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Recombination in PB1 PA NP Genes of H5N1 Henan Chicken 

Recombinomics Commentary

March 7, 2006

The chicken Henan isolate, A/chicken/Henan/210/2004(H5N1), with a recombined PB2 gene, also has recombined PB1, PA, and NP genes.  In each case donor sequences come from a tree sparrow sequences, A/tree sparrow/Henan/1/2004(H5N1), but with different contributions.  The PB1 gene is a recombinant between two tree sparrow sequences (A/tree sparrow/Henan/1/2004(H5N1), A/tree sparrow/Henan/3/2004(H5N1)).  The PA and NP genes are also predominantly from the tree sparrow (the 5' 90% of the gene).  This sequences is also in the wild bird sequence from Guangdong (A/wild bird/Guangdong/314/2004 (H5N1), but the remaining (3') 10% of the gene matches Qinghai sequences.  The NP gene has the same relationship as the PA gene.

Thus, four of the internal genes of the H5N1 isolate from the chicken have strong evidence of recombination, which was also noted for the wild bird sequence from Guangdong.  These data indicate recombination is common, although in other instances the recombined region is not as obvious because the sequence homology is high, or multiple recombinations reduce the size of the sequence homology.

In this recent series of sequences from China, the recombination appears to be shortly before isolation, therefore the stretches of sequence homology are long.  These data highlight the importance of a current an robust database.  The latest H5N1 sequences are being sequestered by WHO in a private database.  WHO comments indicate analysis of the sequences is very limited, focusing on reassortment and random mutations.  The China sequences clearly demonstrate homologous recombination, which is the major drive of influenza genetics. The recombination events are not being analyzed by WHO or consultants.

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

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