Rhiza Labs FluTracker Forum

The USDA has released a large series of H1N2 sequences from 2011 isolates. Most of these sequences have H1N1pdm09 M gene.

_________________
www.twitter.com/hniman

Recent isolates with H1N1pdm09 M gene

A/swine/Illinois/A00907647/2011 EPI_ISL_97017 2011-07-08
A/swine/Michigan/A01202035/2011 EPI_ISL_98875 2011-05-26
A/swine/Michigan/A01202036/2011 EPI_ISL_98874 2011-05-26
A/swine/Michigan/A01202037/2011 EPI_ISL_98873 2011-05-26
A/swine/Iowa/A01049970/2011 EPI_ISL_98881 2011-05-16
A/swine/Indiana/A01049964/2011 EPI_ISL_97121 2011-05-11
A/swine/Minnesota/A01049956/2011 EPI_ISL_97122 2011-05-10
A/swine/Iowa/A01049951/2011 EPI_ISL_97124 H1N2 2011-05-09
A/swine/Indiana/A01049953/2011 EPI_ISL_97123 H1N2 2011-05-07
A/swine/Iowa/A01049887/2011 EPI_ISL_97130 H1N2 2011-04-26
A/swine/Iillinois/A01049871/2011 EPI_ISL_97132 H1N2 2011-04-19
A/swine/Iillinois/A01049872/2011 EPI_ISL_97131 H1N2 2011-04-19
A/swine/Iowa/A01049863/2011 EPI_ISL_97134 H1N2 2011-04-18
A/swine/Iowa/A01049864/2011 EPI_ISL_97133 H1N2 2011-04-18
A/swine/Iowa/A01049858/2011 EPI_ISL_97095 H1N2 2011-04-10
A/swine/Indiana/A01049794/2011 EPI_ISL_97136 H1N2 2011-04-06
A/swine/Iowa/A01049765/2011 EPI_ISL_97138 H1N2 2011-03-29
A/swine/Iowa/A01049766/2011 EPI_ISL_97137 H1N2 2011-03-29
A/swine/Iowa/A01049755/2011 EPI_ISL_97139 H1N2 2011-03-28
A/swine/Iowa/A01049726/2011 EPI_ISL_97096 H1N2 2011-03-22
A/swine/Iowa/A01049722/2011 EPI_ISL_97076 H1N2 2011-03-22
A/swine/Iowa/A01049723/2011 EPI_ISL_97075 H1N2 2011-03-22
A/swine/Iowa/A01049724/2011 EPI_ISL_97074 H1N2 2011-03-22
A/swine/Iowa/A01049728/2011 EPI_ISL_97073 H1N2 2011-03-22
A/swine/Iowa/A01049718/2011 EPI_ISL_97078 H1N2 2011-03-21

_________________
www.twitter.com/hniman

The above list is NOT a complete list. This is a work in progress, but the most recent isolates are clearly HEAVILY weighted with isolates which have H1N1pdm09 M gene
Sequences are almost exclusively limited to HA, NA, and MP.

_________________
www.twitter.com/hniman

A/swine/Iowa/A01049640/2011 EPI_ISL_97099 H1N2 2011-03-07
A/swine/Iowa/A01049646/2011 EPI_ISL_97082 H1N2 2011-03-07
A/swine/Nebraska/A01049648/2011 EPI_ISL_97081 H1N2 2011-03-07
A/swine/South Dakota/6/2011 EPI_ISL_89681 H1N2 2011-02-25
A/swine/South Dakota/5/2011 EPI_ISL_89680 H1N2 2011-02-25
A/swine/Iowa/A01049525/2011 EPI_ISL_97100 H1N2 2011-02-08
A/swine/Iowa/A01049450/2011 EPI_ISL_93365 H1N2 2011-01-19
A/swine/South Dakota/4/2010 EPI_ISL_87532 H1N2 2010-12-28
A/swine/South Dakota/3/2010 EPI_ISL_85051 H1N2 2010-11-23
A/swine/South Dakota/2/2010 EPI_ISL_85050 H1N2 2010-11-23
A/swine/Iowa/A01049071/2010 EPI_ISL_90118 H1N2 2010-11-16
A/swine/North Carolina/226126/2010 EPI_ISL_88840 H1N2 2010-09-08
A/swine/North Carolina/226125/2010 EPI_ISL_88839 H1N2 2010-09-08
A/swine/North Carolina/226124/2010 EPI_ISL_88838 H1N2 2010-09-08

_________________
www.twitter.com/hniman

The above list has 39/56 trH1N2 isolates since Sept 9, 2010 which have H1N1pdm09

For 2011 the numbers are 32/42 with H1N1pdm09

_________________
www.twitter.com/hniman

Here is a full chronological list of H1N2 sequences at GISAID collected after the start of the pandemic, which have an M gene sequence. H1N1pdm09 marked with X

A/swine/Illinois/A00907647/2011 07-08 CY099369 x
A/swine/Michigan/A01202035/2011 05-26 JN863566 x
A/swine/Michigan/A01202036/2011 05-26 JN863567 x
A/swine/Michigan/A01202037/2011 05-26 JN863568 x
A/swine/Iowa/A01049970/2011 05-16 JN863560 x
A/swine/Indiana/A01049964/2011 05-11 JN652586 x
A/swine/Illinois/A01049967/2011 05-11 JN652587
A/swine/Illinois/A01049968/2011 05-11 JN652588
A/swine/Illinois/A01049969/2011 05-11 JN652589
A/swine/Minnesota/A01049956/2011 05-10 JN652585 x
A/swine/Iowa/A01049951/2011 05-09 JN652582 x
A/swine/Illinois/A01049952/2011 05-09 JN652583
A/swine/Indiana/A01049953/2011 05-07 JN652584 x
A/swine/Iowa/A01049887/2011 04-26 JN652571 x
A/swine/Iillinois/A01049871/2011 04-19 JN652569 x
A/swine/Iillinois/A01049872/2011 04-19 JN652570 x
A/swine/Iowa/A01049863/2011 04-18 JN652567 x
A/swine/Iowa/A01049864/2011 04-18 JN652568 x
A/swine/Iowa/A01049846/2011 04-13 JN652565
A/swine/Iowa/A01049858/2011 04-10 JN652489 x
A/swine/Indiana/A01049794/2011 04-06 JN652489 x
A/swine/Iowa/A01049765/2011 03-29 JN652562 x
A/swine/Iowa/A01049766/2011 03-29 JN652563 x
A/swine/Iowa/A01049755/2011 03-28 JN652560 x
A/swine/Iowa/A01049726/2011 03-22 JN652484 x
A/swine/Iowa/A01049722/2011 03-22 JN652481 x
A/swine/Iowa/A01049723/2011 03-22 JN652482 x
A/swine/Iowa/A01049724/2011 03-22 JN652483 x
A/swine/Iowa/A01049728/2011 03-22 JN652485 x
A/swine/Iowa/A01049718/2011 03-21 JN652479 x
A/swine/Iowa/A01049661/2011 03-08 JN652476
A/swine/Iowa/A01049648/2011 03-07 JN652474 x
A/swine/Iowa/A01049640/2011 03-07 JN652470 x
A/swine/Iowa/A01049645/2011 03-07 JN652472
A/swine/Iowa/A01049643/2011 03-07 JN652471
A/swine/Iowa/A01049646/2011 03-07 JN652473 x
A/swine/South Dakota/6/2011 02-25 CY089406 x
A/swine/South Dakota/5/2011 02-25 CY089403 x
A/swine/Iowa/A01049525/2011 02-08 JN652462 x
A/swine/Iowa/A01049506/2011 02-04 JN652461
A/swine/Oklahoma/A01049500/2011 02-03 JN652460
A/swine/Iowa/A01049450/2011 01-19 JN162041 x
A/swine/South Dakota/4/2010 12-28 CY081568 x
A/swine/Iowa/A01049228/2010 12-06 JN162026
A/swine/Illinois/A01049164/2010 12-01 JF833366
A/swine/South Dakota/3/2010 11-23 CY078426 x
A/swine/South Dakota/2/2010 11-23 CY078423 x
A/swine/North Carolina/A0109085/2010 11-16 JF812334
A/swine/Illinois/A01049074/2010 11-16 JF812332
A/swine/Iowa/A01049071/2010 11-16 JF812331 x
A/swine/Iowa/A01049062/2010 11-16 JF812329
A/swine/Iowa/A01049060/2010 11-16 JF812328
A/swine/North Carolina/226126/2010 09-08 CY086907 X
A/swine/North Carolina/226125/2010 09-08 CY086899 X
A/swine/North Carolina/226124/2010 09-08 CY086891 X
A/swine/Oklahoma/44837-5/2010 07-19 HQ424899
A/swine/Minnesota/239106/2010 05-05 CY086931
A/swine/North Carolina/239108/2010 04-21 CY086939 X
A/swine/Indiana/240218/2010 02-21 CY086883 X
A/swine/Minnesota/340304/2010 01-01 CY086941
A/swine/North Carolina/44837-4/2009 12-21 HQ424893
A/swine/Minnesota/44837-3/2009 11-23 HQ424893
A/swine/SD/31813/2009 11-20 GU480920
A/swine/North Carolina/44837-2/2009 11-15 HQ424890
A/swine/South Dakota/152B/2009 09-04 HQ840333

_________________
www.twitter.com/hniman

Commentary

http://www.recombinomics.com/News/12071 ... ine_M.html

_________________
www.twitter.com/hniman

Top 100 NA matches for A/swine/Ohio/FAH10-1/2010

HQ833568.1 Influenza A virus (A/swine/Ohio/FAH10-1/2010(H1N2)) segment 6 neuraminidase (NA) gene, partial cds 2538 2538 100% 0.0 100%
JN652529.1 Influenza A virus (A/swine/Indiana/A01049794/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2533 2533 100% 0.0 99%
CY078425.1 Influenza A virus (A/swine/South Dakota/3/2010(H1N2)) segment 6 sequence 2533 2533 100% 0.0 99%
CY078422.1 Influenza A virus (A/swine/South Dakota/2/2010(H1N2)) segment 6 sequence 2533 2533 100% 0.0 99%
JF312068.1 Influenza A virus (A/swine/Pennsylvania/62170-3/2010(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2524 2524 100% 0.0 99%
JF312066.1 Influenza A virus (A/swine/Pennsylvania/62170-1/2010(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2524 2524 100% 0.0 99%
JN652445.1 Influenza A virus (A/swine/Indiana/A01049653/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2520 2520 100% 0.0 99%
JN652552.1 Influenza A virus (A/swine/Indiana/A01049964/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2520 2520 100% 0.0 99%
JN652550.1 Influenza A virus (A/swine/Indiana/A01049953/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2520 2520 100% 0.0 99%
JQ070791.1 Influenza A virus (A/Indiana/10/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2515 2515 100% 0.0 99%
JQ070783.1 Influenza A virus (A/Indiana/10/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2515 2515 100% 0.0 99%
JN863546.1 Influenza A virus (A/swine/Iowa/A01049970/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2515 2515 100% 0.0 99%
JN652536.1 Influenza A virus (A/swine/Iowa/A01049887/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds
JN652441.1| Influenza A virus (A/swine/Iowa/A01049644/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds
JN652443.1| Influenza A virus (A/swine/Iowa/A01049646/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2515 2515 100% 0.0 99%
JN652523.1 Influenza A virus (A/swine/Indiana/A01049745/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2515 2515 100% 0.0 99%
JN652522.1 Influenza A virus (A/swine/Indiana/A01049744/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2515 2515 100% 0.0 99%
JN863553.1 Influenza A virus (A/swine/Michigan/A01202037/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2511 2511 100% 0.0 99%
JN863552.1 Influenza A virus (A/swine/Michigan/A01202036/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2511 2511 100% 0.0 99%
JN652456.1 Influenza A virus (A/swine/Iowa/A01049858/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2511 2511 100% 0.0 99%
JN652432.1 Influenza A virus (A/swine/Iowa/A01049506/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2511 2511 100% 0.0 99%
JN162021.1 Influenza A virus (A/swine/North Carolina/A01049436/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2511 2511 100% 0.0 99%
JF812312.1 Influenza A virus (A/swine/Indiana/A01049091/2010(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2511 2511 100% 0.0 99%
JF312067.1 Influenza A virus (A/swine/Pennsylvania/62170-2/2010(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2511 2511 100% 0.0 99%
JF312055.1 Influenza A virus (A/swine/Minnesota/A01047604/2010(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2511 2511 100% 0.0 99%
JN638732.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2507 2507 100% 0.0 99%
JQ070799.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2506 2506 100% 0.0 99%
JN652452.1 Influenza A virus (A/swine/Iowa/A01049726/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2506 2506 100% 0.0 99%
JN652453.1 Influenza A virus (A/swine/Iowa/A01049728/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2506 2506 100% 0.0 99%
JN940424.1 Influenza A virus (A/swine/NY/A01104005/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2502 2502 100% 0.0 99%
JN652449.1 Influenza A virus (A/swine/Iowa/A01049722/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2502 2502 100% 0.0 99%
JN652450.1 Influenza A virus (A/swine/Iowa/A01049723/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds
JN652451.1| Influenza A virus (A/swine/Iowa/A01049724/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2502 2502 100% 0.0 99%
JN652532.1 Influenza A virus (A/swine/Iowa/A01049863/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds
JN863559.1| Influenza A virus (A/swine/Iowa/A01202063/2011(N2)) segment 6 neuraminidase (NA) gene, complete cds 2502 2502 100% 0.0 99%
JN652530.1 Influenza A virus (A/swine/Iowa/A01049846/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2502 2502 100% 0.0 99%
JN162022.1 Influenza A virus (A/swine/Iowa/A01049450/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds
JN652439.1| Influenza A virus (A/swine/Iowa/A01049640/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds
JN652447.1| Influenza A virus (A/swine/Iowa/A01049718/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2502 2502 100% 0.0 99%
JF812308.1 Influenza A virus (A/swine/Iowa/A01049071/2010(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2502 2502 100% 0.0 99%
JF312069.1 Influenza A virus (A/swine/Pennsylvania/62170-4/2010(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2502 2502 100% 0.0 99%
CY081567.1 Influenza A virus (A/swine/South Dakota/4/2010(H1N2)) neuraminidase (NA) gene, complete cds 2502 2502 100% 0.0 99%
JN652551.1 Influenza A virus (A/swine/Minnesota/A01049956/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2497 2497 100% 0.0 99%
JN652533.1 Influenza A virus (A/swine/Iowa/A01049864/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2497 2497 100% 0.0 99%
CY099368.1 Influenza A virus (A/swine/Illinois/A00907647/2011(H1N2)) neuraminidase (NA) gene, complete cds 2493 2493 100% 0.0 99%
JN652548.1 Influenza A virus (A/swine/Iowa/A01049951/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2488 2488 100% 0.0 99%
JN652535.1 Influenza A virus (A/swine/Iillinois/A01049872/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2488 2488 100% 0.0 99%
JN655545.1 Influenza A virus (A/Pennsylvania/11/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2480 2480 98% 0.0 99%
JN655557.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2477 2477 98% 0.0 99%
JN652553.1 Influenza A virus (A/swine/Illinois/A01049967/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2475 2475 100% 0.0 99%
JN652554.1 Influenza A virus (A/swine/Illinois/A01049968/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds
JN652555.1| Influenza A virus (A/swine/Illinois/A01049969/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2475 2475 100% 0.0 99%
JN652549.1 Influenza A virus (A/swine/Illinois/A01049952/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2475 2475 100% 0.0 99%
JN652534.1 Influenza A virus (A/swine/Iillinois/A01049871/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2470 2470 100% 0.0 99%
JN992752.1 Influenza A virus (A/Indiana/10/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2462 2462 97% 0.0 99%
JN866185.1 Influenza A virus (A/Maine/06/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2462 2462 98% 0.0 99%
JN655533.1 Influenza A virus (A/Pennsylvania/09/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2459 2459 98% 0.0 99%
CY045601.1 Influenza A virus (A/swine/Oklahoma/010226-17/2008(H1N2)) segment 6 sequence 2439 2439 100% 0.0 98%
CY045649.1 Influenza A virus (A/swine/Oklahoma/011521-5/2008(H1N2)) segment 6 sequence 2434 2434 100% 0.0 98%
CY045697.1 Influenza A virus (A/swine/Oklahoma/020736-2/2008(H1N2)) segment 6 sequence 2434 2434 100% 0.0 98%
CY045705.1 Influenza A virus (A/swine/Oklahoma/020736-1/2008(H1N2)) segment 6 sequence 2434 2434 100% 0.0 98%
CY045625.1 Influenza A virus (A/swine/Oklahoma/011289-9/2008(H1N2)) segment 6 sequence 2434 2434 100% 0.0 98%
CY045633.1 Influenza A virus (A/swine/Oklahoma/011289-10/2008(H1N2)) segment 6 sequence
CY045641.1| Influenza A virus (A/swine/Oklahoma/011289-8/2008(H1N2)) segment 6 sequence
CY045689.1| Influenza A virus (A/swine/Oklahoma/020734-3/2008(H1N2)) segment 6 sequence 2434 2434 100% 0.0 98%
CY045609.1 Influenza A virus (A/swine/Oklahoma/010710-9/2008(H1N2)) segment 6 sequence 2430 2430 100% 0.0 98%
CY045593.1 Influenza A virus (A/swine/Oklahoma/010226-16/2008(H1N2)) segment 6 sequence 2430 2430 100% 0.0 98%
JQ070775.1 Influenza A virus (A/Iowa/09/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2426 2426 98% 0.0 99%
HQ424898.1 Influenza A virus (A/swine/Oklahoma/44837-5/2010(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2425 2425 100% 0.0 98%
CY045681.1 Influenza A virus (A/swine/Oklahoma/020734-2/2008(H1N2)) segment 6 sequence 2425 2425 100% 0.0 98%
CY045617.1 Influenza A virus (A/swine/Oklahoma/010710-8/2008(H1N2)) segment 6 sequence 2425 2425 100% 0.0 98%
CY045537.1 Influenza A virus (A/swine/Texas/050625/2008(H1N2)) segment 6 sequence 2425 2425 100% 0.0 98%
CY045521.1 Influenza A virus (A/swine/Oklahoma/032726/2008(H1N2)) segment 6 sequence 2425 2425 100% 0.0 98%
JQ070767.1 Influenza A virus (A/Iowa/08/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2421 2421 97% 0.0 99%
CY045673.1 Influenza A virus (A/swine/Oklahoma/016179-9/2008(H1N2)) segment 6 sequence 2421 2421 100% 0.0 98%
CY045665.1 Influenza A virus (A/swine/Oklahoma/016179-8/2008(H1N2)) segment 6 sequence 2421 2421 100% 0.0 98%
CY045657.1 Influenza A virus (A/swine/Oklahoma/011521-4/2008(H1N2)) segment 6 sequence 2421 2421 100% 0.0 98%
CY045529.1 Influenza A virus (A/swine/Texas/050593/2008(H1N2)) segment 6 sequence 2421 2421 100% 0.0 98%
CY045545.1 Influenza A virus (A/swine/Oklahoma/053259/2008(H1N2)) segment 6 sequence 2412 2412 100% 0.0 98%
JQ070759.1 Influenza A virus (A/Iowa/07/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2397 2397 96% 0.0 99%
CY045713.1 Influenza A virus (A/swine/Oklahoma/042169/2008(H1N2)) segment 6 sequence 2394 2394 100% 0.0 98%
CY045561.1 Influenza A virus (A/swine/Kansas/015252/2009(H3N2)) segment 6 sequence 2388 2388 100% 0.0 98%
CY086930.1 Influenza A virus (A/swine/Minnesota/239106/2010(H1N2)) neuraminidase (NA) gene, complete cds 2385 2385 100% 0.0 98%
CY045553.1 Influenza A virus (A/swine/Oklahoma/001142/2009(H3N2)) segment 6 sequence 2385 2385 100% 0.0 98%
CY089402.1 Influenza A virus (A/swine/South Dakota/5/2011(H1N2)) neuraminidase (NA) gene, complete cds 2361 2361 100% 0.0 97%
CY089405.1 Influenza A virus (A/swine/South Dakota/6/2011(H1N2)) neuraminidase (NA) gene, complete cds 2352 2352 100% 0.0 97%
JN652543.1 Influenza A virus (A/swine/Arkansas/A01049917/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2345 2345 100% 0.0 97%
HQ424889.1 Influenza A virus (A/swine/North Carolina/44837-2/2009(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2340 2340 100% 0.0 97%
CY099209.1 Influenza A virus (A/swine/Minnesota/02324/2008(H1N2)) neuraminidase (NA) gene, complete cds 2331 2331 100% 0.0 97%
CY099177.1 Influenza A virus (A/swine/Minnesota/SG1133/2008(H1N2)) neuraminidase (NA) gene, complete cds 2325 2325 100% 0.0 97%
EU735820.1 Influenza A virus (A/turkey/OH/313053/2004(H3N2)) neuraminidase (NA) gene, complete cds 2322 2322 100% 0.0 97%
DQ335773.1 Influenza A virus (A/turkey/Ohio/313053/04(H3N2)) neuraminidase (NA) gene, complete cds 2322 2322 100% 0.0 97%
CY099029.1 Influenza A virus (A/swine/Iowa/01700/2007(H3N2)) neuraminidase (NA) gene, complete cds 2313 2313 100% 0.0 96%
EU735828.1 Influenza A virus (A/turkey/NC/353568/2005(H3N2)) neuraminidase (NA) gene, complete cds 2307 2307 100% 0.0 96%
EF551055.1 Influenza A virus (A/swine/North Carolina/2003(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2307 2307 100% 0.0 96%
EF551047.1 Influenza A virus (A/turkey/Illinois/2004(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2307 2307 100% 0.0 96%
DQ469976.1 Influenza A virus (A/swine/British Columbia/28103/2005(H3N2)) neuraminidase (NA) gene, complete cds 2307 2307 100% 0.0 96%
CY099249.1 Influenza A virus (A/swine/Minnesota/00484/2005(H3N2)) neuraminidase (NA) gene, complete cds 2304 2304 100% 0.0 96%
CY099145.1 Influenza A virus (A/swine/Minnesota/00611/2005(H3N2)) neuraminidase (NA) gene, complete cds 2304 2304 100% 0.0 96%
CY099088.1 Influenza A virus (A/swine/Nebraska/00722/2005(mixed)) neuraminidase (NA) gene, complete cds 2304 2304 100% 0.0 96%
CY099054.1 Influenza A virus (A/swine/Illinois/02450/2008(mixed)) neuraminidase (NA) gene, complete cds 2298 2298 100% 0.0 96%
EU826544.2 Influenza A virus (A/swine/Quebec/4001/2005(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2298 2298 100% 0.0 96%
HQ825168.1 Influenza A virus (A/turkey/BC/1529-3/2005(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2295 2295 100% 0.0 96%
EU697211.1 Influenza A virus (A/turkey/North Carolina/353568/2005(H3N2)) neuraminidase (NA) gene, complete cds 2295 2295 100% 0.0 96%
DQ469992.1 Influenza A virus (A/swine/Ontario/33853/2005(H3N2)) neuraminidase (NA) gene, complete cds 2295 2295 100% 0.0 96%
DQ469984.1 Influenza A virus (A/swine/Manitoba/12707/2005(H3N2)) neuraminidase (NA) gene, complete cds 2295 2295 100% 0.0 96%
DQ469960.1 Influenza A virus (A/Ontario/RV1273/2005(H3N2)) neuraminidase (NA) gene, complete cds 2295 2295 100% 0.0 96%
CY099063.1 Influenza A virus (A/swine/Minnesota/00709/2005(H3N2)) neuraminidase (NA) gene, complete cds 2289 2289 100% 0.0 96%
DQ470000.1 Influenza A virus (A/turkey/Ontario/31232/2005(H3N2)) neuraminidase (NA) gene, complete cds 2289 2289 100% 0.0 96%

_________________
www.twitter.com/hniman

Top 100 NA matches at GISAID

EPI338590 A/swine/Indiana/A01049794/2011 (A/H1N2) segment 6 (NA) 2593.8 0.000000e+00 1406/1407 (99%)
EPI298488 A/swine/South Dakota/3/2010 (A/H1N2) segment 6 (NA) 2593.8 0.000000e+00 1406/1407 (99%)
EPI298485 A/swine/South Dakota/2/2010 (A/H1N2) segment 6 (NA) 2593.8 0.000000e+00 1406/1407 (99%)
EPI314799 A/swine/Pennsylvania/602170-3/2010 (A/H3N2) segment 6 (NA) 2582.7 0.000000e+00 1404/1407 (99%)
EPI314797 A/swine/Pennsylvania/602170-1/2010 (A/H3N2) segment 6 (NA) 2582.7 0.000000e+00 1404/1407 (99%)
EPI291871 A/Pennsylvania/14/2010 (A/H3N2) segment 6 (NA) 2582.7 0.000000e+00 1404/1407 (99%)
EPI291869 A/Pennsylvania/14/2010 (A/H3N2) segment 6 (NA) 2582.7 0.000000e+00 1404/1407 (99%)
EPI338569 A/swine/Indiana/A01049953/2011 (A/H1N2) segment 6 (NA) 2577.2 0.000000e+00 1403/1407 (99%)
EPI338567 A/swine/Indiana/A01049964/2011 (A/H1N2) segment 6 (NA) 2577.2 0.000000e+00 1403/1407 (99%)
EPI338447 A/swine/Indiana/A01049653/2011 (A/H3N2) segment 6 (NA) 2577.2 0.000000e+00 1403/1407 (99%)
EPI344396 A/Indiana/10/2011 (A/H3N2) segment 6 (NA) 2571.7 0.000000e+00 1402/1407 (99%)
EPI344388 A/Indiana/10/2011 (A/H3N2) segment 6 (NA) 2571.7 0.000000e+00 1402/1407 (99%)
EPI338597 A/swine/Indiana/A01049744/2011 (A/H3N2) segment 6 (NA) 2571.7 0.000000e+00 1402/1407 (99%)
EPI338596 A/swine/Indiana/A01049745/2011 (A/H3N2) segment 6 (NA) 2571.7 0.000000e+00 1402/1407 (99%)
EPI338583 A/swine/Iowa/A01049887/2011 (A/H1N2) segment 6 (NA) 2571.7 0.000000e+00 1402/1407 (99%)
EPI338451 A/swine/Iowa/A01049644/2011 (A/H1N2) segment 6 (NA) 2571.7 0.000000e+00 1402/1407 (99%)
EPI338449 A/swine/Iowa/A01049646/2011 (A/H1N2) segment 6 (NA) 2571.7 0.000000e+00 1402/1407 (99%)
EPI341756 A/swine/Iowa/A01049970/2011 (A/H1N2) segment 6 (NA) 2569.8 0.000000e+00 1401/1407 (99%)
EPI341750 A/swine/Michigan/A01202036/2011 (A/H1N2) segment 6 (NA) 2566.1 0.000000e+00 1401/1407 (99%)
EPI341749 A/swine/Michigan/A01202037/2011 (A/H1N2) segment 6 (NA) 2566.1 0.000000e+00 1401/1407 (99%)
EPI338459 A/swine/Iowa/A01049506/2011 (A/H1N2) segment 6 (NA) 2566.1 0.000000e+00 1401/1407 (99%)
EPI338436 A/swine/Iowa/A01049858/2011 (A/H1N2) segment 6 (NA) 2566.1 0.000000e+00 1401/1407 (99%)
EPI324819 A/swine/North Carolina/A01049436/2011 (A/H3N2) segment 6 (NA) 2566.1 0.000000e+00 1401/1407 (99%)
EPI317026 A/swine/Indiana/A0109091/2010 (A/H3N2) segment 6 (NA) 2566.1 0.000000e+00 1401/1407 (99%)
EPI314798 A/swine/Pennsylvania/602170-2/2010 (A/H3N2) segment 6 (NA) 2566.1 0.000000e+00 1401/1407 (99%)
EPI314786 A/swine/Minnesota/A01047604/2010 (A/H1N2) segment 6 (NA) 2566.1 0.000000e+00 1401/1407 (99%)
EPI333151 A/Indiana/08/2011 (A/H3N2) segment 6 (NA) 2562.4 0.000000e+00 1400/1407 (99%)
EPI344404 A/Indiana/08/2011 (A/H3N2) segment 6 (NA) 2560.6 0.000000e+00 1400/1407 (99%)
EPI338440 A/swine/Iowa/A01049726/2011 (A/H1N2) segment 6 (NA) 2560.6 0.000000e+00 1400/1407 (99%)
EPI338439 A/swine/Iowa/A01049728/2011 (A/H1N2) segment 6 (NA) 2560.6 0.000000e+00 1400/1407 (99%)
EPI342601 A/swine/NY/A01104005/2011 (A/H3N2) segment 6 (NA) 2555.0 0.000000e+00 1397/1404 (99%)
EPI341743 A/swine/Iowa/A01202063/2011 (A/H0N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI338589 A/swine/Iowa/A01049846/2011 (A/H1N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI338587 A/swine/Iowa/A01049863/2011 (A/H1N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI338453 A/swine/Iowa/A01049640/2011 (A/H1N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI338445 A/swine/Iowa/A01049718/2011 (A/H1N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI338443 A/swine/Iowa/A01049722/2011 (A/H1N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI338442 A/swine/Iowa/A01049723/2011 (A/H1N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI338441 A/swine/Iowa/A01049724/2011 (A/H1N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI324820 A/swine/Iowa/A01049450/2011 (A/H1N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI317022 A/swine/Iowa/A01049071/2010 (A/H1N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI314800 A/swine/Pennsylvania/602170-4/2010 (A/H3N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI307830 A/swine/South Dakota/4/2010 (A/H1N2) segment 6 (NA) 2555.0 0.000000e+00 1399/1407 (99%)
EPI338586 A/swine/Iowa/A01049864/2011 (A/H1N2) segment 6 (NA) 2549.5 0.000000e+00 1398/1407 (99%)
EPI338568 A/swine/Minnesota/A01049956/2011 (A/H1N2) segment 6 (NA) 2549.5 0.000000e+00 1398/1407 (99%)
EPI291863 A/Pennsylvania/14/2010 (A/H3N2) segment 6 (NA) 2549.5 0.000000e+00 1388/1392 (99%)
EPI338190 A/swine/Illinois/A00907647/2011 (A/H1N2) segment 6 (NA) 2544.0 0.000000e+00 1397/1407 (99%)
EPI338584 A/swine/Iillinois/A01049872/2011 (A/H1N2) segment 6 (NA) 2538.4 0.000000e+00 1396/1407 (99%)
EPI338571 A/swine/Iowa/A01049951/2011 (A/H1N2) segment 6 (NA) 2538.4 0.000000e+00 1396/1407 (99%)
EPI335620 A/Pennsylvania/11/2011 (A/H3N2) segment 6 (NA) 2536.6 0.000000e+00 1383/1388 (99%)
EPI335631 A/Indiana/08/2011 (A/H3N2) segment 6 (NA) 2531.0 0.000000e+00 1382/1388 (99%)
EPI338570 A/swine/Illinois/A01049952/2011 (A/H1N2) segment 6 (NA) 2521.8 0.000000e+00 1393/1407 (99%)
EPI338566 A/swine/Illinois/A01049967/2011 (A/H1N2) segment 6 (NA) 2521.8 0.000000e+00 1393/1407 (99%)
EPI338565 A/swine/Illinois/A01049968/2011 (A/H1N2) segment 6 (NA) 2521.8 0.000000e+00 1393/1407 (99%)
EPI338564 A/swine/Illinois/A01049969/2011 (A/H1N2) segment 6 (NA) 2521.8 0.000000e+00 1393/1407 (99%)
EPI340983 A/Indiana/10/2011 (A/H3N2) segment 6 (NA) 2518.1 0.000000e+00 1373/1378 (99%)
EPI338585 A/swine/Iillinois/A01049871/2011 (A/H1N2) segment 6 (NA) 2516.3 0.000000e+00 1392/1407 (98%)
EPI339170 A/Maine/06/2011 (A/H3N2) segment 6 (NA) 2514.4 0.000000e+00 1379/1388 (99%)
EPI335612 A/Pennsylvania/09/2011 (A/H3N2) segment 6 (NA) 2508.9 0.000000e+00 1378/1388 (99%)
EPI220781 A/swine/Oklahoma/010226-17/2008 (A/H1N2) segment 6 (NA) 2477.5 0.000000e+00 1385/1407 (98%)
EPI342703 A/Iowa/09/2011 (A/H3N2) segment 6 (NA) 2471.9 0.000000e+00 1366/1380 (98%)
EPI220885 A/swine/Oklahoma/020736-2/2008 (A/H1N2) segment 6 (NA) 2471.9 0.000000e+00 1384/1407 (98%)
EPI220877 A/swine/Oklahoma/020736-1/2008 (A/H1N2) segment 6 (NA) 2471.9 0.000000e+00 1384/1407 (98%)
EPI220869 A/swine/Oklahoma/020734-3/2008 (A/H1N2) segment 6 (NA) 2471.9 0.000000e+00 1384/1407 (98%)
EPI220837 A/swine/Oklahoma/011521-5/2008 (A/H1N2) segment 6 (NA) 2471.9 0.000000e+00 1384/1407 (98%)
EPI220821 A/swine/Oklahoma/011289-9/2008 (A/H1N2) segment 6 (NA) 2471.9 0.000000e+00 1384/1407 (98%)
EPI220813 A/swine/Oklahoma/011289-8/2008 (A/H1N2) segment 6 (NA) 2471.9 0.000000e+00 1384/1407 (98%)
EPI220805 A/swine/Oklahoma/011289-10/2008 (A/H1N2) segment 6 (NA) 2471.9 0.000000e+00 1384/1407 (98%)
EPI342695 A/Iowa/08/2011 (A/H3N2) segment 6 (NA) 2466.4 0.000000e+00 1363/1377 (98%)
EPI220797 A/swine/Oklahoma/010710-9/2008 (A/H1N2) segment 6 (NA) 2466.4 0.000000e+00 1383/1407 (98%)
EPI220773 A/swine/Oklahoma/010226-16/2008 (A/H1N2) segment 6 (NA) 2466.4 0.000000e+00 1383/1407 (98%)
EPI292300 A/swine/Oklahoma/44837-5/2010 (A/H1N2) segment 6 (NA) 2460.9 0.000000e+00 1382/1407 (98%)
EPI220934 A/swine/Texas/050625/2008 (A/H1N2) segment 6 (NA) 2460.9 0.000000e+00 1382/1407 (98%)
EPI220893 A/swine/Oklahoma/032726/2008 (A/H1N2) segment 6 (NA) 2460.9 0.000000e+00 1382/1407 (98%)
EPI220861 A/swine/Oklahoma/020734-2/2008 (A/H1N2) segment 6 (NA) 2460.9 0.000000e+00 1383/1408 (98%)
EPI220789 A/swine/Oklahoma/010710-8/2008 (A/H1N2) segment 6 (NA) 2460.9 0.000000e+00 1382/1407 (98%)
EPI220926 A/swine/Texas/050593/2008 (A/H1N2) segment 6 (NA) 2455.3 0.000000e+00 1381/1407 (98%)
EPI220853 A/swine/Oklahoma/016179-9/2008 (A/H1N2) segment 6 (NA) 2455.3 0.000000e+00 1381/1407 (98%)
EPI220845 A/swine/Oklahoma/016179-8/2008 (A/H1N2) segment 6 (NA) 2455.3 0.000000e+00 1381/1407 (98%)
EPI220829 A/swine/Oklahoma/011521-4/2008 (A/H1N2) segment 6 (NA) 2455.3 0.000000e+00 1381/1407 (98%)
EPI342687 A/Iowa/07/2011 (A/H3N2) segment 6 (NA) 2444.2 0.000000e+00 1349/1362 (99%)
EPI220909 A/swine/Oklahoma/053259/2008 (A/H1N2) segment 6 (NA) 2444.2 0.000000e+00 1380/1408 (98%)
EPI220901 A/swine/Oklahoma/042169/2008 (A/H1N2) segment 6 (NA) 2422.1 0.000000e+00 1375/1407 (97%)
EPI219362 A/swine/Kansas/015252/2009 (A/H3N2) segment 6 (NA) 2416.5 0.000000e+00 1374/1407 (97%)
EPI312699 A/swine/Minnesota/239106/2010 (A/H1N2) segment 6 (NA) 2411.0 0.000000e+00 1373/1407 (97%)
EPI219370 A/swine/Oklahoma/001142/2009 (A/H3N2) segment 6 (NA) 2411.0 0.000000e+00 1373/1407 (97%)
EPI315843 A/swine/South Dakota/5/2011 (A/H1N2) segment 6 (NA) 2383.3 0.000000e+00 1368/1407 (97%)
EPI315846 A/swine/South Dakota/6/2011 (A/H1N2) segment 6 (NA) 2372.2 0.000000e+00 1366/1407 (97%)
EPI338576 A/swine/Arkansas/A01049917/2011 (A/H1N2) segment 6 (NA) 2363.0 0.000000e+00 1364/1407 (96%)
EPI292291 A/swine/North Carolina/44837-2/2009 (A/H1N2) segment 6 (NA) 2355.6 0.000000e+00 1364/1408 (96%)
EPI337507 A/swine/Minnesota/02324/2008 (A/H1N2) segment 6 (NA) 2344.5 0.000000e+00 1361/1407 (96%)
EPI337475 A/swine/Minnesota/SG1133/2008 (A/H1N2) segment 6 (NA) 2339.0 0.000000e+00 1360/1407 (96%)
EPI229374 A/turkey/OH/313053/2004 (A/H3N2) segment 6 (NA) 2333.4 0.000000e+00 1359/1407 (96%)
EPI101393 A/turkey/Ohio/313053/04 (A/H3N2) segment 6 (NA) 2333.4 0.000000e+00 1359/1407 (96%)
EPI337343 A/swine/Iowa/01700/2007 (A/H3N2) segment 6 (NA) 2322.4 0.000000e+00 1357/1407 (96%)
EPI235273 A/swine/North Carolina/2003 (A/H3N2) segment 6 (NA) 2316.8 0.000000e+00 1357/1408 (96%)
EPI228924 A/turkey/Illinois/2004 (A/H3N2) segment 6 (NA) 2316.8 0.000000e+00 1357/1408 (96%)
EPI227576 A/turkey/NC/353568/2005 (A/H3N2) segment 6 (NA) 2316.8 0.000000e+00 1357/1408 (96%)
EPI103158 A/swine/British Columbia/28103/2005 (A/H3N2) segment 6 (NA) 2316.8 0.000000e+00 1356/1407 (96%)
EPI337547 A/swine/Minnesota/00484/2005 (A/H3N2) segment 6 (NA) 2311.3 0.000000e+00 1355/1407 (96%)

_________________
www.twitter.com/hniman

trH1N2 South Dakota reassortants noted in Feb, 2011

South Dakota trH1N2 Swine Reassortants Raise Concerns
Recombinomics Commentary 15:50
February 11, 2011


South Dakota State University has released HA, NA, and MP sequences from three recent H1N2 swine reassortants (collected in November and December, 28, 2010). The sequences (A/swine/South Dakota/2/2010, A/swine/South Dakota/3/2010, and A/swine/South Dakota/4/2010) are related to each other, and the NA sequences are closely related to the human trH3N2 from Pennsylvania, A/Pennsylvania/14/2010........

http://www.recombinomics.com/News/02111 ... tants.html

_________________
www.twitter.com/hniman