Rhiza Labs FluTracker Forum

The recently released H1N1v sequence from A/Wisconsin/28/2011 (WI/08/11) is extremely diverse. The isolate has two H1N1pdm09 gene segements (M and PA) as well as one gene segment (NP) from H3N2v. It also has PB2 and PB1 genes from the lineage from multiple human cases including the Huron County fair (A/Ohio/01/2007 and A/Ohio/02/2007), where two dozen attendees had ILI.

CORRECTION. The comments below are for T2001C which is SYNONYMOUS and doe NOT code for T637N
In addition, WI/0811 has PB2 T637N which was in A/South Dakota/03/2008 which was associate with a large number of students who subsequently were sero-positive for H1N1v.

T637N is also in A/Pennsylvania/14/2010, who had no swine contact, as well as H3N2 cases in Maine and West Virginia, site of longest confirmed H3N2v transmission reported to date.

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T2001C polymorphism pedigree (NOT T637N)

EPI346913 A/Wisconsin/28/2011 (A/H1N1) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI346490 A/West Virginia/06/2011 (A/H3N2) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI339168 A/Maine/06/2011 (A/H3N2) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI337528 A/swine/Minnesota/001581/2007 (A/H1N1) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI302688 A/swine/Pennsylvania/62170-4/2010 (A/H3N2) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI302677 A/swine/Pennsylvania/62170-3/2010 (A/H3N2) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI302676 A/swine/Pennsylvania/62170-2/2010 (A/H3N2) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI302665 A/swine/Pennsylvania/62170-1/2010 (A/H3N2) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI291880 A/South Dakota/03/2008 (A/H1N1) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI291868 A/Pennsylvania/14/2010 (A/H3N2) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI291853 A/Missouri/04/2006 (A/H1N1) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI291810 A/Iowa/05/2007 (A/H1N1) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI180353 A/duck/Primorie/2621/01 (A/H5N2) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI166269 A/swine/Minnesota/SG-00240/2007 (A/H1N1) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI117869 A/ostrich/South Africa/AI1091/2006 (A/H5N2) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI105949 A/Bewick's swan/Netherlands/2/2005 (A/H6N8) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI100296 A/goose/Guangxi/2112/2004 (A/H5N1) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI100284 A/duck/Guangxi/1311/2004 (A/H5N1) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)
EPI25653 A/chicken/TX/167280-4/02 (A/H5N3) segment 1 (PB2) 27.0 7.400712e+00 14/14 (100%)

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LOCUS JF758485 1296 bp cRNA linear VRL 10-APR-2011
DEFINITION Influenza A virus (A/South Dakota/03/2008(H1N1)) segment 1
polymerase PB2 (PB2) gene, partial cds.
ACCESSION JF758485
VERSION JF758485.1 GI:327506392
KEYWORDS .
SOURCE Influenza A virus (A/South Dakota/03/2008(H1N1))
ORGANISM Influenza A virus (A/South Dakota/03/2008(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1296)
AUTHORS Garten,R.
TITLE Direct Submission
JOURNAL Submitted (01-APR-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 GenBank Accession Numbers JF758480-JF758487 represent sequences
from the 8 segments of Influenza A virus (A/South
Dakota/03/2008(H1N1)).

##GISAID_EpiFlu(TM)Data-START##
Isolate :: A/South Dakota/03/2008
Subtype :: H1N1
Segment_name :: PB2
Host_gender :: M
Host_age :: 19
Passage_history :: M2
Adamantane_resistance :: unknown
Zanamivir_resistance :: unknown
Oseltamivir_resistance :: unknown
Peramivir_resistance :: unknown
Other_resistance :: unknown
Country :: United States
State/Province :: South Dakota
Localization_detail :: USA
Collection_day :: 04
Collection_month :: 12
Collection_year :: 2008
Isolate_note :: comment: Human case of H1N1 triple
reassortant Swine-origin influenza virus
EPI_accession :: EPI291880
##GISAID_EpiFlu(TM)Data-END##
FEATURES Location/Qualifiers
source 1..1296
/organism="Influenza A virus (A/South
Dakota/03/2008(H1N1))"
/mol_type="viral cRNA"
/strain="A/South Dakota/03/2008"
/serotype="H1N1"
/host="Homo sapiens; gender M; age 19"
/db_xref="taxon:1003428"
/segment="1"
/country="USA"
/collection_date="04-Dec-2008"
gene <1..1296
/gene="PB2"
CDS <1..1296
/gene="PB2"
/codon_start=1
/product="polymerase PB2"
/protein_id="AEA92638.1"
/db_xref="GI:327506393"
/translation="TFKRTSGSSVKKEEEVLTGNLQTLKIRVHEGFEEFTMVGRRATA
ILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNP
MHQLLRHFQKDAKVLFQNWGIEPIDSVMGMIGILPDMTPSTEMSLRGIRVSKMGVDEY
SSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVL
VNTYQWIIRNWESLKIQWSQDPTMLYNKMEFEPFQSLVPKATRSRYSGFVRTLFQQMR
DVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGLRILVRGNSPVFNYNKAT
KRLTILGKDAGALTEDPDEGTAGVESAVLRGFLILGKEDKRYGPALSINELNNLAKGE
KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN"
ORIGIN
1 accttcaaaa gaacaagcgg atcatcagtt aagaaagaag aagaagtgct cacgggcaat
61 ctccaaacac taaaaataag agtacatgaa ggatttgaag aattcacaat ggtcgggaga
121 agagcaacag ctattctcag aaaagcaacc aggagattga tccagttaat agtaagtggg
181 agagacgagc agtcaattgc tgaggcaata attgtggcca tggtattttc acaagaggac
241 tgcatgatca aggcagttag gggcgatctg aactttgtca atagggcaaa ccagcgactg
301 aatcccatgc accaactttt gaggcatttc caaaaagatg caaaagtgct tttccagaac
361 tggggaattg agcccatcga cagtgtgatg ggaatgatcg gaatattgcc tgatatgacc
421 ccaagcacgg aaatgtcgct gagagggata agagtcagca aaatgggagt agatgaatat
481 tccagcacgg agagagtggt ggtaagcatt gaccgatttt tgagggttcg ggatcaacgg
541 gggaacgtac tattgtctcc cgaagaggtc agtgagacac aaggaacgga gaaattgaca
601 ataacctatt cgtcatcaat gatgtgggag atcaatggtc ctgagtcagt gctggtcaac
661 acttatcaat ggatcataag gaactgggaa agtttgaaaa ttcaatggtc acaagatccc
721 acgatgttat acaacaaaat ggaatttgaa ccattccagt ctcttgtccc taaggcaacc
781 agaagtcgtt acagtgggtt tgtaaggaca ctgttccagc aaatgcggga tgtgcttgga
841 acatttgaca ctgtccaaat aataaaactt ctcccctttg ctgctgctcc accggaacag
901 agtaggatgc agttctcctc actgactgtg aatgtgagag gatcagggtt gaggatactg
961 gtaagaggca attctccagt attcaattac aacaaagcaa ccaaaaggct tacaatcctt
1021 ggaaaggatg caggtgcatt gactgaagat ccggatgaag gcacagctgg agtggagtct
1081 gctgtcctaa ggggatttct cattttgggc aaagaagaca agagatatgg cccagcatta
1141 agcatcaatg aactgaacaa tcttgcaaaa ggagagaagg ctaatgtgct aattgggcaa
1201 ggagacgtgg tgttggtaat gaaacggaaa cgggactcta gcatacttac tgacagccag
1261 acagcgacca aaagaattcg gatggccatc aattag

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