Rhiza Labs FluTracker Forum

These sequences are now available at Genbank.

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www.twitter.com/hniman

LOCUS CY086933 2314 bp cRNA linear VRL 22-SEP-2011
DEFINITION Influenza A virus (A/swine/North Carolina/239108/2010(H1N2))
polymerase PB2 (PB2) gene, complete cds.
ACCESSION CY086933
VERSION CY086933.1 GI:325111552
KEYWORDS .
SOURCE Influenza A virus (A/swine/North Carolina/239108/2010(H1N2))
ORGANISM Influenza A virus (A/swine/North Carolina/239108/2010(H1N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2314)
AUTHORS Ducatez,M.F., Hause,B., Stigger-Rosser,E., Darnell,D., Corzo,C.,
Juleen,K., Simonson,R., Brockwell-Staats,C., Rubrum,A., Wang,D.,
Webb,A., Crumpton,J.C., Lowe,J., Gramer,M. and Webby,R.J.
TITLE Multiple Reassortment between Pandemic (H1N1) 2009 and Endemic
Influenza Viruses in Pigs, United States
JOURNAL Emerging Infect. Dis. 17 (9), 1624-1629 (2011)
PUBMED 21892996
REFERENCE 2 (bases 1 to 2314)
AUTHORS Ducatez,M.F., Webby,R.J., Hause,B., Evelyn,S.-R., Darnel,D.,
Corzo,C., Juleen,K., Simonson,R., Rubrum,A., Lowe,J. and Gramer,M.
TITLE Direct Submission
JOURNAL Submitted (02-MAR-2011) Infectious Diseases, St. Jude Children's
Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee
38105, USA
FEATURES Location/Qualifiers
source 1..2314
/organism="Influenza A virus (A/swine/North
Carolina/239108/2010(H1N2))"
/mol_type="viral cRNA"
/strain="A/swine/North Carolina/239108/2010"
/serotype="H1N2"
/host="swine"
/db_xref="taxon:991772"
/segment="1"
/country="USA: North Carolina"
/collection_date="21-Apr-2010"
misc_feature 1..2314
/db_xref="IRD:CEIRS-SJC001-239108.1"
gene 1..2280
/gene="PB2"
CDS 1..2280
/gene="PB2"
/codon_start=1
/product="polymerase PB2"
/protein_id="ADY80116.1"
/db_xref="GI:325111553"
/translation="MERIKELRDLMSQSRTREILTRTTVDHMAIIKKYTSGRQEKNPA
LRMKWMMAMKYPITAEKRIMDVIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRS
GPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPGHADLSAKEAQ
DVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKIAPLMVAYMLERELVRKTRFL
PVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRAAVSADP
LASLLEMCHSTQIGGIRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTS
GSSIKKEEEVLTGNLQTLKMRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDDQ
SIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLSQNWG
IESIDSVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEYSSTERVVVSIDRFLRVRDQR
GNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLINTYQWIIRNWESLKIQWSQ
DPTMLYNKMEFEPFQSIVPKATRSRYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAA
PPEQSRMQFSSLTVNVRGSGLRILVRGNSPVFNFNKATKRLTILGKDAGALTEDPDEG
TAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRD
SSILTDSQTATKRIRMAIN"
ORIGIN
1 atggagagaa taaaagaact aagagaccta atgtcgcagt cccgcactcg cgagatactc
61 actaggacca ctgtggacca tatggccata atcaaaaagt acacatcagg aaggcaagag
121 aagaaccccg cactcagaat gaaatggatg atggcaatga aatacccaat tacagcagaa
181 aagagaataa tggacgtgat tccagagagg aatgaacaag gacaaaccct ctggagcaaa
241 acaaacgatg ctggatcgga ccgtgtgatg gtatcacccc tggccgtaac atggtggaat
301 aggagtggcc caacaacaag cacagttcac taccctaagg tatacaaaac ttacttcgaa
361 aaagtcgaaa ggttaaaaca tggtaccttt ggccctgtcc acttcagaaa tcaagttaaa
421 ataagaagga gggttgacac aaaccctggt catgcagatc tcagtgccaa ggaggcacag
481 gatgtgatca tggaagttgt tttcccaaat gaagtggggg caagaatact gacatcagag
541 tcacagctga caataacaaa agaaaagaaa gaagagctcc aggattgtaa aattgctccc
601 ttgatggtgg catacatgct agaaagagag ttggttcgta agacgaggtt tctcccggtg
661 gctggtggaa caagcagtgt ttatatcgaa gtgctgcact taactcaggg aacatgctgg
721 gagcaaatgt acactccagg aggagaagtg agaaacgatg atgttgacca aagtttgatt
781 atcgctgcta gaaacatagt aagaagagca gcagtgtcag cagacccatt agcatctctc
841 ttggaaatgt gccacagcac acagattgga ggaataagga tggtggacat ccttagacag
901 aacccaacgg aggaacaagc cgtagacata tgcaaggcag caatggggct gaggattagc
961 tcctctttca gctttggtgg gttcaccttc aaaagaacaa gcggatcatc aattaagaaa
1021 gaagaagaag tgctcacggg caacctccaa acactgaaaa tgagagtaca tgaagggtat
1081 gaagaattca caatggtcgg gagaagagca acagctattc tcagaaaagc aaccaggaga
1141 ttgatccagt taatagtaag tgggagagac gatcaatcaa ttgctgaggc aataattgtg
1201 gccatggtat tttcacaaga ggattgcatg atcaaggcag ttaggggcga tctgaatttt
1261 gtcaataggg caaaccagcg actgaatcct atgcaccaac tcttgaggca tttccaaaaa
1321 gatgcaaaag tgctttccca gaactgggga attgaatcca tcgacagtgt gatgggaatg
1381 atcgggatat tgcctgatat gaccccaagc acggaaatgt cgctgagggg tataagagtc
1441 agcaaaatgg gagtagatga gtattccagc actgagagag tggtagtgag cattgaccga
1501 tttttgagag tccgggatca acgagggaac gtactattgt ctcccgaaga ggtcagcgag
1561 acacaaggaa ctgagaaatt gacaataact tattcgtcat caatgatgtg ggagatcaat
1621 ggtcctgagt cagtgctgat caacacttat caatggatca taaggaactg ggaaagcttg
1681 aaaattcagt ggtcacaaga tcccacgatg ttatacaaca aaatggaatt tgaaccattc
1741 cagtctattg tccctaaggc aaccagaagt cgttacagtg gattcgtgag gacactgttc
1801 cagcaaatgc gggatgtgct tggaacattt gacactgtcc aaataataaa acttctcccc
1861 tttgctgctg ctccaccgga acagagtagg atgcagttct cctcgctgac tgtgaatgtg
1921 agaggatcag gactgaggat actggtaaga ggcaattctc cagtgttcaa tttcaacaaa
1981 gcaactaaaa ggctcacaat tcttggaaaa gatgcaggtg cgttgactga agatccagat
2041 gaaggcacag ctggagtgga gtctgctgtt ctgaggggat tcctcatttt gggtaaagaa
2101 gacaagagat atggcccagc attaagcatc aatgaactga gcaatcttgc caaaggagag
2161 aaggctaatg tgctaattgg gcaaggagac gtggtgttgg taatgaaacg gaaacgggac
2221 tctagcatac ttactgacag ccagacagcg accaaaagaa ttcggatggc catcaattag
2281 tgtcgaattg tttaaaaacg accttgtttc tact

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What would happen if this M found its way into H5N1?

Answer

http://www.newscientist.com/article/mg2 ... nline-news

Nonsense. The question is on reassortment, not single nucleotide changes.

_________________
www.twitter.com/hniman

That is a good question. For the trH3N2 sub-clade, the swap is between different M's found in triple reassortants. The polymerase cpmplex first formed in the 1990's and the version in pandemic H1N1 has evolved independently, so the M gene in pandmeic H1N1 is distinct from the M in North American triple reassortants, but swapping still involes triple reassortants with the same general polynmerase complex (human PB1 and avian PA and PB2).

Thus, it is not clear how well a pandemic H1N1 M gene would interact with the internal H5N1 genes, although in general H1N1 genes are closer to H5N1 than seasonal H3N2 genes,

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www.twitter.com/hniman

Thanks.

Looks like it was pretty quiet down here this winter - I wonder what your winter will bring with trH3N2?

Recent H1N2, A/swine/Illinois/A00907647/2011, with M gene from pandemic H1N1 and N2 cloely related to recent trH3N2 sequences.

_________________
www.twitter.com/hniman

Serious isues.

_________________
www.twitter.com/hniman

LOCUS CY099368 1448 bp cRNA linear VRL 23-SEP-2011
DEFINITION Influenza A virus (A/swine/Illinois/A00907647/2011(H1N2))
neuraminidase (NA) gene, complete cds.
ACCESSION CY099368
VERSION CY099368.1 GI:347605596
KEYWORDS .
SOURCE Influenza A virus (A/swine/Illinois/A00907647/2011(H1N2))
ORGANISM Influenza A virus (A/swine/Illinois/A00907647/2011(H1N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1448)
AUTHORS Odyniec,L. and Gramer,M.R.
TITLE USDA NAHLN Voluntary Swine Influenza Surveillance
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1448)
AUTHORS Odyniec,L. and Gramer,M.R.
TITLE Direct Submission
JOURNAL Submitted (23-SEP-2011) VDL, University of Minnesota VDL, 1333
Gortner Ave., St. Paul, MN 55108, USA
FEATURES Location/Qualifiers
source 1..1448
/organism="Influenza A virus
(A/swine/Illinois/A00907647/2011(H1N2))"
/mol_type="viral cRNA"
/strain="A/swine/Illinois/A00907647/2011"
/serotype="H1N2"
/host="swine"
/db_xref="taxon:1089353"
/segment="6"
/lab_host="P1 passage(s)"
/country="USA: Illinois"
/collection_date="08-Jul-2011"
gene 1..1410
/gene="NA"
CDS 1..1410
/gene="NA"
/codon_start=1
/product="neuraminidase"
/protein_id="AEP16574.1"
/db_xref="GI:347605597"
/translation="MNPNQKIITIGSVSLIIATICFLMQIAILVTTVTLHFKQHDYNS
PPNNQAMLCEPTIIERNTTEIVYLTNITIEKEICPKLAEYRNWSKPQCNITGFAPFSK
DNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNGHSNNTVHDRTPYRTLLM
NELGVPFHLGTRQVCMAWSSSSCHDGKAWLHVCITGNDNNATASFIYNGRLVDSIGSW
SKNILRTQESECVCINGTCTVVMTDGSASGRADTKILFVEEGKIVHISTLSGSAQHVE
ECSCYPRFSGVRCVCRDNWRGSNRPIVDINVKNYSIVSSYVCSGLVGDTPRESDSVSS
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 tttgaccaac atcaccatag agaaagaaat atgccccaaa
241 ctagcagaat atagaaactg gtcaaagccg caatgtaaca ttacaggatt tgcacctttt
301 tctaaggaca attcaattcg gctttctgct ggtggggaca tctgggtgac aagagaacct
361 tatgtgtcat gcgatcctga caagtgttat caatttgccc ttgggcaggg aacaacatta
421 aacaacggac attcaaataa cactgtacat gataggaccc cttatcgaac cctattgatg
481 aatgaattgg gtgttccatt tcatttagga accaggcaag tgtgcatggc atggtccagc
541 tcaagttgtc acgatggaaa agcatggctg catgtttgta taactgggaa tgataacaat
601 gcaacagcta gcttcattta caatgggagg cttgtagata gtattggttc atggtccaaa
661 aatatactca gaacccagga gtcggaatgc gtctgtatca atggaacctg tacagtagta
721 atgactgatg ggagcgcttc aggaagagct gatactaaaa tactattcgt tgaggagggg
781 aagatcgttc atattagcac attgtcagga agtgctcagc atgttgagga gtgctcctgt
841 tatcctcgat tttctggtgt cagatgtgtc tgcagagaca actggagagg ctccaatagg
901 cccatcgtag atataaatgt aaagaattat agcattgttt ccagttatgt atgctcagga
961 cttgttggag acacacccag agaaagcgac agcgtcagca gtagttattg cctagatcct
1021 aacaatgaga aaggtggtca tggggtgaaa ggatgggcct ttgatgatgg gaatgacgtg
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 atggcctgat
1381 ggagcggata tcaatctcat gcctatataa gctttcgcaa ttttagaaaa aaactccttg
1441 tttctact

_________________
www.twitter.com/hniman