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  • Re: Sequences at Genbank!

    I stand corrected. First cases were Yokohama area - flight from Canada - around May 9th.

    http://blog.taragana.com/n/japan-con...fection-57396/

    Comment


    • Re: Sequences at Genbank!

      27.June, more sequences (full genomes !) from New York are released.
      81 Newflu-genomes from New York are now available at genbank (=public).
      Most are from the first small peak in late April, early May.
      Only 5 are from 5.May or later, these 5 are all the Cancun strain.

      In total we have 68/81 = 84% from the Cancun-strain.
      All those 68 have all the 11 Cancun markers. Remember,
      A/Shanghai/71T supposedly imported from New York was
      lacking 2 of these markers.

      It would be interesting to know the sequence-numbers from the
      deaths in New York or better : a severety-index of the disease
      for each(most,many,some) of the 81 humans.

      I speculate that the Cancun-strain is particularly mild.
      Much better than seasonal flu. This should be examined,tested,verified !

      Unfortunate most people, most reporters are not even aware
      that there are sequences, that there are different strains already.

      all 81 viruses here:

      http://h5n1experts.org/forum/showpost.php?p=1132
      I'm interested in expert panflu damage estimates
      my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

      Comment


      • Re: Sequences at Genbank!

        What are the new strains? Ive been looking at these for a while.

        A/New York/20/2009 is just like...

        a/california/04/2009
        A/Mexico/4115/2009

        How is A/New York/20/2009 Cancun? It looks more like Canada than Cancun.

        Comment


        • Re: Sequences at Genbank!

          don't know, what you want.
          NY/20 has all 11 Cancun-markers
          I'm interested in expert panflu damage estimates
          my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

          Comment


          • Re: Sequences at Genbank!

            Originally posted by gsgs View Post
            don't know, what you want.
            NY/20 has all 11 Cancun-markers
            How? No Cancun Strain. 11 Markers to Canada.

            Comment


            • Re: Sequences at Genbank!

              Code:
              ******-substrains
              ------------------
              
              name (markers) [#30.May,#12.June]   marker1(segment),...
              ----------------------------------------------------------------
              early Mex (0)[6,6]
                 Northern (2)[8,9]         A1741C(3),C1118T(5)
                    swine (6)[6,6]         A0588G(3),A1741C(3),C0022A(4),C1118T(5),A0283G(6),C0738A(8)
                    Jersey (6)[6,8]        G0799A(1),A1741C(3),G0687T(4),A0877G(4),G1173A(4),C1118T(5)
                    Hamburg (3)[10,12]     A1577G(1),A1741C(3),C1118T(5)
                 Texas (7)[9,9]            G1308A(1),T0450C(2),A0561C(3),G1173A(4),G1563A(4),G0522A(7),A0775G(8)
                 early US (3)[4,5]         A1218G(1),G1986T(3),A1044G(6) 
                 airplane (1)[6,7]         G0546A(1)
                   England (7)[7,9]        G0546A(1),A2030G(1),A0300G(2),A1058G(2),A0008G(3),C0145A(4),C0132T(5)
                 Korea (3)[1,2]            G0298A(5),G1143A(5),G0316A(6)
                    Japan (9)[9,9]            T1711C(1),G1945A(1),G0636A(2),T2000C(2),G0936A(3),G0298A(5),G1143A(5),G0316A(6),G0658A(8)
                    pre-Cancun (5)[11,14]  C1408T(4),G0298A(5),G1143A(5),G0316A(6),A0742G(6)
                       Cancun (11)[73,111] G2163A(1),T0658A(4),C1408T(4),G0298A(5),G1143A(5),G1248A(5),G0316A(6),A0742G(6),G0492A(7),G0600A(7),A0367G(8)

              the 11 Cancun-markers:
              G2163A(1),T0658A(4),C1408T(4),G0298A(5),G1143A(5), G1248A(5),G0316A(6),A0742G(6),G0492A(7),G0600A(7), A0367G(8)

              in brackets is the segment
              segment 1 = PB2
              segment 2=PB1
              etc.
              I'm interested in expert panflu damage estimates
              my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

              Comment


              • Re: Sequences at Genbank!

                "markers" (={characteristic}mutations) as compared with the
                calculated index strain:
                http://h5n1experts.org/forum/showpost.php?p=1099
                I'm interested in expert panflu damage estimates
                my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

                Comment


                • Re: Sequences at Genbank!

                  Originally posted by gsgs View Post
                  El reporte "Brote de Influenza Humana A H1N1", de la Dirección General Adjunta de Epidemiología de la Secretaría de Salud
                  ------------------------------------------
                  I'm not sure how to translate.
                  did they say the outbreak in La Gloria was until 17.March ?
                  ----edit----
                  http://portal.salud.gob.mx/contenido...adisticas.html

                  Is that report available ? Brote de Influenza Humana ...
                  From the Sciencemag paper: "We cited two sources (1, 6) for confirmed and suspected deaths in Mexico, reported by 4 May 2009 and 30 April 2009, respectively. These sources are not publicly available at present."

                  They still are not listed on the Mexico site:
                  #1 México Dirección General Adjunta de Epidemiología, Brote de influenza humana A H1N1 México (4 and 5 May 2009).
                  #6 Mexico Dirección General Adjunta de Epidemiología, Brote de influenza porcina México (30 April 2009).)

                  Links to the paper, supplement and a table:
                  http://www.sciencemag.org/cgi/conten.../324/5934/1557
                  http://www.sciencemag.org/cgi/data/1176062/DC1/3
                  http://www.sciencemag.org/cgi/conten...4/5934/1557/F3
                  The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

                  Comment


                  • Re: Sequences at Genbank!

                    Originally posted by gsgs View Post
                    Code:
                    ******-substrains
                    ------------------
                    
                    name (markers) [#30.May,#12.June]   marker1(segment),...
                    ----------------------------------------------------------------
                    early Mex (0)[6,6]
                       Northern (2)[8,9]         A1741C(3),C1118T(5)
                          swine (6)[6,6]         A0588G(3),A1741C(3),C0022A(4),C1118T(5),A0283G(6),C0738A(8)
                          Jersey (6)[6,8]        G0799A(1),A1741C(3),G0687T(4),A0877G(4),G1173A(4),C1118T(5)
                          Hamburg (3)[10,12]     A1577G(1),A1741C(3),C1118T(5)
                       Texas (7)[9,9]            G1308A(1),T0450C(2),A0561C(3),G1173A(4),G1563A(4),G0522A(7),A0775G(8)
                       early US (3)[4,5]         A1218G(1),G1986T(3),A1044G(6) 
                       airplane (1)[6,7]         G0546A(1)
                         England (7)[7,9]        G0546A(1),A2030G(1),A0300G(2),A1058G(2),A0008G(3),C0145A(4),C0132T(5)
                       Korea (3)[1,2]            G0298A(5),G1143A(5),G0316A(6)
                          Japan (9)[9,9]            T1711C(1),G1945A(1),G0636A(2),T2000C(2),G0936A(3),G0298A(5),G1143A(5),G0316A(6),G0658A(8)
                          pre-Cancun (5)[11,14]  C1408T(4),G0298A(5),G1143A(5),G0316A(6),A0742G(6)
                             Cancun (11)[73,111] G2163A(1),T0658A(4),C1408T(4),G0298A(5),G1143A(5),G1248A(5),G0316A(6),A0742G(6),G0492A(7),G0600A(7),A0367G(8)

                    the 11 Cancun-markers:
                    G2163A(1),T0658A(4),C1408T(4),G0298A(5),G1143A(5), G1248A(5),G0316A(6),A0742G(6),G0492A(7),G0600A(7), A0367G(8)

                    in brackets is the segment
                    segment 1 = PB2
                    segment 2=PB1
                    etc.
                    Travel locations within Mexico for hamburg and jersey are unknown.

                    England is Cancun - but you have this similar to Texas / Early Mex. It's similar tex because Cancun flu is not Mexico City flu, it's us flu.

                    There is more suspect early outbreak data for San Antonio / Dallas Texas than anywhere else...

                    http://maps.google.com/maps/ms?ie=UT...,10.524902&z=7

                    Comment


                    • Re: Sequences at Genbank!

                      47 out of 104 HAs from Europe have T658A which is characteristic
                      for the Cancun-strain. (Also 30/83 NAs have the Cancun mutations)

                      that's 45%(36%), as compared with 85% of the published viruses from New York.
                      I'm interested in expert panflu damage estimates
                      my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

                      Comment


                      • Re: Sequences at Genbank!

                        acquisition of mutations of Cancun-viruses over time




                        3049,3262,3264,/11,3247 have some obvious lab-errors or alignment errors
                        additional suspicious mutations in the first ~15 positions of PB2
                        which are ignored
                        I'm interested in expert panflu damage estimates
                        my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

                        Comment


                        • Re: Sequences at Genbank!

                          12 full genomes from Europe now:
                          (Italy/05 looks a bit like reassortment)


                          Code:
                          Cancun:                                                                  
                            1 >A/Luxembourg/43/2009/06/01           ..A ... .. .AT .A.AA AG AA G  
                            3 >A/Moscow/02/2009/05/26               ..A ... .. .AT .A.AA AG AA G  
                            4 >A/Moscow/01/2009/05/21               ..A ... .. .AT .A.AA AG AA G  
                            5 >A/Moscow/IIV03/2009/06/03            ..A ... .. .AT .A.AA AG AA G  
                                                                                                   
                          pre-Cancun                                                               
                            6 >A/Paris/2591/2009/05/01              ... ... .. ..T .A.A. AG .. .  
                                                                                                   
                          northern                                                                 
                            7 >A/Italy/05/2009/05/03                ... ... .C ... .A... AG .. .  
                            8 >A/Paris/2629/2009/05/11              ... ... .C ... ..T.. .. .. .  
                            9 >A/Hamburg/4/2009//                   ... ... .C ... ..T.. .. .. .  
                                                                                                   
                          airplane                                                                 
                           10 >A/England/195/2009/04/28             AG. .GG G. A.. T.... .. .. .  
                           11 >A/Paris/2592/2009/05/01              AG. TGG G. A.. T.... .. .. .  
                           12 >A/Paris/2580/2009/04/30              AG. TGG G. A.. T.... .. .. .  
                           14 >A/Paris/2590/2009/04/30              A.. T.. .. ... ..... .. .. .  
                                                                                                  
                          ---Index-----------------------------------GAG CAA AA CTC CGCGG GA GG A  
                          -codon-position---------------------------- 2  1 2 21 111  12   11    1  
                                                                     022 001 01 001 00111 00 00 0  
                                                                     501 030 07 164 12112 37 46 3  
                                                                     436 105 04 450 39144 14 90 6  
                                                                     603 908 81 588 28838 62 20 7
                          I'm interested in expert panflu damage estimates
                          my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

                          Comment


                          • Re: Sequences at Genbank!

                            add above Italy/58 (Cancun-strain)

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

                            mutations-watch muhan1a.bas , mexfluaa.s1 , mus1.l3 (85 mutations)

                            HA,F251L GTA ATA : >M Moscow/02/2009/05/26
                            HA,K189Q GAA GAG : >L Philippines/2009/2009/05/23
                            HA,V229A CCG CCT : >D Delaware/02/2009/04/28
                            ...(21)
                            HA,V229A CCG CCT : >J Moscow/226/2009//
                            HA,Y258F ACA ATA : >D Stockholm/29/2009/05/08
                            HA,Y258F ACA ATA : >L Shiga/1/2009//
                            M1,I15V ATC ATA : >L Shandong/1/2009/05/10
                            M1,N207S AAT AAK : >D Wash.DC/03/2009/04/27
                            M1,N224S AGC AAC : >A Catalonia/154/2009/05/02
                            M1,V115I GTG ATG : >H Beijing/01/2009/05/15
                            M2,L26F CTC CTT : >L NY/12/2009/04/25
                            NA,E119? GAA GAG : >G Fukuoka-C/1/2009//
                            NA,E119? GAA RAA : >L NY/13/2009/04/25
                            NA,H275Y CAC TAC : >L Hong Kong/2369/2009/06/11
                            NA,N294S GAT GAC : >L Mexico City/40/2009/05/02
                            NA,R152K AGG AGA : >B Arizona/09/2009/05/19
                            NP,G16D GGT GAT : >G Texas/15/2009/04/15
                            NP,G16D GGT GRT : >M Georgia/01/2009/04/27
                            NP,L283P CTT CCT : >I South Dakota/05/2009/04/30
                            NP,R100V GTA ATA : >J Connecticut/01/2009/04/27
                            ...(192)
                            NP,R100V GTA ATA : >M Zhejiang/2/2009/05/31
                            NS1,T92E GAC GGC : >M NY/3184/2009/04/28
                            NS1,T92E GAC GGC : >M NY/3223/2009//
                            PA,A404S GCA GCG : >M NY/3264/2009/04/29
                            PA,R57Q CGG CAG : >L Nebraska/03/2009/04/27
                            PB1,I100A CCA CCG : >H Sichuan/1/2009/05/10
                            ...(8)
                            PB1,I100A CCA CCG : >I South Carolina/09/2009/04/26
                            PB2,K702R AAG ACG : >D New Jersey/02/2009/04/



                            list mus1.l3: (please help to correct,expand,improve)

                            Code:
                            1,PB2,A44S,130
                            1,PB2,M64T,190
                            1,PB2,A199S,595
                            1,PB2,T271A,811
                            1,PB2,L475M,1423
                            1,PB2,D567N,1699
                            1,PB2,A588I,1762
                            1,PB2,E627K,1879
                            1,PB2,A661T,1981
                            1,PB2,V667I,1999
                            1,PB2,A674T,2020
                            1,PB2,D701N,2101
                            1,PB2,K702R,2104
                            2,PB1,P28L,82
                            2,PB1,D55N,163
                            2,PB1,I100A,298
                            2,PB1,N375S,1123
                            2,PB1,T552S,1654
                            2,PB1-F2,P28L,176
                            2,PB1-F2,P48Q,236
                            2,PB1-F2,D55N,257
                            2,PB1-F2,N66S,290
                            2,PB1-F2,I100A,392
                            2,PB1-F2,T552S,1748
                            3,PA,P28L,82
                            3,PA,D55N,163
                            3,PA,R57Q,169
                            3,PA,V100A,298
                            3,PA,T129I,385
                            3,PA,S225C,673
                            3,PA,L268I,802
                            3,PA,A337S,1009
                            3,PA,A404S,1210
                            3,PA,S409N,1225
                            3,PA,T552S,1654
                            4,HA,D160K,478
                            4,HA,K189Q,565
                            4,HA,E190D,568
                            4,HA,S221P,661
                            4,HA,V229A,685
                            4,HA,F251L,751
                            4,HA,Y258F,772
                            5,NP,G16D,46
                            5,NP,V33I,97
                            5,NP,I61L,181
                            5,NP,R100V,298
                            5,NP,L136M,406
                            5,NP,L283P,847
                            5,NP,R305K,913
                            5,NP,F313Y,937
                            5,NP,Q357K,1069
                            6,NA,E119A,355
                            6,NA,E119G,355
                            6,NA,E119N,355
                            6,NA,E119V,355
                            6,NA,R152K,454
                            6,NA,H274Y,820
                            6,NA,H275Y,823
                            6,NA,R293K,877
                            6,NA,N294S,880
                            6,NA,N295S,883
                            7,M2,A16G,734
                            7,M2,E16G,734
                            7,M2,S20N,746
                            7,M2,L26F,764
                            7,M2,V27A,767
                            7,M2,A30T,776
                            7,M2,S31N,779
                            7,M2,G34E,788
                            7,M2,C55F,851
                            7,M1,I15V,43
                            7,M1,K27R,79
                            7,M1,K101R,301
                            7,M1,V115I,343
                            7,M1,T121A,361
                            7,M1,T137A,409
                            7,M1,A166V,496
                            7,M1,I168T,502
                            7,M1,N207S,619
                            7,M1,N224S,670
                            8,NS2,F55L,641
                            8,NS1,I81M,241
                            8,NS1,T92E,274
                            8,NS1,P215T,643
                            8,NS1,E227R,679

                            amino acids:
                            Code:
                            Alanine,Ala,A,4,GCT,GCC,GCA,GCG
                            Arginine,Arg,R,6,CGT,CGC,CGA,CGG,AGA,AGG
                            Asparagine,Asn,N,2,AAT,AAC
                            AsparticAcid,Asp,D,2,GAT,GAC
                            Cysteine,Cys,C,2,TGT,TGC
                            GlutamicAcid,Glu,E,2,GAA,GAG
                            Glutamine,Gln,Q,2,CAA,CAG
                            Glycine,Gly,G,4,GGT,GGC,GGA,GGG
                            Histidine,His,H,2,CAT,CAC
                            Isoleucine,Ile,I,3,ATT,ATC,ATA
                            Leucine,Leu,L,6,TTA,TTG,CTT,CTC,CTA,CTG
                            Lysine,Lys,K,2,AAA,AAG
                            Methionine,Met,M,1,ATG
                            Phenylalanine,Phe,F,2,TTT,TTC
                            Proline,Pro,P,4,CCT,CCC,CCA,CCG
                            Serine,Ser,S,6,TCT,TCC,TCA,TCG,AGT,AGC
                            Threonine,Thr,T,4,ACT,ACC,ACA,ACG
                            Tryptophan,Trp,W,1,TGG
                            Tyrosine,Tyr,Y,2,TAT,TAC
                            Valine,Val,V,4,GTT,GTC,GTA,GTG
                            STOP,Sto,},3,TAG,TGA,TAA
                            
                            
                            
                            hydrophobic:GAVLIMFWP
                            hydrophilic:STCYNQ,DE,KRH
                            HA ,F251L GTA=V,ATA=I : >M Moscow/02/2009/05/26
                            HA ,Y258F ACA=T,ATA=I : >D Stockholm/29/2009/05/08
                            HA ,Y258F ACA=T,ATA=I : >L Shiga/1/2009//
                            M1 ,N207S AAT=N,AAK=- : >D Wash.DC/03/2009/04/27
                            M1 ,N224S AGC=S,AAC=N : >A Catalonia/154/2009/05/02
                            M1 ,V115I GTG=V,ATG=M : >H Beijing/01/2009/05/15
                            NA ,E119A GAA=E,RAA=P : >L NY/13/2009/04/25
                            NA ,H275Y CAC=H,TAC=Y : >L Hong Kong/2369/2009/06/11
                            NP ,G 16D GGT=G,GAT=D : >G Texas/15/2009/04/15
                            NP ,G 16D GGT=G,GRT=- : >M Georgia/01/2009/04/27
                            NP ,L283P CTT=L,CCT=P : >I South Dakota/05/2009/04/30
                            NP ,R100V GTA=V,ATA=I : >J Connecticut/01/2009/04/27
                            ...(194)
                            NP ,R100V GTA=V,ATA=I : >M Zhejiang/2/2009/05/31
                            NS1,T 92E GAC=D,GGC=G : >M NY/3184/2009/04/28
                            NS1,T 92E GAC=D,GGC=G : >M NY/3223/2009//
                            PA ,R 57Q CGG=R,CAG=Q : >L Nebraska/03/2009/04/27
                            PB2,K702R AAG=K,ACG=T : >D New Jersey/02/2009/04/




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

                            edit----------
                            I'm interested in expert panflu damage estimates
                            my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

                            Comment


                            • Re: Sequences at Genbank!

                              looks like reassortment in A/Israel/276/2009(H1N1) !
                              They say it's from April, no exact date is given.
                              So Israel kept the reassortment secret for >2 months ?

                              Combination of the 2 Cancun-strains (Newberry+St.Francis)
                              Segments 1,3,5,6,8 from St.Francis, 2,4,7 from Newberry

                              Also has the AGA in PB1 positions 156,159,162 from Norway,
                              which looked like a sampling error.
                              I'm interested in expert panflu damage estimates
                              my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

                              Comment


                              • Re: Sequences at Genbank!

                                Originally posted by gsgs View Post
                                looks like reassortment in A/Israel/276/2009(H1N1) !
                                They say it's from April, no exact date is given.
                                So Israel kept the reassortment secret for >2 months ?

                                Combination of the 2 Cancun-strains (Newberry+St.Francis)
                                Segments 1,3,5,6,8 from St.Francis, 2,4,7 from Newberry

                                Also has the AGA in PB1 positions 156,159,162 from Norway,
                                which looked like a sampling error.
                                I cant find A/Israel/276/2009 in GenBank, do you have accession numbers?

                                Comment

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