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Acquisition of H5N1Polymorphisms by H5N2 Bavarian Mallard
Recombinomics Commentary
February 28, 2006
The most recent influenza sequence available at GenBank is the HA sequence from a 2005 H5N2 mallard isolate from Bavaria, A/mallard/Bavaria/1/2005(H5N2). The submission is entitled "Molecular characterization of novel avian influenza viruses". The submitted sequence is novel because although it is most closely related to H5N2 isolates from Sweden and has an LPAI HA cleavage site, it has a number of polymorphisms from H5N1, including various Qinghai strains.
Two of these polymorphisms, G496A and C508T are found in only one isolate, A/chicken/Crimea/1/2005, a Qinghai strain from the Crimea peninsula. However a probe using G496A and the intervening sequences identifies the Crimea sequence as well as 14 Hunan sequences from 2003 to 2005 (see below). Similarly, a probe with C508T and the intervening sequences identifies 38 H5N1 Qinghai sequences.
The acquisition of the adjacent polymorphism are not due to random mutations, The were acquired via homologous recombination from a Qinghai sequence like the Crimea isolate.
The acquisition of H5N1 sequences by LPAI H5 isolates is cause for concern. These acquisitions signal dual infections and genetic exchanges via recombination. The number of H5 sequences reported by Canada was unexpectedly high. 24% of the ducks tested in British Columbia were H5 and acquisition of North American polymorphisms by H5N1 Qinghai strains from Astrakhan suggest the Qinghai strain has been in North America since the summer of 2005.
The confirmation of H5N1 in Sweden indicates further recombinations have been happening since the fall and new H5N1 isolates from Africa should be migrating into the region in the next few months.
The presence of H5N1 in new regions, coupled with frequent recombination with LPAI H5 is cause for concern. The lack of new sequences from these regions is also cause for concerns and sequences should be released to public databases as soon as possible.
G496A
DQ340848 A/chicken/Crimea/1/2005 2005 H5N1
DQ320910 A/chicken/Hunan/999/2005 2005 H5N1
DQ095630 A/Duck/Hunan/114/05 2005 H5N1
DQ320902 A/duck/Hunan/127/2005 2005 H5N1
DQ320903 A/duck/Hunan/139/2005 2005 H5N1
DQ320904 A/duck/Hunan/149/2005 2005 H5N1
DQ320905 A/duck/Hunan/152/2005 2005 H5N1
DQ320906 A/duck/Hunan/157/2005 2005 H5N1
DQ320907 A/duck/Hunan/160/2005 2005 H5N1
DQ320908 A/duck/Hunan/166/2005 2005 H5N1
DQ320909 A/duck/Hunan/182/2005 2005 H5N1
DQ095631 A/Duck/Hunan/191/05 2005 H5N1
DQ387854 A/mallard/Bavaria/120/05 2005 H5N2
AY651365 A/Dk/HN/101/2004 2004 H5N1
AY651364 A/Dk/HN/303/2004 2004 H5N1
AY651363 A/Dk/HN/5806/2003 2003 H5N1
C508T
DQ406728 A/chicken/Nigeria/641/2006 2006 H5N1
ISDN136919 A/swan/Italy/179/2006 2006 H5N1
AB233319 A/bar-headed goose/Mongolia/1/05 2005 H5N1
DQ095621 A/Bar-headed Goose/Qinghai/12/05 2005 H5N1
DQ095617 A/Bar-headed Goose/Qinghai/5/05 2005 H5N1
DQ095612 A/Bar-headed Goose/Qinghai/59/05 2005 H5N1
DQ095615 A/Bar-headed Goose/Qinghai/60/05 2005 H5N1
DQ095618 A/Bar-headed Goose/Qinghai/61/05 2005 H5N1
DQ095620 A/Bar-headed Goose/Qinghai/62/05 2005 H5N1
DQ095622 A/Bar-headed Goose/Qinghai/65/05 2005 H5N1
DQ095623 A/Bar-headed Goose/Qinghai/67/05 2005 H5N1
DQ095613 A/Bar-headed Goose/Qinghai/68/05 2005 H5N1
DQ095619 A/Bar-headed Goose/Qinghai/75/05 2005 H5N1
DQ100554 A/black-headed goose/Qinghai/1/2005 2005 H5N1
DQ100555 A/black-headed goose/Qinghai/2/2005 2005 H5N1
DQ100556 A/black-headed gull/Qinghai/1/2005 2005 H5N1
DQ095616 A/Brown-headed Gull/Qinghai/3/05 2005 H5N1
DQ320932 A/chicken/Bantul/BBVet-I/2005 2005 H5N1
DQ340848 A/chicken/Crimea/1/2005 2005 H5N1
DQ323672 A/chicken/Kurgan/3/2005 2005 H5N1
DQ320928 A/chicken/Salatiga/BBVet-I/2005 2005 H5N1
DQ279301 A/chicken/Tula/10/2005 2005 H5N1
DQ343502 A/Cygnus olor/Astrakhan/Ast05-2-2/2005 2005 H5N1
DQ358746 A/Cygnus olor/Astrakhan/Ast05-2-3/2005 2005 H5N1
DQ363918 A/Cygnus olor/Astrakhan/Ast05-2-4/2005 2005 H5N1
DQ365004 A/Cygnus olor/Astrakhan/Ast05-2-5/2005 2005 H5N1
DQ364996 A/Cygnus olor/Astrakhan/Ast05-2-6/2005 2005 H5N1
DQ363923 A/Cygnus olor/Astrakhan/Ast05-2-7/2005 2005 H5N1
DQ230522 A/duck/Novosibirsk/56/2005 2005 H5N1
DQ320922 A/Environment/Qinghai/31/2005 2005 H5N1
DQ212792 A/goose/Novosibirsk/4/2005 2005 H5N1
DQ100557 A/great black-headed gull/Qinghai/1/2005 2005 H5N1
DQ095614 A/Great Black-headed Gull/Qinghai/2/05 2005 H5N1
DQ230521 A/grebe/Novosibirsk/29/2005 2005 H5N1
DQ387854 A/mallard/Bavaria/120/05 2005 H5N2
DQ320919 A/migratory duck/Jiangxi/2136/2005 2005 H5N1
DQ320920 A/migratory duck/Jiangxi/2295/2005 2005 H5N1
DQ320921 A/migratory duck/Jiangxi/2300/2005 2005 H5N1
DQ320137 A/swan/Astrakhan/1/2005 2005 H5N1
AB233320 A/whooper swan/Mongolia/3/05 2005 H5N1
AB233321 A/whooper swan/Mongolia/4/05 2005 H5N1
AB233322 A/whooper swan/Mongolia/6/05 2005 H5N1
DQ320931 A/chicken/Kulon Progo/BBVet-XII-1/2004 2004 H5N1
DQ320930 A/chicken/Yogjakarta/BBVet-IX/2004 2004 H5N1
AY651324 A/Ck/Indonesia/4/2004 2004 H5N1
AY651325 A/Ck/Indonesia/5/2004 2004 H5N1
AY651322 A/Dk/Indonesia/MS/2004 2004 H5N1
ISDN40917 A/Thailand/SP83/2004 2004 H5N1
ISDN111352 A/Chicken/Indonesia/11/2003 2003 H5N1
ISDN111351 A/Chicken/Indonesia/7/2003 2003 H5N1
DQ320929 A/chicken/Wonosobo/BPPV4/2003 2003 H5N1
AY651323 A/Ck/Indonesia/2A/2003 2003 H5N1
AY651321 A/Ck/Indonesia/BL/2003 2003 H5N1
AY651320 A/Ck/Indonesia/PA/2003 2003 H5N1
U20460 A/tern/South Africa/61 1961 H5N3
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