Rhiza Labs FluTracker Forum

PA DOH again warns of trH3n2 in week 7 report

In addition to seasonal viruses, two unrelated infections with a swine origin influenza A/H3N2 virus have been identified in Pennsylvania with onset dates in September 2010 and October 2010. In recent years this virus has also produced human illness elsewhere in the country, generally in association with direct contact with ill pigs. It has not been associated with person-to-person transmission. Clinicians should remain alert to the possibility of infection with this virus in persons with influenza-like illness who have a history of recent exposure to swine populations, and collect appropriate diagnostic specimens.

_________________
www.twitter.com/hniman

More unsubtypables reported in week 7

_________________
www.twitter.com/hniman

week 8:

In addition to seasonal viruses, two unrelated infections with a swine origin influenza A/H3N2 virus have been identified in Pennsylvania with onset dates in September 2010 and October 2010. In recent years this virus has also produced human illness elsewhere in the country, generally in association with direct contact with ill pigs. It has not been associated with person-to-person transmission. Clinicians should remain alert to the possibility of infection with this virus in persons with influenza-like illness who have a history of recent exposure to swine populations, and collect appropriate diagnostic specimens.

_________________
www.twitter.com/hniman

LOCUS JF312065 1711 bp cRNA linear VRL 27-MAR-2011
DEFINITION Influenza A virus (A/swine/Pennsylvania/62170-4/2010(H3N2)) segment
4 hemagglutinin (HA) gene, complete cds.
ACCESSION JF312065
VERSION JF312065.1 GI:326579184
KEYWORDS .
SOURCE Influenza A virus (A/swine/Pennsylvania/62170-4/2010(H3N2))
ORGANISM Influenza A virus (A/swine/Pennsylvania/62170-4/2010(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1711)
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..1711
/organism="Influenza A virus
(A/swine/Pennsylvania/62170-4/2010(H3N2))"
/mol_type="viral cRNA"
/strain="A/swine/Pennsylvania/602170-4/2010"
/serotype="H3N2"
/host="swine"
/db_xref="taxon:938272"
/segment="4"
/country="USA"
/collection_date="25-Oct-2010"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADZ96091.1"
/db_xref="GI:326579185"
/translation="MKTIIAFSCFLCLIFDQKLPGSDDSTATPCLGHHAVPNGTLVKT
ITDDQIEVTNATELVQSSSTGRICNSPHQILDGKNCTLIDALLGDPHCDDFQNKEWDL
FVERSTAYSNCYPYYVPDYVSLRSLVASSGTLEFTQENFNWTGVAQDGSSYACRRKSV
NSFFSRLNWLYNLNYKYPALNVTMPNNDNFDKLYIWGVHHPGTDKDQTNLYIQASGRV
TVSTKRSQQTVIPNIGSRPWVRGVSSIISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QSGKSSIMRSDAPIGNCKSECITPNGSIPNDKPFQNVNRITYGVCPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGYRHQNSEGTGQAADLKSTQAAINQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQ
HTIDLTDSEMNKLFERTRKQLRENAEDMGNGCFKIYHKCDNTCIGSIRNGTYDHAVYR
DEALNNRFQIKGVQLKSGYKDWILWISFAMSCFLLCVVLLGFIMWACQKGNIRCNICI
"
ORIGIN
1 atgaagacta tcattgcttt tagctgcttt ttatgtctga ttttcgatca aaaacttccc
61 gggagtgacg acagcacggc aacgccgtgc ctgggacacc atgcagtacc aaacggaacg
121 ttagtgaaaa caatcacgga tgaccaaatt gaagtgacta atgctaccga gctggttcag
181 agttcctcaa caggtagaat atgcaacagt cctcaccaaa tccttgatgg gaaaaattgc
241 acactgatag atgctctatt gggagaccct cattgtgatg acttccaaaa caaggaatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgtt acccttatta tgtgccggat
361 tatgtctccc ttaggtcact agttgcctca tccggcaccc tggaatttac ccaagaaaac
421 ttcaattgga ctggagttgc tcaagatgga tcaagctatg cttgcagaag gaaatctgtt
481 aacagtttct ttagtagatt gaattggttg tataatttga attacaaata tccagcgctg
541 aacgtaacta tgccaaacaa tgacaatttt gacaaattgt acatttgggg ggttcaccac
601 ccgggtacag acaaagacca aaccaaccta tatattcaag catcagggag agttacagtc
661 tccaccaaaa gaagccaaca aactgtaatc ccgaatatcg ggtccagacc ctgggtaagg
721 ggtgtctcca gcataataag catctattgg acaatagtaa aaccgggaga catacttttg
781 attaacagca cagggaatct aattgcccct cggggttact tcaaaataca aagtgggaaa
841 agctcaataa tgaggtcaga tgcacccatt ggcaattgca aatctgaatg cattactcca
901 aatggaagca ttcccaatga caaacccttt caaaatgtaa acaggatcac atatggggtc
961 tgtcccagat atgttaagca aaacactctg aaattggcaa caggaatgcg gaatgtacca
1021 gagaaacaaa ctagaggcat atttggcgca atcgcaggtt tcatagaaaa tggttgggag
1081 gggatggtgg acggttggta cggttacagg catcagaatt ctgaaggcac aggacaagca
1141 gcagatctta aaagcactca ggcagcaatc aaccaaatca ccgggaaact aaatagagta
1201 atcaagaaga caaatgaaaa attccatcag atcgaaaaag aattctcaga agtagaaggg
1261 agaattcagg atctagagaa atacgttgaa gacactaaaa tagatctctg gtcttacaac
1321 gcggagcttc ttgttgccct ggagaaccaa catacaattg atttaactga ctcagaaatg
1381 aacaaactgt tcgaaagaac aagaaagcaa ctgcgggaaa atgctgagga catgggcaat
1441 ggttgcttca aaatatacca caaatgtgac aatacctgca taggatcaat cagaaatgga
1501 acttatgacc atgctgtata cagagacgag gcattaaaca atcggttcca gatcaaaggt
1561 gttcagctga agtcaggata caaagattgg atcctatgga tttcctttgc catgtcatgc
1621 tttttgcttt gtgttgttct gctggggttc attatgtggg cctgccaaaa aggcaacatt
1681 aggtgcaaca tttgcatttg agtacattaa t

_________________
www.twitter.com/hniman

The CDC just released another set of trH3N2 sequences from PA, A/Pennsylvania/40/2010 from a 3F. Sample was collected Sept 13, 2010 so it is unclear if this was the prior case, which did not have an associated sequence. or if this is the third PA trH3N2 case.

_________________
www.twitter.com/hniman

Top 100 HA matches

FJ519977.1 Influenza A virus (A/swine/Minnesota/7931/2007(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2901 2901 100% 0.0 97%
HQ825166.1 Influenza A virus (A/turkey/BC/1529-3/2005(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2877 2877 100% 0.0 97%
EU735818.1 Influenza A virus (A/turkey/OH/313053/2004(H3N2)) hemagglutinin (HA) gene, complete cds 2874 2874 100% 0.0 97%
DQ469994.1 Influenza A virus (A/swine/Ontario/33853/2005(H3N2)) hemagglutinin (HA) gene, complete cds 2874 2874 99% 0.0 97%
DQ469962.1 Influenza A virus (A/Ontario/RV1273/2005(H3N2)) hemagglutinin (HA) gene, complete cds 2874 2874 99% 0.0 97%
DQ469986.1 Influenza A virus (A/swine/Manitoba/12707/2005(H3N2)) hemagglutinin (HA) gene, complete cds 2865 2865 99% 0.0 97%
DQ469970.1 Influenza A virus (A/swine/Alberta/14722/2005(H3N2)) hemagglutinin (HA) gene, complete cds 2865 2865 99% 0.0 97%
DQ335771.1 Influenza A virus (A/turkey/Ohio/313053/04(H3N2)) hemagglutinin (HA) gene, complete cds 2865 2865 99% 0.0 97%
HQ315643.1 Influenza A virus (A/swine/Minnesota/1300/2007(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2859 2859 100% 0.0 97%
EU743210.1 Influenza A virus (A/turkey/MN/366767/2005(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2859 2859 100% 0.0 97%
EU697204.1 Influenza A virus (A/turkey/Minnesota/366767/2005(H3N2)) hemagglutinin (HA) gene, complete cds 2847 2847 100% 0.0 97%
DQ470002.1 Influenza A virus (A/turkey/Ontario/31232/2005(H3N2)) hemagglutinin (HA) gene, complete cds 2843 2843 99% 0.0 97%
EF551045.1 Influenza A virus (A/turkey/Illinois/2004(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2841 2841 100% 0.0 97%
EU697209.1 Influenza A virus (A/turkey/North Carolina/353568/2005(H3N2)) hemagglutinin (HA) gene, complete cds 2837 2837 100% 0.0 96%
EU735826.1 Influenza A virus (A/turkey/NC/353568/2005(H3N2)) hemagglutinin (HA) gene, complete cds 2837 2837 100% 0.0 96%
CY035416.1 Influenza A virus (A/swine/Minnesota/SG-00234/2005(H3N2)) segment 4 sequence 2832 2832 99% 0.0 97%
FJ519972.1 Influenza A virus (A/swine/Minnesota/66853/2006(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2828 2828 100% 0.0 96%
DQ150425.1 Influenza A virus (A/swine/MI/PU243/04 (H3N1)) hemagglutinin (HA) gene, complete cds 2825 2825 100% 0.0 96%
FJ410140.1 Influenza A virus (A/swine/Minnesota/1145/2007(H3N2)) segment 4, complete sequence 2819 2819 100% 0.0 96%
EU826543.2 Influenza A virus (A/swine/Quebec/4001/2005(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2819 2819 99% 0.0 96%
EU399751.1 Influenza A virus (A/Ontario/1252/2007(H3N2)) hemagglutinin (HA) gene, complete cds 2816 2816 99% 0.0 96%
FJ519973.1 Influenza A virus (A/swine/Minnesota/66960/2006(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2814 2814 100% 0.0 96%
CY045567.1 Influenza A virus (A/swine/Oklahoma/008722/2007(H3N2)) segment 4 sequence 2814 2814 100% 0.0 96%
CY035419.1 Influenza A virus (A/swine/Minnesota/SG-00235/2007(H3N2)) segment 4 sequence 2814 2814 99% 0.0 96%
HQ825243.1 Influenza A virus (A/swine/QC/2108-2/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2810 2810 100% 0.0 96%
FJ519971.1 Influenza A virus (A/swine/Minnesota/65767/2006(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2810 2810 100% 0.0 96%
CY041847.1 Influenza A virus (A/swine/North Carolina/R08-001877-D08-013371/2008 (H3N2)) segment 4 sequence 2810 2810 99% 0.0 96%
CY035422.1 Influenza A virus (A/swine/Minnesota/SG-00236/2007(H3N2)) segment 4 sequence 2809 2809 99% 0.0 96%
FJ519974.1 Influenza A virus (A/swine/Minnesota/578/2007(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2807 2807 99% 0.0 96%
DQ469978.1 Influenza A virus (A/swine/British Columbia/28103/2005(H3N2)) hemagglutinin (HA) gene, complete cds 2807 2807 99% 0.0 96%
FJ519976.1 Influenza A virus (A/swine/Minnesota/5947/2007(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2805 2805 100% 0.0 96%
CY035442.1 Influenza A virus (A/swine/Minnesota/SG-00242/2006(H3N2)) segment 4 sequence 2803 2803 99% 0.0 96%
HQ825182.1 Influenza A virus (A/swine/QC/414/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2796 2796 100% 0.0 96%
FJ519975.1 Influenza A virus (A/swine/Minnesota/761/2007(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2792 2792 99% 0.0 96%
JF263536.1 Influenza A virus (A/swine/Pennsylvania/62170-3/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2789 2789 99% 0.0 96%
JF263535.1 Influenza A virus (A/swine/Pennsylvania/62170-1/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2789 2789 99% 0.0 96%
HM217202.1 Influenza A virus (A/swine/Minnesota/03008/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2789 2789 99% 0.0 96%
CY086920.1 Influenza A virus (A/swine/Minnesota/239105/2009(H3N2)) hemagglutinin (HA) gene, complete cds 2783 2783 99% 0.0 96%
EU826551.2 Influenza A virus (A/mink/Nova Scotia/1055488/2007(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2783 2783 99% 0.0 96%
JF312065.1 Influenza A virus (A/swine/Pennsylvania/62170-4/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2774 2774 100% 0.0 96%
CY045575.1 Influenza A virus (A/swine/Oklahoma/011506/2007(H3N2)) segment 4 sequence 2774 2774 99% 0.0 96%
HQ825223.1 Influenza A virus (A/swine/QC/1698-2/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2771 2771 99% 0.0 96%
HQ825218.1 Influenza A virus (A/swine/QC/1698-1/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2771 2771 99% 0.0 96%
HQ825190.1 Influenza A virus (A/swine/QC/382/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2769 2769 100% 0.0 96%
HQ825226.1 Influenza A virus (A/swine/QC/1698-4/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2765 2765 99% 0.0 96%
HQ825229.1 Influenza A virus (A/swine/QC/1698-5/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2762 2762 99% 0.0 96%
JF312071.1 Influenza A virus (A/swine/Iowa/A01057188/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2762 2762 99% 0.0 96%
GU937743.1 Influenza A virus (A/Kansas/13/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2756 2756 99% 0.0 95%
HQ734189.1 Influenza A virus (A/swine/Illinois/53612-2/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2756 2756 99% 0.0 95%
HQ734186.1 Influenza A virus (A/swine/Illinois/53612-1/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2756 2756 99% 0.0 95%
HQ825235.1 Influenza A virus (A/swine/QC/1840-2/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2753 2753 99% 0.0 95%
AY779254.1 Influenza A virus (A/turkey/Minnesota/764-2/03(H3N2)) hemagglutinin (HA) gene, complete cds 2751 2751 100% 0.0 95%
JF312064.1 Influenza A virus (A/swine/Pennsylvania/62170-2/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2747 2747 99% 0.0 95%
GU289666.1 Influenza A virus (A/swine/Wisconsin/R7c/2001(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2747 2747 99% 0.0 95%
CY045559.1 Influenza A virus (A/swine/Kansas/015252/2009(H3N2)) segment 4 sequence 2747 2747 100% 0.0 95%
AY779253.1 Influenza A virus (A/turkey/North Carolina/12344/03(H3N2)) hemagglutinin (HA) gene, complete cds 2747 2747 100% 0.0 95%
HQ825203.1 Influenza A virus (A/swine/QC/1685-1/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2738 2738 99% 0.0 95%
HQ825174.1 Influenza A virus (A/quail/QC/FAV-10/2008(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2738 2738 100% 0.0 95%
HQ825198.1 Influenza A virus (A/swine/QC/440-A/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2735 2735 100% 0.0 95%
HQ825210.1 Influenza A virus (A/swine/QC/1685-5/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2729 2729 99% 0.0 95%
HQ734198.1 Influenza A virus (A/swine/Illinois/53612-5/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2729 2729 99% 0.0 95%
HQ734195.1 Influenza A virus (A/swine/Illinois/53612-4/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2726 2726 99% 0.0 95%
GU135891.1 Influenza A virus (A/swine/Iowa/H03BF5/2003(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2726 2726 99% 0.0 95%
CY045551.1 Influenza A virus (A/swine/Oklahoma/001142/2009(H3N2)) segment 4 sequence 2724 2724 100% 0.0 95%
JF312073.1 Influenza A virus (A/swine/Illinois/A01057088/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2720 2720 99% 0.0 95%
JF312072.1 Influenza A virus (A/swine/Illinois/A01057087/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2717 2717 99% 0.0 95%
HQ734201.1 Influenza A virus (A/swine/Illinois/53612-6/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2717 2717 99% 0.0 95%
DQ145537.1 Influenza A virus (A/swine/Minnesota/00395/2004(H3N1)) hemagglutinin gene, complete cds 2715 2715 99% 0.0 95%
HQ734204.1 Influenza A virus (A/swine/Illinois/53612-7/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2708 2708 99% 0.0 95%
JF703684.1 Influenza A virus (A/swine/Quebec/1265553/2010(H3N2)) segment 4 hemagglutinin (HA) gene, partial cds 2700 2700 99% 0.0 95%
EU422988.1 Influenza A virus (A/swine/Iowa/H03HO7/2003(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2688 2688 99% 0.0 95%
JF316643.1 Influenza A virus (A/swine/Pennsylvania/057108-1/2010(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2681 2681 99% 0.0 94%
DQ150433.1 Influenza A virus (A/swine/IN/PU542/04 (H3N1)) hemagglutinin (HA) gene, complete cds 2679 2679 100% 0.0 94%
CY009716.1 Influenza A virus (A/New York/587/1996(H3N2)) segment 4, complete sequence 2679 2679 100% 0.0 94%
CY009692.1 Influenza A virus (A/New York/581/1997(H3N2)) segment 4, complete sequence 2679 2679 100% 0.0 94%
CY009516.1 Influenza A virus (A/New York/579/1997(H3N2)) segment 4, complete sequence 2679 2679 100% 0.0 94%
AF363502.1 Influenza A virus (A/Paris/896/97(H3N2)) hemagglutinin gene, complete cds 2679 2679 100% 0.0 94%
CY006475.1 Influenza A virus (A/New York/518/1998(H3N2)) segment 4, complete sequence 2679 2679 100% 0.0 94%
EU857004.1 Influenza A virus (A/Hong Kong/CUHK4147/1997(H3N2)) hemagglutinin (HA) gene, complete cds 2675 2675 99% 0.0 94%
CY011128.1 Influenza A virus (A/New York/599/1996(H3N2)) segment 4, complete sequence 2675 2675 100% 0.0 94%
CY010588.1 Influenza A virus (A/New York/572/1996(H3N2)) segment 4, complete sequence 2675 2675 100% 0.0 94%
CY010068.1 Influenza A virus (A/New York/600/1996(H3N2)) segment 4, complete sequence 2675 2675 100% 0.0 94%
CY010044.1 Influenza A virus (A/New York/594/1996(H3N2)) segment 4, complete sequence 2675 2675 100% 0.0 94%
CY009668.1 Influenza A virus (A/New York/574/1996(H3N2)) segment 4, complete sequence 2675 2675 100% 0.0 94%
CY009524.1 Influenza A virus (A/New York/583/1997(H3N2)) segment 4, complete sequence 2675 2675 100% 0.0 94%
CY009508.1 Influenza A virus (A/New York/575/1996(H3N2)) segment 4, complete sequence 2675 2675 100% 0.0 94%
CY009684.1 Influenza A virus (A/New York/580/1996(H3N2)) segment 4, complete sequence 2675 2675 100% 0.0 94%
CY009676.1 Influenza A virus (A/New York/576/1997(H3N2)) segment 4, complete sequence 2670 2670 100% 0.0 94%
CY009476.1 Influenza A virus (A/New York/565/1996(H3N2)) segment 4, complete sequence 2670 2670 100% 0.0 94%
CY009460.1 Influenza A virus (A/New York/560/1997(H3N2)) segment 4, complete sequence 2670 2670 100% 0.0 94%
AF363503.1 Influenza A virus (A/Paris/906/97(H3N2)) hemagglutinin gene, complete cds 2670 2670 100% 0.0 94%
CY009652.1 Influenza A virus (A/New York/566/1997(H3N2)) segment 4, complete sequence 2666 2666 100% 0.0 94%
CY009468.1 Influenza A virus (A/New York/564/1997(H3N2)) segment 4, complete sequence 2666 2666 100% 0.0 94%
CY006587.1 Influenza A virus (A/New York/541/1998(H3N2)) segment 4, complete sequence 2666 2666 100% 0.0 94%
CY035426.1 Influenza A virus (A/swine/Minnesota/SG-00237/2007(H3N2)) segment 4 sequence 2664 2664 99% 0.0 95%
CY009740.1 Influenza A virus (A/New York/590/1996(H3N2)) segment 4, complete sequence 2661 2661 100% 0.0 94%
HQ734192.1 Influenza A virus (A/swine/Illinois/53612-3/2009(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2659 2659 99% 0.0 94%
EF551053.1 Influenza A virus (A/swine/North Carolina/2003(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2648 2648 100% 0.0 94%
CY010036.1 Influenza A virus (A/New York/592/1996(H3N2)) segment 4, complete sequence 2648 2648 100% 0.0 94%
GU135918.1 Influenza A virus (A/swine/Iowa/H03HB4/2003(H3N2)) segment 4 hemagglutinin (HA) gene, complete cds 2645 2645 99% 0.0 94%

_________________
www.twitter.com/hniman

HA sequence of A/Pennsylvania/40/2010 is almost identical to A/Wisconsin/12/2010 and A/Minnesota/11/2010, two trH3n2 sequences isolated in a similar time frame.

_________________
www.twitter.com/hniman

PA/40 has PB1 E618D

EPI312979 A/Pennsylvania/40/2010 (A/H3N2) segment 2 (PB1) 27.0 6.27592
EPI302685 A/swine/Pennsylvania/62170-4/2010 (A/H3N2) segment 2 (PB1) 27.0 5.97859
EPI302680 A/swine/Pennsylvania/62170-3/2010 (A/H3N2) segment 2 (PB1) 27.0 5.97859
EPI302673 A/swine/Pennsylvania/62170-2/2010 (A/H3N2) segment 2 (PB1) 27.0 5.97859
EPI302668 A/swine/Pennsylvania/62170-1/2010 (A/H3N2) segment 2 (PB1) 27.0 5.97859
EPI293963 A/Minnesota/11/2010 (A/H3N2) segment 2 (PB1) 27.0 5.96979
EPI291895 A/Wisconsin/12/2010 (A/H3N2) segment 2 (PB1) 27.0 5.64229
EPI291867 A/Pennsylvania/14/2010 (A/H3N2) segment 2 (PB1) 27.0 5.64229
EPI291840 A/Minnesota/09/2010 (A/H3N2) segment 2 (PB1) 27.0 5.64229
EPI244299 A/Kansas/13/2009 (A/H3N2) segment 2 (PB1) 27.0 5.67207

_________________
www.twitter.com/hniman

The above comments indicate attempts to culture the virus from the Sept PA case were unsuccessful. It is unclear if PA/40 represents the sequence from a virus subsequently isolate from this case, or yet another PA trH3N2 case in the fall and the second case in September, 2010. The October case (PA/14) is clearly distinct from PA/40, which is like Wisconsin/12 and Minnestota/11 HA sequences

_________________
www.twitter.com/hniman

T177C pedigree. Human trH3N2 sequences in bold

EPI312980 A/Pennsylvania/40/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI305419 A/KOBE/419/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI301352 A/Argentina/28372/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI301348 A/Argentina/28367/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI301346 A/Argentina/28342/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI297897 A/swine/Italy/526/1985 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI293965 A/Minnesota/11/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI291898 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI291893 A/Wisconsin/12/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI291838 A/Minnesota/09/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI259504 A/swine/Minnesota/03008/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI254209 A/Incheon/1909/2004 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI254187 A/Gyeongnam/7/2005 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI254181 A/Gyeongnam/1865/2004 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI254137 A/Daegu/1819/2004 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI254127 A/Chungbuk/5/2005 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI249481 A/Nagasaki/N35/2007 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI246027 A/swine/Minnesota/02952/2009 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI244116 A/swine/Illinois/02940/2010 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI239939 A/Guizhou/3/1987 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI239938 A/Guizhou/1/1987 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI232556 A/Kenya/1165/2009 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI230165 A/Myanmar/JP228/2009 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI230162 A/Myanmar/JP192/2009 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI229420 A/Chungbuk/1927/2004 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI226664 A/Daegu/234/2005 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI185879 A/Massachusetts/01/2009 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI167246 A/British Columbia/0627/2007 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI157451 A/Brazil/1898/2006 (A/H3) segment 4 (HA) 27.0 6.27592
EPI154384 A/Texas/AF1743/2008 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI145974 A/Brazil/BR-1898-ORIGINAL/2006 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI145601 A/SHIZUOKA/3/2005 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI119858 A/Trieste/07/2003 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI106542 A/Oslo/737/99 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI102838 A/TW/3446/02 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI98728 A/swine/IN/PU542/04 (A/H3N1) segment 4 (HA) 27.0 6.27592
EPI96751 A/Memphis/7/1990 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI52776 A/New York/59/2003 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI24064 A/Madrid/G101/93 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI24062 A/Madrid/G116/93 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI9327 A/Finland/702/99 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI3733 A/Spain/118/93 (A/H3N2) segment 4 (HA) 27.0 6.27592
EPI3729 A/Wellington/66/92 (A/H3N2) segment 4 (HA) 27.0 6.27592

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