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Efficient Human Transmission of H5N1 Via Recombination

Recombinomics Commentary
March 5 2005

>>Fauci  indicated that efficient human to human transmission H5N1 would involve evolution via mutations, recombinations, and reassortments.<<

The comment above was made by Anthony Fauci, director, National Institutes of Allergy and Infectious Disease, National Institutes of Health, during an NPR Bird Flu Update.  Also interviewed was Klaus Stohr, project leader, WHO Global Influenza Program, World Health Organization.  Fauci expects the acquisition of efficient human-to-human transmission by H5N1 to involve many steps, and he specifically said recombination.  Since he also mentioned mutation and reassortment, he was clearly acknowledging recombination in bird flu, which has been actively ignored by many of the influenza labs.

However, examples of clear cut recombination have begun to accumulate.  Although all forms are still not well appreciated or understood, this should soon change.  Sequence databases have many partial sequences, some of which are in very strategic places as noted for the PB2 H9N2 swine sequences with WSN/33 in Korea, as well as avian PB2 and NP in Korean chickens.  However, the partial sequences are widespread and NIAID has recently announced an initiative to expand sequence databases for influenza.  The expansion will include completion of the many partial sequences.  A large number of full H3N2 sequences from New York have been added to GenBank under the program.

Completion of these sequences will greatly expand the number of recombinants.  It will also expand the definition of recombination, because many of the mutations in the databases were generated long ago, and are simply recycled via recombination.

Influenza has been evolving throughout recorded history, but it follows very well defined rules which allow future sequences to be predicted before they emerge.

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