Rhiza Labs FluTracker Forum

A new series of swine sequences have been released by the FDA at Genbank, which are largely from May and June 2011 isolates. All are H1, signaling an absence of trH3N2 sequences matching the human trH3N2 sequences

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JN863540 Swine 4 H1N1 USA 2011/05/17 1701 Influenza A virus (A/swine/Illinois/A01049980/2011(H1N1)) yes
JN863547 Swine 6 H1N1 USA 2011/05/17 1410 Influenza A virus (A/swine/Illinois/A01049980/2011(H1N1)) yes
JN863561 Swine 7 H1N1 USA 2011/05/17 982 Influenza A virus (A/swine/Illinois/A01049980/2011(H1N1)) yes
JN863548 Swine 6 H1N1 USA 2011/05/17 1410 Influenza A virus (A/swine/Illinois/A01049981/2011(H1N1)) yes
JN863562 Swine 7 H1N1 USA 2011/05/17 982 Influenza A virus (A/swine/Illinois/A01049981/2011(H1N1)) yes
JN863546 Swine 6 H1N2 USA 2011/05/16 1410 Influenza A virus (A/swine/Iowa/A01049970/2011(H1N2)) yes
JN863560 Swine 7 H1N2 USA 2011/05/16 982 Influenza A virus (A/swine/Iowa/A01049970/2011(H1N2)) yes
JN863541 Swine 4 H1N1 USA 2011/05/26 1701 Influenza A virus (A/swine/Iowa/A01202023/2011(H1N1)) yes
JN863549 Swine 6 H1N1 USA 2011/05/26 1410 Influenza A virus (A/swine/Iowa/A01202023/2011(H1N1)) yes
JN863563 Swine 7 H1N1 USA 2011/05/26 982 Influenza A virus (A/swine/Iowa/A01202023/2011(H1N1)) yes
JN863542 Swine 4 H1N1 USA 2011/05/27 1701 Influenza A virus (A/swine/Iowa/A01202033/2011(H1N1)) yes
JN863550 Swine 6 H1N1 USA 2011/05/27 1410 Influenza A virus (A/swine/Iowa/A01202033/2011(H1N1)) yes
JN863564 Swine 7 H1N1 USA 2011/05/27 982 Influenza A virus (A/swine/Iowa/A01202033/2011(H1N1)) yes
JN863543 Swine 4 H1N1 USA 2011/05/27 1701 Influenza A virus (A/swine/Iowa/A01202034/2011(H1N1)) yes
JN863551 Swine 6 H1N1 USA 2011/05/27 1410 Influenza A virus (A/swine/Iowa/A01202034/2011(H1N1)) yes
JN863565 Swine 7 H1N1 USA 2011/05/27 982 Influenza A virus (A/swine/Iowa/A01202034/2011(H1N1)) yes
JN863544 Swine 4 H1N1 USA 2011/06/02 1701 Influenza A virus (A/swine/Iowa/A01202041/2011(H1N1)) yes
JN863554 Swine 6 H1N1 USA 2011/06/02 1410 Influenza A virus (A/swine/Iowa/A01202041/2011(H1N1)) yes
JN863569 Swine 7 H1N1 USA 2011/06/02 982 Influenza A virus (A/swine/Iowa/A01202041/2011(H1N1)) yes
JN863545 Swine 4 H1N1 USA 2011/06/02 1701 Influenza A virus (A/swine/Iowa/A01202048/2011(H1N1)) yes
JN863555 Swine 6 H1N1 USA 2011/06/02 1410 Influenza A virus (A/swine/Iowa/A01202048/2011(H1N1)) yes
JN863570 Swine 7 H1N1 USA 2011/06/02 982 Influenza A virus (A/swine/Iowa/A01202048/2011(H1N1)) yes
JN863556 Swine 6 H1N1 USA 2011/06/02 1410 Influenza A virus (A/swine/Iowa/A01202049/2011(H1N1)) yes
JN863571 Swine 7 H1N1 USA 2011/06/02 982 Influenza A virus (A/swine/Iowa/A01202049/2011(H1N1)) yes
JN863557 Swine 6 H1N1 USA 2011/06/06 1410 Influenza A virus (A/swine/Iowa/A01202056/2011(H1N1)) yes
JN863572 Swine 7 H1N1 USA 2011/06/06 982 Influenza A virus (A/swine/Iowa/A01202056/2011(H1N1)) yes
JN863559 Swine 6 N2 USA 2011/06/07 1410 Influenza A virus (A/swine/Iowa/A01202063/2011(N2)) yes
JN863574 Swine 7 N2 USA 2011/06/07 982 Influenza A virus (A/swine/Iowa/A01202063/2011(N2)) yes
JN863566 Swine 7 H1N2 USA 2011/05/26 982 Influenza A virus (A/swine/Michigan/A01202035/2011(H1N2)) yes
JN863552 Swine 6 H1N2 USA 2011/05/26 1410 Influenza A virus (A/swine/Michigan/A01202036/2011(H1N2)) yes
JN863567 Swine 7 H1N2 USA 2011/05/26 982 Influenza A virus (A/swine/Michigan/A01202036/2011(H1N2)) yes
JN863553 Swine 6 H1N2 USA 2011/05/26 1410 Influenza A virus (A/swine/Michigan/A01202037/2011(H1N2)) yes
JN863568 Swine 7 H1N2 USA 2011/05/26 982 Influenza A virus (A/swine/Michigan/A01202037/2011(H1N2)) yes
CY086912 Swine 4 H1N1 USA 2010/09/08 1746 Influenza A virus (A/swine/Minnesota/226128/2010(H1N1)) yes
CY086915 Swine 7 H1N1 USA 2010/09/08 1002 Influenza A virus (A/swine/Minnesota/226128/2010(H1N1)) yes
CY086914 Swine 6 H1N1 USA 2010/09/08 1436 Influenza A virus (A/swine/Minnesota/226128/2010(H1N1)) yes
CY086916 Swine 8 H1N1 USA 2010/09/08 864 Influenza A virus (A/swine/Minnesota/226128/2010(H1N1)) yes
CY086913 Swine 5 H1N1 USA 2010/09/08 1520 Influenza A virus (A/swine/Minnesota/226128/2010(H1N1)) yes
CY086911 Swine 3 H1N1 USA 2010/09/08 2142 Influenza A virus (A/swine/Minnesota/226128/2010(H1N1))
CY086910 Swine 2 H1N1 USA 2010/09/08 1450 Influenza A virus (A/swine/Minnesota/226128/2010(H1N1))
CY086909 Swine 1 H1N1 USA 2010/09/08 1899 Influenza A virus (A/swine/Minnesota/226128/2010(H1N1))
JN863558 Swine 6 H1N1 USA 2011/06/08 1410 Influenza A virus (A/swine/Mississippi/A01202059/2011(H1N1)) yes
JN863573 Swine 7 H1N1 USA 2011/06/08 982 Influenza A virus (A/swine/Mississippi/A01202059/2011(H1N1)) yes
CY081566 Swine 4 H1N2 USA 2010/12/28 1686 Influenza A virus (A/swine/South Dakota/4/2010(H1N2)) yes
CY081568 Swine 7 H1N2 USA 2010/12/28 1009 Influenza A virus (A/swine/South Dakota/4/2010(H1N2)) yes
CY081567 Swine 6 H1N2 USA 2010/12/28 1410 Influenza A virus (A/swine/South Dakota/4/2010(H1N2)) yes

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No H sequence

LOCUS JN863559 1410 bp cRNA linear VRL 12-NOV-2011
DEFINITION Influenza A virus (A/swine/Iowa/A01202063/2011(N2)) segment 6
neuraminidase (NA) gene, complete cds.
ACCESSION JN863559
VERSION JN863559.1 GI:356471571
KEYWORDS .
SOURCE Influenza A virus (A/swine/Iowa/A01202063/2011(N2))
ORGANISM Influenza A virus (A/swine/Iowa/A01202063/2011(N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1410)
AUTHORS Nezami,S.G., Sun,D., Zhang,J., Stensland,W.R., Strait,E.L. and
Yoon,K.-J.
TITLE SIV surveillance
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1410)
AUTHORS Nezami,S.G., Sun,D., Zhang,J., Stensland,W.R., Strait,E.L. and
Yoon,K.-J.
TITLE Direct Submission
JOURNAL Submitted (17-OCT-2011) VDPAM, Iowa State University, 1600 S 16th
Str., Ames, IA 50010, USA
FEATURES Location/Qualifiers
source 1..1410
/organism="Influenza A virus
(A/swine/Iowa/A01202063/2011(N2))"
/mol_type="viral cRNA"
/strain="A/swine/Iowa/A01202063/2011"
/serotype="N2"
/host="pig"
/db_xref="taxon:1096800"
/segment="6"
/country="USA: Iowa"
/collection_date="07-Jun-2011"
gene 1..1410
/gene="NA"
CDS 1..1410
/gene="NA"
/codon_start=1
/product="neuraminidase"
/protein_id="AET09998.1"
/db_xref="GI:356471572"
/translation="MNPNQKIITIGSVSLIIATICFLMQIAILVTTVTLHFKQHDYNS
PPNNQAMLCEPTIIERNTTEIVYLINTTIEKEICPKLAEYRNWSKPQCNITGFAPFSK
DNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNGHSNNTVHDRTPYRTLLM
NELGVPFHLGTRQVCMAWSSSSCHDGKAWLHVCITGNDNNATASFIYNGRLVDSIGSW
SKNILRTQESECVCINGTCTVVMTDGSASGKADTKILFVEEGKIVHISTLSGSAQHVE
ECSCYPRFPGVRCVCRDNWKGSNRPIVDINVKNYSIVSSYVCSGLVGDTPRKSDSVSS
SYCLDPNNEKGGHGVKGWAFDDGNDVWMGRTINETLRLGYETFKVIEGWSKANSKLQT
NRQVIVEKGDRSGYSGIFSVEGKSCINRCFYVELIRGRKEETKVWWTSNSIVVFCGTS
GTYGTGSWPDGADINLMPI"
ORIGIN
1 atgaatccaa atcaaaagat aataacaatt ggctctgttt ctctcatcat tgccacaata
61 tgtttcctta tgcaaattgc tatcctagta actactgtaa cattacattt caagcagcat
121 gactacaact cccccccaaa caaccaagca atgctgtgtg aaccaacaat aatagaaaga
181 aacacaacag agattgtgta tttgatcaac accaccatag agaaagaaat atgccccaaa
241 ctagcagaat atagaaactg gtcaaagccg caatgtaaca ttacaggatt tgcacctttt
301 tctaaggaca attcaattcg gctttctgct ggtggggaca tttgggtgac aagagaacct
361 tatgtgtcat gcgatcctga caagtgttat caatttgccc ttgggcaggg aacaacatta
421 aacaacggac attcaaataa cactgtacat gataggaccc cttatcgaac cctattgatg
481 aatgaattgg gtgttccatt tcatttagga accaggcaag tgtgcatggc atggtccagc
541 tcaagttgcc acgatggaaa agcatggctg catgtttgta taactgggaa tgataacaat
601 gcaacagcta gcttcattta caatgggagg cttgtagata gtattggttc atggtccaaa
661 aatatactca gaacccagga gtcggaatgc gtctgtatca atggaacctg tacagtagta
721 atgactgatg ggagcgcttc aggaaaagct gatactaaaa tactattcgt tgaggagggg
781 aagatcgttc atattagcac attgtcagga agtgctcagc atgttgagga gtgctcctgt
841 tatcctcgat ttcctggtgt cagatgtgta tgcagagaca actggaaagg ctccaatagg
901 cccatcgtag atataaatgt aaagaattat agcattgttt ccagttatgt atgctcagga
961 cttgttggag acacacccag aaaaagcgac agcgtcagca gtagttattg cctagatcct
1021 aacaatgaga aaggtggtca tggggtgaaa ggctgggcct ttgatgatgg aaatgacgtg
1081 tggatgggaa ggacaatcaa cgagacgtta cgcttaggtt atgaaacctt caaagtcatt
1141 gaaggctggt ccaaagctaa ctccaaatta cagacaaata ggcaagtcat agttgaaaaa
1201 ggtgacaggt ccggttattc tggtattttc tccgttgaag gtaaaagctg catcaatcgg
1261 tgcttttatg tggagttgat aaggggaagg aaagaggaaa ctaaagtctg gtggacctca
1321 aacagtattg ttgtgttttg tggcacctca ggtacatatg gaacaggctc atggcccgat
1381 ggagcggata tcaatctcat gcctatataa

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Top N2 matches are from H1N2 (as expected), including identity with A/swine/Iowa/A01049863/2011

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 2604 2604 100% 0.0 100%
JN652533.1 Influenza A virus (A/swine/Iowa/A01049864/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2599 2599 100% 0.0 99%
JN652551.1 Influenza A virus (A/swine/Minnesota/A01049956/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2588 2588 100% 0.0 99%
JN652535.1 Influenza A virus (A/swine/Iillinois/A01049872/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2588 2588 100% 0.0 99%
JF812308.1 Influenza A virus (A/swine/Iowa/A01049071/2010(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2582 2582 100% 0.0 99%
JF312068.1 Influenza A virus (A/swine/Pennsylvania/62170-3/2010(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2577 2577 100% 0.0 99%
JF312066.1 Influenza A virus (A/swine/Pennsylvania/62170-1/2010(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2577 2577 100% 0.0 99%
JN652445.1 Influenza A virus (A/swine/Indiana/A01049653/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2571 2571 100% 0.0 99%
JN652552.1 Influenza A virus (A/swine/Indiana/A01049964/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2571 2571 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 2566 2566 100% 0.0 99%
JN652534.1 Influenza A virus (A/swine/Iillinois/A01049871/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2566 2566 100% 0.0 99%
JN652529.1 Influenza A virus (A/swine/Indiana/A01049794/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2566 2566 100% 0.0 99%
JN652523.1 Influenza A virus (A/swine/Indiana/A01049745/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2566 2566 100% 0.0 99%
JN652522.1 Influenza A virus (A/swine/Indiana/A01049744/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2566 2566 100% 0.0 99%
JN863546.1 Influenza A virus (A/swine/Iowa/A01049970/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2564 2564 100% 0.0 99%
JN863553.1 Influenza A virus (A/swine/Michigan/A01202037/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2560 2560 100% 0.0 99%
JN863552.1 Influenza A virus (A/swine/Michigan/A01202036/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2560 2560 100% 0.0 99%
JN652456.1 Influenza A virus (A/swine/Iowa/A01049858/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2560 2560 100% 0.0 99%
JN652432.1 Influenza A virus (A/swine/Iowa/A01049506/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2560 2560 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 2560 2560 100% 0.0 99%
JN162021.1 Influenza A virus (A/swine/North Carolina/A01049436/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2560 2560 100% 0.0 99%
JF812312.1 Influenza A virus (A/swine/Indiana/A01049091/2010(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2560 2560 100% 0.0 99%
JF312067.1 Influenza A virus (A/swine/Pennsylvania/62170-2/2010(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2560 2560 100% 0.0 99%
JF312055.1 Influenza A virus (A/swine/Minnesota/A01047604/2010(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2560 2560 100% 0.0 99%
JN638732.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2556 2556 100% 0.0 99%
JN652452.1 Influenza A virus (A/swine/Iowa/A01049726/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2555 2555 100% 0.0 99%
JN652453.1 Influenza A virus (A/swine/Iowa/A01049728/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2555 2555 100% 0.0 99%
CY078425.1 Influenza A virus (A/swine/South Dakota/3/2010(H1N2)) segment 6 sequence 2555 2555 100% 0.0 99%
CY078422.1 Influenza A virus (A/swine/South Dakota/2/2010(H1N2)) segment 6 sequence 2555 2555 100% 0.0 99%
JN652449.1 Influenza A virus (A/swine/Iowa/A01049722/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2549 2549 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 2549 2549 100% 0.0 99%
JN652550.1 Influenza A virus (A/swine/Indiana/A01049953/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2549 2549 100% 0.0 99%
JN652530.1 Influenza A virus (A/swine/Iowa/A01049846/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2549 2549 100% 0.0 99%
JF312069.1 Influenza A virus (A/swine/Pennsylvania/62170-4/2010(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2549 2549 100% 0.0 99%
CY081567.1 Influenza A virus (A/swine/South Dakota/4/2010(H1N2)) neuraminidase (NA) gene, complete cds 2549 2549 100% 0.0 99%
CY099368.1 Influenza A virus (A/swine/Illinois/A00907647/2011(H1N2)) neuraminidase (NA) gene, complete cds 2538 2538 100% 0.0 99%
JN652548.1 Influenza A virus (A/swine/Iowa/A01049951/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2532 2532 100% 0.0 99%
JN655545.1 Influenza A virus (A/Pennsylvania/11/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2525 2525 98% 0.0 99%
JN655557.1 Influenza A virus (A/Indiana/08/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2519 2519 98% 0.0 99%
JN652553.1 Influenza A virus (A/swine/Illinois/A01049967/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2516 2516 100% 0.0 98%
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 2516 2516 100% 0.0 98%
JN652549.1 Influenza A virus (A/swine/Illinois/A01049952/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2516 2516 100% 0.0 98%
JN866185.1 Influenza A virus (A/Maine/06/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2503 2503 98% 0.0 99%
JN655533.1 Influenza A virus (A/Pennsylvania/09/2011(H3N2)) segment 6 neuraminidase (NA) gene, partial cds 2497 2497 98% 0.0 99%
CY045601.1 Influenza A virus (A/swine/Oklahoma/010226-17/2008(H1N2)) segment 6 sequence 2471 2471 100% 0.0 98%
CY045649.1 Influenza A virus (A/swine/Oklahoma/011521-5/2008(H1N2)) segment 6 sequence 2466 2466 100% 0.0 98%
CY045697.1 Influenza A virus (A/swine/Oklahoma/020736-2/2008(H1N2)) segment 6 sequence 2466 2466 100% 0.0 98%
CY045705.1 Influenza A virus (A/swine/Oklahoma/020736-1/2008(H1N2)) segment 6 sequence 2466 2466 100% 0.0 98%
CY045625.1 Influenza A virus (A/swine/Oklahoma/011289-9/2008(H1N2)) segment 6 sequence 2466 2466 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 2466 2466 100% 0.0 98%
CY045609.1 Influenza A virus (A/swine/Oklahoma/010710-9/2008(H1N2)) segment 6 sequence 2460 2460 100% 0.0 98%
CY045593.1 Influenza A virus (A/swine/Oklahoma/010226-16/2008(H1N2)) segment 6 sequence 2460 2460 100% 0.0 98%
HQ424898.1 Influenza A virus (A/swine/Oklahoma/44837-5/2010(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2455 2455 100% 0.0 98%
CY045681.1 Influenza A virus (A/swine/Oklahoma/020734-2/2008(H1N2)) segment 6 sequence 2455 2455 100% 0.0 98%
CY045617.1 Influenza A virus (A/swine/Oklahoma/010710-8/2008(H1N2)) segment 6 sequence 2455 2455 100% 0.0 98%
CY045537.1 Influenza A virus (A/swine/Texas/050625/2008(H1N2)) segment 6 sequence 2455 2455 100% 0.0 98%
CY045521.1 Influenza A virus (A/swine/Oklahoma/032726/2008(H1N2)) segment 6 sequence 2453 2453 99% 0.0 98%
CY045673.1 Influenza A virus (A/swine/Oklahoma/016179-9/2008(H1N2)) segment 6 sequence 2449 2449 100% 0.0 98%
CY045665.1 Influenza A virus (A/swine/Oklahoma/016179-8/2008(H1N2)) segment 6 sequence 2449 2449 100% 0.0 98%
CY045657.1 Influenza A virus (A/swine/Oklahoma/011521-4/2008(H1N2)) segment 6 sequence 2449 2449 100% 0.0 98%
CY045529.1 Influenza A virus (A/swine/Texas/050593/2008(H1N2)) segment 6 sequence 2449 2449 100% 0.0 98%
CY045545.1 Influenza A virus (A/swine/Oklahoma/053259/2008(H1N2)) segment 6 sequence 2438 2438 100% 0.0 97%
CY045713.1 Influenza A virus (A/swine/Oklahoma/042169/2008(H1N2)) segment 6 sequence 2416 2416 100% 0.0 97%
CY045561.1 Influenza A virus (A/swine/Kansas/015252/2009(H3N2)) segment 6 sequence 2410 2410 100% 0.0 97%
CY086930.1 Influenza A virus (A/swine/Minnesota/239106/2010(H1N2)) neuraminidase (NA) gene, complete cds 2405 2405 100% 0.0 97%
CY045553.1 Influenza A virus (A/swine/Oklahoma/001142/2009(H3N2)) segment 6 sequence 2405 2405 100% 0.0 97%
CY089402.1 Influenza A virus (A/swine/South Dakota/5/2011(H1N2)) neuraminidase (NA) gene, complete cds 2377 2377 100% 0.0 97%
CY089405.1 Influenza A virus (A/swine/South Dakota/6/2011(H1N2)) neuraminidase (NA) gene, complete cds 2366 2366 100% 0.0 96%
JN652543.1 Influenza A virus (A/swine/Arkansas/A01049917/2011(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2357 2357 100% 0.0 96%
HQ424889.1 Influenza A virus (A/swine/North Carolina/44837-2/2009(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2350 2350 100% 0.0 96%
CY099209.1 Influenza A virus (A/swine/Minnesota/02324/2008(H1N2)) neuraminidase (NA) gene, complete cds 2338 2338 100% 0.0 96%
CY099177.1 Influenza A virus (A/swine/Minnesota/SG1133/2008(H1N2)) neuraminidase (NA) gene, complete cds 2333 2333 100% 0.0 96%
EU735820.1 Influenza A virus (A/turkey/OH/313053/2004(H3N2)) neuraminidase (NA) gene, complete cds 2327 2327 100% 0.0 96%
DQ335773.1 Influenza A virus (A/turkey/Ohio/313053/04(H3N2)) neuraminidase (NA) gene, complete cds 2327 2327 100% 0.0 96%
CY099029.1 Influenza A virus (A/swine/Iowa/01700/2007(H3N2)) neuraminidase (NA) gene, complete cds 2316 2316 100% 0.0 96%
EU735828.1 Influenza A virus (A/turkey/NC/353568/2005(H3N2)) neuraminidase (NA) gene, complete cds 2311 2311 100% 0.0 96%
EF551055.1 Influenza A virus (A/swine/North Carolina/2003(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2311 2311 100% 0.0 96%
EF551047.1 Influenza A virus (A/turkey/Illinois/2004(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2311 2311 100% 0.0 96%
DQ469976.1 Influenza A virus (A/swine/British Columbia/28103/2005(H3N2)) neuraminidase (NA) gene, complete cds 2309 2309 99% 0.0 96%
CY099249.1 Influenza A virus (A/swine/Minnesota/00484/2005(H3N2)) neuraminidase (NA) gene, complete cds 2305 2305 100% 0.0 96%
CY099145.1 Influenza A virus (A/swine/Minnesota/00611/2005(H3N2)) neuraminidase (NA) gene, complete cds 2305 2305 100% 0.0 96%
CY099088.1 Influenza A virus (A/swine/Nebraska/00722/2005(mixed)) neuraminidase (NA) gene, complete cds 2305 2305 100% 0.0 96%
CY099054.1 Influenza A virus (A/swine/Illinois/02450/2008(mixed)) neuraminidase (NA) gene, complete cds 2300 2300 100% 0.0 96%
EU826544.2 Influenza A virus (A/swine/Quebec/4001/2005(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2300 2300 100% 0.0 96%
HQ825168.1 Influenza A virus (A/turkey/BC/1529-3/2005(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2294 2294 100% 0.0 96%
EU697211.1 Influenza A virus (A/turkey/North Carolina/353568/2005(H3N2)) neuraminidase (NA) gene, complete cds 2294 2294 100% 0.0 96%
DQ469992.1 Influenza A virus (A/swine/Ontario/33853/2005(H3N2)) neuraminidase (NA) gene, complete cds 2294 2294 100% 0.0 96%
DQ469984.1 Influenza A virus (A/swine/Manitoba/12707/2005(H3N2)) neuraminidase (NA) gene, complete cds 2294 2294 100% 0.0 96%
DQ469960.1 Influenza A virus (A/Ontario/RV1273/2005(H3N2)) neuraminidase (NA) gene, complete cds 2294 2294 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 95%
DQ470000.1 Influenza A virus (A/turkey/Ontario/31232/2005(H3N2)) neuraminidase (NA) gene, complete cds 2287 2287 99% 0.0 95%
GU480921.1 Influenza A virus (A/swine/SD/31813/2009(H1N2)) segment 6 neuraminidase (NA) gene, complete cds 2283 2283 100% 0.0 95%
EU743212.1 Influenza A virus (A/turkey/MN/366767/2005(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2283 2283 100% 0.0 95%
CY099037.1 Influenza A virus (A/swine/Minnesota/01146/2006(H3N2)) neuraminidase (NA) gene, complete cds 2278 2278 100% 0.0 95%
FJ519965.1 Influenza A virus (A/swine/Minnesota/1300/2007(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2278 2278 100% 0.0 95%
FJ519962.1 Influenza A virus (A/swine/Minnesota/66960/2006(H3N2)) segment 6 neuraminidase (NA) gene, complete cds 2278 2278 100% 0.0 95%
EU697206.1 Influenza A virus (A/turkey/Minnesota/366767/2005(H3N2)) neuraminidase (NA) gene, complete cds 2278 2278 100% 0.0 95%
DQ469968.1 Influenza A virus (A/swine/Alberta/14722/2005(H3N2)) neuraminidase (NA) gene, complete cds 2278 2278 100% 0.0 95%
CY099233.1 Influenza A virus (A/swine/Minnesota/001332/2006(H3N2)) neuraminidase (NA) gene, complete cds 2272 2272 100% 0.0 95%
CY099217.1 Influenza A virus (A/swine/Minnesota/001444/2007(H3N2)) neuraminidase (NA) gene, complete cds 2272 2272 100% 0.0 95%

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A quick count identifies 15 isolates from 2011 (May and June), all H1N1 or H1N2.

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H1N1

A/swine/Illinois/A01049980/2011 05/17
A/swine/Illinois/A01049981/2011 05/17
A/swine/Iowa/A01202023/2011 05/26
A/swine/Iowa/A01202033/2011 05/27
A/swine/Iowa/A01202034/2011 05/27
A/swine/Iowa/A01202041/2011 06/02
A/swine/Iowa/A01202048/2011 06/02
A/swine/Iowa/A01202049/2011 06/02
A/swine/Iowa/A01202056/2011 06/02
A/swine/Mississippi/A01202059/2011 06/08



H1N2
A/swine/Iowa/A01049970/2011 05/16
A/swine/Michigan/A01202035/2011 05/26
A/swine/Michigan/A01202036/2011 05/26
A/swine/Michigan/A01202037/2011 05/26
A/swine/Iowa/A01202063/2011 06/07

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LOCUS JN863558 1410 bp cRNA linear VRL 12-NOV-2011
DEFINITION Influenza A virus (A/swine/Mississippi/A01202059/2011(H1N1))
segment 6 neuraminidase (NA) gene, complete cds.
ACCESSION JN863558
VERSION JN863558.1 GI:356471569
KEYWORDS .
SOURCE Influenza A virus (A/swine/Mississippi/A01202059/2011(H1N1))
ORGANISM Influenza A virus (A/swine/Mississippi/A01202059/2011(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1410)
AUTHORS Nezami,S.G., Sun,D., Zhang,J., Stensland,W.R., Strait,E.L. and
Yoon,K.-J.
TITLE SIV surveillance
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1410)
AUTHORS Nezami,S.G., Sun,D., Zhang,J., Stensland,W.R., Strait,E.L. and
Yoon,K.-J.
TITLE Direct Submission
JOURNAL Submitted (17-OCT-2011) VDPAM, Iowa State University, 1600 S 16th
Str., Ames, IA 50010, USA
FEATURES Location/Qualifiers
source 1..1410
/organism="Influenza A virus
(A/swine/Mississippi/A01202059/2011(H1N1))"
/mol_type="viral cRNA"
/strain="A/swine/Mississippi/A01202059/2011"
/serotype="H1N1"
/host="pig"
/db_xref="taxon:1096796"
/segment="6"
/country="USA: Mississippi"
/collection_date="08-Jun-2011"
gene 1..1410
/gene="NA"
CDS 1..1410
/gene="NA"
/codon_start=1
/product="neuraminidase"
/protein_id="AET09997.1"
/db_xref="GI:356471570"
/translation="MNTNQRIITIGTVCMIVGIISLLLQIGSIVSLWISHSIQTGWEN
HTEMCNQSVITYVNNTWVNRTYVNISNTNIATIQDVTSIILAGNSSLCPVSGWAIYSK
DNSIRIGSKGDIFVIREPFISCSQLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMS
CPIGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKS
WRNKILRTQESECVCMNGSCFTVLTDGPSNGQASYKIFKVEKGKIIKSIELDAPNYHY
EECSCYPDTGKVMCVCRDNWHASNRPWVSFNQDLDYQIGYICSGVFGDNPRSNDGKGN
CGPVLSNGANGVKGFSYRYGNGVWIGRTKSINSRRGFEIIWDPNGWTETDSSFSMKQD
IIALTDWSGYSGSFVQHPELTGMNCIRPCFWVELIRGQPKESTIWASGSSISFCGVNS
ETASWSWPDGADLPFTIDK"
ORIGIN
1 atgaatacaa atcaaagaat aataaccatt gggacagttt gtatgatagt tggaataatc
61 agtctattgt tacagatagg aagcatagtc tcgttatgga ttagccattc aattcagacc
121 ggatgggaaa atcacactga gatgtgcaac caaagtgtca ttacatatgt aaataacaca
181 tgggtgaacc gaacttatgt gaacattagc aataccaaca ttgctactat acaggatgtg
241 acttcgatta tactagccgg caattcctca ctttgcccag taagtggatg ggctatatac
301 agcaaagaca atagcataag aattggttct aaaggggaca tttttgtcat aagagaacca
361 ttcatttcat gctctcaatt ggaatgcaga accttttttc tgacccaagg cgccttgctg
421 aatgacaagc attctaatgg aaccgtcaag gacaggagtc cctatagaac cctgatgagc
481 tgccccatcg gtgaagcgcc atctccatac aactcaaggt tcgaatcagt tgcttggtca
541 gcaagtgcat gccatgatgg gatgggatgg ctaacaatcg ggatctctgg tccagataat
601 ggagcagtag ctgttttaaa atacaacggt ataataacag atacaataaa aagttggaga
661 aacaaaatat taagaacaca agagtcggaa tgtgtttgta tgaacggttc ttgttttact
721 gtattaactg atggcccaag caatgggcaa gcctcgtaca aaatatttaa agtggaaaaa
781 ggaaaaataa ttaagtcaat tgagctggat gcccccaatt accactatga ggaatgctca
841 tgttatcctg atacaggcaa agtaatgtgt gtttgcagag acaattggca tgcctcgaac
901 cggccatggg tctctttcaa tcaggatctt gattatcaaa tagggtacat atgcagtgga
961 gttttcggtg ataacccgcg ttctaatgat ggaaagggca attgtggccc agtactttct
1021 aatggagcaa atggagtgaa aggattctca tatagatatg gtaatggtgt ttggatagga
1081 agaactaaga gtatcaactc cagaagaggg tttgagatca tttgggatcc aaatgggtgg
1141 actgaaactg atagtagttt ctctatgaag caggacatta tagcattaac tgattggtca
1201 ggatacagtg gaagttttgt ccaacatcct gaattaacag gaatgaattg cataaggcct
1261 tgtttctggg tggaattaat cagagggcaa cccaaggaaa gcacaatctg ggctagcgga
1321 agcagcatct ctttctgtgg cgtaaatagt gaaaccgcaa gctggtcatg gccagacgga
1381 gctgatctgc cattcaccat tgacaagtag

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Commentary

http://www.recombinomics.com/News/11141 ... 6_NOT.html

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