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Homologous Recombination in PB2 in Korean Swine

Recombinomics Commentary
March 3, 2005

>>  "There are some very, very rare examples proven where one has to postulate that it's recombination," he said. One case occurred last year during a flu outbreak in British Columbia. <<

The recombination in British Columbia was non-homologous recombination between the HA gene and the MP gene.  It is similar to the non-homologous recombination in Chile between HA and NP genes.  Both are rare because the recombination requires genetic information from one gene to be incorporated into another.  However, because these recombinations facilitate cleavage of HA, which is a required step for viral entry into a cell, there are strong selection pressures for the rare event.  The highly pathogenic avian influenza (HPAI) H5N1 has acquired a number of basic amino acids at the cleavage site, which allows ubiquitous proteases to cleave the HA precursor.  Similarly, WSN/33 has a missing glycosylation site in NA which allows plasminogen to be sequestered, and that protease also cleaves the HA precursor.

However, it is homologous recombination that is used by influenza to evolve rapidly.  The homologous recombination is much more efficient because it happens during dual infections and the new gene is a hybrid of the same gene from two parents.

One example  is in the PB2 gene from two Korean swine isolates.  Sequences at GenBank are depicted on the computer screen.  The avian polymorphisms (from H9N2 bird flu) are gold, and human (from WSN/33) are grey.  The top panel shows the data at GenBank, which are only partial sequences for the two PB2 genes with WSN/33 sequences.  The lower panel is the actual sequence which shows the 5' half of the gene is from WSN/33 (grey), while the 3' half is avian (gold).

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