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Deadly bird flu strain found in Germany

Re: Deadly bird flu strain found in Germany

gsgs said:
other sequences usually don't have the markers either, I think.
(Vietnam,Indonesia,Korea/2004,..)
PB2:C222A,G361A,A362G,G564A


Code: 
                                                000000000000000000000000000011111111111111111111111111111111111111111111111112222222222222 0000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111112222222222222 0000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111222 000000000000000000000000011111111111111111111 0000000000000000000000000000000000000111111111111111 0000000000000011111111111 00000000000000000001 0000000000000000000000000000000 
                                                000122333344445556778888899900011111122223333455555666777778888888999999999990000001111123 0011222444555666667788888999999990000011111111222222223333333334444444444555556677788888888888880000000223333 0011222223334444555556667788888888899999900011111111122222233344444555556666667777778888888888999999011 011222234455555667777888900011223344555566777 1122233333333444455566666666666778899000001122222235 1122333677788911111223344 22345555777778888990 1222233333344444555666666667788 
                                                456026666878893685082458869900201247713380569600358169123451136689222346689991334472246923 5844348258248336891302567333668892346803677799013589990111222590223455677012244414803334466667791234677570013 2416445780173389034497999911355778914578924901234588933359925704478346793666660488990123457899146689947 648359957713667773559159837829582299125907667 5728945555569145701501122346669190366344484856888944 4519034217844100136365956 04447888345894559135 0023401456844559047022455881928 
                                                871827129772521484268985604625499886933615957206077152984323553473489415720289076960423645 9206501225451258667274813039034899242304634639924416795279369924087026905611757840840355803890899516736062906 9278098680522592110620692846728690725524001848666525901373660410165063830245677025029573818869492513280 135610623486470078181886681576692839422619458 7785082457963419473335814623596727406846709036157348 7924916417727635132784391 89621039984430082068 1124918247478698140635938248911 
-codon-position---------------------------------  1   12   22           1 1   12  2  1      21             1 2 1  12 2  221   2    2    11 21221 22222222222    2         1      2 2 1 22  1   1  1 2      1    12 2 2    11  1  2    2 1          212 2 2                   11    1      1   1       212    2 1         1   1   1 2 12    21       1   2  111 1 122222212 22   12 1222 22  222222222211 22 12 1   2 1 1 2        1        2          2   12  1       2  11   12112112112111  1 11111111111 1 11 2 2    1   1  1    1  211211 1122 
---Index----------------------------------------GGTAAGGATCTCATCGATGCTGGGCACGTTGGGGAATAGAACTGCAAATTTGCCGAGAGGTGACGAAAGGGGGGAACCCATTGGGGAAGG TTGGAATGAAGGGAGGAGTTTGATGTACTTTAGGAGCAGGATCTTATAGCCTCGCTCTAGACCGCAATTTACGGTGTTAAAGAGATTCACTTCTATCAGTCGTGAACAG TTGTCGAAGTTAGGGGAGATCAGCGTTGCGTACCCCAGGGGGCCAAAGCCGCGAGATCGGTTCCCTTTACTTTCTCGATCAATCAAAAGGCAGCAGGGTTTGG AGCTAGATAGGTAAGGTAGGTAATCGGAGCGCAATCCGGTACATA ACTGGTAGAGAGCGGCAGGTAGAGAGTCACGTGTTTAGATAGGGAAAATCAG AACCCTATTAAGTTGCCTTACGTTC TAGTAAGGGGACGATGGGGA TAGAGCCCCACTGAGACACATAAAGGTAGCA 
  1 >A/bar-headed Gs/Qinghai/2/2005             ------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------- .......C.......A..................G.........C G.........G............AG..T.TA.A.AC.A...A.A..C.G... .G.....C.......T.G....G-- -------------------- -------------------------------      833    379 ,     35     24      1:>A/bar-headed Gs/Qinghai/2/2005             
  2 >A/migratory Dk/Jiangxi/2300/2005           ------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------- ..........................................--- G.........G...................A...............C..... .......C......AT.......-- -------------------- -------------------------------      815    365 ,     11      7      2:>A/migratory Dk/Jiangxi/2300/2005           
  3 >A/Ck/ST/4231/2003                          ------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------- ..T....CC..CG.A....AC.T.A.A...............--- G........AG....T.........A....A.......TGG----------- .....C.C.......T......G-- -------------------- -------------------------------      894    393 ,     52     24      3:>A/Ck/ST/4231/2003                          
  4 >A/bar-headed Gs/Qinghai/9/2005             ......A.C.G.........C.ACT...C.........AGG..A....GC........AAGATAAC.C.A..AAGG...GCCA..A...- ..AA.....G.AA......CC..............ATGA..CTG...................A....C...C.GA..GGCAG..CC..TGCTG..............- -......GAA..AA...ACCT..TA...........G.A.....G.G.......AGCTAA.C..T.C.C....TCTCGG...CTG.G.AA..ATG.TACC..A ......T..A.C...A.G.A.C..A........GG...ACC.... ..G.A........A...........A......A.ACTA...AAA..CGG..A ..T.......C.C..T.......-- .G.C.G.A.TGTA..AA.-- ............................---      225    162 ,    173    152      4:>A/bar-headed Gs/Qinghai/9/2005             
  5 >A/bar-headed Gs/Qinghai/10/2005            ..........GT.G..G.....C..G..C....A...GAG.........C........A..A..AC.CAA..AA.GT..GCC....C.A- ..AAG......A...AG...C.CCA........AT.TGA..CTGCGCG..TCTAT...G.G.AAGGGCC...C.GA...GCAG..CC..TGCTG.C.GA..C......- -.....G...C.AA..CACCT.....C...CGT..........................A.....CC.......CTCG....CT....AA..A.G.TA.CCAA ....CAT..A.C...A...AC.............G..AAC...G. .TG.ACCAGAGA..A.C.A.GAC.GA.T....A.ACTA..GA.A..CGG..A ......G.....C..T.......-- .G.C.G.A.TGT..C..A-- ..........T.A.A.AGG.........---      259    186 ,    207    176      5:>A/bar-headed Gs/Qinghai/10/2005            
  6 >A/great black-headed gull/Qinghai/3/2005   ..............T.....C....G..CC........................A......A.......A..AA...............- ..AAC...............C.CCAAGTCCCCAA.......CTGCGC.......T........A...CC...CAGA.CGGCCG..CC.GTGCTG...GA..C......- -........AC.AAA..ACCT...............G...A...G.GATT....A.C.AA.C.T..C......TCTCGGT..C.G...AA..ATG.TA....A ..T.C.T..ATC...A.G.ACCT..AA..T....G..AACC.... .TG.ACCAGAGA....C.A.GAC.GA......A.A.TA.....A..CGG.GA GG........C....T.......-- .G.......T.T.GCA..-- ...G..T......GA..G.........G---      239    170 ,    187    160      6:>A/great black-headed gull/Qinghai/3/2005   
  7 >A/great black-headed gull/Qinghai/2/2005   ..........G.........C.ACT...CC.A.AG..GAG.........C....A......A..A...A...AA.G.........A..A- .....C..G..AA.A....CC.CCA.............A..CTGCGC...T...T...G.G......C.A..CAGACCGGCCG..CC.G.GCTG...GA..C......- -........A...AA.CACC..T.A...........G......TGG.ATT....A.C.AA.C.T.CC...C..TCTCGG......G..AA..A...T.C..AA .....AT..AT....A...A.CT..A......G.G..A...T... ...................................................- G.....G...C.C..T.......-- .........T.T.GCA..-- ...............G..............-      202    139 ,    153    130      7:>A/great black-headed gull/Qinghai/2/2005   
  8 >A/bar-headed Gs/Qinghai/8/2005             ......A.C...........C.A.....C....A...GAG........GC.........AG.TAA........A............C..- ..AA.......AA.A.........A..........A..A.GCTGCGC..T....T.......AAGGGCCCCTCAGA....CA........GCTG.A..A..C......- -......G.AC..A..CACCT.T..CC...C.......A.AA...G.........GC.AA.C.TT........TCTCGG...C.GGG.AA......TACC.AA ....C.T..A.C...A.G.A............GG.T..A...... .............A...................................... ..T..CG...C.C..T.......-- .G.......T.T....A.-- .TT.A.....T.A.A......C.....G---      198    140 ,    146    130      8:>A/bar-headed Gs/Qinghai/8/2005             
  9 >A/bar-headed Gs/Qinghai/5/2005             ......A.............C....GT.C........GA....A.....C.........A..T.A..C.......G.....CA..AC..- ............................................................................................................- -......G..CG.AA.CACCT.T.A...........G.A.AA.T.GGAT.....A...A.....TCC.C....TCTCGGT.....GGGAA..AT..T.C..AA ...........................................G- .................................................... .......................-- .................... ...............G..............C      108     72 ,     70     66      9:>A/bar-headed Gs/Qinghai/5/2005             
 10 >A/bar-headed Gs/Qinghai/65/2005            ...................................................A...................................... ............................................................................................................A -.......................................A.............................................................. ..........................................--- .................................................... .......................-- .................... ...............G..............-       45     11 ,      9      4     10:>A/bar-headed Gs/Qinghai/65/2005            
 11 >A/bar-headed Gs/Qinghai/68/2005            ...................T.....................................................................- .............................Y..............................................................T...............- -............................A.......A................................................................. ..........................................--- .................................................... .......................-- .................... ...............G......T.......-       48     16 ,      8      7     11:>A/bar-headed Gs/Qinghai/68/2005            
 12 >A/bar-headed Gs/Qinghai/0510/2005          ...................T.....................................................................- .............................Y..............................................................T...............- -............................A.......A................................................................. G.........................................--- .................................................... .......................-- .................... ...............G......T.......-       61     17 ,     17      8     12:>A/bar-headed Gs/Qinghai/0510/2005          
 13 >A/bar-headed Gs/Qinghai/60/2005            ......................................................................A..................- ............................................................................................................- --......................................A.............................................................. .........................A................--- .................................................... .......................CT .................... ..............................C       45     13 ,     19      6     13:>A/bar-headed Gs/Qinghai/60/2005            
 14 >A/brown-headed Gull/Qinghai/3/2005         .............................................G.....................................A.....- .............................C..............................................................................- -...................................................................................................... .........................A....A...........--- ...................................................- .......................-- .................... ..............................-       47     15 ,      5      5     14:>A/brown-headed Gull/Qinghai/3/2005         
 15 >A/bar-headed Gs/Qinghai/67/2005            .........................................................................................- ............................................................................................................- -.....................................A................................................................ .........................A................--- .................................................... .......................-- .................... ..............................-       43     11 ,      3      2     15:>A/bar-headed Gs/Qinghai/67/2005            
 16 >A/Dk/Novosibirsk/02/2005                   ....C.AG.......A.............................C....................G......................T ..........A.................................................................................................. C...................................................................................................C.. ..............A................T............. ..........G...................A....................- ...............T.......CT .................... C.............................-       62     20 ,     46     18     16:>A/Dk/Novosibirsk/02/2005                   
 17 >A/Ck/Inner Mongolia/64/2005                ....C.AG.......A..............C..........................................................- ..A.......A......A...............................................G..........................................- -......................T................AA.....A....................................................C.. G..................A...C.......T............. ..........G......................................... .............C.T.......-- ..................-- C...A...................A...---      102     34 ,     50     24     17:>A/Ck/Inner Mongolia/64/2005                
 18 >A/grebe/Novosibirsk/29/2005                ....C.AGC......A...................................AT........................T............ ..........A............................................................................................A..... ...................................T.......................................................G........C.. ............................................. ..........G...................A..................... ........................- .................... C..............................       60     17 ,     44     16     18:>A/grebe/Novosibirsk/29/2005                
 19 >A/swan/Germany/R65/2006                    ....C.AG.T.....A..A.........C.............................T............................... ..........A.............A.................................................................................... ....T............A..................................................................................C.. ............G..............................C. ..........G....T..............A..................... ......................... .................... C............G.................       61     20 ,     61     20     19:>A/swan/Germany/R65/2006                    
 20 >A/bar-headed Gs/Qinghai/75/2005            .........................................................................................- .......................................................................................................------ -...................................................................................................... ..........................................--- .................................................... .......................-- .................... ...............G..............-       50     15 ,      1      1     20:>A/bar-headed Gs/Qinghai/75/2005            
 21 >A/bar-headed Gs/Qinghai/59/2005            .........................................................................................T ...........................................................................................................C- -...................................................................................................... ..........................................T-- .................................................... .......................-- .................... ...............G..............C       44     11 ,     10      5     21:>A/bar-headed Gs/Qinghai/59/2005            
 22 >A/Environment/Qinghai/31/2005              ---......................................................................................- .......................................................C...................---------------------------------- -...................................................................................................... .........................A................--- ...................................................- .......................-- ...........T........ ..............................-      121     49 ,      4      3     22:>A/Environment/Qinghai/31/2005              
 23 >A/black-headed Gs/Qinghai/2/2005           ---.C...........G........................................................................- -......................................................C----------------------------------------------------- --....................................................................................................- -........................A...............T--- ...................................................- .....................---- ...................G -...........................AT-      195     80 ,     11      8     23:>A/black-headed Gs/Qinghai/2/2005           
 24 >A/great black-headed gull/Qinghai/1/2005   ---....................................................................................G.- -..............................................G.......C----------------------------------------------------- --...........................................................CT..C.A..................................- ..................A......A...T....G......T... ....................G..A....C...A......GG........... ......G....AC..T.......-- ..................-- ...G........................---      201     91 ,     38     23     24:>A/great black-headed gull/Qinghai/1/2005   
 25 >A/bar-headed Gs/Qinghai/1/2005             A....A......C.......C.A.....C..A.....GA...CA.....CC......................................- .C.........A....G........................CTA..CGA.......TC.AGA.A...C..CTC.GA.C...A.A.....T.CTGGC..A..CC.....- -..............A..........................................................................A............ ....C..C.......A...A.....AA.......G.........C .T...C........A.........G.AT.T...........A.A....GT.A ............C..T.G.....-- .G.......T.......A-- ..............A..........A.G---      136     87 ,     84     77     25:>A/bar-headed Gs/Qinghai/1/2005             
 26 >A/whooper swan/Qinghai/1/2005              A....A......C.......C.A.....C..A.....GA...CA.....CC......................................- .C.........A....G........................CTA..CGA.......TC.AGA.A...C..CTC.GA.C...A.A.....T.CTGGC..A..CC.....- -..............A..........................................................................A............ .A....T............AA....A..A.S.....T..C..T.. .T...C........A.........G.AT.T...........A.A....GT.A GG.A.......A...T...G...-- ..................-- ..............A..........A.G---      135     89 ,     83     79     26:>A/whooper swan/Qinghai/1/2005              
 27 >A/brown-headed gull/Qinghai/1/2005         ..C.................C....GT.C..A.....GAG...................A....................C.A.....A- .CA.C..A.G.AAGA.....C.CCA.G.C..CA....CA..CTGCGC................A.....C.....................CTG....A..C......- -.....T.......A.CAC..C...CCTT................G.A...TCCAG..A.CCTTT.C......TCTCGG...C.....AA..A.GCTACC..A ....C.....TC...A...A.C....A......G......C...C .TG........A..A.C.AAG.C.G...CT...................... G......................-- ..................-- ...............G......T....G---      172    122 ,    120    112     27:>A/brown-headed gull/Qinghai/1/2005         
 28 >A/bar-headed Gs/Qinghai/4/2005             ..........G......G..C.A.....C....AG..GAG...A.....C.........A..T.A..........G...G.CA...C..- ..A.CC.....AA.A....CC............A.A.GA.GCTGCGCG.T.CTAT.T...G..A.....C.T...A....C..........CTG.......A...G..- C.....T.......A.CAC..C...CCTT................G.A...TCCAG..A.CCTTT.C......TCTCGG...C.....AA..A.GCTACC..A ....C.T..............C............GT.AS....G. .TG..CCAGA.A....CT..G.C.GA.T.........A.....A..C.G.G. ..........C.C..T.......-- .GT.GG...T.....AA.-- ..T.......T.ATA............G---      220    152 ,    172    143     28:>A/bar-headed Gs/Qinghai/4/2005             
 29 >A/bar-headed Gs/Qinghai/3/2005             ..........G..GT..G..C....GT.C....A...GAG..CA.....C.........A.......C.......G......A..AC.A- .......AG..AA.......C.CCACG.CCCCA.T...A..CTGCGCG......T........A...C....C.GACC.......C...TCCTG...GA..C......- -..........G...................GTT......................C..A.............TCTCG........................A ........CATC...A...A.C...AA.A....G..T..C..... ..................A.G..AGA.T.T.....CTA....AA...CG.GA ............C.........G-- .GT......CGT......-- ............................---      187    121 ,    135    111     29:>A/bar-headed Gs/Qinghai/3/2005             
 30 >A/great cormorant/Qinghai/3/2005           .................G..C.A..GT.C..A.AG..GAG..CA....GC.....G...A..T.A..C..A...GGT...C.......A- ..A........AAGA....CC.CCAAGTCC...........CTGCGC................A...........A...............CTG...........G..- -............A...A.C....................A....G.A...T....C..A.C........C..TCTCGG....................C..A ..................A......AA.......G.......... ............T.A.C.AAG.C.G........................T.. GG....G................-- .G................-- ...G............AGG.CC......---      158    106 ,    106     96     30:>A/great cormorant/Qinghai/3/2005           
 31 >A/peregrine falcon/Hong Kong/D0028/2004    .AC.C.AG.T.T...AG...........C........G..G..AT.G.....T..GA.........G..........T.G....A....- ..........A..GAA.AC....C...............A...........C.A.C.................................T........A.......A.- -C..T...A.C....................G.T.....C.A.....A.........T..............C.......G......G.....T......C.. --------------------------------------------- ---------------------------------------------------- ------------------------- ....GG.............. C........G....A..G..C...AA....-      494    186 ,     98     60     31:>A/peregrine falcon/Hong Kong/D0028/2004    
 32 >A/Ck/Fujian/1042/2005                      .A..C.AG.......AG...................C...G...T.G........GA.........G............G....A....- C.........A.......C..................................A.................................T...........C......A.- -C............A................G..T....C.A.....A..A......T...........T..C.......G......G............C.. --------------------------------------------- ---------------------------------------------------- ------------------------- ......A.A.........A. CT.......G.C..................-      446    169 ,     51     43     32:>A/Ck/Fujian/1042/2005                      
 33 >A/Gs/Shantou/2216/2005,China,2005          .A..C.AG.......AG.................G.....G..AT.G........GA.........G............G....A....- C.........A.......C....................A.............A....................................................A.- -C.............................G.......C.A.....A.........T..............C.......G......G............C.. --------------------------------------------- ---------------------------------------------------- ------------------------- ......A.A........... C.....T..G....................-      450    163 ,     56     37     33:>A/Gs/Shantou/2216/2005,China,2005          
 34 >A/Dk/Fujian/897/2005                       .A..C.AG.......AG...................C...G...T.G........GA.........G............G....A....- C.........A.......C..................................A.................................T......G....C......A.- -C.............................G..T....C.A.....A..A......T...........T..C.......G......G............C.. --------------------------------------------- ---------------------------------------------------- ------------------------- ......A.A.........A. C........G.C..................-      446    168 ,     51     42     34:>A/Dk/Fujian/897/2005                       
 35 >A/Ck/Liaoning/23/2005                      ....C.AG.......A...........T....A.............................................T.........A- ......C...A..........A........................................T.....................T...............T...G...- -.T.......................................T........................G.............G...............A..C.. --------------------------------------------- G.........G...................A.......G......T...... ...............T.......-- C...........A.....-- C..................G........---      235     86 ,     36     31     35:>A/Ck/Liaoning/23/2005                      
 36 >A/guinea fowl/Shantou/1341/2006            ....C.AG.......A...........T..................................................T..........- ......C...A..........A........................................T.....................T...............T...G...- -.T.......................................T........................G..C..........G...............A..C.. ................C..........G...T..........--- G.........G...................A.......G......T...... ...............T.....A.-- C................... C..................G..........-       91     42 ,     48     33     36:>A/guinea fowl/Shantou/1341/2006            
 37 >A/pied magpie/Liaoning/7/2005              ....C.AG.......A...........T..C...............................................T...A...C.A- ......C...A..........A........................................T......A.............AC...............T...G...- -.T.......................................T........................G.............G...............A..C.. ................C..........G...T............. G.........G................T..A.......G......T...... ..............AT.......-- C.................-- C..................G.......G---      107     50 ,     55     40     37:>A/pied magpie/Liaoning/7/2005              
 38 >A/Dk/Novosibirsk/56/2005                   ....C.AG.......A.........................................................................A ..........A...A.............................................................C................................ ...............................................................................T............A.......C.. ...............................T............. ..........G...................A..................... ...............T....T...- .................... C..............................       50     18 ,     34     17     38:>A/Dk/Novosibirsk/56/2005                   
 39 >A/Azerbaijan/008-208/2006                  ---GC.AG.......A..A.............A..............G.....T...G...............................- ..........A.A..A................A........................................................T..................- --.C.A..............T..............T.......................................................GA.......CA. -..C.........G.........C..................... ..........G......A............AC.C..........G......- ........C....C.TT.C....-- -------------------- C....T..T..............G..C...-      183     74 ,     73     42     39:>A/Azerbaijan/008-208/2006                  
 40 >A/Ck/Afghanistan/1207/2006                 ...GC.AG.......A..A............................G.....T...G................................ ..........A....A.........................................................................T..................- -..C.A..............T...........T..T....................................................A...........C.. ...C.........G.........C..................... ..........G...................AC.C..........G....... ....T...C......TT...T..-- .................... C....T..T..............G..C...-       87     42 ,     62     37     40:>A/Ck/Afghanistan/1207/2006                 
 41 >A/Egypt/902782/2006                        ---.C.AG.......A.....A.............T...................................T.................- ..........A..............................................................................T......T..........CA -................................................................C..................................C.. -...........G............A.....T............. ...A......G.T....A............A....................- ....T....G.....T..C..A.-- .................... C......T...........G..........-      136     40 ,     83     30     41:>A/Egypt/902782/2006                        
 42 >A/whooper swan/Mongolia/13/2005            ....C.AG.......A.....A.............T............................A......TA................- ..........A.....................................................................................T......A....- -...................................................................................................C.C .......C.......A..........A.................C ...A......G...................A.................C... .........G.....T......... ..................-- C......T...........G........---       90     35 ,     47     27     42:>A/whooper swan/Mongolia/13/2005            
 43 >A/ruddy shelDk/Qinghai/1/2005              ------------------------------------------------------------------------------------------ ............................................................................................................- -..............A..........................................................................A............ .A.......................A..A.......T........ .................................................... ...A...............G...-- ..................-- ......................M.....---      285    108 ,     15      9     43:>A/ruddy shelDk/Qinghai/1/2005              
 44 >A/bar-headed Gs/Qinghai/62/2005            .........................................................................................- ............................................................................................................A -...................................................................................................... ..........................................--- .................................................... .......................-- .................... ..............................-       39      9 ,      3      1     44:>A/bar-headed Gs/Qinghai/62/2005            
 45 >A/bar-headed Gs/Qinghai/12/2005            .........................................T...............................................- ............................................................................................................- -......................................................................C............................... .........................A................--- .................................................... .......................-- .................... ..............................-       50     12 ,      7      3     45:>A/bar-headed Gs/Qinghai/12/2005            
 46 >A/bar-headed Gs/Qinghai/61/2005            .........................................................................................- .............................C..............................................................................- -.....................A................................................................................ .........................A................--- ...................................................- .......................-- .................... ..............................-       49     13 ,      7      3     46:>A/bar-headed Gs/Qinghai/61/2005            
 47 >A/black-headed gull/Qinghai/1/2005         ---..........................................G.....................................A.....- -......................................................C----------------------------------------------------- --....................................................................................................- -........................A....A..........T--- ...................................................- .....................---- ...................G -............................T-      192     80 ,      8      8     47:>A/black-headed gull/Qinghai/1/2005         
 48 >A/black-headed Gs/Qinghai/1/2005           ---......................................T.............................................G.- -......................................................C----------------------------------------------------- --.....................................................................C..............................- -.T......................A...............T--- ...................................................- .....................---- .................... -...........................AT-      197     81 ,     13      9     48:>A/black-headed Gs/Qinghai/1/2005           
 
---Index----------------------------------------GGTAAGGATCTCATCGATGCTGGGCACGTTGGGGAATAGAACTGCAAATTTGCCGAGAGGTGACGAAAGGGGGGAACCCATTGGGGAAGG TTGGAATGAAGGGAGGAGTTTGATGTACTTTAGGAGCAGGATCTTATAGCCTCGCTCTAGACCGCAATTTACGGTGTTAAAGAGATTCACTTCTATCAGTCGTGAACAG TTGTCGAAGTTAGGGGAGATCAGCGTTGCGTACCCCAGGGGGCCAAAGCCGCGAGATCGGTTCCCTTTACTTTCTCGATCAATCAAAAGGCAGCAGGGTTTGG AGCTAGATAGGTAAGGTAGGTAATCGGAGCGCAATCCGGTACATA ACTGGTAGAGAGCGGCAGGTAGAGAGTCACGTGTTTAGATAGGGAAAATCAG AACCCTATTAAGTTGCCTTACGTTC TAGTAAGGGGACGATGGGGA TAGAGCCCCACTGAGACACATAAAGGTAGCA 
-codon-position---------------------------------  1   12   22           1 1   12  2  1      21             1 2 1  12 2  221   2    2    11 21221 22222222222    2         1      2 2 1 22  1   1  1 2      1    12 2 2    11  1  2    2 1          212 2 2                   11    1      1   1       212    2 1         1   1   1 2 12    21       1   2  111 1 122222212 22   12 1222 22  222222222211 22 12 1   2 1 1 2        1        2          2   12  1       2  11   12112112112111  1 11111111111 1 11 2 2    1   1  1    1  211211 1122 
                                                000000000000000000000000000011111111111111111111111111111111111111111111111112222222222222 0000000000000000000000000000000001111111111111111111111111111111111111111111111111111111111111112222222222222 0000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111222 000000000000000000000000011111111111111111111 0000000000000000000000000000000000000111111111111111 0000000000000011111111111 00000000000000000001 0000000000000000000000000000000 
                                                000122333344445556778888899900011111122223333455555666777778888888999999999990000001111123 0011222444555666667788888999999990000011111111222222223333333334444444444555556677788888888888880000000223333 0011222223334444555556667788888888899999900011111111122222233344444555556666667777778888888888999999011 011222234455555667777888900011223344555566777 1122233333333444455566666666666778899000001122222235 1122333677788911111223344 22345555777778888990 1222233333344444555666666667788 
                                                456026666878893685082458869900201247713380569600358169123451136689222346689991334472246923 5844348258248336891302567333668892346803677799013589990111222590223455677012244414803334466667791234677570013 2416445780173389034497999911355778914578924901234588933359925704478346793666660488990123457899146689947 648359957713667773559159837829582299125907667 5728945555569145701501122346669190366344484856888944 4519034217844100136365956 04447888345894559135 0023401456844559047022455881928 
                                                871827129772521484268985604625499886933615957206077152984323553473489415720289076960423645 9206501225451258667274813039034899242304634639924416795279369924087026905611757840840355803890899516736062906 9278098680522592110620692846728690725524001848666525901373660410165063830245677025029573818869492513280 135610623486470078181886681576692839422619458 7785082457963419473335814623596727406846709036157348 7924916417727635132784391 89621039984430082068 1124918247478698140635938248911
Click to expand...
Qinghai isolates are easily identified. You have not listed any Qinghai isolates from South Korea, Japan, India, or China (other than the isolates from Qinghai Lake). Without those isolates, comments out Qinghai H5N1 dying out has no scientific basis.
 
Re: Deadly bird flu strain found in Germany

Liaoning,inner Mongolia are Qinghai-viruses from China.
Not "Qinghai"-virus is dying out but Qinghai-lake-2005-virus.
 
Re: Deadly bird flu strain found in Germany

gsgs said:
Liaoning,inner Mongolia are Qinghai-viruses from China.
Not "Qinghai"-virus is dying out but Qinghai-lake-2005-virus.
Click to expand...
There are several hundred Qinghai sequences from countries west of China, there are three from China, 0 from South Korea, 0 from Japan, 0 from India. Without more from China, or the countries with 0, little can be said about what died out at Qinghai Lake in May, 2005, since these countries in Asia clearly have Qinghai infections.
 
Re: Deadly bird flu strain found in Germany

that's the point.
They have Qinghai-strain but none of the public sequences
other than Qinghai-lake has the Qinghai-lake-markers.
Also non-Qinghai H5N1. Those markers are specific to
Qinghai-lake.
 
Re: Deadly bird flu strain found in Germany

gsgs said:
that's the point.
They have Qinghai-strain but none of the public sequences
other than Qinghai-lake has the Qinghai-lake-markers.
Also non-Qinghai H5N1. Those markers are specific to
Qinghai-lake.
Click to expand...
H5N1 does not live in public database. They are heavily biased and do not reflect nature.

H5N1 (including Qinghai) is in nature, not public databases.
 
Re: Deadly bird flu strain found in Germany

Is it definite clear, that the positive birds in Nuremberg are from the sub-clade 2.2.2.2? Or, when we can expect an answer?
 
Re: Deadly bird flu strain found in Germany

Coleman said:
Is it definite clear, that the positive birds in Nuremberg are from the sub-clade 2.2.2.2? Or, when we can expect an answer?
Click to expand...
To my knowledge, sequence data on Germany and Czech 2007 isolates have not been released (and may not even have been generated yet).
 
Re: Deadly bird flu strain found in Germany

The H5N1-Virus was proven in the meantime in 13 dead birds.
All originate from the environment of the Woehrder lake
and the silver lake. The number of dead birds with the dangerous
Asia variant remained however constant with six.
On Monday of yesterday the signs increased
that the virus from Nuernberg is the same as in the outbreak
in the winter 2005/2006 or at least very similar.

Mettenleitner: "the risk for humans remains small.
The outbreak is not really surprising after the Czech outbreak.

Bogner: "so far the bird flu for us was an epidemic in the winter,
when the birds are weakened. Now in the early summer we did not really expect it."

The one speculate, the birds just carried the virus
while dying from something else. As example the Botulismus
bacterium is called, which produces a nerve poison.
Others assume a connection to the outbreak in Czech.

Schoepf: "H5N1-Virus is more common as so far assumed under
wild birds without all get sick from it". In the opposite,
there are species, which the virus does obviously no harm.
Schoepf and other experts assume also that the epidemic could
well remain limited to the region Nuernberg.
 
Re: Deadly bird flu strain found in Germany

machinetranslation

Puzzling bird flu

For the experts the outbreak of the epidemic comes completely surprisingly. And over the reasons can be so far only speculated. Whether there is a connection with the cases in Tschechien?

By Christian Sebald

After the outbreak of the bird flu in Nuremberg Federal Ministers of Health Horst Seehofer (CSU) have and bird experts forwards panic-make warned. They reminded at the same time however to the caution with finds of dead birds.

The H5N1-Virus was proven in the meantime with 13 dead birds. All originate from the environment of the W?hrder of lake and the silver lake. The number of the dead birds with the Asia variant dangerous for humans remained however constant with six.

On Monday of yesterday the signs multiplied themselves that the virus is in Nuremberg the same as with the outbreak in the winter 2005/2006 or at least this very similarly. ?With it is and remains very small the risk for humans?, said Thomas Mettenleiter, president of the Friedrich Loeffler institute, which maintains the reference laboratory for bird flu on the Baltic Sea island Riems.


Mettenleiter called nevertheless to increased watchfulness: ?We must ensure that the virus does not jump over on utilizable bird existence.?

On federal level main header a debate over precaution inoculation for poultry on. While B?rbel H?hn, deputy parliamentary group boss of the Greens in the Bundestag, called their introduction overdue, she rejected the consumer Minister of Baden-Wuerttemberg Peter Hauk (CDU) strictly:

?As long there is no vaccine, which leaves the virus inactive so it can not be passed , we see in the inoculation no suitable measure.?

The N?rnberger authorities strengthened its precautionary measures. The restricted area and the observation zone around the W?hrder lake and the silver lake cover large local recreation areas it city, in addition, the zoo, parts of the center as well as the circle F?rth. Forces of the fire-brigade, in addition, Parkw?chter looked for them off for dead birds.

Caution also in the zoo

In addition they controlled the adherence to the guideline for dogs to be as well as the a stable obligation for poultry. The existence of the 57 poultry owners in the security zones are however rather small with 2600 chickens and other utilizable birds.

Also in the zoo precaution measures were seized. To ?we set up, said disinfection tubs natural? the deputy director of zoo Helmut farm servant woman. ?Also the Voli?re is closed.? But the game birds have still much liberty. ?We can kill not hundreds of animals as a precaution?, said farm servant woman. It did not want to describe the scenario, if zoo birds with H5N1 are infected.

Over background the recent outbreak go the estimates of the experts apart. ? Since last week bird flu was discovered in a Czech Turkeyfarm, it is not not really surprising ?, says Mettenleiter.

So far an epidemic in the winter

Differently Karl-Heinz Bogner, the boss of the veterinary laboratory at the national office for health and food security in attaining: ?So far the bird flu for us was an epidemic in the winter, if the birds are weakened, said? it. ?Now in the early summer we did not count really on it.? Like that all kinds of attempts at explanation are in the circulation.

The one speculate, the game birds the virus possibly only in itself would have carried, are however at another illness ends. As example the Botulismus bacterium is called, which produces a nerve poison.

Others assume a connection to the outbreak in Tschechien. ?We examine that everything?, said Bogner. On Monday in addition also specialists of the Friedrich Loeffler Institus in Nuremberg arrived.

For the ornithologist Heiner draw, which leads the bird protection control room in mixing part churches, confirm the N?rnberger of cases above all that the H5N1-Virus under game birds is common further as so far thought, ?without all get sick with it?. On the contrary, there are strong species , which don?t care about the virus obviously.

Draw and other experts assume also that the epidemic could quite remain limited to the region Nuremberg.

http://www.sueddeutsche.de/bayern/artikel/471/120320/
 
Re: Deadly bird flu strain found in Germany

No additional bird flu cases in German wild birds

26 Jun 2007 08:42:06 GMT

HAMBURG, June 26 (Reuters) - No new cases of the lethal strain of bird flu have been discovered in Germany since six wild birds tested positive for the disease over the weekend, Germany's national animal disease institute said on Tuesday.

Six wild birds tested positive in Germany for the dangerous H5N1 strain of the disease. They were found in Nuremberg in south Germany and examined as part of a national testing programme.

"The number remains at six, we have no additional cases," a spokeswoman for Germany's Friedrich Loeffler animal disease institute said.

Authorities continued to investigate the outbreak, the first in Germany this year, but the Agriculture Ministry believes the incident could be isolated.

Poultry farmers in the Nuremberg region have been ordered to confine all poultry to closed stalls. As of Saturday, a 21-day ban was imposed on bringing poultry or poultry products in or out of the area, which is now a quarantine zone.

Last year, some 13 European Union member states had confirmed cases of bird flu -- Germany, Austria, Denmark, Italy, Greece, Britain, the Czech Republic, Poland, Slovakia, Slovenia, Sweden, France and Hungary.

http://www.alertnet.org/thenews/newsdesk/L26393183.htm
 
Re: Deadly bird flu strain found in Germany

one additinal suspected sample sent to FLI now.

PR inside.com 26.06.2007 11:05:09) - in Nuernberg a further dead bird with the suspicion on an infection with the aggressive H5N1-Virus was found. "at present the tenth sample is on the way to us", said the spokeswoman of the Friedrich Loeffler institute on the island Riems, Elke Reinking, on Tuesday on strip packing-inquires. The LGL can test only whether a Kadaver is infected with the H5N1-Erreger. Whether the dangerous or the less sticking on variant of the virus is present, must tighten Friedrich Loeffler Friedrich-Loeffler-Institut. So far Friedrich Loeffler Friedrich-Loeffler-Institut examined nine samples from Nuernberg. With six the highpathogenic variant of the H5N1-Virus was found, a sample was not not infected. With the remaining two samples the H5N1-Virus was identified, the variants is however still unclear (strip packing)

LGL:Erlanden
FLI:Riems
LGL-laboratory:Oberschleissheim

I'm curious, can the LGL do the HA and NA sequencing ?
Are the /Bavaria sequences from the LGL ?
Then they should quite well be capable to determine the strain -
and probably knew it since Friday- and the shipping
to FLI is only proforma.


-----------------------

Press release, 17 March 2006, NR. 110/06 snatch on: High Tech laboratory in enterprise - immediately H5N1-proof in Bavaria possible +++ the new High Tech laboratory of the national office for health and food security (LGL) in Oberschleissheim can accomplish immediately the H5N1-proof. This avowed Bayerns consumer protection Minister Werner snatch on today in Munich. So far only Friedrich Loeffler Friedrich-Loeffler-Institut (LFI) on the island was Riems in a the position to determine H5N1. Snatch on: ' by the own laboratory capacities Bavaria provides a time projection/lead with the analyses. On the basis of the first results of analysis the responsible district administration authorities can be already forewarned and the animal you fight be prepared.' The official confirmation of the poultry plague case takes place also further via the national reference laboratory on the island Riems. The H5N1-Proben positively before-tested at the LGL lands then with highest priority with the FLI. This raid Bayerns takes place in coordination with the FLI. Bavaria is thereby the first country in Germany, which can make the Subtypisierung of the Influenzavirus with own know-how and laboratory equipment. The Free State for it invested approximately 400,000 euro. +++ Beyond that snatch on a scientific advisor committee and its line at the LGL furnished in Oberschleissheim settled. The 10 scientist team is to regenerate relevant questions scientifically. Prioritaer concern themselves the scientists with the inoculation strategy of house poultry and domestic animals as well as a any epidemic spreading over feeds. To the team belong experts from the Infektiologie, the animal you fight, the industrial safety, the environmental sanitation, the animal body removal, the water protection, the chemical compatibility with disinfections and the animal protection. The H5N1-Diagnostik accomplished by means of one ' ' validated material time PCR ''. Over a polymerase nuclear chain reaction (PCR) the h and n-components (Haemagglutinin and Neuraminidase) are proven the influenza-viren. This analytics take place in a S3-security and a molecular biology laboratory. The devices are sucked. ' ' material time Thermocycler ' '.
 
Re: Deadly bird flu strain found in Germany

still 6 confirmed cases in Nuremberg, 19 suspects

3 dead swans found in Saxony. A preliminary test confirmed H5N1.
Location is Frohburg south of Leipzig


http://www.gesundheitpro.de/Vogelgrippe-Neue-Verdachtsfaelle-in-Vogelgrippe-A070626KOA0P051615.html

(in German)


found in Eschefeld near a big pond

lots of ponds in that region :


esch2.jpg
 
Last edited:
Re: Deadly bird flu strain found in Germany

Bird flu found in second German state
Posted : Tue, 26 Jun 2007 11:18:00GMT





Berlin - A summer outbreak of bird flu in Germany was confirmed Tuesday to have spread to a second state, with three swans killed by the deadly form of avian influenza in a small town close to Leipzig. At the end of last week, half a dozen swans killed by the virus were found in a turgid urban pond in Nuremberg in Bavaria state.

Some 190 people around the world have died of bird flu since 2003, mainly through coming into close contact with infected poultry, according to the World Health Organization.

Scientists fear the virus could mutate into a form easily transmissible between humans, which could touch off a global pandemic that would kill millions of people.

The health ministry in Saxony state in Germany's east said three dead swans were found in the Frohburg district, south of Leipzig, and a quick test established they were infected with the dangerous H5N1 virus.

Saxony state had to exterminate a flock of farm birds last year after they caught H5N1.

More tissue tests are being done at Germany's federal animal- disease laboratory on the Baltic Sea island of Riems.

In Nuremberg, a municipal spokeswoman said none of the other dead birds in the city apart from the six swans had H5N1.

Scientists on Riems are trying to establish if the virus is connected to outbreaks of avian influenza at a Czech poultry farm and in Hungary. The disease has not been detected in Germany between August 2006 and its appearance late last week in Nuremberg.



http://www.earthtimes.org/articles/show/76482.html
 
Re: Deadly bird flu strain found in Germany

Translation:

H5N1 also in Saxonia - no further cases in Nuernberg 26.06.2007 12:39 o'clock Frohburg/Nuernberg/Riems - after the occurance of of the bird flu in Nuernberg also in Saxonia infected animals were found. Three dead swans were discovered in glad castle south of Leipzig, reported the Saxonian Ministry of Health. A first test proved the dangerous bird flu virus H5N1. At present further investigations ran at Bundesinstitut for animal health on the Baltic Sea island Riems. Only if the results were present, concrete measures were decided. In Saxonia in the previous year the bird flu in a utilizable animal existence had broken out. In Nuernberg meanwhile no further H5N1-Infektionen was proven with animals. "it remains with the six cases of bird flu", reported a spokeswoman of the city. Bundesinstitut for animal health on the island Riems examines further bird flu suspicion from Nuernberg according to own data still another. The sample comes from a swan, which was found likewise dead in the city, said the president of the Friedrich Loeffler institute, Thomas's C Mettenleiter. The results were expected on Wednesday. The origin of the exciter is further unclear. In molecular-biological investigations the Genomsequenzen in Nuernberg with game birds found of the virus is to be compared with those of the H5N1-Erregers proven in Tschechien and Hungary, said Mettenleiter. With the comparison family relations are not to be uncovered (with dpa) H5N1 also in Saxonia - no further cases in Nuernberg H5N1 also in Saxonia - further cases in Nuernberg
 
Re: Deadly bird flu strain found in Germany

niman said:
Translation:

H5N1 also in Saxonia The origin of the exciter is further unclear. In molecular-biological investigations the Genomsequenzen in Nuernberg with game birds found of the virus is to be compared with those of the H5N1-Erregers proven in Tschechien and Hungary, said Mettenleiter. With the comparison family relations are not to be uncovered (with dpa) H5N1 also in Saxonia - no further cases in Nuernberg H5N1 also in Saxonia - further cases in Nuernberg
Click to expand...

The above appears to suggest that Clade 2.2.2.3 is being detected. This clade has HA M230I and NA G743A, which were acquired by isolates in Egypt this season (including the Gharbiya cluster).
 
Re: Deadly bird flu strain found in Germany

Immediate notification report​
Report reference: , Ref OIE: 5632, Report Date: 26/06/2007 , Country: Germany​
Report Summary​
Disease​
​
​
Highly pathogenic avian influenza Animal type Terrestrial​

Causal Agent​
​
​
Highly pathogenic avian influenza virus Serotype(s) H5N1​

Clinical Signs​
​
​
Yes Reason Reoccurrence of a listed disease​

Date of confirmation of Event​
​
​
24/06/2007 Date of Start of Event 24/06/2007​

Date of report​
​
​
26/06/2007 Diagnosis Laboratory (advanced), Necropsy​

Date of last occurrence​
​
​
03/08/2006 Number of reported outbreaks Submitted= 6, Draft= 0​

Name of Sender of the report​
​
​
Mr Werner Zwingmann Address Rochusstr. 1 Bonn D-53123​

Position​
​
​
Ministerialdirigent Telephone (+49) 228 529 4176​

Fax​
​
​
(+49) 228 529 3867 Email ual32@bmelv.bund.de​

Entered by​
​
​
Mme Margarita Alonso​

Outbreak (this report - submitted) ( 09564A070005 )​
Province District Sub-district Unit Type Location Latitude Longitude Start End​
BAYERN N?rnberg N?rnberg Not applicable N?rnberg 1 49,422482 11,111161 24/06/2007​
Species Measuring units Susceptible Cases Deaths Destroyed Slaughtered​
Wild species Animals ... 1 1 0 0​
Affected Population​
Outbreak (this report - submitted) ( 09564A070004 )​
Province District Sub-district Unit Type Location Latitude Longitude Start End​
BAYERN N?rnberg N?rnberg Not applicable N?rnberg 3 49,451741 11,10286 24/06/2007​
Species Measuring units Susceptible Cases Deaths Destroyed Slaughtered​
Wild species Animals ... 1 1 0 0​
Affected Population​
Outbreak (this report - submitted) ( 09564A070007 )​
Province District Sub-district Unit Type Location Latitude Longitude Start End​
BAYERN N?rnberg N?rnberg Not applicable N?rnberg 5 49,451846 11,103044 25/06/2007​
Species Measuring units Susceptible Cases Deaths Destroyed Slaughtered​
Wild species Animals ... 1 1 0 0
Printed on: Tue Jun 26 13:10:42 Paris, Madrid (heure d'?t?) 2007 Page 1/4​
Affected Population​
Outbreak (this report - submitted) ( 09564A070008 )​
Province District Sub-district Unit Type Location Latitude Longitude Start End​
BAYERN N?rnberg N?rnberg Not applicable N?rnberg 6 49,451421 11,098225 25/06/2007​
Species Measuring units Susceptible Cases Deaths Destroyed Slaughtered​
Wild species Animals ... 1 1 0 0​
Affected Population​
Outbreak (this report - submitted) ( 09564A070006 )​
Province District Sub-district Unit Type Location Latitude Longitude Start End​
BAYERN N?rnberg N?rnberg Not applicable N?rnberg 4 49,450911 11,099059 25/06/2007​
Species Measuring units Susceptible Cases Deaths Destroyed Slaughtered​
Wild species Animals ... 1 1 0 0​
Affected Population​
Outbreak (this report - submitted) ( 09564A070003 )​
Province District Sub-district Unit Type Location Latitude Longitude Start End​
BAYERN N?rnberg N?rnberg Not applicable N?rnberg 2 49,453948 11,101671 24/06/2007​
Species Measuring units Susceptible Cases Deaths Destroyed Slaughtered​
Wild species Animals ... 1 1 0 0​
Affected Population​
Outbreak summary: Total outbreaks = 6 (Submitted)​
Species Susceptible Cases Deaths Destroyed Slaughtered​
Wild species 6 6 0 0​
Epidemiology​
Epidemiological comments​
Affected birds: swans and ducks.
Movement control is applied in the restriction zones as well as disinfection and sensitization of staff in poultry holdings in the restricted zones and reinforcement of wild birds monitoring.​
Source of Infection​
​
​
? Unknown or inconclusive​

Control Measures​
Applied​
​
​
? Screening
? Control of wildlife reservoirs
? Zoning​

To be applied​
​
​
? No Planned Control Measures
Immediate notification report. Report reference: , Ref OIE: 5632, Report Date: 26/06/2007 , Country: Germany
Printed on: Tue Jun 26 13:10:43 Paris, Madrid (heure d'?t?) 2007 Page 2/4​

Vaccination Prohibited​
​
​
No​

Animals treated​
​
​
No​

Country / Zone​
Country or zone​
​
​
a zone or compartment​

Diagnostic test results​
Laboratory Type Name of Laboratory Species Test Type Date Results Provided Result​
National laboratory Friedrich-Loeffler-Institut Wild species polymerase chain reaction (PCR) 25/06/2007 Positive​
Future Reporting​
What further reports will be submitted in relation to this event?​
There are 6outbreaks that are still recorded as unresolved. It is not possible to declare this event resolved until these individual outbreaks are resolved.​
Immediate

http://www.oie.int/wahid-prod/reports/en_imm_0000005632_20070626_131042.pdf
 
Re: Deadly bird flu strain found in Germany

Locations can be mapped using latitude and logitude in OIE report (the comma in the OIE report numbers needs to be replaced with a period, but using the link below and zooming in allows for identication of the 5 locations in the northern lake, and the one location in the southern lake - the detail in the figures is quite remarkable).

http://www.satelliteviews.net/latlong.htm?latitude=49%2C422482+&longitude=11%2C111161+
 
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Re: Deadly bird flu strain found in Germany

Who defines clades? How is it decided that a new one needs to be defined etc.? How many levels can it go to 2.2.2.1 etc.?

Just wondered.
 
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