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Recombination in PB2 Gene of H5N1 Henan Chicken 

Recombinomics Commentary

March 6, 2006

Recent H5N1 sequences from China deposited at GenBank until the title, "A cohort of AIV H5N1 subtypes isolated from wild aquatic birds and domestic poultry revealed rapid transmission, frequent reassortment, and identifiable recombination." have several examples of recombination.  The genetic background is closely related to 2004 H5N1 Henan chicken and swan sequences.  However, in the wild bird Guangdong M sequence there are regions of identity with H5N1 Qinghai sequences.  In the PB2 gene the Henan genetic background is interrupt with alternating stretches of sequence identity with two clades of Henan tree sparrow sequences.

In addition, one of the poultry sequences, A/chicken/Henan/210/2004, also has a recombinant PB2.  It has a Henan genetic background interrupted with sequence identity with A/tree sparrow/Henan/1/2004, at positions 664-866, 913-1056, 1058-1244, 1305-1564.  These long stretches of sequence identity qualify as "identifiable recombination" and provide clear examples of recombination between prevalent H5N1 strains in Henan in 2004.

These sequences are some of the more obvious examples of recombination in H5N1.  Other regions are smaller and may be a small as single nucleotides in regions of high homology.  These recombinations are called "random mutations' by WHO and consultants, although the polymorphism distribution is far from random and is due to recombination.

These various degrees of recombination are evident in most isolates and these recombined polymorphisms can be used to create a historical tracing of the polymorphisms which can be used to predict future movement.  Similarly, the prevalent strains can be used to predict future strains.

These predictions are dependent on an up to date database, which is being sequestered in a private WHO database.  WHO should release the data immediately, so they can be properly analyzed.

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