Here is a story in today's Wired News about Henry Niman and his ideas about viral evolution in the Avian Flu (H5N1). While the text of the story is a bit unclear about the difference between recombination and reassortment, one of the associated images is quite nice. This is yet another take on the specific mechanisms of viral evolution. The figure defines reassortment as the emergence of a new strain via the replacement of whole genes from another (related) virus, and defines recombination as the insertion of fragments of genes into a new viral strain from another genome, potentially from the host.
Ignoring what labels are used, it seems the important point is that there may be two mechanisms for introduction of new sequences into an influenza viral genome; 1) inclusion of whole genes into a segmented genome or 2) insertion of gene fragments from another strain or species within a given viral gene.
Niman seems to think that not only is there evidence that the current H5N1 strain is evolving via the second mechanism, but that this is also the origin of the Spanish Flu (see my post "The Spanish Flu Story"), despite the fact that there appears to be a historically low occurrence of homologous recombination in negative sense RNA viruses (see my post "A Confluence of Concerns").
Currently many eyes are on Egypt where the H5N1 Case Fatality Rate is 100% (4 confirmed infections / 4 deaths) in this Influenza season. More compelling is the fact the 3 of the deaths are from the same family group suggesting potential human to human transmission (H2H).
We have recently had NAMRU-3 release H5N1 viral isolate genetic sequences from 2 of the Egypt deaths. Cytokinic Dysregulation is indicated in the clinical presentation. The topics, including in-depth analysis on the Indonesian and other worldwide clusters, are being discussed at Pandemic Flu Information.
Dr. Henry Niman, who predicted the S227N polymorphism in H5N1, is also discussing the Receptor Binding Domain recombinations (V223I and M230I) in the current isolates and their implications on human transmissibility.
Gharbiya Cluster in Egypt.
At this moment, a significant area of identity within the critical Hemagglutinin Receptor Binding Domain (RBD) exists between the Egypt strains and the current circulating Influenza B seasonal strain. The current Influenza B seasonal strain is highly transmissible between humans.
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http://pfiforum.com/ - Pandemic Flu Information
http://www.pfiforum.com/viewtopic.php?t=186 - Gharbiya Cluster in Egypt