.
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
G738A
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
Map