PB1 Genes Recombinations

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More Recombination in PB1 Genes of H5N1 Henan Chickens  

Recombinomics Commentary
March 8, 2006

Recently submitted H5N1 sequences by researchers in Beijing contain a series of "identifiable recombinations". Details of recombination in M and PB2 a wild bird isolate from Guangdong, A/wild bird/Guangdong/314/2004(H5N1) have been described as have recombinations in a chicken isolate, A/chicken/Henan/210/2004(H5N1) in PB1, PB2, PA, and NP.  All of these recombinations have included donor sequences from a tree sparrow isolate from Henna, A/tree sparrow/Henan/1/2004(H5N1).

The involvement of the tree sparrow genes in "identifiable recombinations" above, allows for analysis of recombinations that are not as obvious as the above examples, which are found in large segments of the recombined genes.

Evidence of more recombination can be found in two additional 2004 H5N1 poultry isolates from Henan, A/chicken/Henan/12/2004(H5N1) and A/chicken/Henan/13/2004(H5N1) in PB1.  The PB1 sequences are virtually identical to other Henan sequences in the 5' portion of the gene.  However, the sequence abruptly changes at position 1419.  Five polymorphisms are closely clusters between positions 1419 and 1440 (G1419A, T1422C, T1431C, T1434C, A1440A).  These five polymorphisms are all third base transitions, which is commonly found in recombined regions.  The Los Alamos flu database has only one isolate with these five polymorphisms and adjacent sequences and the one isolate is the tree sparrow sequence.

The two chicken isolates above also share another polymorphism at position 1572 (G1572A).  This is also a third base transition, but it is also present in the tree sparrow sequence (the only recent sequence at Los Alamos with G1572).

These data provide additional evidence for acquisition of polymorphisms via homologous recombination, including single nucleotide polymorphisms, which WHO and consultants call "random mutations".  These acquisitions happen frequently and can be used to predict future acquisitions, as was done with HA S227N.  

These acquisitions via recombination can be used to predict emerging viruses which can be targets for vaccine development.

This analysis is dependent on a complete and up to date sequence data base.  The current public database has a number of partial H5N1 sequences which are missing information at recombination positions.  Completion of these partial sequences would be useful.  In addition, immediate deposit of recent H5N1 would also be useful.

Currently, WHO has sequestered the sequences in a private database.  WHO has repeatedly stated that H5N1 evolves via reassortment and random mutations.  

The above examples provide compelling evidence of H5N1 evolution via recombination.  

WHO should immediately release this sequences so they can be fully analyzed.

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