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Recombination in PB2 Gene of H5N1 Guangdong Wild Bird 

Recombinomics Commentary

March 6, 2006

A recent sequence from a wild duck in Guangdong, A/wild bird/Guangdong/314/2004(H5N1), was deposited by researchers in Beijing under the title, "A cohort of AIV H5N1 subtypes isolated from wild aquatic birds and domestic poultry revealed rapid transmission, frequent reassortment, and identifiable recombination."  Examples of recombination in the M gene were clear..  Sequence of the M gene are usually stable but the wild bird sequence had a genetic background from recent H5N1 Henan isolates or older isolates from Hong Kong, with stretches of polymorphism from the H5N1 Qinghai strain.

The PB2 sequence has additional evidence of recombination.  The genetic background is like that of the M gene, but the recombined sequences come from two sources, which can be represented by two clades of H5N1 tree sparrow sequences from Henen also isalted in 2004 (see below).  Thus, there are three sets of H5N1 sequences from Henen that recombine multiple times to form the PB2 sequence in the wild bird from Guangdong.

One example is give below.  A 30 BP probe contain five polymorphisms (C663T, C666A, A669G, G684A, A690T) matches three of  the four tree sparrow sequences as well as H9N2 and H3N2 isolates from Korea.  Adjacent to this stretch is a region that matches the other tree sparrow sequence as well as the earlier sequences from Hong Kong.  These were identifies with a 25 BP probe containing polymorphisms A690T, T714C and the sequences between the two polymorphism.

A 18 BP probe of the next polymorphism, G738A identifies the three tree sparrow sequences plus the Qinghai isolates and a series of isolates that trace back to the 1918 pandemic strain.

This series of recombinations is repeated for the next 400 BPs, which has a high density of polymorphisms, clearly showing extensive recombination.

The extensive recombination between three sets H5N1 sequences from Henan, including tree sparrows and long range migratory birds, is cause for concern.  They demonstrate the ability of H5N1 to rapidly evolve via recombination.  Similar sets of recombination are expected worldwide as H5N1 establishes regional strains of H5N1, which then recombine with migratory H5N1 sequences, which continually circle the globe.

Monitoring these changes requires a robust and current database.  Most of the most recent H5N1 sequences are being held in a private WHO database.  The WHO consultants indicate the changes are due to random mutation and are not predictive.  The H5N1 sequences from China clearly show that this is not the case.  The recombination between the prevalent strains in the area and is not random.

WHO should immediately release the sequestered sequences so they can be properly analyzed by the scientific community.

C663T C666A A669G G684A A690T

AY950284   A/WildDuck/Guangdong/314/2004  2004 H5N1
DQ073400  A/tree sparrow/Henan/2/2004           2004  H5N1   
DQ073401  A/tree sparrow/Henan/3/2004           2004  H5N1   
DQ073402  A/tree sparrow/Henan/4/2004           2004  H5N1   
AY862713  A/chicken/Korea/S12/03                     2003  H9N2   
AY862716  A/chicken/Korea/S15/03                     2003  H9N2   
AY862724  A/dove/Korea/S11/03                          2003  H3N2   
AY862723  A/duck/Korea/S10/03                          2003  H3N2   
AY862714  A/duck/Korea/S13/03                          2003  H9N2   
AY862720  A/duck/Korea/S7/03                            2003  H3N2   
AY862721  A/duck/Korea/S8/03                            2003  H3N2   
AY862722  A/duck/Korea/S9/03                            2003  H3N2 

A690T T714C

AY950284 A/WildDuck/Guangdong/314/2004      2004  H5N1
AY950280 A/Chicken/Henan/210/2004                  2004  H5N1
DQ073399  A/tree sparrow/Henan/1/2004             2004  H5N1   
CY005690  A/duck/Australia/749/1980                   1980  H1N1   
CY005545  A/duck/Hong Kong/319/1978               1978  H2N2   
CY005589  A/goose/Hong Kong/23/1978               1978  H5N3   
CY005618  A/duck/Hong Kong/d134/1977             1977  H6N2   
CY005604  A/duck/Hong Kong/d73/1976               1976  H9N1   
CY005745  A/duck/New Zealand/164/1976            1976  H11N3   
CY005827  A/shearwater/Australia/1/1973             1973  H6N5  


AY950284 A/WildDuck/Guangdong/314/2004             2004  H5N1
AB239300  A/bar-headed goose/Mongolia/1/05          2005  H5N1   
DQ095761  A/Bar-headed Goose/Qinghai/12/05        2005  H5N1   
DQ095757  A/Bar-headed Goose/Qinghai/5/05          2005  H5N1   
DQ095752  A/Bar-headed Goose/Qinghai/59/05        2005  H5N1   
DQ095755  A/Bar-headed Goose/Qinghai/60/05        2005  H5N1   
DQ095758  A/Bar-headed Goose/Qinghai/61/05        2005  H5N1   
DQ095760  A/Bar-headed Goose/Qinghai/62/05         2005  H5N1   
DQ095762  A/Bar-headed Goose/Qinghai/65/05         2005  H5N1   
DQ095763  A/Bar-headed Goose/Qinghai/67/05         2005  H5N1   
DQ095753  A/Bar-headed Goose/Qinghai/68/05         2005  H5N1   
DQ095759  A/Bar-headed Goose/Qinghai/75/05         2005  H5N1   
DQ100542  A/black-headed goose/Qinghai/1/2005     2005  H5N1   
DQ100543  A/black-headed goose/Qinghai/2/2005     2005  H5N1   
DQ100544  A/black-headed gull/Qinghai/1/2005          2005  H5N1   
DQ095756  A/Brown-headed Gull/Qinghai/3/05             2005  H5N1   
DQ320810  A/chicken/Fujian/1042/2005                        2005  H5N1   
DQ320832  A/chicken/Guangxi/604/2005                       2005  H5N1   
DQ323675  A/chicken/Kurgan/3/2005                             2005  H5N1   
DQ343506  A/Cygnus olor/Astrakhan/Ast05-2-2/2005  2005  H5N1   
DQ358750  A/Cygnus olor/Astrakhan/Ast05-2-3/2005  2005  H5N1   
DQ363916  A/Cygnus olor/Astrakhan/Ast05-2-4/2005  2005  H5N1   
DQ365011  A/Cygnus olor/Astrakhan/Ast05-2-5/2005  2005  H5N1   
DQ365001  A/Cygnus olor/Astrakhan/Ast05-2-6/2005  2005  H5N1   
DQ363921  A/Cygnus olor/Astrakhan/Ast05-2-7/2005  2005  H5N1   
DQ386305  A/Cygnus olor/Astrakhan/Ast05-2-8/2005  2005  H5N1   
DQ320809  A/duck/Fujian/897/2005                                2005  H5N1   
DQ320833  A/duck/Guangxi/793/2005                            2005  H5N1   
DQ320835  A/duck/Guangzhou/20/2005                         2005  H5N1   
DQ232608  A/duck/Novosibirsk/56/2005                        2005  H5N1   
DQ320856  A/Environment/Qinghai/31/2005                  2005  H5N1   
DQ320849  A/goose/Shantou/2216/2005                        2005  H5N1   
DQ100545  A/great black-headed gull/Qinghai/1/2005 2005  H5N1   
DQ095754  A/Great Black-headed Gull/Qinghai/2/05   2005  H5N1   
DQ232607  A/grebe/Novosibirsk/29/2005                      2005  H5N1   
AB239307  A/whooper swan/Mongolia/3/05                   2005  H5N1   
AY653193  A/chicken/Jilin/9/2004                                    2004  H5N1   
AY856861  A/duck/Shandong/093/2004                          2004  H5N1   
AY651714  A/Qa/Thailand/57/2004                                  2004  H5N1   
DQ073400  A/tree sparrow/Henan/2/2004                       2004  H5N1   
DQ073401  A/tree sparrow/Henan/3/2004                       2004  H5N1   
DQ073402  A/tree sparrow/Henan/4/2004                       2004  H5N1   
DQ351872  A/chicken/Hebei/108/02                                2002  H5N1   
AY585504  A/duck/Fujian/01/2002                                    2002  H5N1   
AY585505  A/duck/Fujian/13/2002                                    2002  H5N1   
AY585517  A/duck/Guangxi/53/2002                                2002  H5N1   
AY585521  A/duck/Shanghai/37/2002                              2002  H5N1   
AY651730  A/Gf/HK/38/2002                                             2002  H5N1   
AF468840  A/Duck/Anyang/AVL-1/2001                          2001  H5N1   
AY585514  A/duck/Guangxi/22/2001                                2001  H5N1   
AY585522  A/duck/Shanghai/38/2001                              2001  H5N1   
AY684874  A/black-headed gull/Netherlands/1/00          2000  H13N8   
DQ064555  A/chicken/Heilongjiang/35/00                       2000  H9N2   
DQ064557  A/chicken/Henan/26/00                                  2000  H9N2   
AF508654  A/Chicken/Henan/62/00                                 2000  H9N2   
AJ410501  A/chukka/Hong Kong/FY295/00                    2000  H6N1   
AJ427305  A/pheasant/Hong Kong/FY294/00                 2000  H6N1   
AJ410500  A/pheasant/Hong Kong/NT261/00                 2000  H6N1   
AJ410498  A/quail/Hong Kong/SF550/00                        2000  H6N1   
AJ410499  A/quail/Hong Kong/SF595/00                        2000  H6N1   
AY684875  A/black-headed gull/Sweden/1/99                 1999  H13N6   
AY684876  A/black-headed gull/Sweden/2/99                 1999  H16N3   
AY684877  A/black-headed gull/Sweden/5/99                 1999  H16N3   
DQ064552  A/chicken/Guangxi/10/99                               1999  H9N2   
DQ064553  A/chicken/Guangxi/9/99                                  1999  H9N2   
AF508648  A/Chicken/Korea/99029/99                            1999  H9N2   
AJ291395  A/Chicken/Pakistan/2/99                                 1999  H9N2   
AF508641  A/Chicken/Pakistan/4/99                                 1999  H9N2   
AF508642  A/Chicken/Pakistan/5/99                                 1999  H9N2   
AY043030  A/Guangzhou/333/99                                        1999  H9N2   
AF258835  A/Hong Kong/1073/99                                      1999  H9N2   
AJ404630  A/Hong Kong/1073/99                                       1999  H9N2   
AJ404631  A/Hong Kong/1074/99                                       1999  H9N2   
AF258836  A/Hong Kong/1074/99                                       1999  H9N2   
AJ410495  A/pheasant/Hong Kong/SH39/99                     1999  H6N1   
AJ410496  A/quail/Hong Kong/1721-20/99                        1999  H6N1   
AJ410497  A/quail/Hong Kong/1721-30/99                        1999  H6N1   
AB049154  A/parakeet/Narita/92A/98                                 1998  H9N2   
AF046086  A/Chicken/Hong Kong/220/97                          1997  H5N1   
AF098577  A/Chicken/Hong Kong/258/97                          1997  H5N1   
AF098579  A/Chicken/Hong Kong/728/97                          1997  H5N1   
AF098580  A/Chicken/Hong Kong/786/97                          1997  H5N1   
AF098578  A/Chicken/Hong Kong/y388/97                        1997  H5N1   
AF036363  A/Hong Kong/156/97                                         1997  H5N1   
AF046093  A/Hong Kong/156/97                                         1997  H5N1   
AF258837  A/Hong Kong/481/97                                         1997  H5N1   
AF115290  A/Hong Kong/481/97                                         1997  H5N1   
AF258839  A/Hong Kong/483/97                                         1997  H5N1   
AF084262  A/Hong Kong/483/97                                         1997  H5N1   
AF258843  A/Hong Kong/532/97                                         1997  H5N1   
AF258845  A/Hong Kong/542/97                                         1997  H5N1   
AB049153  A/parakeet/Chiba/1/97                                      1997  H9N2   
AF156435  A/Quail/Hong Kong/G1/97                                 1997  H9N2   
AF250476  A/Teal/Hong Kong/W312/97                             1997  H6N1   
CY004398  A/herring gull/New Jersey/402/1989                1989  H5N3   
CY004976  A/herring gull/New Jersey/406/1989                1989  H5N3   
CY004880  A/herring gull/Delaware/665/1988                    1988  H4N6   
CY005297  A/ruddy turnstone/Delaware/637/1988             1988  H11N9   
CY005071  A/laughing gull/Delaware/2838/1987               1987  H13N2   
CY003901  A/herring gull/Delaware/475/1986                    1986  H13N2  
CY004389  A/herring gull/New Jersey/780/1986                 1986  H1N3   
M73516      A/Gull/Astrakhan/227/84                                    1984  H13N6   
CY003727  A/Hong Kong 26/83                                            1983  H3N2   
CY005865  A/gull/MN/945/1980                                            1980  H13N6   
M38277      A/Kiev/59/79                                                        1979  H1N1   
CY005646  A/duck/Hong Kong/147/1977                            1977  H9N6   
CY005596  A/duck/Hong Kong/205/1977                            1977  H5N3   
M73525      A/Gull/Maryland/704/77                                      1977  H13N6   
CY005800  A/quail/Italy/1117/1965                                       1965  H10N8   
CY005819  A/duck/Ukraine/1/1963                                       1963  H3N8   
CY008995  A/Denver/57                                                          1957  H1N1   
CY009371  A/Connecticut/9/56                                              1956  H1N1   
CY009347  A/Malaysia/54                                                      1954  H1N1   
CY009339  A/Fort Worth/50                                                   1950  H1N1   
X99035      A/Fort Monmouth/1/47                                         1947  H1N1   
X99036      A/Fort Monmouth/1/47 (Mouse adapted)          1947  H1N1   
NC_002023  A/Puerto Rico/8/34                                           1934  H1N1   
DQ208309  A/Brevig Mission/1/1918                                   1918  H1N1   


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