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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.


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


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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