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H5N1 Bird Flu Recombinant in Ivory Coast

Recombinomics Commentary

July 25, 2006

The HA sequence from an H5N1 bird flu sequence from the Ivory Coast , A/chicken/Ivory Coast/1787/2006(H5N1), shares a number of polymorphisms with other Qinghai isolates.  However, the haplotype containing these polymorphisms indicate the Ivory Coast isolate is a recombinant and was independently introduced into the area.  It has little in common with the three different sets of sequences from Nigeria, or the sequences from Niger.  These data indicate migrating birds have brought in multiple versions of the Qinghai strain into western Africa.  The Ivory Coast lies within the East Atlantic Flyway, which connects western Africa with western Europe and northeast Canada.

The Qinghai isolates have a discrete number of polymorphism over laid onto the Qinghai genetic background.  Discordance among these newly acquired polymorphisms identify recombination.  The Ivory Coast isolate has tandem polymorphisms, G195A and C211T as well as C1261T.  The polymorphisms are common, but found in non-overlapping haplotypes.  G195A and C1261T are in isolates from Mongolia in 2005, Turkey, Iraq, and northern Nigeria.  C211T is in Italy, Iran, Kasnodor, Afghanistan, and 2006 isolates from Mongolia and Tyva.  Additional discordance is seen because the Ivory Coast isolate has A74G, which is in a Crimean isolate, as well as Kurgan / Nigeria polymorphisms, H433A, G643A, G1708A

The recombinants in the Ivory Coast will increase the genetic diversity in the Qunbghai isolate in western Africa.  Efforts to discount the role of migratory birds in the increase and distribution of this diversity are cause for concern.

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