An insight to segment based genetic exchange in Influenza A virus: an in silico study

Influenza virus is well recognized for high level of mutations that lead to development of new strains and subtypes, primarily through genetic shifts and drifts. Another mechanism of genetic change is through recombination, often observed in mammalian genes but controversial in viral genomes, which involves exchanges of short nucleotide sequences between two strains that coinfect the same cell. While evidence of such recombinations is rare to disputed in influenza genomes, we have observed that well-defined segments of influenza genes such as the hemagglutinin and neuraminidase have shown identical sequences between various strains that is best explained by segment exchange. Thus we had in our earlier study of the spread and proliferation of H5N1 bird flu observed that the neuraminidase with three segments – the transmembrane, stalk and body – shows evidence of exchange of one or other segments between different strains. Extending our work to the hemagglutinin of various subtypes, we noticed the same phenomena: Hemagglutinin has two segments, HA1 and HA2, where we found several instances where the segments seem to have been exchanged. Our analyses was based on RNA descriptors calculated in a 2D graphical representation scheme which have been proved to easily identify identical sequences. In this paper we discuss some of the details of this phenomenon in influenza genes which could be important in monitoring development of new highly pathogenic strains