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Similarities in H5N1 Sequences from Nigeria and Sudan
Recombinomics Commentary
September 28, 2006

Full sequences from all eight gene segments of four isolates from Africa were released today, (A/chicken/Nigeria/641/2006, A/chicken/Nigeria/957-20/2006, A/chicken/Sudan/1784-7/2006, A/chicken/Sudan/1784-10/2006).  These were sequenced under the NIAID Influenza Genome Sequencing Project. Thirty eight additional sequences have been submitted by Istituto Zooprofilattico Sperimentale delle Venezie, Italy.  The samples are in the process of validation or sequencing.

As expected, all four of the above sequences were the Qinghai strain and had PB2 E627K.  Moreover, the two sequences from Nigeria had the common HA cleavage site in the Qinghai strain GERRRKKR.  The two isolates from the Sudan have the previously described novel variation, GEGRRKKR.

The release of full sequences allowed for a fuller comparision with previously released sequences as well as each other.  The two isolates from Sudan were similar with each other, but also shared many polymorphisms with the 641 isolate from Nigeria.  In contrast the 957 isolate from Nigeria was distinct from the other three isolates from Africa, but shared many polymorphism with the isolates from Astrakhan (see discussion).  The differences between the isolates supported independent introductions by migratory birds.

The sequences from the additional gene segments identified many additional polymorphisms found in isolates from human cases in Indonesia, providing additional evidence form the evolution of Indonesian sequences via recombination with wild birds sequences.  Similarly, the newly released genes also shared polymorphisms with human and swine isolates.  The acquisition of mammalian polymorphisms, including the E627K, is cause for concern.

The release of the full sequences allow for a closer monitoring of such changes.  Many mammalian acquisitions were in the PB1 gene segment (see discussion).  Human PB1 has been identified in a number of constellations found in swine in North America and Asia  Some of these constellations also include avian genes, allowing for transfer of polymorphisms in human, swine, and avian hosts.

The acquisition of mammalian polymorphisms has been noted in wild birds in North America and Asia, including fatal cases in southeast Asia.  The acquisitions remain a cause for concern.

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