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New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

OIE would be the international organisation I guess, collecting data on the spread of H5N1 and receiving samples.

My feeling is OIE knows (much) more than they make public, may be because of a deal with the countries who sent the samples?



.
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

they uploaded some pika-sequences recently - I haven't looked yet ...
6 Pika sequences in total ... give me some minutes ...

--------edit-----------

hmm...
not the Qinghai virus and a recombination !
I have to look closer later


Code: 
p0 e0 f0 h0 s2
maxl=51
#differences
                                                     1   2   3   4   5   6   7   PB2 PB1  PA  HA  NP  NA   M  NS
--------------------------------------------------------------------------------------------------------------------------
  1 >A/plateau pika/Qinghai/04/2007(H5N1/04/19/      0 850 925 907 905 917 917   540 716 596 433 675 330 591 861   584#  774   13250   5491      1:>A/plateau pika/Qinghai/04/2007(H5N1/04/19/   
  2 >Index Qinghai                                 850   0 231 540 539 550 553   193 193 649 336 295 269 681 335   353#  466   13183   5479      2:>Index Qinghai                                
  3 >A/pika/Qinghai/BI/2007(H5N1/04/22/            925 231   0 485 490 501 502   244 220 334 409 317 344 714 401   340#  447   13163   5470      3:>A/pika/Qinghai/BI/2007(H5N1/04/22/           
  4 >A/pika/Qinghai/HMH/2007(H5N1/12/03/           907 540 485   0  19  29  31   155 165 256 221 218 194 397 246   218#  287   13170   5477      4:>A/pika/Qinghai/HMH/2007(H5N1/12/03/          
  5 >A/pika/Qinghai/SHK/2007(H5N1/12/02/           905 539 490  19   0  28  30   149 167 254 222 218 199 397 255   218#  287   13154   5482      5:>A/pika/Qinghai/SHK/2007(H5N1/12/02/          
  6 >A/pika/Qinghai/GRL/2007(H5N1/12/04/           917 550 501  29  28   0  37   157 171 260 225 232 194 414 246   223#  294   13170   5477      6:>A/pika/Qinghai/GRL/2007(H5N1/12/04/          
  7 >A/pika/Qinghai/QW/2007(H5N1/12/05/            917 553 502  31  30  37   0   155 168 260 238 232 205 392 255   224#  295   13170   5481      7:>A/pika/Qinghai/QW/2007(H5N1/12/05/           
-------------------------------------------------------------------------------------------------------------------------------------
                                                     1   2   3   4   5   6   7   227 257 372 297 312 247 512 371


#differences in total to index
#differences in total to index , considering only polymorphisms that occur more than once in this table
#differences in total to index, where defined
#differences in total to index, where defined, considering only polymorphisms that occur more than once in this table


                                                   000000000000011111111111111111112222 00000000000000011111111122 00000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111112222 0000000000000000000000000000000000000000000000000000000111111111111111111111 000000000000000000000000000011111111111111111111 000000000000000000000000000000000001111111111111111 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 0000000000000000000000000 
                                                   112223344579900122345556677778990012 01244666666789912356779912 01111222222333334444445556777788888888889999999999990000000011111111222222222333333345555566777778888889999990111 0000112222222233333444444455555666667777777888899999999000012223344444666777 111223333334555677788888889900011122222233333335 001111112222222223335567777788888990011111222222223 001111111111222222222233333333333334444444444444555555555666666666666667777777777778888889999 1222223333444455666677778 
                                                   594586807727806868784582611239071600 62604011159354555600138812 60268235578000230124670126088801134667790012233677990113456901234559223345668011457711188927033365679991445688178 5678462235688912227133569903669122473556999356801127789034756780923569559003 458160035694167022601457894747906804667803467893 553455571344558991292594458956778283500233015667891 670112345679000156789900113346668990344445689999012245667012344567789990011124566990015670137 4124880166035633014701484 
                                                   359526401015485831925743806589629768 53727015819052424533674529 33980834595067795794967986806950629171376924739328038173405879446586121481391548134765817037114744580395179897283 0462803640578863477845825686152978240473369063163920627563204389633954199586 233353661394049606879956272814242668372422487248 039801796958584261082123902441258937325109273284029 924176516055147387321706896950697362212494592358737835479354624795910593513841356095873658674 0272122402192478563561561 
-codon-position------------------------------------       1  1       2         1 11     2     2    1       1  12    1    22     1      12        1  1   1                 1      2    2 111       1                  2    1     2  2 21111111 112 112  212 2  112 111 1 211111112122 1111111 1211111111211 1 1112 1   1                           11   1       222 2211 112 222  212222 2222 222 22 222 11222222222222   2      11              1            1 21   1    2           2   1  2 1  211   1111111222112 22222 22 22122 1211 1 1 1 
---Index-------------------------------------------TGGGGACCCGCCCTGCGATGTTTACGAGCAGGGCAA CAGCTGTGAACCACCCTTAAAAGCTC CACCTATAGATCCATCCCAATATGACTGCCAAACCAGTACTACATGTTCATAACTGGACGGAATAAGAGCTTGCACTGAAGAGTTGACACAAAGTAGGCGGGTAAAACTGTAA TCCTTTCGAAAACAAGCGTAGAATATCAACCTATGAAATCCCCTAGGGGGGGATGATAGTAGGTCTAAGATTTCGG GTGGAAACAGATGACATGAGCGGACAAATTATATGTCGAATTAGTAAT TGGTAATTGTATACTAATACTCCAAACATCGCCGTTCAACAATGCTCTGCG TAGGTGATAAAGTAGGGATGCCCCATGGGAATTGTCACGAGCATCGCACGCTTTAAGTAAAAGATGGCCGCAAAAGATGACCACTATCTAGAT GAGAGACAGGCTAGGGGCGAGGGGG 
   1 >A/plateau pika/Qinghai/04/2007(H5N1/04/19/   CA..AGTT.A...CATAG.A.CC.T..A.C...T.G ..A...C..G.TGTTTCC.GT.AGCT TGTTCGC.AGCTTTGTTTCC.CCAGTCA..TG.T.G..G.CGTGG..AT.C.G.CA.GTA.G..GGAG.TAG.T...A.GAGACCATTGTGGGACCAAAAAACGCGGTCACG. CTTG..TCGT...GG...CTAGTCGG..G.T.CGAG.GG..T..G.TAAAACGCAGC.A.TAACTCCG...CCTAA ..A..GG.GA.C.GTGCAGATA.TTCCGAA.C.CTA..G.CCG.CGGA CACAC.C..CCAG.C.GAGTA..G.GTGC.ATTACCACG..CAA.CT.AT. CG.AC....C...G....C......CA........T..A.T...TTACTA.CCC..A.GGG...G.ATA..G.G...C..A..TC.CT.G.GG AG.GAG..A...GA.AA...A..AA      904    301 ,    904    301       1:>A/plateau pika/Qinghai/04/2007(H5N1/04/19/   
   2 >Index Qinghai                                CAAAAGTTTATTTCATAGCACCC.TAGATCAAATGG TGTTCACAGGTTGTTTCCGGGGAGCT TGTTCGC.AGCTTTGTTTCC.CCAGTCATTTGGTTGACGTCGTGGACAGGCGGTCAAGT.AGGCGGAGATCG.TGTCAGGAGACCATTGTGGGACCAAAAAACGCGGTCACG. CTTGCCTAGTGCTGGATACTAGTCGGTGGTTACG.GGGGTA.TAGATAAAACGCAGCGACTAACTCCGTGCCCTAA ACATCGGTGAGCAGTGCAGATAATTTTGACGCGCTAAAGGCCTACGGA CACACGCA.CCAGTCGGAGTATTGGGTGCAATTACCACGTGCAATCTC.TT CGAACACCGC.AGGAACGCATTTTGCAAATGCCACTCTAGTTGATTAGTATCCCGGAGGGGTAGAAATTATGTGGACCAGATCTCCCTCGAGG AGAGAGTGAATAGAAAATTGAAA.A      532    456 ,    530    456       2:>Index Qinghai                                
   3 >A/pika/Qinghai/BI/2007(H5N1/04/22/           CAAAAGTTTATTTCATAGCACCC.TAG.TCAAATGG TGTTCACAG.TTGTTTC.GGGGAGCT .......G............C.......TTT.GTTGAC.TCGTGGACAGGCGGTCAAGTAA.GCGGAGATCG.TGTCAG.................................G CTTGCCTAGTGCTGGATACTAGTCGGTGGTTACGAGGGGTATTAGATAAAACGCAGCGACTAACTCCGTGCCCT-- ACATCGGTGAGCAGTGCAGATAATTTTGACGCGCTAAAGGCCTACGG. CACACGCA.CCAGTCGGAGTATTGGGTGCAATTAC.ACGTGCAATCTCATT CGAACACCGC.AGGAACGCATTTTGCAAATGCCACTCTAGTTGATTAGTATCCCGGAGGGGTAGAAATTATGTGGACCAGATCTCCCTCGAGG AGAGAGTGAATAGAAAATTGAAAAA      485    397 ,    480    395       3:>A/pika/Qinghai/BI/2007(H5N1/04/22/           
   4 >A/pika/Qinghai/HMH/2007(H5N1/12/03/          .......................G............ .......................... .......G............C...........................................................................................G ............................................................................ ................................................ ........A.......................................... ............................................................................................. .........................       20      5 ,     11      5       4:>A/pika/Qinghai/HMH/2007(H5N1/12/03/          
   5 >A/pika/Qinghai/SHK/2007(H5N1/12/02/          .......................G............ .......................... ........................................................................A........................................ ............................................................................ ................................................ ................................................... ............................................................................................. .........................       20      2 ,     10      2       5:>A/pika/Qinghai/SHK/2007(H5N1/12/02/          
   6 >A/pika/Qinghai/GRL/2007(H5N1/12/04/          .......................C............ .......................... ........................................................................A........................................ ............................................................................ ................................................ ........A.......................................... ..........C.................................................................................. .........................       30      4 ,     21      4       6:>A/pika/Qinghai/GRL/2007(H5N1/12/04/          
   7 >A/pika/Qinghai/QW/2007(H5N1/12/05/           .......................G............ .......................... ........................................................................A........................................ ..................................A......................................... ................................................ ........A.......................................... ..........C.................................................................................. .........................       33      5 ,     24      5       7:>A/pika/Qinghai/QW/2007(H5N1/12/05/           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
---Index-------------------------------------------TGGGGACCCGCCCTGCGATGTTTACGAGCAGGGCAA CAGCTGTGAACCACCCTTAAAAGCTC CACCTATAGATCCATCCCAATATGACTGCCAAACCAGTACTACATGTTCATAACTGGACGGAATAAGAGCTTGCACTGAAGAGTTGACACAAAGTAGGCGGGTAAAACTGTAA TCCTTTCGAAAACAAGCGTAGAATATCAACCTATGAAATCCCCTAGGGGGGGATGATAGTAGGTCTAAGATTTCGG GTGGAAACAGATGACATGAGCGGACAAATTATATGTCGAATTAGTAAT TGGTAATTGTATACTAATACTCCAAACATCGCCGTTCAACAATGCTCTGCG TAGGTGATAAAGTAGGGATGCCCCATGGGAATTGTCACGAGCATCGCACGCTTTAAGTAAAAGATGGCCGCAAAAGATGACCACTATCTAGAT GAGAGACAGGCTAGGGGCGAGGGGG 
-codon-position------------------------------------       1  1       2         1 11     2     2    1       1  12    1    22     1      12        1  1   1                 1      2    2 111       1                  2    1     2  2 21111111 112 112  212 2  112 111 1 211111112122 1111111 1211111111211 1 1112 1   1                           11   1       222 2211 112 222  212222 2222 222 22 222 11222222222222   2      11              1            1 21   1    2           2   1  2 1  211   1111111222112 22222 22 22122 1211 1 1 1 
                                                   000000000000011111111111111111112222 00000000000000011111111122 00000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111111111111112222 0000000000000000000000000000000000000000000000000000000111111111111111111111 000000000000000000000000000011111111111111111111 000000000000000000000000000000000001111111111111111 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 0000000000000000000000000 
                                                   112223344579900122345556677778990012 01244666666789912356779912 01111222222333334444445556777788888888889999999999990000000011111111222222222333333345555566777778888889999990111 0000112222222233333444444455555666667777777888899999999000012223344444666777 111223333334555677788888889900011122222233333335 001111112222222223335567777788888990011111222222223 001111111111222222222233333333333334444444444444555555555666666666666667777777777778888889999 1222223333444455666677778 
                                                   594586807727806868784582611239071600 62604011159354555600138812 60268235578000230124670126088801134667790012233677990113456901234559223345668011457711188927033365679991445688178 5678462235688912227133569903669122473556999356801127789034756780923569559003 458160035694167022601457894747906804667803467893 553455571344558991292594458956778283500233015667891 670112345679000156789900113346668990344445689999012245667012344567789990011124566990015670137 4124880166035633014701484 
                                                   359526401015485831925743806589629768 53727015819052424533674529 33980834595067795794967986806950629171376924739328038173405879446586121481391548134765817037114744580395179897283 0462803640578863477845825686152978240473369063163920627563204389633954199586 233353661394049606879956272814242668372422487248 039801796958584261082123902441258937325109273284029 924176516055147387321706896950697362212494592358737835479354624795910593513841356095873658674 0272122402192478563561561


Code: 
                                                       000000000000000000000000000000001111111111111111111111111111111111111111122222 0000000000000000000000000000000000000000011111111111111111111111111111111111111111112222222222 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111122222222222222 00000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111 000000000000000000000000000000000000000000111111111111111111111 0000000000000000000000000000000000000000000000000000000000000000001111111111111111111111 0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 00000000000000000000000000 
                                                       001122222233334445555666778999990000012223344444555555666666677777788889900011 0001112234444445566666666777778889999999900000111112222223333444445555677788889999990000111122 0011111111111122222222222333333444444444444444455555555566666677778888888888999999999999000000001111111112222222223333333333444455555555566666666677777777778888888888888899999999999900000111111112 00000111222222222333333344444444445555555556666666777777888899999999900000001122223333444445666667 001112222223333333444555567778888888899999000011222222223333335 0000111111111222222222222333333344445566667777777888888889999999990001111111112222222233 0011111111112222222222333333333333334444444444444445555555555556666666666666677777777777788888889999999 01222222333344455566666678 
                                                       123703336855680570057367054567890134971466924568223467045568900124758895605909 3662332630048891901112699013894560344567926788155995788990467113450238013648991577881159013829 3602355567899912235567899000233001122223456778901123566833466608880113466779001223367799011345670122345592233456680114567788126801156688911125778902333446770123567788999901244455668823678135677891 56678466022356889122226713345669990346678991112247355699356801125778903444674567780019235691455590 393470045790133459038045701260144477923799368958045566792367783 3559344555789114445568899012377913472503990455689125677880134457893350011123480125667927 7701123456790001567899001223446678990233444556999990112222456680112344577889900011124566900015670113457 24124668044823522902369932 
                                                       767930396706841566948582520987327619424753785867395184702818409222303906131082 6053255792870953701584849810363516625433365102625474817495454098623764367121394447450324626591 3339203987056822834579517067709580703692469670270987514256836980695062917137692473932803817340577924465861214813915481324769624805843617017830479518147364063519452847036955614739891900167268989337 04762809936405788634787784558235678621593263797824047339063163928062756138324043980956339540514995 936774739070801573283468304021337906146209586860021716866821682 6146809128105790696975837921958973873266038401935675236596202542472843678921023844395301 0352876271662584984328179057061708473736235056034698243689465804365735806021604624952467106984769478185 21383788068758034129812717 
-codon-position----------------------------------------2222222222222 222222222  2 2222222222222212 2 222222222222222222 2 222  222222   2               2   21   1 1         1     2         1       1      1        1  12       1 2   1         1 2  22        1     2        12            2         1  1   1                 1       2    2 111       1                      1                     2         1       11 12  2  1  12   21111111211 112 112  11212 12 1 12122 1 112121 1 21111112122 11111111 1 211111111111111211 1111 11   1     1     1                 1             11    1       222      22122   1    11   2         11 1        11   2 1   1        1  12212                11 1111112211111111111111211111111111111121 211121112111 111111111111 111211 1211 221112222222   22221  1     1  1  2  12 22212122 
---Index-----------------------------------------------GATGAAGGGTACCTCCTGCGGAGGCCCTCCCTAAGGGCAGATAAAAGGTTGTCCGGCCCCGAGCCTGCAGGGGGCAGA TGTAAACGCCTTGGAAAGCGAAGCCAGTCCCGAAATATGAAAGGGAATTGACCACCTAACCAACACGTTGGGGATCACAACGAGTACGTCAATA CCACCAACTCCAACTCACAGGATAATCTTGCTCTCAAAATACTCTACTCGACTGATGAAGTCTACCAGACCGGTACTACATGTACACAACTGGGCGGAAATGAAAGCTTGCACTAAGGACGTGTTTCGAGATTCCGCCGCATAACGATGTCCGGGCGGGAACAGATGAATGAGAAAAACCCTCTAGATAAGATATA CCTTGTTCGTGGTAATGGGCATCCTAGATTAAGTCAGGCAATGCCTCGAGAGTCCCTGGGAAAAACGCAATAAGAATTTATAGCGCCCGGATGTCCCT CAGTAGGCAAGGATAAGGTTTGGGTACAAATAGGTTAGTGAGACGCGCTAACGGGCTTGCGGA GTAAGCACACCTAGGCAAGCGTTAGTTACCGCATGAACCATTGGAGGCACCCAATATAAACCAGCGTCACAAGCCAACAATCCTTCGG CGAGCACCGCAATGAACGCATTTTGCTAAATGCCATTAAATAGTTGATTAGTAAACTCCCGGAGTGGGTAGAGATTATGTGGACCAGATCTCCCTCGAAGCAG AAAGAGACAGGTTAGGGGCGAAAGGG 
   1 >A/peregrine falcon/Hong Kong/2142/2008(H5N1///   ....G..................T.T...T.........A........C.........T........T........A. ......T...C..ACGG....C.T....T......CC...........C........C..A.GTG.ACCA.T.G..GTGG.A......C..... ........C.T......T.............C...............................G...A...............T..T........A.......G..........G..A..A..............A......C...G..C....................................G....G...G .......T..A....A.....C.....C..GT.C..A.....ATT.A..........A.............T.A..........A......CT..... ....G......A.C...A..C..AC....GC....C.AAA..T.ATATGT....AT.A..AA. A.C..GTA.T..G..T.T..A.......T............C.A.A.....TCGC.C.......T...CG........T..TTC...A TAG.TGATAA.G.AGGGATGCCCCATCGGGAATTG.C...CGAGCATCGCAC.GGTCTTTAAGT.AAAA.AT.GCCGCAAAAGATGACCACTA..TA.GAT.T GG....................G...      462    220 ,    460    220       1:>A/peregrine falcon/Hong Kong/2142/2008(H5N1///   
   2 >A/pika/Qinghai/HMH/2007(H5N1/12/03/              --...........C.............C........................T......................... .AC.......C..AC.G.T..CA...AC.TTAG..CTC...GAAAGGC.A.TTG.TC..T...T..A...AAAGCT.TGG..GC.GT..T..CC ........C.T......TG......C.A...C.......C..CA................C..G...A...A...........T..T......A....G..A.G..........G.A..........A.......A......C.......A.........G......G...........T......G......G.. T..CT....C.AA..CAA..G..TAGA.A...T....A...C....ATGA.A.....A..GGGG.GATG......G..AG.G.T..TAA......TTC -...G.....AA.C...A.....AC.TG.GCG..AC..AA..TTATATGT...AAT.A.TAAT ..G..GTA.T...A.T.TA.....A...........T....C.A.A.....TCGC.C..G....T..TCA........TG..TC.... TAG.TGATAA.G.AGGGATGCCCCATCGGGAATTG.C...CGAGCATCGCAC.GGTCTTTAAGT.AAAAGAT.GCCGCAAAAGATGACCACTATCTA.GAT.T -G.........C..........G...      300    285 ,    287    281       2:>A/pika/Qinghai/HMH/2007(H5N1/12/03/              
   3 >A/pika/Qinghai/GRL/2007(H5N1/12/04/              --...........C.............C........................T.C....................... .AC.......C..AC.G.T..CA...AC.TTAG..CTC...GAAAGGC.A.TTG.TC..T...T..A...AAAGCT.TGG..GC.GT..T..CC ........C.T......T.......C.A...C.......C...A................C..G...A...A...........T..T......A....G..A.G.....A....G.A..........A.......A......C.......A.........G......G...........T......G......... T..CT....C.AA..CAA..G..TAGA.A...T....A...C....ATGA.A.....A..GGGG.GATG......G..AG.G.T..TAA......TTC -...G.....AA.C...A.....AC.TG.GCG..AC..AA..TTATATGT...AAT.A.TAAT ..G..GTA.T...A.T.TA.....A...........T....C.A.A.....TCGC.C..G....T..TCA........TG..TC.... TAG.TGATAACG.AGGGATGCCCCATCGGGAATTG.C...CGAGCATCGCAC.GGTCTTTAAGT.AAAAGAT.GCCGCAAAAGATGACCACTATCTA.GAT.T -G.........C..........G...      311    285 ,    298    281       3:>A/pika/Qinghai/GRL/2007(H5N1/12/04/              
   4 >A/pika/Qinghai/QW/2007(H5N1/12/05/               --...........C.............C........................T......................... .AC.......C..AC.G.T..CA...AC.TTAG..CTC...GAAAGGC.A.TTG.TC..T...T..A...AAAGCT.TGG..GC.GT..T..CC ........C.T......T.......C.A...C.......C...A................C..G...A...A...........T..T......A....G..A.G.....A....G.A..........A.......A......C.......A.........G......G...........T......G......... T..CT....C.AA..CAA..G..TAGA.A...T....A...C....AT.A.A.....A..GGGG.GATG......G..AG.G.T..TAA......TTC -...G.....AA.C...A.....AC.TG.GCG..AC..AA..TTATATGT...AAT.A.TAAT ..G..GTA.T...A.T.TA.....A...........T....C.A.A.....TCGC.C..G....T..TCA........TG..TC.... TAG.TGATAACG.AGGGATGCCCCATCGGGAATTG.C...CGAGCATCGCAC.GGTCTTTAAGT.AAAAGAT.GCCGCAAAAGATGACCACTATCTA.GAT.T -G.........C..........G...      311    283 ,    298    279       4:>A/pika/Qinghai/QW/2007(H5N1/12/05/               
   5 >A/pika/Qinghai/SHK/2007(H5N1/12/02/              --...........C.............C........................T......................... .AC.......C..AC.G.T..CA...AC.TTAG..CTC...GAAAGGC.A.TTG.TC..T...T..A...AAAGCT.TGG..GC.GT..T..CC ........C.T......T.......C.A...C.......C...A................C..G...A...A...........T..T......A....G..A.G.....A....G.A..........A.......A......C.......A.........G......G...........T......G......... T..CT....C.AA..CAA..G..TAGA.A...T....A...C....ATGA.A.....A..GGGG.GATG......G..AG.G.T..TAA......TTC -...G.....AA.C...A.....AC.TG.GCG..AC..AA..TTATATGT...AAT.A.TAAT ..G..GTA.T.....T.TA.....A....T......T....C.A.A.....TCGC.C..G....T..TCA........TG..TC...A TAG.TGATAA.G.AGGGATGCCCCATCGGGAATTG.C...CGAGCATCGCAC.GGTCTTTAAGT.AAAAGAT.GCCGCAAAAGATGACCACTATCTA.GAT.T -G.........C..........G...      300    284 ,    286    280       5:>A/pika/Qinghai/SHK/2007(H5N1/12/02/              
   6 >A/magpie robin/Hong Kong/1097/2008(H5N1///       A........C.......AT..G....T...T..G..A.G...GCGG.A.......A.......T.CA..T........ C....G..T...A..G.........C.......GG...A.G.......C.G...T...G.TG..GT.C...A............C..A..GC.. ............G.C.G...............................T..T.A...G...T...................A......G......A.....................A..........G...C..................T....................A..................G...G T..CT...A..AAG..AA....TTAGA...G.T..G.A...C....A.GA.A.....AA.GGGG..AT.......GC.AG.G.....AA......TTC TG...A.T.G....CGA.C...A..............A..GA....A...G..A......... ...GA.....A.C.T.....A.G..A.GTTA.GCAG.TTGA.A...AT.TT....G..T.GAGA......GGAAT..T..C....T.. .A..........C...T....................G.G..........................A.C............................G...G. ....................G.....      245    168 ,    243    168       6:>A/magpie robin/Hong Kong/1097/2008(H5N1///       
   7 >A/peregrine falcon/Hong Kong/1143/2007(H5N1///   A........C.......AT..G....T...T..G..A.G....C...A.......A.........CA..T..A..... C...G...T...A..G.......T.C.......GG...A.G.......C.G...T...G..G..GT.....A........TA..C..AC.GC.. ............G.C.G...............................T................................A..........A..A.....................A..............C..................T.......................................G...- ---CT...A..AA....A....TTAGA...G.T..G.A...C....A.GA.A.....AA.GGGG..AT.......GC.A..G.....AA......TTC TG...A.T.G....C.......A.................G.........G............ ...GA.....A.C.......A.G..A.GT.A.GC.G.TTGA.A...AT.TT....G.GT.GAGA.A....GGAAT.....CA...T.- ............C...T....................G.G........................C................................G...G. ....................G.....      192    151 ,    176    146       7:>A/peregrine falcon/Hong Kong/1143/2007(H5N1///   
   8 >A/duck/Guangxi/4428/2005(H5N1///                 .....................................................................A........ C.......T........................GG...A.G.........G..........GG.GT..............T............. ............G...G..................................................................................................................C...........................................................----- .......T...................C.C.C.C..A...G.ATT..........................T.A..........A......CT.T... -G...A.T.G....C.......A..G..............G.........G...........- ...GA.....A.C.......A....A.GT.A..C...T....A...AT.TT....G.......A.A....G.A.T.....C....T.- ...............G.....................G.G........................C................................G...G. -..........C..............       97     81 ,     78     72       8:>A/duck/Guangxi/4428/2005(H5N1///                 
   9 >A/duck/Hunan/5106/2005(H5N1///                   --...........C.............C........................T......................... C.......T........................GG...AGG.........G..........GG.GT..........G...T......A...... ............G...G......................................C..............................................................................................................................T........----- ..C....T.............C.....C.C.C.C..A..GG.ATT..............A...........T.A......C...A......CT.T... -G...A.T.G....C.......A..G..............G.........G...........- ...GA.....A.C.......A....A.GT.A..C........A...AT.TT....G.......A.A....G.A.T.....C....T.- .....................................G.G............C...........C................................G...G. -.........................      105     92 ,     82     81       9:>A/duck/Hunan/5106/2005(H5N1///                   
  10 >A/duck/Hunan/5152/2005(H5N1///                   .............C.............C........................T......................... C.......T........................GG...AGG.........G..........GG.GT..........G...T......A...... ............G...G......................................C..............................................................................................................................T........----- ..C....T.............C.....C.C.C.C..A..GG.ATT..............A...........T.A......C...A......CT.T... -G...A.T.G....C.......A..G..............G.........G...........- ...GA.....A.C.......A....A.GT.A..C........A...AT.TT....G.......A.A....G.A.T.....C....T.- .....................................G.G............C...........C................................G...G. -.........................      100     90 ,     81     81      10:>A/duck/Hunan/5152/2005(H5N1///                   
  11 >A/goose/Guangxi/224/2006(H5N1///                 ................................G............................................. C.......T........................GG...A.G.........G.........TGG.GT..CA..........T......A...... ................G...............................................................................................................G..........................T..................................A----- .......T.............C.....C...C.C..A...G.ATT..........................T.A..........A......CT.T.-- -G...A.T.G..G.C...C...A..G..............G.........G...........- A.G....A.T.....T..A......................C...A......CGC.C.......T...CG........T...T....- .....................................G.G........................C................................G...G. -.................T.......      106     82 ,     79     71      11:>A/goose/Guangxi/224/2006(H5N1///                 
  12 >A/goose/Guangxi/1633/2006(H5N1///                .......................T...................................................... -.......T...................T....GG...A.G....................GG.GT...A..........T......A...--- ........C........T...............................................................A....T....................................................................T..................................A----- .......T.............C.....C...C.C..A...G.ATT..........................T.A..........A......CT..... -G...A.T.G..G.C.......A..G..............G.........G...........- A.G...TA.T.....T..A......................C...A......CGC.C.......T...CG.......TT...T....A .....................................G.G........................C................................G...G. -.........................      114     82 ,     84     70      12:>A/goose/Guangxi/1633/2006(H5N1///                
  13 >A/duck/Hunan/3315/2006(H5N1/11/30/               ..CAGGA.A.G.T.T...T.....TT.C.T.CGGAAAT..G.G.G...C.A.TAA.TTTT..AT...TC...A....G .A...GT..........................GG.....G.........G......CG..GG..T..............T.....TA....C. ..G....T....G...G........................................G...........T.A....C........G..G..............GG.............................T..........................A......................G...G..----- .....................C.....C.C.C.C..A...G.ATT..........................T.A...A......A.......T.T... -...G......A.C...A.....AC.....C...CC..A...T.ATATGT.....T....A.. ..G......T....TA...............T...........AG.......C......G....T...C..................A ...A.G...............................G.G........................C..A.................G...........G...G. G.G.G....AA...A...........      355    139 ,    342    133      13:>A/duck/Hunan/3315/2006(H5N1/11/30/               
  14 >A/pika/Qinghai/BI/2007(H5N1/04/22/               .GCA..AAA.G.T..T...AA.A.T...T..C...A.T.AGC..G.A..C.C..A.TT..AG..T...C.AA.ATG.G .A.G...T.TCC.AC.GA.AGCA.T.A..TT.G...T....GAAAGG..A..TG.TC..T...T.........G.T.TGG.....GT......C ........C.T......TG......C.A...C.......C..CA................C..GTTTAGTT.AC.TCGTGGAC.GG.GGTCAA.T.A.GGC.G.GATCG.TGTC.GA..........A.......A......C.......A.........G......G...........T......G......G.. .T...CC...A..GC...AT.......G.C.G..TG..T......A....G.GTATA.AT....T....GC.G.G..C.......T...TG..C.... -.AC..T.C......GA..C.A...G..G....A..T..............AA...C.A...T .C......G..A....C..T.C.G..AG...T..A..T......G..TG........G.........T..G...TGCT...T..CTT. ...A........G.............C........C..C...............TT................A...........................T.. -.GAGAGTGAA.AGAAAATT.G.AAA      336    249 ,    325    247      14:>A/pika/Qinghai/BI/2007(H5N1/04/22/               
  15 >A/great crested grebe/Denmark/7498/06(H5N1///    .GCA.GAAA.GTT.TTC..A..A.T......C..AA.T.AGC...GA..C.C.AA.T.TAAGA.T...C.AA.ATG.G ----------------------------.TTAG...T....GAAAGG..A..TG.TC......T.........GCT.TGG..G..GT..T...C TTGTTGGT.T.G.T.AG..AAGCTG.T.GAT.TCTGGGCCCT..AGAC.AGTCAG.A.TA.TC.TTT.GTT.ACGTCGTGGAC.GG.GGTCAA.T.AGGGC.G.GATCG.TGTC.G.AGTACACCCTA.ATC.TT.TTATGCCGTTGCAC..AAA.AAAG.ATAGCA.CCAGACGGGGTTTC.CGA.CGG.GG.C- TT...CC...A..GC.A.AT.........C.G..TG..T......A..G.G.GTATA.AT....C....GC.G.G..C....A..T...TGC.C.... -.AC..T.C......GA....A...G..G...AA..T..............AA...C.A.... .C......G..A....C..T.C.G..AG...T.....T......G..TG.................C...G...TGC....T..CTT. ...A........G......................C..C................T..............A.A...........................T.. -.GAGAGTGAA.AGAAAATT.G.AAA      465    363 ,    356    332      15:>A/great crested grebe/Denmark/7498/06(H5N1///    
  16 >A/chicken/Nigeria/1071-15/2007(H5N1///           .GCA.GAAA.GTT..TC..AA...T...T..C.....T.AGC...GA..CAC..A.T.TAAGA.T...C.AA.ATGAG .A.GGG.T.TCC.AC.GA.AGCA.T.A..TTAG..CTC...GAAAGGC.A.TTG.TC..T...T..A...AAAGCT.TGG..GC.GT..T..CC TTGTTGGT.T.G.T.A...AAGCTG.T.GAT.TCTGGGCCCT..AGACTAGTCAG.A.TA.TC.TTT.GTT.ACGTCGTGGAC.GGTGGTCAA.T.AGGGC.G.GATCG.TGTC.G.AGTACACCCTA.ATC.TT.TTATGCCGTTGCAC..AAA.AAAG.ATAGCA.CCAGACGGGGTTTC.CGA.CGG.GG.C- .T...CC...A..GC...AT.........C.G..TG..T......A..G.G.GTATA.AT....C..T.GC.G.G..C....A..T...TG..C.... ..AC..T.C..A...GA..CCA...G..G...AA..T....A.........AA...C.A.... .C......G..A....C..T.C.G..AG...T....GT......G..TG.................C...G...TGC....T..CTT. ...A........G......................C..C.A..............T..............A.A...........................T.. ..GAGAGTGAA.AGAAAATT.G.AAA      427    366 ,    417    365      16:>A/chicken/Nigeria/1071-15/2007(H5N1///
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

ACT31467 560 Pika HA H5N1 China 2007/04/22 Influenza A virus (A/pika/Qinghai/BI/2007(H5N1))
ACT31478 567 Pika HA H5N1 China 2007/12/03 Influenza A virus (A/pika/Qinghai/HMH/2007(H5N1))
ACT31496 567 Pika HA H5N1 China 2007/12/04 Influenza A virus (A/pika/Qinghai/GRL/2007(H5N1))
ACT31500 567 Pika HA H5N1 China 2007/12/02 Influenza A virus (A/pika/Qinghai/SHK/2007(H5N1))
ACT31511 567 Pika HA H5N1 China 2007/12/05 Influenza A virus (A/pika/Qinghai/QW/2007(H5N1))
Click to expand...

The first one has lots of differences.!

(added) the 4/22 HA has 30 differences from the concensus.

.
 
Last edited:
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

The NS1 has 11 differences in the first sequence.

Unfortunately, they all contained 92E, which confers virulence and resistance to antiviral cytokines.

.
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

we must have discussed this 29.Dec.2008, I have files on my PC,
but I forgot about it. I had thought it were just a normal Qinghai-virus...

but (plateau pika) it's a strange virus, combined from others
but still distant.
Even much worse than quadruple reassortant ******


Code: 
 40 >A/plateau pika/Qinghai/04/07,04/19        

 10: 51, 83, 78,482, 75,477,179,260   A/Dk/HK/7/1975(H3N2)
 17:134, 92,103, 16, 72,116,157, 61   A/Hong Kong/156/97(H5N1)
 32: 72, 75, 63, 12, 47, 21,179,273   A/Goose/Guangdong/1/96(H5N1)
 38: 58, 83, 65, 24, 75, 26,187, 30   A/Ck/Henan/01/04(H5N1)
 39: 41, 73, 52, 22, 20, 20,198, 49   A/Ck/Hubei/wm/97(H5N1)
 41: 78, 63, 83,  8, 68, 32,177, 44   A/Ck/Hubei/wh/97(H5N1)
 44:106, 68, 87, 10, 81, 35,167,  0   A/Ck/Hubei/wj/97(H5N1)
 50: 85, 85, 84, 26, 70, 51,177, 30   A/TSp/Henan/4/04(H5N1)
 53:118, 90, 86, 10, 79, 70,163, 34   A/Ck/Hubei/wi/97(H5N1)
 55:122, 87, 91,377, 91,120,180, 15   A/Ck/HK/17/1977(H6N1)
 63: 51, 69, 87, 79, 72,470,174, 23   A/Dk/HK/312/1978(H5N3)
 68: 51, 70, 84,481, 80,476,170, 13   A/Dk/HK/562/1979(H10N9)
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

Those cute little pikas are carrying a polybasic cleavage site!!!
(This allows the virus to be cleaved by a wide variety of enzymes)

GERRRKKR for the 4/22 sequence - ACT31467

RERRRK_R for the later sequences!

Boy - they don't miss a trick.

Question is - do they live through it & the NS1/E ???

.
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

Are the Chinese Pikas the infamous "unknown reservoir"????

.
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

no, they don't give the virus to birds,humans

------------edit-----------
well, maybe they give it to birds I haven't checked.
similar in most segments to old H5N1 from 1997
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

we must have discussed this 29.Dec.2008
Click to expand...

Submission date = Aug 2009, journal date = 2009.

collection date = 2007, so does that mean they just recently sequenced the samples?

.
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

Conservationists say the small animals are an important source of food for bigger species such as bears, eagles and leopards
Click to expand...

http://ecoworldly.com/2009/03/30/china-tries-to-control-plague-of-pikas-with-contraceptives/

Unfortunately, loss of the plateau pika over vast expanses of the Tibetan Plateau has resulted in a loss of many native species that rely on the pika. Most endemic native birds nest only in pika burrows, and when these collapse following poisoning, the birds disappear. Most predators on the plateau (weasels, ferrets, Pallas's cat, Tibetan fox, wolf, brown bear, upland buzzard, saker falcon, and black-eared kite) rely almost exclusively on pikas in their diet. When the pikas are poisoned, these animals also disappear.
Click to expand...

http://www.answers.com/topic/plateau-pika
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

Roehl_JC said:
IMHO...Pikas and swine (both wild and domesticated) and other mammals need a much more thorough testing and assessment to determine how widely distributed H5N1-postive samples are, and then conduct sequencing to determine the evolutionary changes occurring so that experts like Niman and GSGS can assess the data for the benefit of us all.
Click to expand...

Agreed. One of the lessons of the current H1N1 pandemic (and other diseases from animal / bird reservoirs like ebola, H5N1, etc.) is: we need surveillance, surveillance, surveillance.

The new H1N1 has been roaming around for years before going pandemic, right under our nose.

We see all kinds of scattered projects, not easy to get funding, to coordinate efforts, to avoid political problems.

Individual countries and research institutes may prioritize viral research, send the virologists to fieldtrips, let them catch virusses and analyse them.

May be OIE needs more support and should hit the drums more and harder and try to do more than they do now. More coordination with WHO?

OIE operates in a political minefield. For instance : it would not surprise me if Indonesia still sends their positive H5N1 samples to the OIE regional office in Australia. It is not clear to me what happens next.

Also commercial interests could hamper research: collecting and analysing samples in poultry and pig farms.

We need surveillance .
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

I missed one pika sequence. It's listed as "plateau pika". it's similar to the other early pika, having even more differences from the later pikas and an RERRRKKR cleavage site.

ACO83271 568 Plateau pika HA H5N1 China 2007/04/19 Influenza A virus (A/plateau pika/Qinghai/04/2007(H5N1))
Click to expand...
.
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

yes, distant sequences. Goes back to Hubei/1997(H5N1)

maybe they share the virus with other species, also environment.

E.g. HA of the plateau pika is only .6% different from 1997 H5
conserved in permafrost ?


no mention of the recombination in BI (or lab error ?) in the JVI-paper ?

the Qinghai-strain pika-flu (A/pika/Qinghai/BI/) is similar to Korean chicken from Nov.2006
in 7 segments plus in the middle part of PA
showing that the two outbreaks in Korea Nov/2006 have entirely different sources
in location but not in time, one of which is linked to the Qinghai-pika
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

It's intriguing that a 2007 sample from Chinese high plateau pikas can match (somewhat well) 1997 H5N1 infected Hubei chickens.

I wonder what % of captured pikas were H5N1-infected?

If it's been in the Pikas since 1997 or soon thereafter, how many other mammals have carried the polybasic cleavage site for years?

.
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

the 1997 was a quick check from a 48-genomes database
the match was in HA

checking the whole database, the best matches are:

segment: number of differences, virus name


A/Plateau Pika/Qinghai/2007/04/19(H5N1)
----------------------------------
PB2: 9,A/Dk/Fujian/19/2000(H5N1)
PB1: 9,A/Dk/Fujian/19/2000(H5N1)
PA : 6,A/Dk/Fujian/19/2000(H5N1)
HA : 4,A/Ck/Hubei/wn/2003(H5N1)
NP : 2,A/Sw/Shandong/2/2003(H5N1)
NA : 2,A/Ck/Hubei/wn/2003(H5N1)
M : 4,A/silkyCk/Shantou/1818/2000(H9N2)
NS : 0,A/Ck/Hubei/wn/2003(H5N1)

A/Pika/Qinghai/HMH/2007/12/03(H5N1)
---------------------------------
PB2: 2,A/Dk/Hunan/5106/2005(H5N1)
PB1: 22,A/Ck/Nigeria/1071-15/2007(H5N1)
PA : 28,A/Dk/Guangxi/288/2006(H5N1)
HA : 20,A/MagpieRobin/HK/1097/2008(H5N1)
NP : 16,A/PeregrineFalcon/HK/2142/2008(H5N1)
NA : 14,A/Ck/Guangxi/463/2006(H5N1)
M : 9,A/PeregrineFalcon/HK/2142/2008(H5N1)
NS : 2,A/Dk/Guangxi/4428/2005(H5N1)

A/Pika/Qinghai/BI/2007/04/22(H5N1)
------------------------------------------
PB2: 3,A/Dk/Korea/Asan5/2006/11/25(H5N1)
PB1: 0,A/Environment/Korea/W149/2006/11/25(H5N1)
PA : 69(recombination),A/WhooperSwan/Hokkaido/2/2008(H5N1)
HA : 12,A/Ck/Korea/CA7/2006(H5N1)
NP : 0,A/CommonGull/Chany/P/2006(H5N1)
NA : 11,A/CommonGull/Chany/P/2006(H5N1)
M : 3,A/Dk/Korea/Asan5/2006/11/25(H5N1)
NS : 2,A/Ck/Krasnodar/2/2007(H5N1)


a file with the 100 best matches for each of these 3 viruses and each
segment is attached
 

Attachments

Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

How do the hawk sequences compare?
 
Re: New Study Finds Wild Pikas Are Natural Mammalian Hosts To H5N1 Avian Influenza Virus

gsgs said:
t
A/Pika/Qinghai/HMH/2007/12/03(H5N1)
---------------------------------
PB2: 2,A/Dk/Hunan/5106/2005(H5N1)
PB1: 22,A/Ck/Nigeria/1071-15/2007(H5N1)
PA : 28,A/Dk/Guangxi/288/2006(H5N1)
Click to expand...

Nigeria makes sense: H5N1 outbreak suspected to be related with imported live poultry (chicks) from China.
 
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