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new sequences

gsgs

gsgs

Registered User
all currently available sequences at genbank from New York:

Code: 
                                    00000000001122 000011122 001112 00000000111 0000001111 0000001 00 0000    
                                    00000255885601 346700900 040791 00126789124 0123481122 0377791 46 1234    
                                    00011148097436 051969648 164557 15527094892 2692214737 4147843 90 0875    
                                    23434282109125 740656903 755038 81932114762 7056516146 8840843 97 9241    
-codon-position---------------------2 11222  21 12 1111 11 1 2 11      1 2 22    11221 111    2222 11 1 21    
---Index----------------------------TATTAGGCGCAGAG ACGCAGCGC AACATT AGCGTGAGGGC CCTGCGCGCG AGACGAG GG TAAG    
  2 >A/Mexflu/index/2009-02-01      -............. ......... .....- ........... -......... ....... .. ....    

--  4  rest
  1 >A/New York/3178/2009/04/28     ---AT......... ......... .....- ........... .......... ....... .. ....    
  3 >A/New York/3177/2009/05/02     ......A.....G. G...G.... G....- ..A........ TT........ ....... .. ....    
  4 >A/New York/3181/2009/04/28     ......A.....G. G...G.... G....- ..A........ TT........ ....... .. ....    
  5 >A/New York/3307/2009/05/01     -............. ......... .....- ........... .......... ....... .. ....    

-- 10  Northern
  6 >A/New York/3099/2009/04/29     -.......A..... ......... ...C.- .....TG.A.. ......T... ....... .. ....    
  7 >A/New York/3100/2009/04/30     -.......A..... ......... ...C.- .....TG.A.. ......T... ...T... .. ....    
  8 >A/New York/3183/2009/04/28     ---.....A..... ......... ...C.. .....TG.A.. ......T... ....... .. ....    
  9 >A/New York/1682/2009/04/27     -.......A..... ......... ...C.. .....TG.A.. ......T... ...T... .. ....    
 10 >A/New York/1669/2009/04/26     -.........G... ......... ...C.. ........... ..C.A.T... ....A.. .. ....    
 11 >A/New York/3323/2009/05/06     ..........G... ......... ...C.- .A......... ..C.A.T.T. ....A.. .. ....    
 12*>A/New York/3454/2009/05/11     ..........G... ......... .G.C.. .A......... ..C.A.T.T. ....A.. .. ....    
 13*>A/New York/3455/2009/05/11     ..........G... ......... .G.C.- .A......... ..C.A.T.T. ....A.. .. ....    
 14*>A/New York/3460/2009/05/04     ..........G... ......... ...C.- ........... ......T... ....... .. ....    
 15 >A/New York/3240/2009//         -.........G... ......... ...C.- ........... ......T... ....... .. ....    


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

-- 11 Mexico-City
 16 >A/New York/3351/2009/05/06     .............. ......... ...... ..........T ...A...A.. .AG.... .. ....    

 17*>A/New York/3514/2009/05/14     .........T.... ..A.....T .....- G......T..T ...A...A.. .AG.... .. ....    
 18*>A/New York/3338/2009/05/04     .....A...T.... ..A.....T .....- G......T..T ...A...A.. .AG.... .. ....    
 19 >A/New York/3348/2009/04/28     .........T.... ..A.....T .....- G......T..T ...A...A.. .AG.... .. ....    
 20*>A/New York/3499/2009/05/16     .........T.... ..A.....T ...... G......T..T ...A...A.. .AG.... .. ....    
 21*>A/New York/3389/2009/05/08     .....A...T.... ..A.....T .....- G......T..T ...A...A.. .AG.... .. ....    
 22 >A/New York/3337/2009/05/04     .....A...T.... ..A.....T .....- G......T..T ...A...A.. .AG.... .. ....    
 23*>A/New York/3498/2009/05/12     .........T.... ..A.....T ...... G......T..T ...A...A.. .AG.... .. ....    
 24*>A/New York/3449/2009/05/13     .....A...T.... ..A.....T .....- G......T..T ...A...A.. .AG.... .. ....    
 25*>A/New York/3324/2009/05/06     -........T.... ..A.....T .....- G......T..T ...A...A.. .AG.... .. ....    
 26 >A/New York/3352/2009/05/06     .........T.... ..A.....T ...... G......T..T ...A...A.. .AG.... .. ....    


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

--130 CancunA
 58 >A/Cancun-NY/Index/2009-04-15   -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    

 27 >A/New York/37/2009/04/25       -..----------- --------- ------ ....A.....T -..A...A.A .AG.... -- ----    
 28 >A/New York/3463/2009/05/14     .............A ......T.. .....- ....A.....T ...A...A.A .AG.... AA C.G.    
 29 >A/New York/35/2009/04/25       -..----------- --------- ------ ....A.....T -..A...A.A .AG.... -- ----    
 30 >A/New York/11/2009/04/25       -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
 31 >A/New York/31/2009/04/24       -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
 32 >A/New York/3222/2009//         -............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 33*>A/New York/3563/2009/05/19     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 34 >A/New York/3255/2009//         -............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 35 >A/New York/3232/2009/04/30     -............A ......... .....- G...A.....T ...A...A.A .AG.... AA ..G.    
 36 >A/New York/3204/2009/04/27     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 37 >A/New York/06/2009/04/25       -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
 38 >A/New York/3260/2009/04/27     -............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 39 >A/New York/3211/2009/04/28     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 40 >A/New York/3220/2009//         .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 41 >A/New York/3252/2009//         -............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 42 >A/New York/3173/2009/04/28     -............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 43 >A/New York/3170/2009/05/02     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 44 >A/New York/3231/2009//         .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 45*>A/New York/3651/2009/05/25     .............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
 46 >A/New York/3012/2009/04/27     -............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 47 >A/New York/3193/2009/04/28     -............A .......A. .....- ....A.....T ...A...A.A .AG.... AA ..GA    
 48 >A/New York/18/2009/04/25       -............A .......A. .....- ....A.....T -..A...A.A .AG.... AA ..GA    
 49 >A/New York/08/2009/04/25       -..----------- --------- ------ ....A.....T ---------- .AG.... AA ----    
 50 >A/New York/33/2009/04/25       -..----------- --------- ------ ....A.....T -..A...A.A .AG.... AA ----    
 51 >A/New York/05/2009/04/         -..----------- --------- ------ ....A.....T ---------- ------- -- ----    
 52 >A/New York/25/2009/04/24       -............A ...T..... ------ ....A.....T -..A...A.A .AG.... AA ..G.    
 53 >A/New York/13/2009/04/25       -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
 54 >A/New York/3189/2009/04/29     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 55 >A/New York/3313/2009/05/04     -............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 56 >A/New York/3257/2009//         .............A ......... .....C ....A.....T ...A...A.A .AG.... AA ..G.    
 57 >A/New York/3218/2009//         .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 59 >A/New York/3194/2009/04/30     -............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 60 >A/New York/3195/2009/04/28     ...........A.A .....A... ...... ...AA.....T ...A...A.A .AG...A AA ..G.    
 61 >A/New York/3199/2009/04/28     ...........A.A .....A... ...... ...AA.....T ...A...A.A .AG...A AA ..G.    
 62 >A/New York/3002/2009/04/25     .............A ......... ...... ....A.....T ...A...A.A .AG...A AA ..G.    
 63 >A/New York/3166/2009/04/26     .............A ...T..... .....- ....A.....T ...A...A.A .AG...A AA ..G.    
 64 >A/New York/3238/2009/04/28     -----........A ......... -....- -...A.....T ...A...A.A .AG...A AA ..G.    
 65 >A/New York/3202/2009//         .............A ......... .....C ....A.....T ...A...A.A .AG...A AA ..G.    
 66 >A/New York/17/2009/04/         -..----------- --------- ------ ....A.....T ---------- .AG...A -- ----    
 67 >A/New York/27/2009/04/         -..----------- --------- ------ ....A.....T ---------- .AG.... -- ----    
 68*>A/New York/3509/2009/05/16     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 69 >A/New York/34/2009/04/25       -..----------- --------- ------ ....A.....T ---------- .AG.... -- ----    
 70 >A/New York/21/2009/04/24       -............A ......... .....- ....A.....T -..A.A.A.A .AG.... AA ..G.    
 71 >A/New York/3207/2009/04/26     ---..........A ......... .....- ....A.....T ...A.A.A.A .AG.... AA ..G.    
 73 >A/New York/3149/2009//         ---..........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 74*>A/New York/3418/2009/05/12     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 75 >A/New York/3225/2009/04/27     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 76 >A/New York/3203/2009/04/27     -............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
 77 >A/New York/39/2009/04/25       -..----------- --------- ------ ....A.....T -..A...A.A .AG.... AA ----    
 78 >A/New York/3049/2009/04/27     ---AT........A ......T.. .....- ....A.....T ...A...A.A .AG.... AA C.G.    
 79 >A/New York/3261/2009/04/29     --.-T........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 80 >A/New York/3244/2009//         --.-T........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 81 >A/New York/3247/2009/04/29     .GG-T........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 82 >A/New York/3239/2009//         ---..........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 83 >A/New York/3187/2009/05/01     ---....A.....A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
 84 >A/New York/3184/2009/04/28     .......A.....A ......... .....- ....A.....T ...A...A.A .AG.... AA .GG.    
 85 >A/New York/3223/2009//         -......A.....A ......... .....- ....A.....T ...A...A.A .AG.... AA .GG.    
 86 >A/New York/57/2009/05/08       -..----------- --------- ------ ....A....AT ---------- .AG.... -- ----    
 87 >A/New York/3007/2009/04/27     .............A ......... .....- ....A....AT ...A...A.A .AG.... AA ..G.    
 88*>A/New York/3502/2009/05/16     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 89*>A/New York/3552/2009/05/20     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 90 >A/New York/3186/2009/04/26     .............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
 91 >A/New York/3168/2009/04/26     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 92 >A/New York/3242/2009//         ---..........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 72 >A/New York/3245/2009//         ATG..........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 93 >A/New York/3263/2009//         ATG..........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 95 >A/New York/3262/2009/04/27     ATG..........A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
 94 >A/New York/3246/2009//         ---..........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
 96 >A/New York/3205/2009/04/26     ---..........A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
 97 >A/New York/20/2009/04/25       -............A ......... .....- -...A...--- -..A...A.A .AG.... AA ..G.    
 98 >A/New York/15/2009/04/25       -............A ......... .....- ----------- -..A...A.A .AG.... AA ..G.    
 99 >A/New York/04/2009/04/         -..----------- --------- ------ ....A.....T ---------- ------- -- ----    
100 >A/New York/16/2009/04/24       -..----------- --------- ------ ....A.....T ---------- .AG.... AA ----    
101 >A/New York/28/2009/04/         -..----------- --------- ------ ....A.....T ---------- ------- -- ----    
102 >A/New York/14/2009/04/         -..----------- --------- ------ ....A.....T ---------- .AG.... -- ----    
103 >A/New York/26/2009/04/24       -..----------- --------- ------ ....A.....T ---------- ------- -- ----    
104 >A/New York/3258/2009//         ---..........A ...Y..... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
105 >A/New York/45/2009/04/25       -..----------- --------- ------ ....A.....T ---------- .AG.... AA ----    
106 >A/New York/3265/2009/04/29     -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
107 >A/New York/59/2009/05/18       -............A --------- ------ ....A.....T ---------- .AG.... AA ----    
108*>A/New York/3420/2009/05/13     .............A .T....... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
109 >A/New York/09/2009/04/25       -............A ......... ------ ....A.....T -..A...A.A .AG.... -- ..G.    
110 >A/New York/3413/2009/05/11     .............A ......... ....C. ....A.....T ...A...A.A .AG.... AA ..G.    
111 >A/New York/3408/2009/05/02     .............A ......... ....C. ....A.....T ...A...A.A .AG.... AA ..G.    
112 >A/New York/3206/2009/04/26     -............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
113 >A/New York/3237/2009/04/28     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
114 >A/New York/3354/2009/05/08     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
115 >A/New York/10/2009/04/25       -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
116*>A/New York/3529/2009/05/19     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
117 >A/New York/3264/2009/04/29     ---..........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
118 >A/New York/3230/2009/04/28     .............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
119 >A/New York/3219/2009//         .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
120 >A/New York/3196/2009/04/28     -............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
121*>A/New York/3488/2009/05/12     .............A .T....... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
122 >A/New York/3215/2009/04/25     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
123 >A/New York/3014/2009/04/27     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
124 >A/New York/3236/2009/04/28     .............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
125 >A/New York/3253/2009//         ---..........A ......... .....- ....A.....T ...A...A.A TAG.... AA ..G.    
126 >A/New York/3172/2009/04/27     -............A ......... ...... ....A.....T ...A...A.A TAG.... AA ..G.    
127 >A/New York/19/2009/04/25       -..----------- ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
128 >A/New York/3532/2009/05/16     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
129 >A/New York/3214/2009/04/25     -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
130 >A/New York/3235/2009/04/28     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
131 >A/New York/3234/2009/04/28     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
132 >A/New York/3201/2009//         .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
133 >A/New York/3191/2009/04/25     -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
134 >A/New York/3221/2009//         .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
135 >A/New York/3188/2009/04/28     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
136*>A/New York/3534/2009/05/17     -............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
137 >A/New York/23/2009/04/24       -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
138 >A/New York/3185/2009/04/29     ---..........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
139 >A/New York/22/2009/04/24       -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
140 >A/New York/12/2009/04/25       -............A ......... ------ ....A.....T -..A...A.A .AG.... AA ..G.    
141 >A/New York/3243/2009//         -............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
142 >A/New York/3008/2009/04/27     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
143*>A/New York/3545/2009/05/16     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
144 >A/New York/3227/2009/04/28     .............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
145 >A/New York/3210/2009/04/24     .............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
146 >A/New York/3259/2009//         ---..........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
147*>A/New York/3501/2009/05/17     .............A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
148 >A/New York/3209/2009/04/25     .............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
149 >A/New York/3176/2009/04/26     -............A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
150 >A/New York/3169/2009/04/26     ---..........A ......... ...... ....A.....T ...A...A.A .AG.... AA ..G.    
151*>A/New York/3469/2009/05/16     .............A ......... .....- ....A.....T ...A...A.A .AG..T. AA ..G.    
152 >A/New York/3468/2009/05/17     .............A ......... ..A..- ....A.....T ...A...A.A .AG..T. AA ..G.    
153*>A/New York/3551/2009/05/20     .............A ......... ..A..- ....A.....T ...A...A.A .AG..T. AA ..G.    
154 >A/New York/30/2009/04/         -..----------- --------- ------ ....A.....T ---------- ------- -- ----    
155 >A/New York/3190/2009/04/29     ---..........A ......... .....- ....A.....T ...A...A.A .AG.... AA ..G.    
156 >A/New York/24/2009/04/24       -..----------- --------- ------ ....A.....T ---------- .AG.... AA ----    
157 >A/New York/58/2009/05/23       -..----------- --------- ------ ....A.....T -..A...A.A .AG.... -- ----    

 58 >A/Cancun-NY/Index/2009-04-15   -............A ......... .....- ....A.....T -..A...A.A .AG.... AA ..G.    
                                                                                                              
---Index----------------------------TATTAGGCGCAGAG ACGCAGCGC AACATT AGCGTGAGGGC CCTGCGCGCG AGACGAG GG TAAG    
-codon-position---------------------2 11222  21 12 1111 11 1 2 11      1 2 22    11221 111    2222 11 1 21    
                                    00000000001122 000011122 001112 00000000111 0000001111 0000001 00 0000    
                                    00000255885601 346700900 040791 00126789124 0123481122 0377791 46 1234    
                                    00011148097436 051969648 164557 15527094892 2692214737 4147843 90 0875    
                                    23434282109125 740656903 755038 81932114762 7056516146 8840843 97 9241
 
Re: new sequences

you can see a new strain of 10 sequences, basically Mexico-City/pre-Cancun
-----clade L see here: http://h5n1experts.org/forum/showpost.php?p=1133 -------------------
but with additional mutations.

Most of these were uploaded yesterday. ("*")

here are the 10 with number,sampling date,age,county
*3324:May/06,16,Washington
3337:May/04,12,Nassau
*3338:May/04,10,Nassau
3348:April/28,17,Bronx
3352:May/06,12,Kings
*3389:May/08,12,Suffolk
*3449:May/13,8,Westchester
*3498:May/12,12,Nassau
*3499:May/16,13,Nassau
*3514:May/15,9,Nassau





Let's examine whether these were more virulent than the usual
Cancun-viruses in New York...



we have 155 viruses from New York, most are full genomes.
However the main outbreak in NYC started on ~May 15, see:
http://www.nyc.gov/html/doh/html/cd/cd-h1n1flu-data.shtml

and we have 6 viruses from May 16, 3 from May 17, 1 from May 18,2 from May 19,
2 viruses from May 20, 1 from May 23, 1 from May 25,
nothing later. And 12 of these 16 were only uploaded yesterday.
15 of these 16 are the CancunA-strain



http://www.nytimes.com/2009/04/29/nyregion/29school.html?_r=2&ref=nyregion

April 28
Mayor Michael R. Bloomberg said at a news conference that
two people had been hospitalized with suspected swine flu —
a young boy just admitted to a hospital in the Bronx, and a
woman treated on Sunday at a hospital in Brooklyn.
Both had family members who had traveled to Mexico, he said.
---------------------------------
April 28
There is a 2-year-old boy in the Bronx in the hospital and is recovering,
Bloomberg said, and he has an older brother who also exhibited flu symptoms,
but tests for the flu are not complete.




----I keep editing this------------I have a bad connection since a few days----------
 
Re: new sequences

What are you talking about.

I had to paste your data in post #1 into notepad and do a search just to find the stars ("*"). How is anyone possibly supposed to understand what it is you are presenting here????

What is Mexico-City/pre-Cancun flu???

How should we examine weather or not these are more virulent???

What are you talking about when you mention that "the main outbreak started on May 16th"????

Are you pretending?
 
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