niman wrote:
niman wrote:
Parallel H1N1 Pandemics in 2010?
Recombinomics Commentary 03:50
July 7, 2010
An H1N1 influenza A virus, A/swine/Ohio/24366/07, was isolated from pigs in an Ohio county fair. Twenty-six people who came in contact with the infected pigs developed respiratory disease and two of these people were laboratory confirmed as H1N1 by the Centers for Disease Control and Prevention (CDC). The A/swine/Ohio/24366/07 virus we isolated from swine was shown at the CDC to have 100% identical genome sequence to the human virus associated with the county fair.
Many of the interal genes in MN/11/2010 are closely related to those from human isolates from the above Hudson County fair in 2007. This cluster was the largest reported swine flu outbreak since the Fox Dix outbreak in 1976. These internal genes are present in tha vast majority of trH3N2 human isolates. In the US, all reported trH3N2 cases followed the H1N1 pademic in 2009.
PB2 from the Hudson Valley fair is closely related to human trH3n2 cases including MN/11. The PB2 from MN11 is VERY closley related to swine H1N1 PB2 in Minnesota
http://www.ncbi.nlm.nih.gov/nuccore/JF312057LOCUS JF312057 2280 bp cRNA linear VRL 27-MAR-2011
DEFINITION Influenza A virus (A/swine/Minnesota/A01047613/2010(H1N1)) segment
1 polymerase PB2 (PB2) gene, complete cds.
ACCESSION JF312057
VERSION JF312057.1 GI:326579167
KEYWORDS .
SOURCE Influenza A virus (A/swine/Minnesota/A01047613/2010(H1N1))
ORGANISM Influenza A virus (A/swine/Minnesota/A01047613/2010(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2280)
AUTHORS McGill,J.L. and Gramer,M.
TITLE Direct Submission
JOURNAL Submitted (09-FEB-2011) DVL-BPA, USDA, APHIS, NVSL, 1920 Dayton
Ave., Ames, IA 50010, USA
FEATURES Location/Qualifiers
source 1..2280
/organism="Influenza A virus
(A/swine/Minnesota/A01047613/2010(H1N1))"
/mol_type="viral cRNA"
/strain="A/swine/Minnesota/A01047613/2010"
/serotype="H1N1"
/host="swine"
/db_xref="taxon:983888"
/segment="1"
/country="USA"
/collection_date="10-Dec-2010"
gene 1..2280
/gene="PB2"
CDS 1..2280
/gene="PB2"
/codon_start=1
/product="polymerase PB2"
/protein_id="ADZ96082.1"
/db_xref="GI:326579168"
/translation="MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPA
LRMKWMMAMKYPITADRRIMDMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRN
GPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPGHADLSAKEAQ
DVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKIAPLMVAYMLERELVRKTRFL
PVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRAAVSADP
LASLLEMCHSTQIGGIRMMDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTS
GSSVKKEEEVLTGNLQTLKIKVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDDQ
SIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG
IEPIDSVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEYSSTERVVVSIDRFLRVRDQR
GNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWESLKIQWSQ
DPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAA
PPEQSRMQFSSLTVNVRGSGLRILVRGNSPVFNYNKATKRLTILGKDAGALTEDPDEG
TAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRD
SSILTDSQTATKRIRMAIN"
ORIGIN
1 atggagagaa taaaagaact aagagatcta atgtctcagt cccgcactcg cgagatactc
61 actaagacca ctgtggacca tatggccata atcaaaaagt acacatcagg aaggcaggag
121 aagaaccccg cactcagaat gaagtggatg atggcaatga aatacccaat tacagcagac
181 aggagaataa tggacatgat tccagagagg aatgaacaag gacaaaccct ctggagcaaa
241 acaaacgatg ctggatcgga ccgtgtgatg gtatcacccc tggccgtaac atggtggaat
301 aggaatggcc caacaacaag cacagttcac taccctaagg tatacaaaac ttatttcgaa
361 aaagtcgaaa ggttaaaaca tggtaccttt ggccctgtcc acttcagaaa tcaagttaaa
421 ataagaagga gggttgacac aaaccctggt catgcagatc tcagtgccaa ggaggcacag
481 gatgtgatca tggaagttgt tttccctaat gaagtggggg caagaatact gacatcagag
541 tcacagctga caataacaaa agaaaagaaa gaagagctcc aggattgtaa aattgctccc
601 ttgatggtgg catacatgct agaaagagaa ttggttcgta agacgaggtt tcttccggtg
661 gctggtggaa caagcagtgt ttatattgaa gtgctgcact taactcaggg aacatgctgg
721 gaacaaatgt acactccagg aggagaagtg agaaatgatg atgttgacca aagtttgatt
781 atcgccgcta gaaacatagt aagaagagca gcagtgtcag cagacccatt agcatctctc
841 ttggaaatgt gccacagcac acaaattgga ggaataagga tgatggacat ccttagacag
901 aacccaacgg aggaacaagc cgtagacata tgcaaggcag caatggggct gaggattagc
961 tcctctttca gctttggtgg gttcaccttc aaaaggacaa gcggatcatc tgttaagaaa
1021 gaagaagaag tgctcacggg caacctccaa acactgaaaa taaaagtaca tgaaggatat
1081 gaggaattca caatggtcgg gagaagagca acagctattc tcagaaaagc aaccaggaga
1141 ttgatccagt taatagtaag tgggagagac gatcaatcaa ttgctgaggc aataattgtg
1201 gccatggtat tttcacaaga ggattgcatg atcaaggcag ttaggggcga tctgaacttt
1261 gtcaataggg caaaccagcg actgaatccc atgcaccaac tcttgaggca tttccaaaag
1321 gatgcaaaag tgcttttcca gaactgggga attgaaccca tcgacagtgt aatgggaatg
1381 atcggaatat tgcctgatat gaccccaagc acggaaatgt cgctgagagg tataagagtc
1441 agcaaaatgg gagtagatga atattccagc acggagagag tggtagtgag cattgaccga
1501 tttttgagag ttcgggatca acgggggaac gtactattgt cccccgaaga ggtcagcgag
1561 acacagggaa ctgagaaatt gacaataact tattcgtcat caatgatgtg ggagatcaat
1621 ggtcctgagt cagtgctggt caacacttat caatggatca taaggaactg ggaaagcttg
1681 aaaattcaat ggtcacagga tcccacgatg ttatacaaca aaatggaatt tgaaccattc
1741 cagtctcttg tccctaaggc aaccagaagt cgttacagtg gattcgtgag gacactgttc
1801 cagcaaatgc gggatgtgct tggaacattt gatactgtcc aaataataaa acttctcccc
1861 tttgctgctg ctccaccgga acagagtagg atgcagttct cctcgctgac tgtgaatgtg
1921 agaggatcag ggctgaggat actggtaaga ggcaactctc cagtgttcaa ttacaacaaa
1981 gcaaccaaaa ggcttacaat tcttggaaaa gatgcaggtg cattgactga agatccagat
2041 gaaggcacag ctggagtgga gtctgctgtc ctgaggggat tcctcatttt gggtaaagaa
2101 gacaagagat atggcccagc attaagcatc aatgaactga gcaatcttgc aaaaggagag
2161 aaggctaatg tgctaattgg gcaaggagac gtggtgttgg taatgaaacg gaaacgggac
2221 tctagcatac ttactgacag ccagacagcg accaaaagga ttcggatggc catcaattag
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