Rhiza Labs FluTracker Forum

EPI249352 A/Wisconsin/629-D01904/2009 (A/H1N1 pdm09) segment 8 (NS) 1192.2 0.000000e+00 655/660 (99%)
EPI215376 A/New Bern/WR0670/2009 (A/H1N1 pdm09) segment 8 (NS) 1192.2 0.000000e+00 655/660 (99%)
EPI215178 A/Cherry Point/WR0100/2009 (A/H1N1 pdm09) segment 8 (NS) 1192.2 0.000000e+00 655/660 (99%)
EPI338781 A/canine/Beijing/cau2/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI337867 A/swine/Guangdong/50/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI336747 A/swine/Alberta/25/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI335594 A/Khon Kaen/INS461/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI335417 A/Khon Kaen/INS442/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI335412 A/Khon Kaen/INS444/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI333452 A/South Carolina/WRAIR1645P/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332904 A/Pune/NIV0953725/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332896 A/Pune/NIV10278/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332832 A/Mum/NIV9945/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332537 A/Khon Kaen/INS445/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332521 A/Khon Kaen/INS447/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332513 A/Khon Kaen/INS449/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332505 A/Khon Kaen/INS450/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332497 A/Khon Kaen/INS451/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332481 A/Khon Kaen/INS453/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332473 A/Khon Kaen/INS454/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332449 A/Khon Kaen/INS458/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332441 A/Khon Kaen/INS459/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332433 A/Khon Kaen/INS460/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332425 A/Khon Kaen/INS462/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332129 A/Bangkok/INS511/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI332017 A/Cambridge/INS528/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI327666 A/mallard/California/1154/2010 (A/H0) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI324538 A/Khon Kaen/INS456/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI324522 A/Khon Kaen/INS440/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI324362 A/California/VRDL353/2009 (A/H0) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323377 A/England/H093780034/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323372 A/England/797/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323369 A/England/1213/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323368 A/England/H094220579/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323364 A/England/898/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323363 A/England/902/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323362 A/England/862/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323361 A/England/872/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323360 A/England/854/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323359 A/England/900/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323355 A/England/876/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323352 A/England/451/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323351 A/England/450/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323350 A/England/446/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323347 A/England/435/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323345 A/England/429/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323344 A/England/424/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323343 A/England/421/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323342 A/England/416/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323338 A/Ireland/3/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323335 A/Ireland/2/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323332 A/England/393/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323314 A/England/343/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI323307 A/England/303/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI321095 A/Sydney/DD3-29/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI320935 A/Sydney/DD3-03/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI320699 A/Nanchang/8008/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI320446 A/Changchun/01/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI320299 A/Australia/17/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI317106 A/Bethesda/NIH107-D0/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI317099 A/Bethesda/NIH106-D14/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI317092 A/Bethesda/NIH106-D0/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI317053 A/Managua/4877.02/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI316973 A/Wisconsin/629-D01667/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI316742 A/Wisconsin/629-D02330/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI316637 A/Boston/107/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI316008 A/Finland/671/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI315726 A/Thailand/CU-H2417/2010 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI315683 A/Korea/NAP-1/2009 (A/H1N1 pdm09) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI315591 A/Boston/691/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI315551 A/Boston/680/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI315519 A/Boston/670/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI315479 A/Boston/637/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI315447 A/Boston/630/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI315407 A/Chile/19/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI313338 A/Texas/JMS368/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI313131 A/Boston/694/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI313110 A/Athens/INS152/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI312994 A/New York/4764/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI312990 A/New York/3565/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI312750 A/New York/3251/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI312737 A/New York/3198/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI312721 A/swine/Thailand/CU-M8_2/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI309312 A/Cambodia/NHRCC00006/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI309143 A/New York/6537/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308869 A/San Diego/INS194/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308853 A/Warsaw/INS148/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308805 A/San Diego/INS50/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308797 A/San Diego/INS49/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308757 A/San Diego/INS07/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308752 A/Wroclaw/INS435/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308724 A/Berlin/INS362/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308680 A/Brussels/INS205/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308617 A/Terrassa/INS94/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308588 A/San Diego/INS41/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308497 A/Budapest/WRAIR2393T/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308489 A/Budapest/WRAIR2393N/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308441 A/Mexico City/WRAIR1691N/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308409 A/Mexico City/WRAIR1679N/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)
EPI308401 A/Ft.Benning/WRAIR1669P/2009 (A/H1N1) segment 8 (NS) 1186.7 0.000000e+00 654/660 (99%)

_________________
www.twitter.com/hniman

A/swine/Kansas/11-109700/2011 has a H1N1pdm09 M gene and its HA, NA, and MP match the prior 5 isolates from Texas and Iowa with H1N1pdm09.

The sequences of the remaining 5 genes from the KS isolate indicate NP and NS are also H1N1pdm09.

_________________
www.twitter.com/hniman

Additional isolates from Kansas and Illinois also have #H1N1pdm09 M gene. Analysis in progress.

_________________
www.twitter.com/hniman

Prior M gene thread

viewtopic.php?f=5&t=7460

_________________
www.twitter.com/hniman

http://www.cdc.gov/eid/content/17/9/110338.htm
Multiple Reassortment between Pandemic (H1N1) 2009 and Endemic Influenza Viruses in Pigs, United States
Mariette F. Ducatez, Ben Hause, Evelyn Stigger-Rosser, Daniel Darnell, Cesar Corzo, Kevin Juleen, Randy Simonson, Christy Brockwell-Staats, Adam Rubrum, David Wang, Ashley Webb, Jeri-Carol Crumpton, James Lowe, Marie Gramer, and Richard J. Webby
Author affiliations: St. Jude Children's Research Hospital, Memphis, Tennessee, USA (M.F. Ducatez, E. Stigger-Rosser, D. Darnell, C. Brockwell-Staats, A. Rubrum, D. Wang, A. Webb, J.-C. Crumpton, R.J. Webby); Newport Laboratories, Worthington, Minnesota, USA (B. Hause, R. Simonson); University of Minnesota College of Veterinary Medicine, Saint Paul, Minnesota, USA (C. Corzo, K. Juleen, M. Gramer); and Carthage Veterinary Services, Carthage, Illinois, USA (J. Lowe)
Vol. 17, No. 9 • September 2011

_________________
www.twitter.com/hniman

Also reported in A/swine/North Carolina/226126/2010(H1N2)

_________________
www.twitter.com/hniman

LOCUS JN409431 1701 bp cRNA linear VRL 30-NOV-2011
DEFINITION Influenza A virus (A/swine/Kansas/11-109700/2011(H3N2)) segment 4
hemagglutinin (HA) gene, complete cds.
ACCESSION JN409431
VERSION JN409431.1 GI:342675564
KEYWORDS .
SOURCE Influenza A virus (A/swine/Kansas/11-109700/2011(H3N2))
ORGANISM Influenza A virus (A/swine/Kansas/11-109700/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1701)
AUTHORS Ma,W., Richt,J.A. and Liu,Q.
TITLE Emergence of novel reassortant H3N2 swine influenza viruses in the
United States
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 1701)
AUTHORS Ma,W., Richt,J.A. and Liu,Q.
TITLE Direct Submission
JOURNAL Submitted (29-JUL-2011) Department of Diagnostic
Medicine/Pathobiology, College of Veterinary Medicine, Kansas State
University, 1800 Denison Avenue, Manhattan, KS 66506, USA
COMMENT GenBank Accession Numbers JN409428-JN409435 represent sequences
from the 8 segments of Influenza A virus
(A/swine/Kansas/11-109700/2011(H3N2)).
FEATURES Location/Qualifiers
source 1..1701
/organism="Influenza A virus
(A/swine/Kansas/11-109700/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/swine/Kansas/11-109700/2011"
/serotype="H3N2"
/host="swine"
/db_xref="taxon:1071624"
/segment="4"
/country="USA"
/collection_date="02-Apr-2011"
gene 1..1701
/gene="HA"
CDS 1..1701
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="AEL31715.1"
/db_xref="GI:342675565"
/translation="MKTIIAFSCILYLIFAQKLPGSDNSMATLCLGHHAVPNGTLVKT
ITDDQVEVTNATELVQSSSTGRICNSPYQVLDGKNCTLIDALLGDPHCDEFQNTEWDL
FVERSTAYSNCYPYYVPDYSSLRSLVASSGTLEFTQESFDWTGVAQDGSSYACKRGSV
NSFFSRLNWLHNLNYKYPALNVTMPNNDNFDKLYIWGVHHPGTDRDQANLYVQASGRV
TVSTKRSQQTVIPNIGSRPWVRGVSSVISIYWTIVKPGDILLINSTGNLIAPRGYFKI
QNGKSSIMRSDAHIDNCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLAT
GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHHNSEGTGQAADLKSTQAAINQ
ITGKLNRVIKKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQ
HTIDLTDSEMSKLFEKTRKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYNHDVYR
DEALNNRFQIKGVQLKSEYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIKCNICI
"
ORIGIN
1 atgaagacta tcattgcttt tagctgcatt ttatatctga ttttcgctca aaaacttccc
61 ggaagtgaca acagcatggc aacgttgtgc ttggggcacc atgcagtacc aaacggaacg
121 ttagtgaaaa caatcacgga tgaccaagtt gaagtgacta atgctactga gctggtccag
181 agttcctcaa caggtagaat atgcaacagt ccttatcaag tccttgatgg gaaaaattgc
241 acactgatag atgctctatt gggagatcct cattgtgatg aattccaaaa cacggaatgg
301 gacctttttg ttgaacgaag cacagcctac agcaactgtt acccttatta tgtgccggat
361 tattcatccc ttaggtcact agttgcctca tccggcactc tggaatttac ccaagaaagc
421 tttgattgga ctggagttgc ccaagatgga tcaagctatg cttgcaaaag gggatctgtt
481 aacagtttct ttagtaggtt gaattggttg cataatttga attacaaata tccagcgctg
541 aacgtaacta tgccaaacaa tgacaatttt gacaaattgt acatttgggg ggttcaccac
601 ccggggacgg acagggacca agccaaccta tatgttcaag catcagggag agttacagtc
661 tccaccaaaa gaagccaaca aactgtgatc ccgaatatcg ggtctagacc ctgggtaagg
721 ggtgtctcca gcgtcataag catttattgg acaatagtaa aaccggggga catactttta
781 attaacagca cagggaatct aattgcccct cggggttact tcaaaataca aaatgggaaa
841 agctcaataa tgaggtcaga tgcacacatt gacaactgca attctgaatg cattactcca
901 aatggaagca ttccaaacga caagcctttc caaaatgtaa acaggatcac atatggggcc
961 tgtcccagat atgttaagca aaacactctg aaattggcaa caggaatgcg gaatgtacca
1021 gagaaacaaa caagaggcat atttggcgca atcgcaggtt tcatagaaaa tggttgggag
1081 gggatggtgg acggttggta tggtttcagg catcacaatt ctgaaggcac aggacaagca
1141 gcagatctta aaagcactca agcagctatc aaccaaatca ccgggaaact aaacagagtg
1201 atcaagaaaa cgaacgagaa attccatcag atcgaaaaag aattctcaga agtagaaggg
1261 agaattcagg acctagagaa atacgttgaa gacactaaaa tagatctctg gtcttacaat
1321 gcggagcttc ttgttgccct ggagaaccaa catacaattg atttaactga ctcagaaatg
1381 agcaaactgt tcgaaaaaac aagaaagcag ctgcgggaaa atgctgagga catgggcaat
1441 ggttgcttca aaatatacca caaatgtgac aatgcctgca taggatcaat cagaaatgga
1501 acttataacc atgatgtata cagagacgag gcattaaaca atcggttcca gatcaaaggt
1561 gttcagctga agtcagaata caaagattgg atcctatgga tttcttttgc catatcatgc
1621 tttttgcttt gtgttgttct gctggggttt atcatgtggg cctgccaaaa aggcaacatt
1681 aagtgcaaca tttgcatttg a

_________________
www.twitter.com/hniman

The other Kansas H3N2 sequences, as well as Illinois H1N2 also have H1N1pdm09 M gene.

_________________
www.twitter.com/hniman

None of the 7 Kansas HA sequences match H3N2pdm11. 6 of the 7 are closely related to A/swine/Kansas/11-109700/2011 .

_________________
www.twitter.com/hniman

HA outlier is A/swine/Kansas/11-107824/2011

_________________
www.twitter.com/hniman