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Japan sequences

gsgs

gsgs

Registered User
first was Narita, strangely few mutations and similar to Beijing/1

then some sequences from schools in Osaka area all with 9 characteristic
markers not seen elsewhere. Somehow connected to Korea/1 with
3 of the pre-Cancun markers.

then 2nd introduction Shiba

then 3 sequences from Fukuoka, similar to CA/04, which was thought to have
died out


Fukuoka prefecture (new school infections)
6 pupils of a primary school and 6 students of a junior high school in the same area of Fukuoka have been confirmed infected with novel flu so far. They don’t have record of visiting any foreign country or Kansai area recently. Their schools and another primary school of the same area will be closed until June 14.
A new series of school infections may have started in Fukuoka.
With 50 to 60 other pupils and students having flu-like symptoms on June 6 and 7, the number of confirmed cases is likely to increase.
The first case student was reportedly tested positive for both of novel flu virus and seasonal A(H1N1) virus!! (No reassortment please)



Yokohama,Shigu,Shizuoka similar to Zhejiang/1

one clear line of travel:

Cancun-->NY/3408-->NY/3413-->Zhejiang/1-->Yokohama/1,Shiga/3,Shizuoka/759
19.April-->02.May-->15.May-->23.May-->?,?,02.June



Shiga/1,Utsonomiya,Tokushima : pre-Cancun (5 markers) similar Beijing/3
 
Re: Japan sequences

5 strains in Japan, at least 5 independent introductions
listed are only those mutations which occur more than once

Code: 
                                    111111122 011112 000111111 00000000111 01111 00001 0000 000  
                                    112778912 677890 369124899 25566668014 20012 37790 4668 366  
                                    091127466 356150 073510848 90104589160 98844 14654 9099 615  
                                    328182537 685580 306944246 85650841218 86738 62244 2062 719  
-codon-position---------------------21 1  1 2   1 22  1 12 1   11 211  1 1 1 1   11       1 122  
---Index----------------------------GAATATGGT GGCCAT GTGGGCGTG TGAGGTGGGTC GGGGG GAGCA GGCG AGG  

Cancun,New York  virus
  1 >A/Sapporo/1/2009//             .......A. ...... ......... .....A....T A..AA AG... AA.. G..  
  2 >A/Fukushima/1/2009//           .......A. ...... ......... .....A....T A..AA AG... AA.. G..  
  3 >A/Iwate/2/2009//               .......A. ...... ......... .....A....T A..AA AG... AA.. G..  
  4 >A/Iwate/1/2009//               --------- ------ --------- .....A....T ----- AGA.. ---- ---  
  5 >A/Shizuoka/759/2009/06/02      ....G..A. ...... .......C. .....A....T A..AA AGA.. AA.. G..  
  6 >A/Yokohama/1/2009//            ....G..A. ...... .......C. .....A....T A..AA AGA.. AA.. G..  
  7 >A/Akita/1/2009/06/11           ....G..A. ...... .......C. .....A....T A..AA AGA.. AA.. G..  
  8 >A/Shiga/3/2009//               ....G..A. ...... .......C. .....A....T A..AA AGA.. AA.. G..  

pre-Cancun,Mexico City
  9 >A/Shiga/1/2009//               ......... ...... ......... ..........T A..A. AG... .... ...  
 12 >A/Tokushima/1/2009//           ......... ...... ......... ..........T A..A. AG... .... ...  
 10 >A/Utsunomiya/2/2009//          .G......C ..TT.. .....A... ..GA......T AA.A. AG.T. ..TA .A.  
 11 >A/Utsunomiya/1/2009//          .G......C ..TT.. .....A... ..GA......T AA.A. AG.T. ..TA .A.  

Japan  virus
 13 >A/Amagasaki/2/2009//           ...C..A.. A....C ..A...... ........... A..A. A.... .... ..A  
 14 >A/Osaka-C/1/2009/05/16         ...C..A.. A....C ..A...... ........... A..A. A.... .... ..A  
 15 >A/Himeji/1/2009//              ...C..A.. A....C ..A...... ........... A..A. A.... .... ..A  
 16 >A/Sakai/1/2009//               ...C..A.. A....C ..A.T.... .........A. A..A. A.... .... ..A  
 17 >A/Sakai/2/2009//               ...C..A.. A....C ..A.T.... .........A. A..A. A.... .... ..A  
 18 >A/Amagasaki/1/2009//           ...C..A.. A....C ..A...... .........A. A..A. A.... .... ..A  
 19 >A/Osaka-C/2/2009/05/17         ...C..A.. A....C ..A...... ........... A..A. A.... .... ..A  
 20 >A/Hyogo/2/2009/05/17           ...C..A.. A....C ..A...... ........... A..A. A.... .... ..A  
 21 >A/Shiga/2/2009//               ...C..A.. A....C ..A...... ........... A..A. A.... .... ..A  
 22 >A/Hyogo/1/2009/05/17           ...C..A.. A....C ..A...... ........... A..A. A.... .... ..A  
 23 >A/Osaka/1/2009/05/16           ...C..A.. A....C ..A...... .A......... A..A. A.... .... ..A  
 24 >A/Osaka/180/2009//             --------- ------ --------- .A......... ----- A.... ---- ---  
 25 >A/Kobe/1/2009//                ...C..A.. A....C ..A...... ........... A..A. A.... .... ..A  
 26 >A/Osaka/2/2009/05/16           ...C..A.. A....C ..A...... ........... A..A. A.... .... ..A  

early USA , CA/04-like
 28 >A/Kagoshima/1/2009//           A.G..C... .A.... AC.A..A.T C...A.AAA.. ..A.. ....G .... ...  
 29 >A/Fukuoka-C/3/2009//           A.G..C... .A.... AC.A..A.T C...A.AAA.. ..A.. ....G .... ...  
 30 >A/Fukuoka-C/2/2009//           A.G..C... .A..G. AC.A..A.T C...A.AAA.. ..A.. ....G .... ...  
 31 >A/Fukuoka-C/1/2009//           A.G..C... .A..G. AC.A..A.T C...A.AAA.. ..A.. ....G .... ...  

pre-airplane/Cancun2
 27 >A/Narita/1/2009/05/08          ......... ...... ......... ........... ..... ..... .... ...  

 32 >A/Mexflu/index/2009-02-01      ......... ...... ......... ........... ..... ..... .... ...  
 33 >A/Cancun-NY/Index/2009-04-15   .......A. ...... ......... .....A....T A..AA AG... AA.. G..  
                                                                                                 
---Index----------------------------GAATATGGT GGCCAT GTGGGCGTG TGAGGTGGGTC GGGGG GAGCA GGCG AGG  
-codon-position---------------------21 1  1 2   1 22  1 12 1   11 211  1 1 1 1   11       1 122  
                                    111111122 011112 000111111 00000000111 01111 00001 0000 000  
                                    112778912 677890 369124899 25566668014 20012 37790 4668 366  
                                    091127466 356150 073510848 90104589160 98844 14654 9099 615  
                                    328182537 685580 306944246 85650841218 86738 62244 2062 719
 
Re: Japan sequences

the latest virus is A/Akita/1/2009 from 11.June with 14 mutations.

Assuming the origin in late Jan., this gives 38 mutations per year,
the English group estimated ~70/year earlier, seasonal flu is ~32,
Qinghai H5N1 was ~45
 
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