Rhiza Labs FluTracker Forum

http://www.ncbi.nlm.nih.gov/nuccore/JN866186
LOCUS JN866186 1701 bp cRNA linear VRL 19-OCT-2011
DEFINITION Influenza A virus (A/Maine/06/2011(H3N2)) segment 4 hemagglutinin
(HA) gene, complete cds.
ACCESSION JN866186
VERSION JN866186.1 GI:353331772
KEYWORDS .
SOURCE Influenza A virus (A/Maine/06/2011(H3N2))
ORGANISM Influenza A virus (A/Maine/06/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (19-OCT-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Maine/06/2011
Subtype :: H3N2
Segment_name :: HA
Host_gender :: M
Host_age :: 8
Passage_history :: Original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Maine
Collection_day :: 10
Collection_month :: 10
Collection_year :: 2011
Isolate_note :: comment: Human case of SOIV H3N2 with M
gene from H1N1pdm09 ; Originating
Laboratory: Maine Health and
Environmental Testing Laboratory,
Virology Section Department of Human
Services 221 State St, 04333, Augusta,
United States
EPI_accession :: EPI339171
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus (A/Maine/06/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Maine/06/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 8"
/db_xref="taxon:1097365"
/segment="4"
/country="USA"
/collection_date="10-Oct-2011"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="AEQ92851.1"
/db_xref="GI:353331773"
/translation="MKTIIAFSCILCLIFAQKLPGSDNSMATLCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGRICNSPHQILDGKNCTLIDALLGDPHCDDFQNKEWDL
FVERSTAYSNCYPYYVPDYATLRSLVASSGNLEFTQESFNWTGVAQDGSSYACRRGSV
NSFFSRLNWLYNLNYKYPEQNVTMPNNDKFDKLYIWGVHHPGTDKDQTNLYVQASGRV
IVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QSGKSSIIRSDAHIDECNSECITPNGSIPNDKPFQNVNKITYGACPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQ
HTIDLTDSEMSKLFERTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDIYR
NEALNNRFQIKGVQLKSGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNICI
"
ORIGIN
1 atgaagacta tcattgcttt tagctgcatt ttatgtctga ttttcgctca aaaacttccc
61 ggaagtgaca acagcatggc aacgctgtgc ctgggacacc atgcagtgcc aaacggaaca
121 ttagtgaaaa caatcacgga tgaccaaatt gaagtgacta atgctactga gctggtccag
181 agttcctcaa caggtagaat atgcaacagt cctcaccaaa tccttgatgg gaaaaattgc
241 acactgatag atgctctatt gggggaccct cattgtgatg acttccaaaa caaggaatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgtt acccttatta tgtgccagat
361 tatgccaccc ttaggtcact agttgcctca tctggcaacc tggaatttac ccaagaaagc
421 ttcaattgga ctggagttgc tcaagacgga tcaagctatg cctgcagaag gggatctgtt
481 aacagtttct ttagtagatt gaattggttg tataacttga attacaagta tccagagcag
541 aacgtaacta tgccaaacaa tgacaaattt gacaaattgt acatttgggg ggttcaccac
601 ccgggtacgg acaaggacca aaccaaccta tatgtccaag catcagggag agttatagtc
661 tctaccaaaa gaagccaaca aactgtaatc ccgaatatcg ggtctagacc ctgggtaagg
721 ggtgtctcca gcataataag catctattgg acgatagtaa aaccgggaga catacttttg
781 attaacagca cagggaatct aattgcccct cggggttact tcaaaataca aagtgggaaa
841 agctcaataa taagatcaga tgcacacatt gatgaatgca attctgaatg cattactcca
901 aatggaagca ttcccaatga caaacctttt caaaatgtaa acaagatcac atatggagcc
961 tgtcccagat atgttaagca aaacaccctg aaattggcaa caggaatgcg gaatgtacca
1021 gagaaacaaa ctagaggcat attcggcgca attgcaggtt tcatagaaaa tggttgggag
1081 ggaatggtag acggttggta cggtttcagg catcagaatt ctgaaggcac aggacaagca
1141 gcagatctta aaagcactca agcagcaatc aaccaaatca ccgggaaact aaatagagta
1201 atcaagaaaa cgaacgagaa attccatcaa atcgaaaaag aattctcaga agtagaaggg
1261 agaattcagg acctagagaa atacgttgaa gacactaaaa tagatctctg gtcttacaac
1321 gctgagcttc ttgttgccct ggagaaccaa catacaattg atttaaccga ctcagagatg
1381 agcaaactgt tcgaaagaac aagaaggcaa ctgcgggaaa atgctgagga catgggcaat
1441 ggttgcttca aaatatacca caaatgtgac aatgcctgca taggatcaat cagaaatgga
1501 acttatgacc atgatatata cagaaacgag gcattaaaca atcggttcca gatcaaaggt
1561 gttcagctaa agtcaggata caaagattgg atcctatgga tttcctttgc catatcatgc
1621 tttttgcttt gtgttgttct gctggggttc attatgtggg cctgccaaaa aggcaacatt
1681 aggtgcaaca tttgcatttg a

_________________
www.twitter.com/hniman

LOCUS JN866185 1388 bp cRNA linear VRL 19-OCT-2011
DEFINITION Influenza A virus (A/Maine/06/2011(H3N2)) segment 6 neuraminidase
(NA) gene, partial cds.
ACCESSION JN866185
VERSION JN866185.1 GI:353331770
KEYWORDS .
SOURCE Influenza A virus (A/Maine/06/2011(H3N2))
ORGANISM Influenza A virus (A/Maine/06/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1388)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (19-OCT-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Maine/06/2011
Subtype :: H3N2
Segment_name :: NA
Host_gender :: M
Host_age :: 8
Passage_history :: Original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Maine
Collection_day :: 10
Collection_month :: 10
Collection_year :: 2011
Isolate_note :: comment: Human case of SOIV H3N2 with M
gene from H1N1pdm09 ; Originating
Laboratory: Maine Health and
Environmental Testing Laboratory,
Virology Section Department of Human
Services 221 State St, 04333, Augusta,
United States
EPI_accession :: EPI339170
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..1388
/organism="Influenza A virus (A/Maine/06/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Maine/06/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 8"
/db_xref="taxon:1097365"
/segment="6"
/country="USA"
/collection_date="10-Oct-2011"
gene 1..>1388
/gene="NA"
CDS 1..>1388
/gene="NA"
/codon_start=1
/product="neuraminidase"
/protein_id="AEQ92850.1"
/db_xref="GI:353331771"
/translation="MNPNQKIITIGSVSLIIATICFLMQIAILVTTVTLHFKQHDYNS
PPNNQAMLCEPTIIERNTTEIVYLTNTTIEKEICPKLAEYRNWSKPQCNITGFAPFSK
DNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNGHSNNTVHDRTPYRTLLM
NELGVPFHLGTRQVCMAWSSSSCHDGKAWLHVCITGNDNNATASFIYNGRLVDSIGSW
SKNILRTQESECVCINGTCTVVMTDGSASGKADTKILFVEEGKIVHISTLSGSAQHVE
ECSCYPRFPGVRCVCRDNWKGSNRPIVDINVKNYSIVSSYVCSGLVGDTPRKSDSVSS
SYCLDPNNEKGGHGVKGWAFDDGNDVWMGRTINETLRLGYETFKVIGGWSKSNSKLQT
NRQVIVEKGDRSGYSGIFSVEGKSCINRCFYVELIRGRKEETKVWWTSNSIVVFCGTS
GTYGTGSWPDGA"
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 accaccatag 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 ggagtgcttc aggaaaagct gatactaaaa tactattcgt tgaggagggg
781 aagatcgttc atattagcac attgtcagga agtgctcagc atgttgagga gtgctcctgt
841 taccctcgat ttcctggtgt cagatgtgtc tgcagagaca actggaaagg ctccaatagg
901 cccatcgtag atataaatgt aaagaattat agcattgttt ccagttatgt atgctcagga
961 cttgttggag acacacccag aaaaagcgac agcgtcagca gtagttattg cctagatccc
1021 aacaatgaga aaggtggtca tggggtgaaa ggctgggcct ttgatgatgg aaatgacgtg
1081 tggatgggaa ggacaatcaa cgagacgtta cgcttaggtt atgaaacctt caaagtcatt
1141 ggaggctggt ccaaatctaa ctccaaatta cagacaaata ggcaagtcat agtagaaaaa
1201 ggtgacaggt ccggttattc tggtattttc tccgttgaag gtaaaagctg catcaatcgg
1261 tgcttttatg tggagttgat aaggggaagg aaagaggaaa ctaaagtctg gtggacctca
1321 aacagtattg ttgtgttttg tggcacctca ggtacatatg gaacaggctc atggcctgat
1381 ggagcgga

_________________
www.twitter.com/hniman

LOCUS JN866183 2264 bp cRNA linear VRL 19-OCT-2011
DEFINITION Influenza A virus (A/Maine/06/2011(H3N2)) segment 1 polymerase PB2
(PB2) gene, partial cds.
ACCESSION JN866183
VERSION JN866183.1 GI:353331765
KEYWORDS .
SOURCE Influenza A virus (A/Maine/06/2011(H3N2))
ORGANISM Influenza A virus (A/Maine/06/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2264)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (19-OCT-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Maine/06/2011
Subtype :: H3N2
Segment_name :: PB2
Host_gender :: M
Host_age :: 8
Passage_history :: Original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Maine
Collection_day :: 10
Collection_month :: 10
Collection_year :: 2011
Isolate_note :: comment: Human case of SOIV H3N2 with M
gene from H1N1pdm09 ; Originating
Laboratory: Maine Health and
Environmental Testing Laboratory,
Virology Section Department of Human
Services 221 State St, 04333, Augusta,
United States
EPI_accession :: EPI339168
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..2264
/organism="Influenza A virus (A/Maine/06/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Maine/06/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 8"
/db_xref="taxon:1097365"
/segment="1"
/country="USA"
/collection_date="10-Oct-2011"
gene 1..>2264
/gene="PB2"
CDS 1..>2264
/gene="PB2"
/codon_start=1
/product="polymerase PB2"
/protein_id="AEQ92847.1"
/db_xref="GI:353331766"
/translation="MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPA
LRMKWMMAMKYPITADRRIMDMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRN
GPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDTNPGHADLSAKEAQ
DVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKIAPLMVAYMLERELVRKTRFL
PVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRAAVSADP
LASLLEMCHSTQIGGIRMMDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTS
GSSVKKEEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDDQ
SIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWG
IEPIDSVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEYSSTERVVVSIDRFLRVRDQR
GNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWESLKIQWSQ
DPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAA
PPEQSRMQFSSLTVNVRGSGLRILVRGNSPVFNYNKATKRLTILGKDAGALTEDPDEG
TAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRD
SSILTDSQTATKRIR"
ORIGIN
1 atggagagaa taaaagaact aagagatcta atgtcgcagt cccgcactcg cgagatactc
61 actaagacca ctgtggacca tatggccata atcaaaaagt acacgtcagg aaggcaggag
121 aagaaccccg cactcagaat gaagtggatg atggcaatga aatacccaat tacagcagac
181 aggagaatca tggacatgat tccagagagg aatgaacaag gacaaaccct ctggagcaaa
241 acaaacgatg ctggatcaga ccgtgtgatg gtatcacccc tggccgtaac atggtggaat
301 aggaatggcc caacaacaag cacagttcac taccctaagg tatacaaaac ttacttcgaa
361 aaagtcgaaa ggttaaaaca tggtaccttt ggccctgtcc acttcagaaa tcaagtcaaa
421 ataaggagga gggttgacac aaaccctggt catgcagatc tcagtgccaa ggaggcacag
481 gatgtgatca tggaagttgt tttcccaaat gaagtggggg caagaatact gacatcagag
541 tcacagctga caataacaaa agaaaagaaa gaagagctcc aggattgtaa aattgctccc
601 ttgatggtgg catacatgct agaaagagaa ttggttcgta agacgaggtt ccttccggtg
661 gctggtggaa caagcagtgt ttatattgaa gtgctgcact taactcaggg aacatgctgg
721 gagcaaatgt acactccagg aggagaagtg agaaatgatg atgttgacca aagtttgatt
781 atcgccgcta gaaacatagt aagaagagca gcagtgtcag cagacccatt agcatctctc
841 ttggaaatgt gccacagcac acaaattgga ggaataagga tgatggacat ccttagacag
901 aacccaacgg aggaacaagc tgtagacata tgcaaggcag caatggggct gaggattagc
961 tcctctttca gctttggtgg gttcaccttc aaaaggacaa gcggatcatc tgttaagaaa
1021 gaagaagaag tgctcacggg caacctccaa acactgaaaa taagagtaca 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 gaactggggg attgaaccca tcgacagtgt aatgggaatg
1381 atcggaatat tgcctgatat gaccccaagc acggaaatgt cgctgagagg tataagagtc
1441 agcaaaatgg gagtagatga atattccagt acggagagag tggtagtgag cattgaccga
1501 tttttgagag ttcgggatca acgagggaac gtactattgt cccccgaaga ggtcagcgag
1561 acacagggga ctgagaaatt gacaataact tattcgtcat caatgatgtg ggagatcaat
1621 ggtcctgagt cagtgctggt caacacttat caatggatta 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 ccttggaaaa 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 ttcg

_________________
www.twitter.com/hniman

LOCUS JN866184 2274 bp cRNA linear VRL 19-OCT-2011
DEFINITION Influenza A virus (A/Maine/06/2011(H3N2)) segment 2 polymerase PB1
(PB1) and PB1-F2 protein (PB1-F2) genes, complete cds.
ACCESSION JN866184
VERSION JN866184.1 GI:353331767
KEYWORDS .
SOURCE Influenza A virus (A/Maine/06/2011(H3N2))
ORGANISM Influenza A virus (A/Maine/06/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2274)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (19-OCT-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Maine/06/2011
Subtype :: H3N2
Segment_name :: PB1
Host_gender :: M
Host_age :: 8
Passage_history :: Original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Maine
Collection_day :: 10
Collection_month :: 10
Collection_year :: 2011
Isolate_note :: comment: Human case of SOIV H3N2 with M
gene from H1N1pdm09 ; Originating
Laboratory: Maine Health and
Environmental Testing Laboratory,
Virology Section Department of Human
Services 221 State St, 04333, Augusta,
United States
EPI_accession :: EPI339169
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..2274
/organism="Influenza A virus (A/Maine/06/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Maine/06/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 8"
/db_xref="taxon:1097365"
/segment="2"
/country="USA"
/collection_date="10-Oct-2011"
gene 1..2274
/gene="PB1"
CDS 1..2274
/gene="PB1"
/codon_start=1
/product="polymerase PB1"
/protein_id="AEQ92848.1"
/db_xref="GI:353331768"
/translation="MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVN
RTHQYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGI
FENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANES
GRLIDFLKDVMESMDKEEIEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRVNKRSYL
IRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGN
EKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFR
NILSMAPIMFSNKMARLGKGYMFESKRMKLRTQIPAEMLSSIDLKYFNESTRKKIEKI
RPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTRTTYWWDGLQSSDDFALI
VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINKTGTFEFTSFFYRYGFVANFSME
LPSFGVSGINESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDT
QIQTRRSFELKKLWDQTQSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYRGRL
CNPLNPFVSHKEIDSVNSAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGI
LEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEF
SEIMKICSTIEELRRQK"
gene 95..367
/gene="PB1-F2"
CDS 95..367
/gene="PB1-F2"
/codon_start=1
/product="PB1-F2 protein"
/protein_id="AEQ92849.1"
/db_xref="GI:353331769"
/translation="MEQEQDTPWTQSTEHTNIQKKGNGRQIQRLGHPSSIRLMDHYLK
IMNQVDMHKLTVSWRPWLSLKNPTQGYLRIHALKQWKLSNKQGWIN"
ORIGIN
1 atggatgtca atccgactct acttttccta aaggttccag cgcagaatgc cataagcacc
61 acattccctt atactggaga tcctccatac agccatggaa caggaacagg atacaccatg
121 gacacagtca acagaacaca ccaatattca gaaaaaggga aatggacgac aaatacagag
181 actggggcac cccagctcaa tccgattgat ggaccactac ctgaagataa tgaaccaagt
241 ggatatgcac aaactgactg tgtcctggag gccatggctt tccttgaaga atcccaccca
301 gggatatttg agaattcatg ccttgaaaca atggaaattg tccaacaaac aagggtggat
361 aaactaaccc agggtcgcca gacatatgat tggacattaa atagaaatca accggcagca
421 actgcattgg ccaacaccat agaagttttt agatcaaatg gtctaacagc taatgagtca
481 ggaaggctga tagatttctt aaaagatgta atggaatcaa tggataaaga ggaaatagag
541 ataacaacac actttcaaag aaaaaggaga gtgagggata acatgaccaa gaagatggtc
601 acacaaagaa caatagggaa gaaaaaacaa agagtgaata agaggagtta tttaataaga
661 gcactaacat tgaatacgat gaccaaagat gcagagagag gcaaattgaa aagaagggct
721 attgcaacac ctgggatgca aattagaggg ttcgtgtact ttgttgaaac tctagctaga
781 agcatttgcg agaagcttga acaatccgga ctcccagtag ggggcaatga aaagaaagcc
841 aaattggcaa acgttgtgag aaagatgatg actaattcac aagacacaga gctttccttc
901 acaattactg gggacaacac taaatggaat gaaaaccaaa atcctcgaat gttcctggcg
961 atgattacat acatcaccag aaaccaaccc gagtggttca gaaacatcct gagcatggca
1021 cccataatgt tctcaaacaa aatggcaaga ctaggaaaag ggtacatgtt cgagagtaaa
1081 aggatgaagc tccgaacaca gataccagca gaaatgctat caagcattga cctgaagtat
1141 ttcaatgaat caacaaggaa gaaaattgag aaaataaggc ctctcctaat agatggcaca
1201 gcatcactga gccctgggat gatgatgggc atgttcaaca tgctaagtac ggttttggga
1261 gtctcaatac tgaatcttgg acaaaagaaa tacaccagga caacatactg gtgggacgga
1321 ctccaatcct ccgacgattt tgccctcata gtaaacgcac caaatcatga gggaatccaa
1381 gcaggagtgg atagattcta caggacctgc aagttagtag gaatcaacat gagcaaaaag
1441 aagtcctata taaataagac agggacattt gaattcacaa gcttttttta tcgctatggg
1501 tttgtagcta attttagcat ggagctgccc agttttggag tgtctggaat aaacgaatca
1561 gctgatatga gtattggggt aacagtgata aagaacaaca tgataaacaa tgatcttgga
1621 cctgcaacag ctcagatggc ccttcagttg ttcatcaaag actacagata cacctataga
1681 tgccatagag gggacacaca aattcaaacg agaagatcat tcgagctaaa gaagctgtgg
1741 gatcaaaccc aatcaaaggc aggattacta gtatctgatg gaggaccaaa tttatacaat
1801 atccggaatc ttcacattcc tgaagtctgc ttaaaatggg agctaatgga tgaggattat
1861 cggggaagac tttgcaatcc cctgaatccc tttgtcagcc ataaagagat tgattctgta
1921 aacagtgctg tggtgatgcc agcccatggt ccagccaaaa gcatggaata tgatgccgtt
1981 gcaactacac actcctggat tcccaagagg aaccgctcta ttctcaacac aagccaaagg
2041 ggaattcttg aggatgaaca gatgtaccag aagtgctgca atctgttcga gaaatttttc
2101 cctagtagtt cgtacaggag accggttgga atttctagca tggtagaggc catggtgtct
2161 agggcccgaa ttgatgccag gattgacttc gagtctggac ggattaagaa agaagagttc
2221 tctgagatca tgaagatctg ttccaccatt gaagaactca gacggcaaaa gtaa

_________________
www.twitter.com/hniman

LOCUS JN866182 2151 bp cRNA linear VRL 19-OCT-2011
DEFINITION Influenza A virus (A/Maine/06/2011(H3N2)) segment 3 polymerase PA
(PA) gene, complete cds.
ACCESSION JN866182
VERSION JN866182.1 GI:353331763
KEYWORDS .
SOURCE Influenza A virus (A/Maine/06/2011(H3N2))
ORGANISM Influenza A virus (A/Maine/06/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2151)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (19-OCT-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Maine/06/2011
Subtype :: H3N2
Segment_name :: PA
Host_gender :: M
Host_age :: 8
Passage_history :: Original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Maine
Collection_day :: 10
Collection_month :: 10
Collection_year :: 2011
Isolate_note :: comment: Human case of SOIV H3N2 with M
gene from H1N1pdm09 ; Originating
Laboratory: Maine Health and
Environmental Testing Laboratory,
Virology Section Department of Human
Services 221 State St, 04333, Augusta,
United States
EPI_accession :: EPI339167
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..2151
/organism="Influenza A virus (A/Maine/06/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Maine/06/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 8"
/db_xref="taxon:1097365"
/segment="3"
/country="USA"
/collection_date="10-Oct-2011"
gene 1..2151
/gene="PA"
CDS 1..2151
/gene="PA"
/codon_start=1
/product="polymerase PA"
/protein_id="AEQ92846.1"
/db_xref="GI:353331764"
/translation="MEDFVRQCFNPMIVELAEKAMKEYGEDSKIETNKFAAICTHLEV
CFMYSDFHFIDEQGESIIVESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGVEK
PKFLPDLYDYKENRFVEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKAD
YTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQS
LPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVSAQIEPFLKTTPRPLRLPDGPPC
SQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNY
LLAWKQVLAELQDIENEEKIPKTKNMKRTSQLKWALGENMAPEKVDFDDCKDVGDLKQ
YDSDEPEPRSLASWVQNEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEV
SHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRRTNLYGFIIKGR
SHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAIGQVSRPMFLYVR
TNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPIGES
PKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFD
LGGLYEAIEECLINDPWVLLNASWFNSFLTHALK"
ORIGIN
1 atggaagact ttgtgcgaca atgcttcaat ccaatgatcg tcgagcttgc ggaaaaggca
61 atgaaagaat atggggaaga ctcgaaaatc gaaaccaaca agttcgctgc aatatgcacg
121 cacttggaag tctgtttcat gtactcggat ttccatttca ttgacgaaca gggtgaatca
181 atcattgtag aatctggtga tccaaatgca ttgctgaagc accgatttga gataattgaa
241 ggaagagaca ggactatggc ctggacagta gtgaacagta tctgcaacac cacaggggta
301 gagaagccta aatttcttcc agatttatac gactacaaag aaaatcgatt cgttgaaatt
361 ggagtgacac gaagggaggt ccacatatac tacctagaga aagccaacaa aataaaatcc
421 gagaagacac acattcatat tttttcattc actggagagg agatggccac caaagcggac
481 tacacccttg acgaagagag cagggcaaga atcaaaacca ggctcttcac cataagacaa
541 gagatggcca gtaggggtct atgggattcc tttcgtcagt ccgagagagg cgaagagaca
601 attgaagaaa gatttgaaat tacaggaaca atgcgcaggc ttgccgacca aagtctccca
661 ccgaacttct ccagccttga aaactttaga gcctatgtag atggattcga accaaacggc
721 tgcattgagg gcaagctttc tcaaatgtca aaagaagtga gtgcccaaat tgaaccattc
781 ttgaagacaa caccacgccc tctcagattg cctgatgggc ccccttgctc tcagcggtca
841 aagttcttgc tgatggatgc tctgaaacta agtattgaag acccgagtca tgaaggggaa
901 ggaataccac tatatgatgc aatcaagtgc atgaagacat tttttggctg gaaagagcct
961 aacataatca aacctcatga aaaaggcata aaccccaatt atctactggc ttggaagcaa
1021 gtactagcag agctccagga cattgaaaat gaagagaaga tcccaaagac aaagaacatg
1081 aagagaacaa gccaattgaa gtgggcactt ggtgagaata tggcaccaga gaaagtagat
1141 tttgatgact gcaaagatgt cggtgatctc aaacagtatg acagcgatga gccagagcct
1201 agatctctag caagctgggt ccaaaatgag ttcaacaagg catgtgaatt aaccgattca
1261 agctggatag aacttgatga gataggagaa gatgttgccc cgattgaaca catcgcaagc
1321 atgaggagga actattttac agcagaagtg tcccattgca gggctactga atacataatg
1381 aagggagtgt acataaatac ggctctcctt aatgcatctt gtgcagccat ggatgacttt
1441 cagctgatcc caatgataag caaatgtagg accaaagaag gaagacgaag aacaaatctg
1501 tatggcttca ttataaaagg aaggtcccat ctgagaaatg atactgacgt ggtgaacttt
1561 gtaagcatgg agttctccct cactgacccg aggctggagc cacacaaatg ggaaaagtac
1621 tgtgttcttg aaataggaga catgctcctg aggactgcaa taggccaagt gtcgaggccc
1681 atgttcctat atgtgagaac caatggaacc tccaagatca agatgaaatg gggcatggaa
1741 atgaggcgct gccttctcca gtctcttcag cagattgaga gtatgattga ggctgagtct
1801 tctgtcaaag agaaagacat gaccaaagaa ttctttgaaa acaaatcgga aacatggcca
1861 atcggagaat cacccaaagg agtggaggaa ggctctattg ggaaagtgtg caggacctta
1921 ctggcaaaat ctgtattcaa cagtctatac gcgtctccac agcttgaggg gttttcggct
1981 gaatcgagaa agttgcttct cattgttcag gcacttaggg acaacttgga acctgggacc
2041 tttgatcttg gggggctata tgaagcaatc gaggagtgcc tgattaatga tccctgggtt
2101 ttgcttaatg catcttggtt caactccttc ctcacacatg cactgaaata g

_________________
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LOCUS JN866179 1497 bp cRNA linear VRL 19-OCT-2011
DEFINITION Influenza A virus (A/Maine/06/2011(H3N2)) segment 5 nucleocapsid
protein (NP) gene, complete cds.
ACCESSION JN866179
VERSION JN866179.1 GI:353331755
KEYWORDS .
SOURCE Influenza A virus (A/Maine/06/2011(H3N2))
ORGANISM Influenza A virus (A/Maine/06/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1497)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (19-OCT-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Maine/06/2011
Subtype :: H3N2
Segment_name :: NP
Host_gender :: M
Host_age :: 8
Passage_history :: Original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Maine
Collection_day :: 10
Collection_month :: 10
Collection_year :: 2011
Isolate_note :: comment: Human case of SOIV H3N2 with M
gene from H1N1pdm09 ; Originating
Laboratory: Maine Health and
Environmental Testing Laboratory,
Virology Section Department of Human
Services 221 State St, 04333, Augusta,
United States
EPI_accession :: EPI339164
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..1497
/organism="Influenza A virus (A/Maine/06/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Maine/06/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 8"
/db_xref="taxon:1097365"
/segment="5"
/country="USA"
/collection_date="10-Oct-2011"
gene 1..1497
/gene="NP"
CDS 1..1497
/gene="NP"
/codon_start=1
/product="nucleocapsid protein"
/protein_id="AEQ92841.1"
/db_xref="GI:353331756"
/translation="MASQGTKRSYEQMETGGERQDATEIRASVGRMIGGIGKFYIQMC
TELKLSDYEGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRVDG
KWMRELILYDKEEIRRVWRQANNGEDATAGLTHIMIWHSNLNDATYQRTRALVRTGMD
PRMCSLMQGSTLPRRSGAAGAAVKGVGTIAMELIRMIKRGINDRNFWRGENGRRTRIA
YERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCL
PACVYGLAVASGHDFEREGYSLVGIDPFKLLQNSQVFSLIRPNENPAHKSQLVWMACH
SAAFEDLRVSSFIRGKKVLPRGKLSTRGVQIASNENVEAMDSNTLELRSRYWAIRTRS
GGNTNQQKASAGQISVQPTFSVQRNLPFERATVLAAFSGNNEGRTSDMRTEVIRMMES
AKPEDLSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFFGDNAEEYDS"
ORIGIN
1 atggcgtctc aaggcaccaa acgatcatat gaacaaatgg agactggtgg ggagcgccag
61 gatgccacag aaatcagagc atctgtcgga agaatgattg gtggaatcgg aaaattctac
121 atccaaatgt gcactgaact caaactcagt gattatgagg gacgactaat ccaaaatagc
181 ataacaatag agagaatggt gctctctgct ttcgatgaga gaagaaataa gtacctagaa
241 gagcatccca gtgctgggaa ggatcctaag aaaactggag gacccatata tagaagagta
301 gacggaaagt ggatgagaga actcattctt tatgacaaag aagaaataag gagagtttgg
361 cgccaagcaa acaatggtga agatgcaaca gctggcctta ctcatatcat gatttggcat
421 tccaatctga atgatgccac gtaccagaga acaagagcgc ttgttcgcac tggaatggat
481 cccagaatgt gctctctaat gcaaggttca acacttccca gaaggtctgg ggccgcaggt
541 gctgcagtaa aaggagttgg aacaatagca atggaactaa tcagaatgat caaacgtggg
601 atcaatgacc gaaacttctg gagaggtgaa aatggacgaa gaacaaggat tgcatatgag
661 agaatgtgca atatccttaa aggaaaattt cagacagcag cccagagggc aatgatggat
721 caagtgagag aaagtcgaaa cccaggaaat gctgagattg aagatctcat tttcctggca
781 cggtcagcac ttattctaag gggatcagtt gcacataagt cttgcctgcc tgcttgtgtg
841 tatgggcttg cagtggcaag tggacatgac tttgaaaggg aaggatactc actggtcggg
901 atagacccat ttaaattact ccaaaacagt caagtgttca gcctgataag accaaatgaa
961 aacccagctc acaagagtca attagtgtgg atggcatgcc actctgctgc atttgaggat
1021 ctaagggtat caagtttcat aagagggaag aaagtgcttc caagaggaaa gctttccaca
1081 agaggggtcc agattgcttc aaatgagaat gtggaagcca tggattccaa taccttagag
1141 ctgagaagca gatactgggc cataaggacc agaagtggag gaaataccaa tcaacagaaa
1201 gcatccgcgg gccaaatcag tgtgcaacct acattctcag tgcaacggaa tctccctttt
1261 gaacgagcaa ccgttttggc agctttcagc gggaacaatg aaggacggac atccgatatg
1321 cgaacagaag ttataaggat gatggaaagt gcaaagccag aagatttgtc cttccagggg
1381 cggggagtct tcgagctctc ggacgaaaag gcaacgagcc cgatcgtgcc ttcctttgac
1441 atgagtaatg aaggatctta tttcttcgga gacaatgcag aggagtatga cagttga

_________________
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LOCUS JN866181 966 bp cRNA linear VRL 19-OCT-2011
DEFINITION Influenza A virus (A/Maine/06/2011(H3N2)) segment 7 matrix protein
2 (M2) and matrix protein 1 (M1) genes, partial cds.
ACCESSION JN866181
VERSION JN866181.1 GI:353331760
DBLINK Project: 37813
KEYWORDS .
SOURCE Influenza A virus (A/Maine/06/2011(H3N2))
ORGANISM Influenza A virus (A/Maine/06/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 966)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (19-OCT-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Maine/06/2011
Subtype :: H3N2
Segment_name :: MP
Host_gender :: M
Host_age :: 8
Passage_history :: Original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Maine
Collection_day :: 10
Collection_month :: 10
Collection_year :: 2011
Isolate_note :: comment: Human case of SOIV H3N2 with M
gene from H1N1pdm09 ; Originating
Laboratory: Maine Health and
Environmental Testing Laboratory,
Virology Section Department of Human
Services 221 State St, 04333, Augusta,
United States
EPI_accession :: EPI339166
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..966
/organism="Influenza A virus (A/Maine/06/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Maine/06/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 8"
/db_xref="taxon:1097365"
/segment="7"
/country="USA"
/collection_date="10-Oct-2011"
gene <1..966
/gene="M2"
CDS join(<1..10,699..966)
/gene="M2"
/codon_start=3
/product="matrix protein 2"
/protein_id="AEQ92845.1"
/db_xref="GI:353331762"
/translation="VETPTRSEWECRCSDSSDPLAIAANIIGILHLILWITDRLFFKC
IYRRFKYGLKRGPSTEGVPESMREEYQQEQQSAVDVDDGHFVNIELE"
gene <1..743
/gene="M1"
CDS <1..743
/gene="M1"
/codon_start=3
/product="matrix protein 1"
/protein_id="AEQ92844.1"
/db_xref="GI:353331761"
/translation="VETYVLSIIPSGPLKAEIAQRLESVFAGKNTDLEALMEWLKTRP
ILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLYKKLKREIT
FHGAKEVSLSYSTGALASCMGLIYNRMGTVTTEAAFGLVCATCEQIADSQHRSHRQMA
TTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAAEAMEVANQTRQMVHAMRTIGTHPS
SSTGLKDDLLENLQAYQKRMGVQMQRFK"
ORIGIN
1 aggtcgaaac gtacgttctt tctatcatac cgtcaggccc cctcaaagcc gagatcgcgc
61 agagactgga aagtgtcttt gcaggaaaga acacagatct tgaggctctc atggaatggc
121 taaagacaag accaatcttg tcacctctga ctaagggaat tttaggattt gtgttcacgc
181 tcaccgtgcc cagtgagcga ggactgcagc gtagacgctt tgtccaaaat gccctaaatg
241 ggaatgggga cccaaacaac atggatagag cagttaaact atacaagaag ctcaaaagag
301 aaataacgtt ccatggggcc aaggaggtgt cactaagcta ttcaactggt gcacttgcca
361 gttgcatggg cctcatatac aacaggatgg gaacagtgac cacagaagct gcttttggtc
421 tagtgtgtgc cacttgtgaa cagattgctg attcacagca tcggtctcac agacagatgg
481 ctactaccac caatccacta atcaggcatg agaacagaat ggtgctggct agcactacgg
541 caaaggctat ggaacagatg gctggatcga gtgaacaggc agcggaggcc atggaggttg
601 ctaatcagac taggcagatg gtacatgcaa tgagaactat tgggactcat cctagctcca
661 gtactggtct gaaagatgac cttcttgaaa atttgcaggc ctaccagaag cgaatgggag
721 tgcagatgca gcgattcaag tgatcctctc gccattgcag caaatatcat tgggatcttg
781 cacctgatat tgtggattac tgatcgtctt tttttcaaat gtatttatcg tcgctttaaa
841 tacggtttga aaagagggcc ttctacggaa ggagtgcctg agtccatgag ggaagaatat
901 caacaggaac agcagagtgc tgtggatgtt gacgatggtc attttgtcaa catagagcta
961 gagtaa

_________________
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LOCUS JN866180 844 bp cRNA linear VRL 19-OCT-2011
DEFINITION Influenza A virus (A/Maine/06/2011(H3N2)) segment 8 nuclear export
protein (NEP) and nonstructural protein 1 (NS1) genes, complete
cds.
ACCESSION JN866180
VERSION JN866180.1 GI:353331757
KEYWORDS .
SOURCE Influenza A virus (A/Maine/06/2011(H3N2))
ORGANISM Influenza A virus (A/Maine/06/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 844)
AUTHORS Shu,B., Garten,R., Emery,S., Balish,A., Smith,C., Barnes,J.,
Lindstrom,S., Klimov,A. and Cox,N.
TITLE Direct Submission
JOURNAL Submitted (19-OCT-2011) WHO Collaborating Center for Surveillance,
Epidemiology and Control of Influenza, Influenza Division, Centers
for Disease Control and Prevention, 1600 Clifton Road, N.E.,
Atlanta, GA 30333, USA
COMMENT ##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/Maine/06/2011
Subtype :: H3N2
Segment_name :: NS
Host_gender :: M
Host_age :: 8
Passage_history :: Original
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: Maine
Collection_day :: 10
Collection_month :: 10
Collection_year :: 2011
Isolate_note :: comment: Human case of SOIV H3N2 with M
gene from H1N1pdm09 ; Originating
Laboratory: Maine Health and
Environmental Testing Laboratory,
Virology Section Department of Human
Services 221 State St, 04333, Augusta,
United States
EPI_accession :: EPI339165
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..844
/organism="Influenza A virus (A/Maine/06/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/Maine/06/2011"
/serotype="H3N2"
/host="Homo sapiens; gender M; age 8"
/db_xref="taxon:1097365"
/segment="8"
/country="USA"
/collection_date="10-Oct-2011"
gene 1..838
/gene="NEP"
/gene_synonym="NS2"
CDS join(1..30,503..838)
/gene="NEP"
/gene_synonym="NS2"
/note="nonstructural protein 2"
/codon_start=1
/product="nuclear export protein"
/protein_id="AEQ92843.1"
/db_xref="GI:353331759"
/translation="MDSNTVSSFQDILTRMSKMQLGSSSEDLNGMVTRFESLKIYRDS
LGETVMRMGDLHYLQSRNEKWREQLGQKFEEIRWLIEEVRHRLKATENSFEQITFMQA
LQLLLEVEQEIRTFSFQLI"
gene 1..660
/gene="NS1"
CDS 1..660
/gene="NS1"
/codon_start=1
/product="nonstructural protein 1"
/protein_id="AEQ92842.1"
/db_xref="GI:353331758"
/translation="MDSNTVSSFQVDCFLWHIRKRFADNGLGDAPFLDRLRRDQKSLK
GRGNTLGLDIETATLVGKQIVEWILREESSETLKMTIASVPTSRYIADMTLEEMSRDW
FMLMPRQKIIGPLCVRMDQAIMEKNIILKANFSVIFNRLETLILLRAFTEEGAIVGEI
SPLPSLPGHTNEDVKNAVGVLIGGLEWNGNTVRVSENLQRFAWRNRNEDGRPSLPPEQ
K"
ORIGIN
1 atggactcca atactgtgtc aagttttcag gtagactgtt tcctttggca catccgcaaa
61 cggtttgcag acaatggatt gggtgatgcc ccattccttg atcggctccg ccgagatcaa
121 aagtccctaa aaggaagagg caacacgctt ggcctcgata tcgaaactgc cactcttgtt
181 gggaagcaaa ttgtggagtg gattttgaga gaggaatcca gcgagacact taagatgacc
241 attgcatctg tacctacttc gcgctacata gctgacatga ccctcgagga aatgtcacga
301 gactggttca tgctcatgcc taggcaaaag ataataggcc ctctttgtgt gcgaatggac
361 caggcgatca tggaaaagaa cattatacta aaagcgaact tcagtgtgat ctttaaccga
421 ttagagactt tgatactact aagggctttc actgaggagg gagcaatcgt tggagaaatt
481 tcaccattac cttctcttcc aggacatact aacgaggatg tcaaaaatgc agttggggtc
541 ctcatcggag gacttgaatg gaatggtaac acggttcgag tctctgaaaa tctacagaga
601 ttcgcttgga gaaaccgtaa tgaggatggg agaccttcac tacctccaga gcagaaatga
661 aaagtggcga gagcaattgg gacagaaatt tgaggaaata aggtggttaa ttgaagaagt
721 acgacacaga ttgaaggcaa cagagaatag tttcgaacaa ataacattta tgcaagcctt
781 acaactactg cttgaagtag agcaagagat aaggactttc tcgtttcagc ttatttaatg
841 ataa

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www.twitter.com/hniman

One case of human infection with a novel influenza A virus was reported by the Maine Center for Disease Control and Prevention. The patient was infected with a swine origin influenza A (H3N2) virus. Testing performed at Maine’s Health and Environmental Testing Laboratory on October 14, 2011 indicated a likely swine origin influenza A (H3N2) virus and this result was confirmed at CDC on October 16, 2011. The patient reported attendance at an event where pigs were present in the week preceding symptom onset on October 7, 2011, did not require hospitalization, and continues to recover. No illness has been identified in family members or close contacts, but the investigation is ongoing.

Swine-origin triple reassortant Influenza A (H3N2) viruses have been circulating among North American swine herds since the late 1990's. Human infections with these viruses are detected sporadically, and cases usually occur following direct or indirect contact with pigs. Thirteen human cases of swine-origin influenza A (H3N2) have been reported to CDC since 2005, including five this year. No epidemiologic link has been identified between the case in Maine and recent cases reported in Indiana and Pennsylvania. General information about swine influenza is available at

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www.twitter.com/hniman

Note that CDC confirmed positive on Oct 16 and published sequences on Oct 17 at GISAID.

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www.twitter.com/hniman