A/Kansas/13/2009 Visit local animal fair (July)
A/Iowa/16/2009 No reported exposure (Sept)
A/Minnesota/09/2010 Visit live animal market (May)
A/Wisconsin/12/2010 Visit local animal fair (Sept)
A/Pennsylvania/14/2010 No direct exposure (Oct)
A/Pennsylvania/40/2010 Visit local animal fair (Sept)
A/Minnesota/11/2010 Visited live animal market (Nov)

The above list, from the Nancy Cox presentation at the Feb 2011 FDA advisory committee meeting on vaccines summarizes the swine "expsoure", which is a long way from "close contact" used by ProMed to describe the 2011 trH3N2 cases, which using the same criteria as above would read something like this:
A/Indiana/08/2011 No direct exposure (July)
A/Pennsylvania/09/2011 Visit county fair (Aug)
A/Pennsylvania/10/2011 Exhibited market hogs at local animal fair (Aug)
A/Pennsylvania/11/2011 Visit local animal fair (Aug)
A/Maine/06/2011 Visit local animal fair (Oct)
A/Indiana/10/2011 Veterinarian visit local swine (Oct)
A/Maine/07/2011 Local swine exposure (on farm?) (Oct)

Note that only PA/10 (and possibly ME/07) had close contact with swine and in both cases swine was asymptomatic. Since the all swine associated with veterinarian (IN/10) were asymptomatic, the "contact" with swine is unclear.

The chronological listing of the 2010 cases is curious. Pennsylvania/40/2010 is listed out of order because it was initally characterized as seasonal H3N2 and was not reported unitil Feb 2011 (5 months after infection) and the release of the sequence was six weeks later, on a Sunday. The sequence was remarkable because it was virtually identical to Wisconsin/12/2010, who showed symptoms 6 days after Pennsylvania/40/2010.

The above listing is curious because the WHO pager alert was issued just prior to announcemnt of Minnesota/11/2010 in Nov. Minnesota/11/2010 was the index case for the cluster, that included the daughter with no swine exposure, who's lab confirmation was announced 6 months later.

However, the above list placing PA/40 above MN/11 raises the distinct posiibilty that when the WHO pager alert was issued for WI/12 and PA/14 in Nov, the CDC and WHO were well aware of the fact that PA/40 was trH3N2 (and not seasonal H3N2) and virtually identical to WI/12. Thus, in Nov, 2010 and there were 3 known trH3n2 cases, and not just 2, as indicated in the alert, and the sequence in 2 of 3 were virtually identical.

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Tue Nov 22, 2011 10:29 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

Commentary

http://www.recombinomics.com/News/11221 ... Chron.html

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Tue Nov 22, 2011 2:03 pm

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

Top HA sequences (99% identity). Swine sequence now at GISAID

EPI342603 A/swine/NY/A01104005/2011 (A/H3N2) segment 4 (HA) 3142.3 0.000000e+00 1701/1701 (100%)
EPI339171 A/Maine/06/2011 (A/H3N2) segment 4 (HA) 3136.7 0.000000e+00 1700/1701 (99%)
EPI317003 A/swine/Indiana/A0109091/2010 (A/H3N2) segment 4 (HA) 3131.2 0.000000e+00 1699/1701 (99%)
EPI340984 A/Indiana/10/2011 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI324857 A/swine/North Carolina/A01049436/2011 (A/H3N2) segment 4 (HA) 3120.1 0.000000e+00 1697/1701 (99%)
EPI293965 A/Minnesota/11/2010 (A/H3N2) segment 4 (HA) 3114.6 0.000000e+00 1696/1701 (99%)
EPI338561 A/swine/Indiana/A01049745/2011 (A/H3N2) segment 4 (HA) 3110.9 0.000000e+00 1695/1701 (99%)
EPI338562 A/swine/Indiana/A01049744/2011 (A/H3N2) segment 4 (HA) 3109.0 0.000000e+00 1695/1701 (99%)
EPI291898 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 3109.0 0.000000e+00 1695/1701 (99%)
EPI338421 A/swine/Indiana/A01049653/2011 (A/H3N2) segment 4 (HA) 3103.5 0.000000e+00 1694/1701 (99%)
EPI328900 A/Minnesota/11/2010 X-203A (A/H3N2) segment 4 (HA) 3103.5 0.000000e+00 1694/1701 (99%)
EPI312980 A/Pennsylvania/40/2010 (A/H3N2) segment 4 (HA) 3103.5 0.000000e+00 1694/1701 (99%)
EPI328898 A/Minnesota/11/2010 X-203 (A/H3N2) segment 4 (HA) 3098.0 0.000000e+00 1693/1701 (99%)
EPI333152 A/Indiana/08/2011 (A/H3N2) segment 4 (HA) 3086.9 0.000000e+00 1691/1701 (99%)
EPI335610 A/Pennsylvania/09/2011 (A/H3N2) segment 4 (HA) 3083.2 0.000000e+00 1690/1701 (99%)
EPI291838 A/Minnesota/09/2010 (A/H3N2) segment 4 (HA) 3029.6 0.000000e+00 1664/1676 (99%)
EPI291893 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 2955.8 0.000000e+00 1612/1618 (99%)

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Tue Nov 22, 2011 5:35 pm

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

Commentary

http://www.recombinomics.com/News/11221 ... X_Def.html

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gsgs

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 1:48 am

Joined: Tue Sep 01, 2009 11:54 pm
Posts: 1784
Location: germany

I don't think the NY swine got it from humans.

closest is A/IN/10/2011/10/22 in segments 1,4,7
but A/ME/06/2011/10/10 in 2,3,4,6,7,8
while 5 is better to IN/08 or PA/11

(4,7, match both of the first)

so there are clear signs of reassortment.

Most clear for segments 1 and 6 which are separated this way.

we won't assume it reassorts in humans ...

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

1 has C399T,G1164A,A1281G,G1422A,A1584C,G1920A (NY and IN/10)
(coded-area nucleotides, as compared to ancestor A/Sw/Ontario/33853/2005)

6 has T843C,T1020C,A1142G,T1194A (NY and ME)

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

Code:

                                       0000000000011111111112 00000001112 000001111111111 00000000000000111 0000001111111 00000001111 00000000 0000   
                                       0112234457711224458990 35777891270 347780245556899 11233333345579223 0136990122444 26888990011 01345689 3456   
                                       4141492411267382685250 37039708600 291822500896169 79655779941356162 7107195416588 12234452949 40292067 9114   
                                       2449596707346612741061 33852362611 127843173732528 76417593866930207 2165797054526 07313410824 52428066 0643   
-codon-position------------------------    2                                 22            1    1 22 2    1     2 1  1  1   1  2   2        21  211   
---Index-------------------------------TGGACCACCTAGAGAGCAAGTT GAAGATCCGAC GCCCCAACCCAAAAC CAGTGGCCAACAGCAGC AGACTCCGACAGT CGGGTGATCAT CGAAAAAA GAGC   
   1 >Index                            ...................... ........... ............... ................. ............. ........... ........ ....   
   2 >A/Sw/Ontario/33853/2005+M(Mex)   C...A..TTCG.G......... .......TA.T .T...GGGTT....T T.A.....C.TTA.G.. ...T..A.GA... ........... .AGG.G.. ....   
   3 >A/Sw/MN/02948/2009/05/19         ---------------------- ----------- --------------- T.A.....C.TTA---- ------------- ----------- -------- ----   
   4 >A/Sw/PA/62170-1/2010/10/25       C...A.GTTCG.G.......CC ----------- .TT.TGGT...G... ----------------- GA.....A..GAA ........... -------- ..A.   
   5 >A/Sw/PA/62170-2/2010/10/25       C...A.GTTCG.G.......CC ----------- .TT.TGGT...G... ----------------- GA.....A..GAA ..A..CG.... -------- ..A.   
   6 >A/Sw/PA/62170-3/2010/10/25       C...A.GTTCG.........CC ----------- .TT.TGGT...G... ----------------- GA.....A..G.. ........... -------- ..A.   
   7 >A/Sw/PA/62170-4/2010/10/25       C...A.GTTCG.........CC ----------- .TT.TGGT...G... ----------------- GA.....A..G.. ..A..CG.... -------- ..A.   
   8 >A/Sw/Quebec/1257777/2010/11/08   ---------------------- ----------- --------------- ----------------- ------------- ----------- .AG...-- ----   
   9 >A/Sw/Quebec/1257774/2010/11/09   ---------------------- ----------- --------------- ----------------- ------------- ----------- .AG....- ----   
  10 >A/Sw/IN/A01049091/2010/11/18     ---------------------- ----------- --------------- ..............G.. ------------- T.......... -------- ----   
  11 >A/Sw/NC/A01049436/2011/01/19     ---------------------- ----------- --------------- ................. ------------- T.......... -------- ----   
  12 >A/PA/09/2011/08/20               ..AG.......A.AGAACGA.. A..AG.T..G. ...A..--------- .G...AT..G...A.AA ............. ........... .......G ....   
  13 >A/PA/11/2011/08/25               ..AG.......----------- -------..G. ...A......G.GG. .G.C.AT..G...A--- ..G..T....... .T......A.. .......G .G.T   
  14 >A/PA/10/2011/08/26               ---------------------- ----------- --------------- ------------.A--- ------------- ----------- ...----- .G.T   
  15 >A/PA/10b/2011                    ---------------------- ----------- --------------- ------------.A--- ------------- --......A.. ...----- .G.T   
  16 >A/IN/08_a/2011/07/27             .AA........A.AGAACGA.. A..AGCT..G. ...A......G.GG. .G.C.AT..G.....AA ..G.CT....... .T.A....A.. ......GG .G..   
  17 >A/IN/08_b/2011/07/27             .AA........A.AGAACGA.. A..AGCT..G. ...A......G.GG. .G.C.AT..G.....A- ..G.CT....... .T.A....A.. ......G- .G..   
  18 >A/KA/13/2009/07/27               ---------------------- ----------- --------------- ----------------- ...T..A.GA... ----------- -------- ....   
  19 >A/IN/10/2011/10/22               .....T.....A..GA.C.A.. ...AG.T..G. ..........G..G. ....A..T......G.. ............. ........... AAGGG... ....   
  20 >A/Sw/NY/A01104005/2011/09/13     .....T.....A..GA.C.A.. .GG.G.T.A.. A........TG..G. ....A..T......G.. ..G..T....... ....C..C.GA AAGGG... A...   
  21 >A/ME/06/2011/10/10               C...A.GTTCG.........CC .GG.G.TTA.T A.......T.G..GT ....A..T......G.. .A........... ....C..C.GA AAGGGG.. A...   
                                                                                                                                                      
---Index-------------------------------TGGACCACCTAGAGAGCAAGTT GAAGATCCGAC GCCCCAACCCAAAAC CAGTGGCCAACAGCAGC AGACTCCGACAGT CGGGTGATCAT CGAAAAAA GAGC   
-codon-position------------------------    2                                 22            1    1 22 2    1     2 1  1  1   1  2   2        21  211   
                                       0000000000011111111112 00000001112 000001111111111 00000000000000111 0000001111111 00000001111 00000000 0000   
                                       0112234457711224458990 35777891270 347780245556899 11233333345579223 0136990122444 26888990011 01345689 3456   
                                       4141492411267382685250 37039708600 291822500896169 79655779941356162 7107195416588 12234452949 40292067 9114   
                                       2449596707346612741061 33852362611 127843173732528 76417593866930207 2165797054526 07313410824 52428066 0643   
.
.

.
.

these are the similar sequences from genbank that I found,
difference < 0.13% in some segment
distant (nonmatching) segments are ignored
mutations that occur only once are ignored (--> ancestor Sw/Ont is mostly
"-", this does no harm since it shares none of the recent mutations
in the list)

_________________
no patents on genes, publish the GISAID sequences !

Last edited by gsgs on Fri Dec 02, 2011 2:07 am, edited 1 time in total.

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 2:05 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

gsgs wrote:

Code:

                                       0000000000011111111112 00000001112 000001111111111 00000000000000111 0000001111111 00000001111 00000000 0000 
                                       0112234457711224458990 35777891270 347780245556899 11233333345579223 0136990122444 26888990011 01345689 3456 
                                       4141492411267382685250 37039708600 291822500896169 79655779941356162 7107195416588 12234452949 40292067 9114 
                                       2449596707346612741061 33852362611 127843173732528 76417593866930207 2165797054526 07313410824 52428066 0643 
-codon-position------------------------    2                                 22            1    1 22 2    1     2 1  1  1   1  2   2        21  211 
---Index-------------------------------TGGACCACCTAGAGAGCAAGTT GAAGATCCGAC GCCCCAACCCAAAAC CAGTGGCCAACAGCAGC AGACTCCGACAGT CGGGTGATCAT CGAAAAAA GAGC 
   1 >Index                            ...................... ........... ............... ................. ............. ........... ........ ....        0      0 ,      0      0       1:>Index                            
   2 >A/Sw/Ontario/33853/2005+M(Mex)   C...A..TTCG.G......... .......TA.T .T...GGGTT....T T.A.....C.TTA.G.. ...T..A.GA... ........... .AGG.G.. ....      285     32 ,    285     32       2:>A/Sw/Ontario/33853/2005+M(Mex)   
   3 >A/Sw/MN/02948/2009/05/19         ---------------------- ----------- --------------- T.A.....C.TTA---- ------------- ----------- -------- ----      429     94 ,      6      6       3:>A/Sw/MN/02948/2009/05/19         
   4 >A/Sw/PA/62170-1/2010/10/25       C...A.GTTCG.G.......CC ----------- .TT.TGGT...G... ----------------- GA.....A..GAA ........... -------- ..A.      172     60 ,     25     24       4:>A/Sw/PA/62170-1/2010/10/25       
   5 >A/Sw/PA/62170-2/2010/10/25       C...A.GTTCG.G.......CC ----------- .TT.TGGT...G... ----------------- GA.....A..GAA ..A..CG.... -------- ..A.      179     63 ,     32     27       5:>A/Sw/PA/62170-2/2010/10/25       
   6 >A/Sw/PA/62170-3/2010/10/25       C...A.GTTCG.........CC ----------- .TT.TGGT...G... ----------------- GA.....A..G.. ........... -------- ..A.      170     57 ,     23     21       6:>A/Sw/PA/62170-3/2010/10/25       
   7 >A/Sw/PA/62170-4/2010/10/25       C...A.GTTCG.........CC ----------- .TT.TGGT...G... ----------------- GA.....A..G.. ..A..CG.... -------- ..A.      176     60 ,     29     24       7:>A/Sw/PA/62170-4/2010/10/25       
   8 >A/Sw/Quebec/1257777/2010/11/08   ---------------------- ----------- --------------- ----------------- ------------- ----------- .AG...-- ----      453     97 ,      5      2       8:>A/Sw/Quebec/1257777/2010/11/08   
   9 >A/Sw/Quebec/1257774/2010/11/09   ---------------------- ----------- --------------- ----------------- ------------- ----------- .AG....- ----      445     96 ,      3      2       9:>A/Sw/Quebec/1257774/2010/11/09   
  10 >A/Sw/IN/A01049091/2010/11/18     ---------------------- ----------- --------------- ..............G.. ------------- T.......... -------- ----      320     75 ,      4      2      10:>A/Sw/IN/A01049091/2010/11/18     
  11 >A/Sw/NC/A01049436/2011/01/19     ---------------------- ----------- --------------- ................. ------------- T.......... -------- ----      320     74 ,      4      1      11:>A/Sw/NC/A01049436/2011/01/19     
  12 >A/PA/09/2011/08/20               ..AG.......A.AGAACGA.. A..AG.T..G. ...A..--------- .G...AT..G...A.AA ............. ........... .......G ....       73     33 ,     40     24      12:>A/PA/09/2011/08/20               
  13 >A/PA/11/2011/08/25               ..AG.......----------- -------..G. ...A......G.GG. .G.C.AT..G...A--- ..G..T....... .T......A.. .......G .G.T      120     41 ,     24     20      13:>A/PA/11/2011/08/25               
  14 >A/PA/10/2011/08/26               ---------------------- ----------- --------------- ------------.A--- ------------- ----------- ...----- .G.T      413     95 ,      3      3      14:>A/PA/10/2011/08/26               
  15 >A/PA/10b/2011                    ---------------------- ----------- --------------- ------------.A--- ------------- --......A.. ...----- .G.T      368     87 ,      4      4      15:>A/PA/10b/2011                    
  16 >A/IN/08_a/2011/07/27             .AA........A.AGAACGA.. A..AGCT..G. ...A......G.GG. .G.C.AT..G.....AA ..G.CT....... .T.A....A.. ......GG .G..       38     36 ,     38     36      16:>A/IN/08_a/2011/07/27             
  17 >A/IN/08_b/2011/07/27             .AA........A.AGAACGA.. A..AGCT..G. ...A......G.GG. .G.C.AT..G.....A- ..G.CT....... .T.A....A.. ......G- .G..       49     36 ,     35     34      17:>A/IN/08_b/2011/07/27             
  18 >A/KA/13/2009/07/27               ---------------------- ----------- --------------- ----------------- ...T..A.GA... ----------- -------- ....      380     88 ,     11      4      18:>A/KA/13/2009/07/27               
  19 >A/IN/10/2011/10/22               .....T.....A..GA.C.A.. ...AG.T..G. ..........G..G. ....A..T......G.. ............. ........... AAGGG... ....       45     20 ,     42     20      19:>A/IN/10/2011/10/22               
  20 >A/Sw/NY/A01104005/2011/09/13     .....T.....A..GA.C.A.. .GG.G.T.A.. A........TG..G. ....A..T......G.. ..G..T....... ....C..C.GA AAGGG... A...       38     30 ,     38     30      20:>A/Sw/NY/A01104005/2011/09/13     
  21 >A/ME/06/2011/10/10               C...A.GTTCG.........CC .GG.G.TTA.T A.......T.G..GT ....A..T......G.. .A........... ....C..C.GA AAGGGG.. A...       64     36 ,     61     36      21:>A/ME/06/2011/10/10               
                                                                                                                                                    
---Index-------------------------------TGGACCACCTAGAGAGCAAGTT GAAGATCCGAC GCCCCAACCCAAAAC CAGTGGCCAACAGCAGC AGACTCCGACAGT CGGGTGATCAT CGAAAAAA GAGC 
-codon-position------------------------    2                                 22            1    1 22 2    1     2 1  1  1   1  2   2        21  211 
                                       0000000000011111111112 00000001112 000001111111111 00000000000000111 0000001111111 00000001111 00000000 0000 
                                       0112234457711224458990 35777891270 347780245556899 11233333345579223 0136990122444 26888990011 01345689 3456 
                                       4141492411267382685250 37039708600 291822500896169 79655779941356162 7107195416588 12234452949 40292067 9114 
                                       2449596707346612741061 33852362611 127843173732528 76417593866930207 2165797054526 07313410824 52428066 0643 
.
.

.
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The genes in H3N2pdm11 all were found previously in humans. There is no reason to assume no reassortment in humans. This virus is widespread in humans, just not well tested. There is still just ONE example in pigs (where there is enhanced surveillance), and that was from a collection AFTER the spread in humans, where there are ten example in spite of little testing because on the focus on "swine exposure".

You are saying it didn't happen because you assume it didn't happen based on ZERO data.

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niman

Post subject: Re: First Novel trH3N2 In New York Swine

Posted: Fri Dec 02, 2011 2:08 am

Joined: Wed Aug 19, 2009 10:42 am
Posts: 27549
Location: Pittsburgh, PA USA

gsgs wrote:

Code:

                                       0000000000011111111112 00000001112 000001111111111 00000000000000111 0000001111111 00000001111 00000000 0000   
                                       0112234457711224458990 35777891270 347780245556899 11233333345579223 0136990122444 26888990011 01345689 3456   
                                       4141492411267382685250 37039708600 291822500896169 79655779941356162 7107195416588 12234452949 40292067 9114   
                                       2449596707346612741061 33852362611 127843173732528 76417593866930207 2165797054526 07313410824 52428066 0643   
-codon-position------------------------    2                                 22            1    1 22 2    1     2 1  1  1   1  2   2        21  211   
---Index-------------------------------TGGACCACCTAGAGAGCAAGTT GAAGATCCGAC GCCCCAACCCAAAAC CAGTGGCCAACAGCAGC AGACTCCGACAGT CGGGTGATCAT CGAAAAAA GAGC   
   1 >Index                            ...................... ........... ............... ................. ............. ........... ........ ....   
   2 >A/Sw/Ontario/33853/2005+M(Mex)   C...A..TTCG.G......... .......TA.T .T...GGGTT....T T.A.....C.TTA.G.. ...T..A.GA... ........... .AGG.G.. ....   
   3 >A/Sw/MN/02948/2009/05/19         ---------------------- ----------- --------------- T.A.....C.TTA---- ------------- ----------- -------- ----   
   4 >A/Sw/PA/62170-1/2010/10/25       C...A.GTTCG.G.......CC ----------- .TT.TGGT...G... ----------------- GA.....A..GAA ........... -------- ..A.   
   5 >A/Sw/PA/62170-2/2010/10/25       C...A.GTTCG.G.......CC ----------- .TT.TGGT...G... ----------------- GA.....A..GAA ..A..CG.... -------- ..A.   
   6 >A/Sw/PA/62170-3/2010/10/25       C...A.GTTCG.........CC ----------- .TT.TGGT...G... ----------------- GA.....A..G.. ........... -------- ..A.   
   7 >A/Sw/PA/62170-4/2010/10/25       C...A.GTTCG.........CC ----------- .TT.TGGT...G... ----------------- GA.....A..G.. ..A..CG.... -------- ..A.   
   8 >A/Sw/Quebec/1257777/2010/11/08   ---------------------- ----------- --------------- ----------------- ------------- ----------- .AG...-- ----   
   9 >A/Sw/Quebec/1257774/2010/11/09   ---------------------- ----------- --------------- ----------------- ------------- ----------- .AG....- ----   
  10 >A/Sw/IN/A01049091/2010/11/18     ---------------------- ----------- --------------- ..............G.. ------------- T.......... -------- ----   
  11 >A/Sw/NC/A01049436/2011/01/19     ---------------------- ----------- --------------- ................. ------------- T.......... -------- ----   
  12 >A/PA/09/2011/08/20               ..AG.......A.AGAACGA.. A..AG.T..G. ...A..--------- .G...AT..G...A.AA ............. ........... .......G ....   
  13 >A/PA/11/2011/08/25               ..AG.......----------- -------..G. ...A......G.GG. .G.C.AT..G...A--- ..G..T....... .T......A.. .......G .G.T   
  14 >A/PA/10/2011/08/26               ---------------------- ----------- --------------- ------------.A--- ------------- ----------- ...----- .G.T   
  15 >A/PA/10b/2011                    ---------------------- ----------- --------------- ------------.A--- ------------- --......A.. ...----- .G.T   
  16 >A/IN/08_a/2011/07/27             .AA........A.AGAACGA.. A..AGCT..G. ...A......G.GG. .G.C.AT..G.....AA ..G.CT....... .T.A....A.. ......GG .G..   
  17 >A/IN/08_b/2011/07/27             .AA........A.AGAACGA.. A..AGCT..G. ...A......G.GG. .G.C.AT..G.....A- ..G.CT....... .T.A....A.. ......G- .G..   
  18 >A/KA/13/2009/07/27               ---------------------- ----------- --------------- ----------------- ...T..A.GA... ----------- -------- ....   
  19 >A/IN/10/2011/10/22               .....T.....A..GA.C.A.. ...AG.T..G. ..........G..G. ....A..T......G.. ............. ........... AAGGG... ....   
  20 >A/Sw/NY/A01104005/2011/09/13     .....T.....A..GA.C.A.. .GG.G.T.A.. A........TG..G. ....A..T......G.. ..G..T....... ....C..C.GA AAGGG... A...   
  21 >A/ME/06/2011/10/10               C...A.GTTCG.........CC .GG.G.TTA.T A.......T.G..GT ....A..T......G.. .A........... ....C..C.GA AAGGGG.. A...   
                                                                                                                                                      
---Index-------------------------------TGGACCACCTAGAGAGCAAGTT GAAGATCCGAC GCCCCAACCCAAAAC CAGTGGCCAACAGCAGC AGACTCCGACAGT CGGGTGATCAT CGAAAAAA GAGC   
-codon-position------------------------    2                                 22            1    1 22 2    1     2 1  1  1   1  2   2        21  211   
                                       0000000000011111111112 00000001112 000001111111111 00000000000000111 0000001111111 00000001111 00000000 0000   
                                       0112234457711224458990 35777891270 347780245556899 11233333345579223 0136990122444 26888990011 01345689 3456   
                                       4141492411267382685250 37039708600 291822500896169 79655779941356162 7107195416588 12234452949 40292067 9114   
                                       2449596707346612741061 33852362611 127843173732528 76417593866930207 2165797054526 07313410824 52428066 0643   
.
.

.
.

Your analysis is fatally flawed because you don't use the human trH3N2 sequences from 2009 and 2010 which shows the clustering of the human sequences relative to the swine sequences.
The reassortment in the first H3N2pdm09 was described when the sequence first came out in August. The reassortment involving PB1, NA, MP is a VERY old story.

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